101
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Zhou Z, Zhang J, Zheng X, Pan Z, Zhao F, Gao Y. CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308115. [PMID: 38308181 PMCID: PMC11005702 DOI: 10.1002/advs.202308115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Circular RNAs (circRNAs) are a crucial yet relatively unexplored class of transcripts known for their tissue- and cell-type-specific expression patterns. Despite the advances in single-cell and spatial transcriptomics, these technologies face difficulties in effectively profiling circRNAs due to inherent limitations in circRNA sequencing efficiency. To address this gap, a deep learning model, CIRI-deep, is presented for comprehensive prediction of circRNA regulation on diverse types of RNA-seq data. CIRI-deep is trained on an extensive dataset of 25 million high-confidence circRNA regulation events and achieved high performances on both test and leave-out data, ensuring its accuracy in inferring differential events from RNA-seq data. It is demonstrated that CIRI-deep and its adapted version enable various circRNA analyses, including cluster- or region-specific circRNA detection, BSJ ratio map visualization, and trans and cis feature importance evaluation. Collectively, CIRI-deep's adaptability extends to all major types of RNA-seq datasets including single-cell and spatial transcriptomic data, which will undoubtedly broaden the horizons of circRNA research.
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Affiliation(s)
- Zihan Zhou
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Jinyang Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Xin Zheng
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Zhicheng Pan
- Center for Computational Biology Flatiron InstituteNew York10010USA
| | - Fangqing Zhao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Yuan Gao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
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102
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Degalez F, Charles M, Foissac S, Zhou H, Guan D, Fang L, Klopp C, Allain C, Lagoutte L, Lecerf F, Acloque H, Giuffra E, Pitel F, Lagarrigue S. Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Sci Rep 2024; 14:6588. [PMID: 38504112 PMCID: PMC10951430 DOI: 10.1038/s41598-024-56705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/09/2024] [Indexed: 03/21/2024] Open
Abstract
Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org.
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Affiliation(s)
- Fabien Degalez
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Mathieu Charles
- INRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de Toulouse, 31326, Castanet-Tolosan, France
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Sylvain Foissac
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Dailu Guan
- University of California Davis, Davis, USA
| | | | - Christophe Klopp
- INRAE, BioinfOmics, GenoToul Bioinformatics facility, Sigenae, Université Fédérale de Toulouse, 31326, Castanet-Tolosan, France
| | - Coralie Allain
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | | | | | - Hervé Acloque
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Elisabetta Giuffra
- INRAE, AgroParisTech, GABI, Paris-Saclay University, 78350, Jouy-en-Josas, France
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
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103
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Yang H, Li Q, Stroup EK, Wang S, Ji Z. Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features. Nat Commun 2024; 15:1932. [PMID: 38431639 PMCID: PMC10908861 DOI: 10.1038/s41467-024-46240-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
Studies have revealed dozens of functional peptides in putative 'noncoding' regions and raised the question of how many proteins are encoded by noncanonical open reading frames (ORFs). Here, we comprehensively annotate genome-wide translated ORFs across five eukaryotes (human, mouse, zebrafish, worm, and yeast) by analyzing ribosome profiling data. We develop a logistic regression model named PepScore based on ORF features (expected length, encoded domain, and conservation) to calculate the probability that the encoded peptide is stable in humans. Systematic ectopic expression validates PepScore and shows that stable complex-associating microproteins can be encoded in 5'/3' untranslated regions and overlapping coding regions of mRNAs besides annotated noncoding RNAs. Stable noncanonical proteins follow conventional rules and localize to different subcellular compartments. Inhibition of proteasomal/lysosomal degradation pathways can stabilize some peptides especially those with moderate PepScores, but cannot rescue the expression of short ones with low PepScores suggesting they are directly degraded by cellular proteases. The majority of human noncanonical peptides with high PepScores show longer lengths but low conservation across species/mammals, and hundreds contain trait-associated genetic variants. Our study presents a statistical framework to identify stable noncanonical peptides in the genome and provides a valuable resource for functional characterization of noncanonical translation during development and disease.
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Affiliation(s)
- Haiwang Yang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Qianru Li
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Emily K Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Sheng Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA.
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104
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Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith JJ, Rokhsar DS. The hagfish genome and the evolution of vertebrates. Nature 2024; 627:811-820. [PMID: 38262590 PMCID: PMC10972751 DOI: 10.1038/s41586-024-07070-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution1-3. Here we investigate the complex history, timing and functional role of genome-wide duplications4-7 and programmed DNA elimination8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1RV) that predates the early Cambrian cyclostome-gnathostome split, followed by a mid-late Cambrian allo-tetraploidization (2RJV) in gnathostomes and a prolonged Cambrian-Ordovician hexaploidization (2RCY) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan1,2. Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys10,11. Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates.
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Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | | | | | - Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- UK Dementia Research Institute, University College London, London, UK
| | - Masakazu Suzuki
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kaoru Kubokawa
- Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Sydney Brenner
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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105
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Xu L, Ren Y, Wu J, Cui T, Dong R, Huang C, Feng Z, Zhang T, Yang P, Yuan J, Xu X, Liu J, Wang J, Chen W, Mi D, Irwin DM, Yan Y, Xu L, Yu X, Li G. Evolution and expression patterns of the neo-sex chromosomes of the crested ibis. Nat Commun 2024; 15:1670. [PMID: 38395916 PMCID: PMC10891136 DOI: 10.1038/s41467-024-46052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Bird sex chromosomes play a unique role in sex-determination, and affect the sexual morphology and behavior of bird species. Core waterbirds, a major clade of birds, share the common characteristics of being sexually monomorphic and having lower levels of inter-sexual conflict, yet their sex chromosome evolution remains poorly understood. Here, by we analyse of a chromosome-level assembly of a female crested ibis (Nipponia nippon), a typical core waterbird. We identify neo-sex chromosomes resulting from fusion of microchromosomes with ancient sex chromosomes. These fusion events likely occurred following the divergence of Threskiornithidae and Ardeidae. The neo-W chromosome of the crested ibis exhibits the characteristics of slow degradation, which is reflected in its retention of abundant gametologous genes. Neo-W chromosome genes display an apparent ovary-biased gene expression, which is largely driven by genes that are retained on the crested ibis W chromosome but lost in other bird species. These results provide new insights into the evolutionary history and expression patterns for the sex chromosomes of bird species.
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Affiliation(s)
- Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiahong Wu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Tingting Cui
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Rong Dong
- Research Center for Qinling Giant Panda, Shaanxi Academy of Forestry, Xi'an, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Zhe Feng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Tianmin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jiao Liu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., LTD, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yaping Yan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Luohao Xu
- MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, China.
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
- Guangzhou Wildlife Research Center, Guangzhou Zoo, Guangzhou, China.
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106
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He Z, Lan Y, Zhou X, Yu B, Zhu T, Yang F, Fu LY, Chao H, Wang J, Feng RX, Zuo S, Lan W, Chen C, Chen M, Zhao X, Hu K, Chen D. Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis. PLANT COMMUNICATIONS 2024; 5:100717. [PMID: 37715446 PMCID: PMC10873878 DOI: 10.1016/j.xplc.2023.100717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/14/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
The plant genome produces an extremely large collection of long noncoding RNAs (lncRNAs) that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes. Here, we mapped the transcriptional heterogeneity of lncRNAs and their associated gene regulatory networks at single-cell resolution. We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing (scRNA-seq) datasets from juvenile Arabidopsis seedlings. We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers. We further demonstrated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity. In addition, we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs, and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs. The analysis results are available at the single-cell-based plant lncRNA atlas database (scPLAD; https://biobigdata.nju.edu.cn/scPLAD/). Overall, this work demonstrates the power of integrative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.
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Affiliation(s)
- Zhaohui He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yangming Lan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bianjiong Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Fa Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Liang-Yu Fu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiahao Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Rong-Xu Feng
- Zhejiang Zhoushan High School, Zhoushan 316099, China
| | - Shimin Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Wenzhi Lan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chunli Chen
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Keming Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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107
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Durkin SM, Ballinger MA, Nachman MW. Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice. PLoS Genet 2024; 20:e1010892. [PMID: 38306396 PMCID: PMC10866503 DOI: 10.1371/journal.pgen.1010892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/14/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Changes in gene regulation have long been appreciated as a driving force of adaptive evolution, however the relative contributions of cis- and trans-acting changes to gene regulation over short evolutionary timescales remain unclear. Instances of recent, parallel phenotypic evolution provide an opportunity to assess whether parallel patterns are seen at the level of gene expression, and to assess the relative contribution of cis- and trans- changes to gene regulation in the early stages of divergence. Here, we studied gene expression in liver and brown adipose tissue in two wild-derived strains of house mice that independently adapted to cold, northern environments, and we compared them to a strain of house mice from a warm, tropical environment. To investigate gene regulatory evolution, we studied expression in parents and allele-specific expression in F1 hybrids of crosses between warm-adapted and cold-adapted strains. First, we found that the different cold-adapted mice showed both unique and shared changes in expression, but that the proportion of shared changes (i.e. parallelism) was greater than expected by chance. Second, we discovered that expression evolution occurred largely at tissue-specific and cis-regulated genes, and that these genes were over-represented in parallel cases of evolution. Finally, we integrated the expression data with scans for selection in natural populations and found substantial parallelism in the two northern populations for genes under selection. Furthermore, selection outliers were associated with cis-regulated genes more than expected by chance; cis-regulated genes under selection influenced phenotypes such as body size, immune functioning, and activity level. These results demonstrate that parallel patterns of gene expression in mice that have independently adapted to cold environments are driven largely by tissue-specific and cis-regulatory changes, providing insight into the mechanisms of adaptive gene regulatory evolution at the earliest stages of divergence.
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Affiliation(s)
- Sylvia M. Durkin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mallory A. Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
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108
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Peng J, Zhao L. The origin and structural evolution of de novo genes in Drosophila. Nat Commun 2024; 15:810. [PMID: 38280868 PMCID: PMC10821953 DOI: 10.1038/s41467-024-45028-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
Recent studies reveal that de novo gene origination from previously non-genic sequences is a common mechanism for gene innovation. These young genes provide an opportunity to study the structural and functional origins of proteins. Here, we combine high-quality base-level whole-genome alignments and computational structural modeling to study the origination, evolution, and protein structures of lineage-specific de novo genes. We identify 555 de novo gene candidates in D. melanogaster that originated within the Drosophilinae lineage. Sequence composition, evolutionary rates, and expression patterns indicate possible gradual functional or adaptive shifts with their gene ages. Surprisingly, we find little overall protein structural changes in candidates from the Drosophilinae lineage. We identify several candidates with potentially well-folded protein structures. Ancestral sequence reconstruction analysis reveals that most potentially well-folded candidates are often born well-folded. Single-cell RNA-seq analysis in testis shows that although most de novo gene candidates are enriched in spermatocytes, several young candidates are biased towards the early spermatogenesis stage, indicating potentially important but less emphasized roles of early germline cells in the de novo gene origination in testis. This study provides a systematic overview of the origin, evolution, and protein structural changes of Drosophilinae-specific de novo genes.
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Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA.
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109
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Sturgill D, Wang L, Arda HE. PancrESS - a meta-analysis resource for understanding cell-type specific expression in the human pancreas. BMC Genomics 2024; 25:76. [PMID: 38238687 PMCID: PMC10797729 DOI: 10.1186/s12864-024-09964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND The human pancreas is composed of specialized cell types producing hormones and enzymes critical to human health. These specialized functions are the result of cell type-specific transcriptional programs which manifest in cell-specific gene expression. Understanding these programs is essential to developing therapies for pancreatic disorders. Transcription in the human pancreas has been widely studied by single-cell RNA technologies, however the diversity of protocols and analysis methods hinders their interpretability in the aggregate. RESULTS In this work, we perform a meta-analysis of pancreatic single-cell RNA sequencing data. We present a database for reference transcriptome abundances and cell-type specificity metrics. This database facilitates the identification and definition of marker genes within the pancreas. Additionally, we introduce a versatile tool which is freely available as an R package, and should permit integration into existing workflows. Our tool accepts count data files generated by widely-used single-cell gene expression platforms in their original format, eliminating an additional pre-formatting step. Although we designed it to calculate expression specificity of pancreas cell types, our tool is agnostic to the biological source of count data, extending its applicability to other biological systems. CONCLUSIONS Our findings enhance the current understanding of expression specificity within the pancreas, surpassing previous work in terms of scope and detail. Furthermore, our database and tool enable researchers to perform similar calculations in diverse biological systems, expanding the applicability of marker gene identification and facilitating comparative analyses.
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Affiliation(s)
- David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Li Wang
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - H Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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110
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Gu X, Wang M, Zhang XO. TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS). Nucleic Acids Res 2024; 52:D322-D333. [PMID: 37956335 PMCID: PMC10767810 DOI: 10.1093/nar/gkad1048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.
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Affiliation(s)
- Xiaobing Gu
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Mingdong Wang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao-Ou Zhang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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111
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Xu H, Zhang S, Duan Q, Lou M, Ling Y. Comprehensive analyses of 435 goat transcriptomes provides insight into male reproduction. Int J Biol Macromol 2024; 255:127942. [PMID: 37979751 DOI: 10.1016/j.ijbiomac.2023.127942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
A systematic analysis of genes related to reproduction is crucial for obtaining a comprehensive understanding of the molecular mechanisms that underlie male reproductive traits in mammals. Here, we utilized 435 goat transcriptome datasets to unveil the testicular tissue-specific genes (TSGs), allele-specific expression (ASE) genes and their uncharacterized transcriptional features related to male goat reproduction. Results showed a total of 1790 TSGs were identified in goat testis, which was the most among all tissues. GO enrichment analyses suggested that testicular TSGs were mainly involved in spermatogenesis, multicellular organism development, spermatid development, and flagellated sperm motility. Subsequently, a total of 95 highly conserved TSGs (HCTSGs), 508 middle conserved TSGs (MCTSGs) and 42 no conserved TSGs (NCTSGs) were identified in goat testis. GO enrichment analyses suggested that the HCTSGs and MCTSGs has a more important association with male reproduction than NCTSGs. Additionally, we identified 644 ASE genes, including 88 tissue-specific ASE (TS-ASE) genes (e.g., FSIP2, TDRD9). GO enrichment analyses indicated that both ASE genes and TS-ASE genes were associated with goat male reproduction. Overall, this study revealed an extensive gene set involved in the regulation of male goat reproduction and their dynamic transcription patterns. Data reported here provide valuable insights for a further improvement of the economic benefits of goats as well as future treatments for male infertility.
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Affiliation(s)
- Han Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Sihuan Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Qin Duan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Mengyu Lou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, Anhui, China.
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112
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Betti MJ, Aldrich MC, Gamazon ER. Minimum entropy framework identifies a novel class of genomic functional elements and reveals regulatory mechanisms at human disease loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544507. [PMID: 37398170 PMCID: PMC10312628 DOI: 10.1101/2023.06.11.544507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We introduce CoRE-BED, a framework trained using 19 epigenomic features in 33 major cell and tissue types to predict cell-type-specific regulatory function. CoRE-BED identifies nine functional classes de-novo, capturing both known and new regulatory categories. Notably, we describe a previously undercharacterized class that we term Development Associated Elements (DAEs), which are highly enriched in cell types with elevated regenerative potential and distinguished by the dual presence of either H3K4me2 and H3K9ac (an epigenetic signature associated with kinetochore assembly) or H3K79me3 and H4K20me1 (a signature associated with transcriptional pause release). Unlike bivalent promoters, which represent a transitory state between active and silenced promoters, DAEs transition directly to or from a non-functional state during stem cell differentiation and are proximal to highly expressed genes. CoRE-BED's interpretability facilitates causal inference and functional prioritization. Across 70 complex traits, distal insulators account for the largest mean proportion of SNP heritability (~49%) captured by the GWAS. Collectively, our results demonstrate the value of exploring non-conventional ways of regulatory classification that enrich for trait heritability, to complement existing approaches for cis-regulatory prediction.
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Affiliation(s)
| | | | - Eric R Gamazon
- Vanderbilt University Medical Center, Nashville, TN
- Clare Hall, University of Cambridge, Cambridge, England
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113
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Kozlova A, Sarygina E, Deinichenko K, Radko S, Ptitsyn K, Khmeleva S, Kurbatov L, Spirin P, Prassolov V, Ilgisonis E, Lisitsa A, Ponomarenko E. Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue. BIOLOGY 2023; 12:1494. [PMID: 38132320 PMCID: PMC10740679 DOI: 10.3390/biology12121494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
The long-read RNA sequencing developed by Oxford Nanopore Technologies provides a direct quantification of transcript isoforms, thereby making it possible to present alternative splicing (AS) profiles as arrays of single splice variants with different abundances. Additionally, AS profiles can be presented as arrays of genes characterized by the degree of alternative splicing (the DAS-the number of detected splice variants per gene). Here, we successfully utilized the DAS to reveal biological pathways influenced by the alterations in AS in human liver tissue and the hepatocyte-derived malignant cell lines HepG2 and Huh7, thus employing the mathematical algorithm of gene set enrichment analysis. Furthermore, analysis of the AS profiles as abundances of single splice variants by using the graded tissue specificity index τ provided the selection of the groups of genes expressing particular splice variants specifically in liver tissue, HepG2 cells, and Huh7 cells. The majority of these splice variants were translated into proteins products and appeal to be in focus regarding further insights into the mechanisms underlying cell malignization. The used metrics are intrinsically suitable for transcriptome-wide AS profiling using long-read sequencing.
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Affiliation(s)
- Anna Kozlova
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Elizaveta Sarygina
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Kseniia Deinichenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Sergey Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Konstantin Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Svetlana Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Leonid Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Pavel Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (P.S.); (V.P.)
| | - Vladimir Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (P.S.); (V.P.)
| | - Ekaterina Ilgisonis
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Andrey Lisitsa
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
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114
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Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle. Nat Commun 2023; 14:8054. [PMID: 38052795 PMCID: PMC10698142 DOI: 10.1038/s41467-023-43623-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Hyaluronic acid is a major component of extracellular matrix which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (Heterocephalus glaber) contains abundant high-molecular-mass hyaluronic acid in its tissues, which contributes to this species' cancer resistance and possibly to its longevity. Here we report that abundant high-molecular-mass hyaluronic acid is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These subterranean mammalian species accumulate abundant high-molecular-mass hyaluronic acid by regulating the expression of genes involved in hyaluronic acid degradation and synthesis and contain unique mutations in these genes. The abundant high-molecular-mass hyaluronic acid may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic conditions. Our work suggests that high-molecular-mass hyaluronic acid has evolved with subterranean lifestyle.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Zhizhong Zheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yandong Xu
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Eric Hillpot
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yifei S Lin
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Frances T Zakusilo
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - J Yuyang Lu
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Seyed Ali Biashad
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
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115
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Kurylo C, Guyomar C, Foissac S, Djebali S. TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data. NAR Genom Bioinform 2023; 5:lqad089. [PMID: 37850035 PMCID: PMC10578202 DOI: 10.1093/nargab/lqad089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/11/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023] Open
Abstract
Genome annotation plays a crucial role in providing comprehensive catalog of genes and transcripts for a particular species. As research projects generate new transcriptome data worldwide, integrating this information into existing annotations becomes essential. However, most bioinformatics pipelines are limited in their ability to effectively and consistently update annotations using new RNA-seq data. Here we introduce TAGADA, an RNA-seq pipeline for Transcripts And Genes Assembly, Deconvolution, and Analysis. Given a genomic sequence, a reference annotation and RNA-seq reads, TAGADA enhances existing gene models by generating an improved annotation. It also computes expression values for both the reference and novel annotation, identifies long non-coding transcripts (lncRNAs), and provides a comprehensive quality control report. Developed using Nextflow DSL2, TAGADA offers user-friendly functionalities and ensures reproducibility across different computing platforms through its containerized environment. In this study, we demonstrate the efficacy of TAGADA using RNA-seq data from the GENE-SWiTCH project alongside chicken and pig genome annotations as references. Results indicate that TAGADA can substantially increase the number of annotated transcripts by approximately [Formula: see text] in these species. Furthermore, we illustrate how TAGADA can integrate Illumina NovaSeq short reads with PacBio Iso-Seq long reads, showcasing its versatility. TAGADA is available at github.com/FAANG/analysis-TAGADA.
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Affiliation(s)
- Cyril Kurylo
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Toulouse, France
| | - Cervin Guyomar
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Toulouse, France
| | - Sylvain Foissac
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Toulouse, France
| | - Sarah Djebali
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Univ Toulouse III - Paul Sabatier (UPS), Toulouse, France
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116
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Saul F, Scharmann M, Wakatake T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. NATURE PLANTS 2023; 9:2000-2015. [PMID: 37996654 DOI: 10.1038/s41477-023-01562-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.
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Affiliation(s)
- Franziska Saul
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Mathias Scharmann
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, Germany
| | - Takanori Wakatake
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Louisa Channon
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Emily Carroll
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | | | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station & Program in Ecology, Evolution, and Behavior, Michigan State University, Hickory Corners, MI, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Sachiko Masuda
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerd Vogg
- Botanical Garden, University of Würzburg, Würzburg, Germany
| | - Ken Shirasu
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany.
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117
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Hooper M, Huang M, Hupp M, Jin K, Kroll M, Lathia K, Leon A, Li S, Long B, Madigan Z, Malloy J, Malone J, Maltzer Z, Martin N, McCue R, McGinty R, Mei N, Melchor J, Meyerdierks E, Mollenkopf T, Moonsman S, Nguyen TN, Otto S, Pham T, Rimorin C, Ruiz A, Sanchez R, Sawyer L, Shapovalova N, Shepard N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Valera Cuevas N, Vance S, Wadhwani K, Ward K, Levi B, Farrell C, Young R, Staats B, Wang MQM, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith K, Tasic B, Zhuang X, et alYao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Aitken M, Baker K, Baker P, Barkan E, Bertagnolli D, Bhandiwad A, Bielstein C, Bishwakarma P, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, DiValentin P, Dolbeare T, Ellingwood L, Fiabane E, Fliss T, Gee J, Gerstenberger J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Hooper M, Huang M, Hupp M, Jin K, Kroll M, Lathia K, Leon A, Li S, Long B, Madigan Z, Malloy J, Malone J, Maltzer Z, Martin N, McCue R, McGinty R, Mei N, Melchor J, Meyerdierks E, Mollenkopf T, Moonsman S, Nguyen TN, Otto S, Pham T, Rimorin C, Ruiz A, Sanchez R, Sawyer L, Shapovalova N, Shepard N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Valera Cuevas N, Vance S, Wadhwani K, Ward K, Levi B, Farrell C, Young R, Staats B, Wang MQM, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith K, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 2023; 624:317-332. [PMID: 38092916 PMCID: PMC10719114 DOI: 10.1038/s41586-023-06812-z] [Show More Authors] [Citation(s) in RCA: 311] [Impact Index Per Article: 155.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties1-3. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.0 million cells passing quality control), and a spatial transcriptomic dataset of approximately 4.3 million cells using multiplexed error-robust fluorescence in situ hybridization (MERFISH). The atlas is hierarchically organized into 4 nested levels of classification: 34 classes, 338 subclasses, 1,201 supertypes and 5,322 clusters. We present an online platform, Allen Brain Cell Atlas, to visualize the mouse whole-brain cell-type atlas along with the single-cell RNA-sequencing and MERFISH datasets. We systematically analysed the neuronal and non-neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell-type organization in different brain regions-in particular, a dichotomy between the dorsal and ventral parts of the brain. The dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. Our study also uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types. Finally, we found that transcription factors are major determinants of cell-type classification and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole mouse brain transcriptomic and spatial cell-type atlas establishes a benchmark reference atlas and a foundational resource for integrative investigations of cellular and circuit function, development and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Mike Huang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Su Li
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zach Madigan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ryan McGinty
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nicholas Mei
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Sven Otto
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Lane Sawyer
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Noah Shepard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shane Vance
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Rob Young
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Staats
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
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118
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Rao L, Cai L, Huang L. Single-cell dynamics of liver development in postnatal pigs. Sci Bull (Beijing) 2023; 68:2583-2597. [PMID: 37783617 DOI: 10.1016/j.scib.2023.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/21/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
The postnatal development of the liver, an essential organ for metabolism and immunity, remains poorly characterized at the single-cell resolution. Here, we generated single-nucleus and single-cell transcriptomes of 84,824 pig liver cells at four postnatal time points: day 30, 42, 150, and 730. We uncovered 23 cell types, including three rare cell types: plasmacytoid dendritic cells, CAVIN3+IGF2+ endothelial cells, and EBF1+ fibroblasts. The latter two were verified by multiplex immunohistochemistry. Trajectory and gene regulatory analyses revealed 33 genes that encode transcription factors associated with hepatocyte development and function, including NFIL3 involved in regulating hepatic metabolism. We characterized the spatiotemporal heterogeneity of liver endothelial cells, identified and validated leucine zipper protein 2 (LUZP2) as a novel adult liver sinusoidal endothelial cell-specific transcription factor. Lymphoid cells (NK and T cells) governed the immune system of the pig liver since day 30. Furthermore, we identified a cluster of tissue-resident NK cells, which displayed virus defense functions, maintained proliferative features at day 730, and manifested a higher conservative transcription factor expression pattern in humans than in mouse liver. Our study presents the most comprehensive postnatal liver development single-cell atlas and demonstrates the metabolic and immune changes across the four age stages.
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Affiliation(s)
- Lin Rao
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Liping Cai
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lusheng Huang
- National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang 330045, China.
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119
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Rodríguez-Montes L, Ovchinnikova S, Yuan X, Studer T, Sarropoulos I, Anders S, Kaessmann H, Cardoso-Moreira M. Sex-biased gene expression across mammalian organ development and evolution. Science 2023; 382:eadf1046. [PMID: 37917687 PMCID: PMC7615307 DOI: 10.1126/science.adf1046] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
Abstract
Sexually dimorphic traits are common among mammals and are specified during development through the deployment of sex-specific genetic programs. Because little is known about these programs, we investigated them using a resource of gene expression profiles in males and females throughout the development of five organs in five mammals (human, mouse, rat, rabbit, and opossum) and a bird (chicken). We found that sex-biased gene expression varied considerably across organs and species and was often cell-type specific. Sex differences increased abruptly around sexual maturity instead of increasing gradually during organ development. Finally, sex-biased gene expression evolved rapidly at the gene level, with differences between organs in the evolutionary mechanisms used, but more slowly at the cellular level, with the same cell types being sexually dimorphic across species.
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Affiliation(s)
- Leticia Rodríguez-Montes
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | | | - Xuefei Yuan
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Tania Studer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Simon Anders
- BioQuant, Heidelberg University, D-69120 Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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120
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Nikumbh S, Lenhard B. Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation. PLoS Comput Biol 2023; 19:e1011491. [PMID: 37983292 PMCID: PMC10695386 DOI: 10.1371/journal.pcbi.1011491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/04/2023] [Accepted: 09/05/2023] [Indexed: 11/22/2023] Open
Abstract
Core promoters are stretches of DNA at the beginning of genes that contain information that facilitates the binding of transcription initiation complexes. Different functional subsets of genes have core promoters with distinct architectures and characteristic motifs. Some of these motifs inform the selection of transcription start sites (TSS). By discovering motifs with fixed distances from known TSS positions, we could in principle classify promoters into different functional groups. Due to the variability and overlap of architectures, promoter classification is a difficult task that requires new approaches. In this study, we present a new method based on non-negative matrix factorisation (NMF) and the associated software called seqArchR that clusters promoter sequences based on their motifs at near-fixed distances from a reference point, such as TSS. When combined with experimental data from CAGE, seqArchR can efficiently identify TSS-directing motifs, including known ones like TATA, DPE, and nucleosome positioning signal, as well as novel lineage-specific motifs and the function of genes associated with them. By using seqArchR on developmental time courses, we reveal how relative use of promoter architectures changes over time with stage-specific expression. seqArchR is a powerful tool for initial genome-wide classification and functional characterisation of promoters. Its use cases are more general: it can also be used to discover any motifs at near-fixed distances from a reference point, even if they are present in only a small subset of sequences.
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Affiliation(s)
- Sarvesh Nikumbh
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
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121
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Suresh H, Crow M, Jorstad N, Hodge R, Lein E, Dobin A, Bakken T, Gillis J. Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution. Nat Ecol Evol 2023; 7:1930-1943. [PMID: 37667001 PMCID: PMC10627823 DOI: 10.1038/s41559-023-02186-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
Abstract
Enhanced cognitive function in humans is hypothesized to result from cortical expansion and increased cellular diversity. However, the mechanisms that drive these phenotypic innovations remain poorly understood, in part because of the lack of high-quality cellular resolution data in human and non-human primates. Here, we take advantage of single-cell expression data from the middle temporal gyrus of five primates (human, chimp, gorilla, macaque and marmoset) to identify 57 homologous cell types and generate cell type-specific gene co-expression networks for comparative analysis. Although orthologue expression patterns are generally well conserved, we find 24% of genes with extensive differences between human and non-human primates (3,383 out of 14,131), which are also associated with multiple brain disorders. To assess the functional significance of gene expression differences in an evolutionary context, we evaluate changes in network connectivity across meta-analytic co-expression networks from 19 animals. We find that a subset of these genes has deeply conserved co-expression across all non-human animals, and strongly divergent co-expression relationships in humans (139 out of 3,383, <1% of primate orthologues). Genes with human-specific cellular expression and co-expression profiles (such as NHEJ1, GTF2H2, C2 and BBS5) typically evolve under relaxed selective constraints and may drive rapid evolutionary change in brain function.
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Affiliation(s)
- Hamsini Suresh
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Alexander Dobin
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
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Patil AB, Kar D, Datta S, Vijay N. Genomic and Transcriptomic Analyses Illuminates Unique Traits of Elusive Night Flowering Jasmine Parijat (Nyctanthes arbor-tristis). PHYSIOLOGIA PLANTARUM 2023; 175:e14119. [PMID: 38148217 DOI: 10.1111/ppl.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The night-flowering Jasmine, Nyctanthes arbor-tristis also known as Parijat, is a perennial woody shrub belonging to the family of Oleaceae. It is popular for its fragrant flowers that bloom in the night and is a potent source of secondary metabolites. However, knowledge about its genome and the expression of genes regulating flowering or secondary metabolite accumulation is lacking. In this study, we generated whole genome sequencing data to assemble the first de novo assembly of Parijat and use it for comparative genomics and demographic history reconstruction. The temporal dynamics of effective population size (Ne ) experienced a positive influence of colder climates suggesting the switch to night flowering may have provided an evolutionary advantage. We employed multi-tissue transcriptome sequencing of floral stages/parts to obtain insights into the transcriptional regulation of nocturnal flower development and the production of volatiles/metabolites. Tissue-specific transcripts for mature flowers revealed key players in circadian regulation and flower development, including the auxin pathway and cell wall modifying genes. Furthermore, we identified tissue-specific transcripts responsible for producing numerous secondary metabolites, mainly terpenoids and carotenoids. The diversity and specificity of Terpene Synthase (TPS) and CCDs (Carotenoid Cleavage Deoxygenases) mediate the bio-synthesis of specialised metabolites in Parijat. Our study establishes Parijat as a novel non-model species to understand the molecular mechanisms of nocturnal blooming and secondary metabolite production.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Debojyoti Kar
- Plant Cell and Developmental Biology Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Sourav Datta
- Plant Cell and Developmental Biology Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
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Almeida-Silva F, Pedrosa-Silva F, Venancio TM. The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1041-1051. [PMID: 37681739 DOI: 10.1111/tpj.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/04/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamics of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a fourfold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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Zhang Y, Guo M, Wang L, Weng S, Xu H, Ren Y, Liu L, Guo C, Cheng Q, Luo P, Zhang J, Han X. A tumor-infiltrating immune cells-related pseudogenes signature based on machine-learning predicts outcomes and immunotherapy responses in ovarian cancer. Cell Signal 2023; 111:110879. [PMID: 37659727 DOI: 10.1016/j.cellsig.2023.110879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
Previous researches have provided evidence for the significant involvement of pseudogenes in immune-related functions across different types of cancer. However, the mechanisms by which pseudogenes regulate immunity in ovarian cancer (OV) and their potential impact on clinical outcomes remain unclear. To address this gap in knowledge, our study utilized a novel computational framework to analyze a total of 491 samples from three public datasets. We employed a combination of 10 machine-learning algorithms to construct a signature known as the tumor-infiltrating immune cells-related pseudogenes signature (TIICPS). The TIICPS, consisting of 12 pseudogenes, demonstrated independent prognostic value for overall survival, surpassing conventional clinical traits, 62 published signatures, and TP53 and BRCA mutation status in three cohorts. Patients with low TIICPS exhibited heightened immune-related pathways, intricate genomic alterations, substantial immune infiltration, and greater potential for immunotherapy efficacy. Consequently, TIICPS holds promise as a predictive tool for prognosis and immunotherapy response in ovarian cancer.
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Affiliation(s)
- Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Manman Guo
- Reproductive Medical Center, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410000, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510000, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510000, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
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125
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Liu L, Heidecker M, Depuydt T, Manosalva Perez N, Crespi M, Blein T, Vandepoele K. Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots. PLANT PHYSIOLOGY 2023; 193:1933-1953. [PMID: 37345955 DOI: 10.1093/plphys/kiad360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of 8 annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis (Arabidopsis thaliana). For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation (ChIP) data were used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 15,686 interactions. We found that properties characterizing lincRNA expression, conservation, and regulation differ between plants and animals. Experimental validation confirmed the role of 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs, regulated by these TFs, showing strong root cell type-specific expression or chromatin accessibility, which are linked with genome-wide association studies genetic associations related to root system development and growth. The multilevel genome-wide characterization covering chromatin state information, promoter conservation, and chromatin immunoprecipitation-based TF binding, for all detectable lincRNAs across 769 expression samples, permits rapidly defining the biological context and relevance of Arabidopsis lincRNAs through regulatory networks.
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Affiliation(s)
- Li Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Michel Heidecker
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, 91190 Gif-sur-Yvette, France
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Nicolas Manosalva Perez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Martin Crespi
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, 91190 Gif-sur-Yvette, France
| | - Thomas Blein
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Cité, 91190 Gif-sur-Yvette, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
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126
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Jorstad NL, Close J, Johansen N, Yanny AM, Barkan ER, Travaglini KJ, Bertagnolli D, Campos J, Casper T, Crichton K, Dee N, Ding SL, Gelfand E, Goldy J, Hirschstein D, Kroll M, Kunst M, Lathia K, Long B, Martin N, McMillen D, Pham T, Rimorin C, Ruiz A, Shapovalova N, Shehata S, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Ward K, Callaway EM, Hof PR, Keene CD, Levi BP, Linnarsson S, Mitra PP, Smith K, Hodge RD, Bakken TE, Lein ES. Transcriptomic cytoarchitecture reveals principles of human neocortex organization. Science 2023; 382:eadf6812. [PMID: 37824655 PMCID: PMC11687949 DOI: 10.1126/science.adf6812] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Variation in cytoarchitecture is the basis for the histological definition of cortical areas. We used single cell transcriptomics and performed cellular characterization of the human cortex to better understand cortical areal specialization. Single-nucleus RNA-sequencing of 8 areas spanning cortical structural variation showed a highly consistent cellular makeup for 24 cell subclasses. However, proportions of excitatory neuron subclasses varied substantially, likely reflecting differences in connectivity across primary sensorimotor and association cortices. Laminar organization of astrocytes and oligodendrocytes also differed across areas. Primary visual cortex showed characteristic organization with major changes in the excitatory to inhibitory neuron ratio, expansion of layer 4 excitatory neurons, and specialized inhibitory neurons. These results lay the groundwork for a refined cellular and molecular characterization of human cortical cytoarchitecture and areal specialization.
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Affiliation(s)
| | - Jennie Close
- Allen Institute for Brain Science; Seattle, WA, 98109
| | | | | | | | | | | | - Jazmin Campos
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Tamara Casper
- Allen Institute for Brain Science; Seattle, WA, 98109
| | | | - Nick Dee
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Song-Lin Ding
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Emily Gelfand
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Jeff Goldy
- Allen Institute for Brain Science; Seattle, WA, 98109
| | | | - Matthew Kroll
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Michael Kunst
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Kanan Lathia
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Brian Long
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Naomi Martin
- Allen Institute for Brain Science; Seattle, WA, 98109
| | | | | | | | - Augustin Ruiz
- Allen Institute for Brain Science; Seattle, WA, 98109
| | | | | | - Kimberly Siletti
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; Stockholm, Sweden, 171 77
| | | | - Josef Sulc
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Michael Tieu
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Amy Torkelson
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Herman Tung
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Katelyn Ward
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Edward M. Callaway
- Systems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, 92037
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington; Seattle, WA, 98195
| | - Boaz P. Levi
- Allen Institute for Brain Science; Seattle, WA, 98109
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet; Stockholm, Sweden, 171 77
| | - Partha P. Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724
| | | | | | | | - Ed S. Lein
- Allen Institute for Brain Science; Seattle, WA, 98109
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127
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Kai Y, Liu N, Orkin SH, Yuan GC. Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC. BMC Genomics 2023; 24:614. [PMID: 37833630 PMCID: PMC10571287 DOI: 10.1186/s12864-023-09675-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Chromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and oncogenesis. However, currently the prevalent method for comparative analysis of compartmentalization landscapes between different cell types is limited to the qualitative switched compartments. RESULTS To identify genomic regions with quantitatively differential compartmentalization changes from genome-wide chromatin conformation data like Hi-C, we developed a computational framework named DARIC. DARIC includes three modules: compartmentalization quantification, normalization, and differential analysis. Comparing DARIC with the conventional compartment switching analysis reveals substantial regions characterized by quantitatively significant compartmentalization changes without switching. These changes are accompanied by changes in gene expression, chromatin accessibility, H3K27ac intensity, as well as the interactions with nuclear lamina proteins and nuclear positioning, highlighting the functional importance of such quantitative changes in gene regulation. We applied DARIC to dissect the quantitative compartmentalization changes during human cardiomyocyte differentiation and identified two distinct mechanisms for gene activation based on the association with compartmentalization changes. Using the quantitative compartmentalization measurement module from DARIC, we further dissected the compartment variability landscape in the human genome by analyzing a compendium of 32 Hi-C datasets from 4DN. We discovered an interesting correlation between compartmentalization variability and sub-compartments. CONCLUSIONS DARIC is a useful tool for analyzing quantitative compartmentalization changes and mining novel biological insights from increasing Hi-C data. Our results demonstrate the functional significance of quantitative compartmentalization changes in gene regulation, and provide new insights into the relationship between compartmentalization variability and sub-compartments in the human genome.
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Affiliation(s)
- Yan Kai
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Nan Liu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Howards Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Charles Bronfman Institute for Precision Medicine, New York, NY, 10029, USA.
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128
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Modi A, Lopez G, Conkrite KL, Su C, Leung TC, Ramanan S, Manduchi E, Johnson ME, Cheung D, Gadd S, Zhang J, Smith MA, Guidry Auvil JM, Meshinchi S, Perlman EJ, Hunger SP, Maris JM, Wells AD, Grant SF, Diskin SJ. Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors. Cancer Res 2023; 83:3462-3477. [PMID: 37584517 PMCID: PMC10787516 DOI: 10.1158/0008-5472.can-22-3186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/07/2023] [Accepted: 08/09/2023] [Indexed: 08/17/2023]
Abstract
Long noncoding RNAs (lncRNA) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curated RNA sequencing data for 1,044 pediatric leukemia and extracranial solid tumors and integrated paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. A total of 2,657 lncRNAs were robustly expressed across six pediatric cancers, including 1,142 exhibiting histotype-elevated expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multidimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell type-specific transcription factors further implicated distinct histotype-elevated and developmental lncRNAs. Integration of these analyses prioritized lncRNAs for experimental validation, and silencing of TBX2-AS1, the top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming the computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies. SIGNIFICANCE Comprehensive characterization of lncRNAs in pediatric cancer leads to the identification of highly expressed lncRNAs across childhood cancers, annotation of lncRNAs showing histotype-specific elevated expression, and prediction of lncRNA gene regulatory networks.
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Affiliation(s)
- Apexa Modi
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Genomics and Computational Biology Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Karina L. Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Chun Su
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tsz Ching Leung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Sathvik Ramanan
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elisabetta Manduchi
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew E. Johnson
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daphne Cheung
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland 20892, USA
| | | | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Elizabeth J. Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois 60208, USA
| | - Stephen P. Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Struan F.A. Grant
- Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Divisions of Human Genetics and Endocrinology & Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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129
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Liu Z, Huang YF. Deep multiple-instance learning accurately predicts gene haploinsufficiency and deletion pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555384. [PMID: 37693607 PMCID: PMC10491176 DOI: 10.1101/2023.08.29.555384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Copy number losses (deletions) are a major contributor to the etiology of severe genetic disorders. Although haploinsufficient genes play a critical role in deletion pathogenicity, current methods for deletion pathogenicity prediction fail to integrate multiple lines of evidence for haploinsufficiency at the gene level, limiting their power to pinpoint deleterious deletions associated with genetic disorders. Here we introduce DosaCNV, a deep multiple-instance learning framework that, for the first time, models deletion pathogenicity jointly with gene haploinsufficiency. By integrating over 30 gene-level features potentially predictive of haploinsufficiency, DosaCNV shows unmatched performance in prioritizing pathogenic deletions associated with a broad spectrum of genetic disorders. Furthermore, DosaCNV outperforms existing methods in predicting gene haploinsufficiency even though it is not trained on known haploinsufficient genes. Finally, DosaCNV leverages a state-of-the-art technique to quantify the contributions of individual gene-level features to haploinsufficiency, allowing for human-understandable explanations of model predictions. Altogether, DosaCNV is a powerful computational tool for both fundamental and translational research.
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Affiliation(s)
- Zhihan Liu
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Molecular, Cellular, and Integrative Biosciences Program, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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130
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Wijfjes Z, van Dalen FJ, Le Gall CM, Verdoes M. Controlling Antigen Fate in Therapeutic Cancer Vaccines by Targeting Dendritic Cell Receptors. Mol Pharm 2023; 20:4826-4847. [PMID: 37721387 PMCID: PMC10548474 DOI: 10.1021/acs.molpharmaceut.3c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
Antigen-presenting cells (APCs) orchestrate immune responses and are therefore of interest for the targeted delivery of therapeutic vaccines. Dendritic cells (DCs) are professional APCs that excel in presentation of exogenous antigens toward CD4+ T helper cells, as well as cytotoxic CD8+ T cells. DCs are highly heterogeneous and can be divided into subpopulations that differ in abundance, function, and phenotype, such as differential expression of endocytic receptor molecules. It is firmly established that targeting antigens to DC receptors enhances the efficacy of therapeutic vaccines. While most studies emphasize the importance of targeting a specific DC subset, we argue that the differential intracellular routing downstream of the targeted receptors within the DC subset should also be considered. Here, we review the mouse and human receptors studied as target for therapeutic vaccines, focusing on antibody and ligand conjugates and how their targeting affects antigen presentation. We aim to delineate how targeting distinct receptors affects antigen presentation and vaccine efficacy, which will guide target selection for future therapeutic vaccine development.
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Affiliation(s)
- Zacharias Wijfjes
- Chemical
Immunology group, Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
- Institute
for Chemical Immunology, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
| | - Floris J. van Dalen
- Chemical
Immunology group, Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
- Institute
for Chemical Immunology, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
| | - Camille M. Le Gall
- Chemical
Immunology group, Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
- Institute
for Chemical Immunology, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
| | - Martijn Verdoes
- Chemical
Immunology group, Department of Medical BioSciences, Radboud University Medical Center, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
- Institute
for Chemical Immunology, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
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131
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Lim B, Kim SC, Kim WI, Kim JM. Integrative time-serial networks for genome-wide lncRNA-mRNA interactions reveal interferon-inducible antiviral and T-cell receptor regulations against PRRSV infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104759. [PMID: 37315774 DOI: 10.1016/j.dci.2023.104759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) infection severely affects the swine industry each year. Although the host mechanisms against PRRSV infection have been identified in key target tissues through whole transcriptome sequencing, specific molecular regulators have not been elucidated. Long non-coding RNA (lncRNA) expression is highly specific and could thus be used to effectively identify PRRSV-specific candidates. Here, we identified novel lncRNAs in lungs, bronchial lymph nodes, and tonsils after PRRSV infection and constructed phenotype-based integrative co-expression networks using time-series differentially expressed (DE) lncRNAs and mRNAs. After the analyses, a total of 309 lncRNA-mRNA interactions were identified. During early host innate signalling, interferon-inducible and interferon genes were positively regulated by specific lncRNA. Moreover, T-cell receptor genes in lung adaptive immune signalling were negatively regulated by specific lncRNA. Collectively, our findings provide insights into the genome-wide lncRNA-mRNA interactions and dynamic regulation of lncRNA-mediated mechanisms against PRRSV infection.
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Affiliation(s)
- Byeonghwi Lim
- Functional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Seung-Chai Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea.
| | - Jun-Mo Kim
- Functional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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132
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LaPolice TM, Huang YF. An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data. BMC Bioinformatics 2023; 24:347. [PMID: 37723435 PMCID: PMC10506225 DOI: 10.1186/s12859-023-05481-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/13/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. While the existing methods are highly predictive of essential genes of long length, they have limited power in pinpointing short essential genes due to the sparsity of polymorphisms in the human genome. RESULTS Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. Compared with previous methods, DeepLOF shows unmatched performance in predicting ClinGen haploinsufficient genes, mouse essential genes, and essential genes in human cell lines. Notably, at a false positive rate of 5%, DeepLOF detects 50% more ClinGen haploinsufficient genes than previous methods. Furthermore, DeepLOF discovers 109 novel essential genes that are too short to be identified by previous methods. CONCLUSION The predictive power of DeepLOF shows that it is a compelling computational method to aid in the discovery of essential genes.
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Affiliation(s)
- Troy M LaPolice
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Yi-Fei Huang
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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133
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Sreedasyam A, Plott C, Hossain MS, Lovell J, Grimwood J, Jenkins J, Daum C, Barry K, Carlson J, Shu S, Phillips J, Amirebrahimi M, Zane M, Wang M, Goodstein D, Haas F, Hiss M, Perroud PF, Jawdy S, Yang Y, Hu R, Johnson J, Kropat J, Gallaher S, Lipzen A, Shakirov E, Weng X, Torres-Jerez I, Weers B, Conde D, Pappas M, Liu L, Muchlinski A, Jiang H, Shyu C, Huang P, Sebastian J, Laiben C, Medlin A, Carey S, Carrell A, Chen JG, Perales M, Swaminathan K, Allona I, Grattapaglia D, Cooper E, Tholl D, Vogel J, Weston DJ, Yang X, Brutnell T, Kellogg E, Baxter I, Udvardi M, Tang Y, Mockler T, Juenger T, Mullet J, Rensing S, Tuskan G, Merchant S, Stacey G, Schmutz J. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Res 2023; 51:8383-8401. [PMID: 37526283 PMCID: PMC10484672 DOI: 10.1093/nar/gkad616] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
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Affiliation(s)
| | | | - Md Shakhawat Hossain
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joseph Carlson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shengqiang Shu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Phillips
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mojgan Amirebrahimi
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Zane
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mei Wang
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Goodstein
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Sara S Jawdy
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Yongil Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rongbin Hu
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jenifer Johnson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Marilia R Pappas
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | - Lifeng Liu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muchlinski
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Christine Shyu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Pu Huang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jose Sebastian
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Carol Laiben
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa Medlin
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Sankalpi Carey
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Dario Grattapaglia
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | | | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - John P Vogel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Gerald A Tuskan
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Gary Stacey
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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134
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Zhou C, Wei X, Xiao Y, Liu S, Wang J. Novel compound heterozygous variants in lectin mannose-binding 2-like gene identified in a Chinese autosomal recessive mental retardation-52 (MRT52) patient with phenotype expansion. Chin Med J (Engl) 2023; 136:2107-2109. [PMID: 37667433 PMCID: PMC10476734 DOI: 10.1097/cm9.0000000000002285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Indexed: 09/06/2023] Open
Affiliation(s)
- Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xing Wei
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuanyuan Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan 610041, China
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135
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Liu W, Zhu P, Li M, Li Z, Yu Y, Liu G, Du J, Wang X, Yang J, Tian R, Seim I, Kaya A, Li M, Li M, Gladyshev VN, Zhou X. Large-scale across species transcriptomic analysis identifies genetic selection signatures associated with longevity in mammals. EMBO J 2023; 42:e112740. [PMID: 37427458 PMCID: PMC10476176 DOI: 10.15252/embj.2022112740] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 07/11/2023] Open
Abstract
Lifespan varies significantly among mammals, with more than 100-fold difference between the shortest and longest living species. This natural difference may uncover the evolutionary forces and molecular features that define longevity. To understand the relationship between gene expression variation and longevity, we conducted a comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species. We found that few genes exhibit common expression patterns with longevity in the three organs analyzed. However, pathways related to translation fidelity, such as nonsense-mediated decay and eukaryotic translation elongation, correlated with longevity across mammals. Analyses of selection pressure found that selection intensity related to the direction of longevity-correlated genes is inconsistent across organs. Furthermore, expression of methionine restriction-related genes correlated with longevity and was under strong selection in long-lived mammals, suggesting that a common strategy is utilized by natural selection and artificial intervention to control lifespan. Our results indicate that lifespan regulation via gene expression is driven through polygenic and indirect natural selection.
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Affiliation(s)
- Weiqiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zihao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Yu
- School of Life SciencesUniversity of Science and Technology of ChinaAnhuiChina
| | - Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Jing Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ran Tian
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Inge Seim
- Integrative Biology Laboratory, College of Life SciencesNanjing Normal UniversityNanjingChina
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQLDAustralia
| | - Alaattin Kaya
- Department of BiologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityChengduChina
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of ZoologyChinese Academy of SciencesBeijingChina
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136
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Li Y, Mokrani A, Fu H, Shi C, Li Q, Liu S. Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas. Genomics 2023; 115:110697. [PMID: 37567397 DOI: 10.1016/j.ygeno.2023.110697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The Pacific oyster (Crassostrea gigas) is a widely cultivated shellfish in the world, while its transcriptome diversity remains less unexplored due to the limitation of short reads. In this study, we used Oxford Nanopore sequencing to develop the full-length transcriptome database of C. gigas. We identified 77,920 full-length transcripts from 21,523 genes, and uncovered 9668 alternative splicing events and 87,468 alternative polyadenylation sites. Notably, a total of 16,721 novel transcripts were annotated in this work. Furthermore, integrative analysis of 25 publicly available RNA-seq datasets revealed the transcriptome diversity involved in post-transcriptional regulation in C. gigas. We further developed a Drupal based webserver, Cgtdb, which can be used for transcriptome visualization, sequence alignment, and functional genome annotation analyses. This work provides valuable resources and a useful tool for integrative analysis of various transcriptome datasets in C. gigas, which will serve as an essential reference for functional annotation of the oyster genome.
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Affiliation(s)
- Yin Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Ahmed Mokrani
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Huiru Fu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Chenyu Shi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China.
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137
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Jain A, Begum T, Ahmad S. Analysis and Prediction of Pathogen Nucleic Acid Specificity for Toll-like Receptors in Vertebrates. J Mol Biol 2023; 435:168208. [PMID: 37479078 DOI: 10.1016/j.jmb.2023.168208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Identification of key sequence, expression and function related features of nucleic acid-sensing host proteins is of fundamental importance to understand the dynamics of pathogen-specific host responses. To meet this objective, we considered toll-like receptors (TLRs), a representative class of membrane-bound sensor proteins, from 17 vertebrate species covering mammals, birds, reptiles, amphibians, and fishes in this comparative study. We identified the molecular signatures of host TLRs that are responsible for sensing pathogen nucleic acids or other pathogen-associated molecular patterns (PAMPs), and potentially play important roles in host defence mechanism. Interestingly, our findings reveal that such host-specific features are directly related to the strand (single or double) specificity of nucleic acid from pathogens. However, during host-pathogen interactions, such features were unable to explain the pathogenic PAMP (i.e., DNA, RNA or other) selectivity, suggesting a more complex mechanism. Using these features, we developed a number of machine learning models, of which Random Forest achieved a high performance (94.57% accuracy) to predict strand specificity of TLRs from protein-derived features. We applied the trained model to propose strand specificity of some previously uncharacterized distinct fish-specific novel TLRs (TLR18, TLR23, TLR24, TLR25, TLR27).
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Affiliation(s)
- Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. https://twitter.com/@Anuja334
| | - Tina Begum
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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138
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Li S, Zhang N, Zhang H, Zhou R, Li Z, Yang X, Wu W, Li H, Luo P, Wang Z, Dai Z, Liang X, Wen J, Zhang X, Zhang B, Cheng Q, Zhang Q, Yang Z. Artificial intelligence learning landscape of triple-negative breast cancer uncovers new opportunities for enhancing outcomes and immunotherapy responses. JOURNAL OF BIG DATA 2023; 10:132. [DOI: 10.1186/s40537-023-00809-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/07/2023] [Indexed: 01/12/2025]
Abstract
AbstractTriple-negative breast cancer (TNBC) is a relatively aggressive breast cancer subtype due to tumor relapse, drug resistance, and multi-organ metastatic properties. Identifying reliable biomarkers to predict prognosis and precisely guide TNBC immunotherapy is still an unmet clinical need. To address this issue, we successfully constructed a novel 25 machine learning (ML) algorithms-based immune infiltrating cell (IIC) associated signature of TNBC (MLIIC), achieved by multiple transcriptome data of purified immune cells, TNBC cell lines, and TNBC entities. The TSI index was employed to determine IIC-RNAs that were accompanied by an expression pattern of upregulation in immune cells and downregulation in TNBC cells. LassoLR, Boruta, Xgboost, SVM, RF, and Pamr were utilized for further obtaining the optimal IIC-RNAs. Following univariate Cox regression analysis, LassoCox, CoxBoost, and RSF were utilized for the dimensionality reduction of IIC-RNAs from a prognostic perspective. RSF, Ranger, ObliqueRSF, Rpart, CoxPH, SurvivalSVM, CoxBoost, GlmBoost, SuperPC, StepwiseCox, Enet, LassoCox, CForest, Akritas, BlackBoost, PlsRcox, SurvReg, GBM, and CTree were used for determining the most potent MLIIC signature. Consequently, this MLIIC signature was correlated significantly with survival status validated by four independent TNBC cohorts. Also, the MLIIC signature had a superior predictive capability for TNBC prognosis, compared with 148 previously reported signatures. In addition, MLIIC signature scores developed by immunofluorescent staining of tissue arrays from TNBC patients showed a substantial prognostic value. In TNBC immunotherapy, the low MLIIC profile demonstrated significant immune-responsive efficacy in a dataset of multiple cancer types. MLIIC signature could also predict m6A epigenetic regulation which controls T cell homeostasis. Therefore, this well-established MLIIC signature is a robust predictive indicator for TNBC prognosis and the benefit of immunotherapy, thus providing an efficient tool for combating TNBC.
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139
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Stevenson DW, Ramakrishnan S, de Santis Alves C, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, Loke S, Rossetto M, McPherson H, Nigris S, Moschin S, Little DP, Katari MS, Varala K, Kolokotronis SO, Ambrose B, Croft LJ, Coruzzi GM, Schatz M, McCombie WR, Martienssen RA. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554647. [PMID: 37662366 PMCID: PMC10473749 DOI: 10.1101/2023.08.24.554647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.
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Affiliation(s)
| | | | - Cristiane de Santis Alves
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Laís Araujo Coelho
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Gil Eshel
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Samantha Frangos
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Katherine Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Shujun Ou
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaojin Wang
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Yin Peng Lee
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Stella Loke
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Australian Botanic Garden, Mount Annan, NSW 2567, Australia
| | - Sebastiano Nigris
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Silvia Moschin
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Damon P. Little
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Manpreet S. Katari
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Kranthi Varala
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Barbara Ambrose
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Larry J. Croft
- School of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Gloria M. Coruzzi
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Michael Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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140
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Cui L, Cheng H, Yang Z, Xia C, Zhang L, Kong X. Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3021. [PMID: 37687268 PMCID: PMC10489728 DOI: 10.3390/plants12173021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Wheat (Triticum aestivum L.) is a staple food crop that provides 20% of total human calorie consumption. Gene duplication has been considered to play an important role in evolution by providing new genetic resources. However, the evolutionary fates and biological functions of the duplicated genes in wheat remain to be elucidated. In this study, the resulting data showed that the duplicated genes evolved faster with shorter gene lengths, higher codon usage bias, lower expression levels, and higher tissue specificity when compared to non-duplicated genes. Our analysis further revealed functions of duplicated genes in various biological processes with significant enrichment to environmental stresses. In addition, duplicated genes derived from dispersed, proximal, tandem, transposed, and whole-genome duplication differed in abundance, evolutionary rate, gene compactness, expression pattern, and genetic diversity. Tandem and proximal duplicates experienced stronger selective pressure and showed a more compact gene structure with diverse expression profiles than other duplication modes. Moreover, genes derived from different duplication modes showed an asymmetrical evolutionary pattern for wheat A, B, and D subgenomes. Several candidate duplication hotspots associated with wheat domestication or polyploidization were characterized as potential targets for wheat molecular breeding. Our comprehensive analysis revealed the evolutionary trajectory of duplicated genes and laid the foundation for future functional studies on wheat.
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Affiliation(s)
- Licao Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hao Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Zhe Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
| | - Chuan Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
| | - Lichao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
| | - Xiuying Kong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.C.); (H.C.); (Z.Y.); (C.X.); (L.Z.)
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141
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Li J, Wiebenga A, Lipzen A, Ng V, Tejomurthula S, Zhang Y, Grigoriev IV, Peng M, de Vries RP. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi. J Fungi (Basel) 2023; 9:860. [PMID: 37623631 PMCID: PMC10455118 DOI: 10.3390/jof9080860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.
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Affiliation(s)
- Jiajia Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Sravanthi Tejomurthula
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
| | - Igor V. Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA; (A.L.); (V.N.); (S.T.); (Y.Z.); (I.V.G.)
- Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; (J.L.); (M.P.)
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142
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Li Y, Yang H, Guo J, Yang Y, Yu Q, Guo Y, Zhang C, Wang Z, Zuo P. Uncovering the candidate genes related to sheep body weight using multi-trait genome-wide association analysis. Front Vet Sci 2023; 10:1206383. [PMID: 37662987 PMCID: PMC10469697 DOI: 10.3389/fvets.2023.1206383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
In sheep, body weight is an economically important trait. This study sought to map genetic loci related to weaning weight and yearling weight. To this end, a single-trait and multi-trait genome-wide association study (GWAS) was performed using a high-density 600 K single nucleotide polymorphism (SNP) chip. The results showed that 43 and 56 SNPs were significantly associated with weaning weight and yearling weight, respectively. A region associated with both weaning and yearling traits (OARX: 6.74-7.04 Mb) was identified, suggesting that the same genes could play a role in regulating both these traits. This region was found to contain three genes (TBL1X, SHROOM2 and GPR143). The most significant SNP was Affx-281066395, located at 6.94 Mb (p = 1.70 × 10-17), corresponding to the SHROOM2 gene. We also identified 93 novel SNPs elated to sheep weight using multi-trait GWAS analysis. A new genomic region (OAR10: 76.04-77.23 Mb) with 22 significant SNPs were discovered. Combining transcriptomic data from multiple tissues and genomic data in sheep, we found the HINT1, ASB11 and GPR143 genes may involve in sheep body weight. So, multi-omic anlaysis is a valuable strategy identifying candidate genes related to body weight.
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Affiliation(s)
- Yunna Li
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Jing Guo
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Chaoxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University,, Harbin, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
| | - Peng Zuo
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science,, Shihezi, China
- College of Science, Northeast Agricultural University, Harbin, China
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143
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Cervantes S, Kesälahti R, Kumpula TA, Mattila TM, Helanterä H, Pyhäjärvi T. Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory. Mol Biol Evol 2023; 40:msad183. [PMID: 37565532 PMCID: PMC10457172 DOI: 10.1093/molbev/msad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023] Open
Abstract
The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in a diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intraspecific competition. Evidence from other plant groups is scarce, and results show no support for the masking theory. Here, we have used a gymnosperm Scots pine megagametophyte, a maternally derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue and that this signal of strong selection is not an artifact driven by high expression levels.
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Affiliation(s)
- Sandra Cervantes
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Robert Kesälahti
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Timo A Kumpula
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Tiina M Mattila
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Heikki Helanterä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Tanja Pyhäjärvi
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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144
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Kong W, Zhu Q, Zhang Q, Zhu Y, Yang J, Chai K, Lei W, Jiang M, Zhang S, Lin J, Zhang X. 5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant ( Camellia sinensis L.). HORTICULTURE RESEARCH 2023; 10:uhad126. [PMID: 37560013 PMCID: PMC10407603 DOI: 10.1093/hr/uhad126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
Abstract
In plants, 5mC DNA methylation is an important and conserved epistatic mark involving genomic stability, gene transcriptional regulation, developmental regulation, abiotic stress response, metabolite synthesis, etc. However, the roles of 5mC DNA methylation modification (5mC methylation) in tea plant growth and development (in pre-harvest processing) and flavor substance synthesis in pre- and post-harvest processing are unknown. We therefore conducted a comprehensive methylation analysis of four key pre-harvest tissues (root, leaf, flower, and fruit) and two processed leaves during oolong tea post-harvest processing. We found that differential 5mC methylation among four key tissues is closely related to tissue functional differentiation and that genes expressed tissue-specifically, responsible for tissue-specific functions, maintain relatively low 5mC methylation levels relative to non-tissue-specifically expressed genes. Importantly, hypomethylation modifications of CsAlaDC and TS/GS genes in roots provided the molecular basis for the dominant synthesis of theanine in roots. In addition, integration of 5mC DNA methylationomics, metabolomics, and transcriptomics of post-harvest leaves revealed that content changes in flavor metabolites during oolong tea processing were closely associated with transcription level changes in corresponding metabolite synthesis genes, and changes in transcript levels of these important synthesis genes were strictly regulated by 5mC methylation. We further report that some key genes during processing are regulated by 5mC methylation, which can effectively explain the content changes of important aroma metabolites, including α-farnesene, nerolidol, lipids, and taste substances such as catechins. Our results not only highlight the key roles of 5mC methylation in important flavor substance synthesis in pre- and post-harvest processing, but also provide epimutation-related gene targets for future improvement of tea quality or breeding of whole-tissue high-theanine varieties.
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Affiliation(s)
- Weilong Kong
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Qiufang Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qing Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Yiwang Zhu
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Jingjing Yang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Kun Chai
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Wenlong Lei
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Mengwei Jiang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Shengcheng Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
| | - Jinke Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xingtan Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangzhou 518120, China
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145
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Walker KA, Chen J, Shi L, Yang Y, Fornage M, Zhou L, Schlosser P, Surapaneni A, Grams ME, Duggan MR, Peng Z, Gomez GT, Tin A, Hoogeveen RC, Sullivan KJ, Ganz P, Lindbohm JV, Kivimaki M, Nevado-Holgado AJ, Buckley N, Gottesman RF, Mosley TH, Boerwinkle E, Ballantyne CM, Coresh J. Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life. Sci Transl Med 2023; 15:eadf5681. [PMID: 37467317 PMCID: PMC10665113 DOI: 10.1126/scitranslmed.adf5681] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/28/2023] [Indexed: 07/21/2023]
Abstract
A diverse set of biological processes have been implicated in the pathophysiology of Alzheimer's disease (AD) and related dementias. However, there is limited understanding of the peripheral biological mechanisms relevant in the earliest phases of the disease. Here, we used a large-scale proteomics platform to examine the association of 4877 plasma proteins with 25-year dementia risk in 10,981 middle-aged adults. We found 32 dementia-associated plasma proteins that were involved in proteostasis, immunity, synaptic function, and extracellular matrix organization. We then replicated the association between 15 of these proteins and clinically relevant neurocognitive outcomes in two independent cohorts. We demonstrated that 12 of these 32 dementia-associated proteins were associated with cerebrospinal fluid (CSF) biomarkers of AD, neurodegeneration, or neuroinflammation. We found that eight of these candidate protein markers were abnormally expressed in human postmortem brain tissue from patients with AD, although some of the proteins that were most strongly associated with dementia risk, such as GDF15, were not detected in these brain tissue samples. Using network analyses, we found a protein signature for dementia risk that was characterized by dysregulation of specific immune and proteostasis/autophagy pathways in adults in midlife ~20 years before dementia onset, as well as abnormal coagulation and complement signaling ~10 years before dementia onset. Bidirectional two-sample Mendelian randomization genetically validated nine of our candidate proteins as markers of AD in midlife and inferred causality of SERPINA3 in AD pathogenesis. Last, we prioritized a set of candidate markers for AD and dementia risk prediction in midlife.
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Affiliation(s)
- Keenan A. Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA
| | - Jingsha Chen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Liu Shi
- Novo Nordisk Research Centre Oxford (NNRCO), Oxford OX3 7FZ, UK
| | - Yunju Yang
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School and Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School and Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Pascal Schlosser
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21210, USA
| | - Michael R. Duggan
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA
| | - Zhongsheng Peng
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA
| | - Gabriela T. Gomez
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21210, USA
| | - Adrienne Tin
- MIND Center and Division of Nephrology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ron C. Hoogeveen
- Section of Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin J. Sullivan
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Peter Ganz
- Department of Medicine, University of California-San Francisco, San Francisco, CA 94115, USA
| | - Joni V. Lindbohm
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Mika Kivimaki
- Department of Mental Health of Older People, Faculty of Brain Sciences, University College London, London WC1E 6BT, UK
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki 00100, Finland
| | | | - Noel Buckley
- Department of Psychiatry, University of Oxford, Oxford OX1 2JD, UK
| | - Rebecca F. Gottesman
- National Institute of Neurological Disorders and Stroke, Intramural Research Program, Bethesda, MD 20892, USA
| | - Thomas H. Mosley
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie M. Ballantyne
- Section of Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
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146
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Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera-Maneu S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. A protein-coding gene expression atlas from the brain of pregnant and non-pregnant goats. Front Genet 2023; 14:1114749. [PMID: 37519888 PMCID: PMC10382233 DOI: 10.3389/fgene.2023.1114749] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Background: The brain is an extraordinarily complex organ with multiple anatomical structures involved in highly specialized functions related with behavior and physiological homeostasis. Our goal was to build an atlas of protein-coding gene expression in the goat brain by sequencing the transcriptomes of 12 brain regions in seven female Murciano-Granadina goats, from which three of them were 1-month pregnant. Results: Between 14,889 (cerebellar hemisphere) and 15,592 (pineal gland) protein-coding genes were expressed in goat brain regions, and most of them displayed ubiquitous or broad patterns of expression across tissues. Principal component analysis and hierarchical clustering based on the patterns of mRNA expression revealed that samples from certain brain regions tend to group according to their position in the anterior-posterior axis of the neural tube, i.e., hindbrain (pons and medulla oblongata), midbrain (rostral colliculus) and forebrain (frontal neocortex, olfactory bulb, hypothalamus, and hippocampus). Exceptions to this observation were cerebellum and glandular tissues (pineal gland and hypophysis), which showed highly divergent mRNA expression profiles. Differential expression analysis between pregnant and non-pregnant goats revealed moderate changes of mRNA expression in the frontal neocortex, hippocampus, adenohypophysis and pons, and very dramatic changes in the olfactory bulb. Many genes showing differential expression in this organ are related to olfactory function and behavior in humans. Conclusion: With the exception of cerebellum and glandular tissues, there is a relationship between the cellular origin of sampled regions along the anterior-posterior axis of the neural tube and their mRNA expression patterns in the goat adult brain. Gestation induces substantial changes in the mRNA expression of the olfactory bulb, a finding consistent with the key role of this anatomical structure on the development of maternal behavior.
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Affiliation(s)
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Manel López-Béjar
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Encarna Casas
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sergi Olvera-Maneu
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jaume Gardela
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - María Jesús Palomo
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Uchebuchi Ike Osuagwuh
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Uchechi Linda Ohaneje
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
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147
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Singh AK, Amar I, Ramadasan H, Kappagantula KS, Chavali S. Proteins with amino acid repeats constitute a rapidly evolvable and human-specific essentialome. Cell Rep 2023; 42:112811. [PMID: 37453061 DOI: 10.1016/j.celrep.2023.112811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/30/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023] Open
Abstract
Protein products of essential genes, indispensable for organismal survival, are highly conserved and bring about fundamental functions. Interestingly, proteins that contain amino acid homorepeats that tend to evolve rapidly are enriched in eukaryotic essentialomes. Why are proteins with hypermutable homorepeats enriched in conserved and functionally vital essential proteins? We solve this functional versus evolutionary paradox by demonstrating that human essential proteins with homorepeats bring about crosstalk across biological processes through high interactability and have distinct regulatory functions affecting expansive global regulation. Importantly, essential proteins with homorepeats rapidly diverge with the amino acid substitutions frequently affecting functional sites, likely facilitating rapid adaptability. Strikingly, essential proteins with homorepeats influence human-specific embryonic and brain development, implying that the presence of homorepeats could contribute to the emergence of human-specific processes. Thus, we propose that homorepeat-containing essential proteins affecting species-specific traits can be potential intervention targets across pathologies, including cancers and neurological disorders.
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Affiliation(s)
- Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Ishita Amar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Harikrishnan Ramadasan
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Keertana S Kappagantula
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India.
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148
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Feng T, Pucker B, Kuang T, Song B, Yang Y, Lin N, Zhang H, Moore MJ, Brockington SF, Wang Q, Deng T, Wang H, Sun H. The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation. Commun Biol 2023; 6:706. [PMID: 37429977 DOI: 10.1038/s42003-023-05044-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/14/2023] [Indexed: 07/12/2023] Open
Abstract
Glasshouse plants are species that trap warmth via specialized morphology and physiology, mimicking a human glasshouse. In the Himalayan alpine region, the highly specialized glasshouse morphology has independently evolved in distinct lineages to adapt to intensive UV radiation and low temperature. Here we demonstrate that the glasshouse structure - specialized cauline leaves - is highly effective in absorbing UV light but transmitting visible and infrared light, creating an optimal microclimate for the development of reproductive organs. We reveal that this glasshouse syndrome has evolved at least three times independently in the rhubarb genus Rheum. We report the genome sequence of the flagship glasshouse plant Rheum nobile and identify key genetic network modules in association with the morphological transition to specialized glasshouse leaves, including active secondary cell wall biogenesis, upregulated cuticular cutin biosynthesis, and suppression of photosynthesis and terpenoid biosynthesis. The distinct cell wall organization and cuticle development might be important for the specialized optical property of glasshouse leaves. We also find that the expansion of LTRs has likely played an important role in noble rhubarb adaptation to high elevation environments. Our study will enable additional comparative analyses to identify the genetic basis underlying the convergent occurrence of glasshouse syndrome.
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Affiliation(s)
- Tao Feng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Boas Pucker
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
- CeBiTec & Faculty of Biology, Bielefeld University, Universitaetsstrasse, Bielefeld, 33615, Germany
- Institute of Plant Biology & BRICS, TU Braunschweig, 38106, Braunschweig, Germany
| | - Tianhui Kuang
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Bo Song
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, St. Paul, MN, 55108, USA
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Qingfeng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Tao Deng
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
| | - Hang Sun
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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149
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Bai J, Lin Y, Zhang J, Chen Z, Wang Y, Li M, Li J. Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages. Int J Mol Sci 2023; 24:11076. [PMID: 37446255 DOI: 10.3390/ijms241311076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The study of chromatin accessibility across tissues and developmental stages is essential for elucidating the transcriptional regulation of various phenotypes and biological processes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development remain poorly investigated. Here, we used ATAC-seq and rRNA-depleted RNA-seq to profile open chromatin maps and transcriptional features of heart, kidney, liver, lung, skeletal muscle, and spleen in newborn pigs and porcine liver tissue in the suckling and adult stages, respectively. Specifically, by analyzing a union set of protein-coding genes (PCGs) and two types of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage. As expected, the PCGs with tissue-specific accessible promoters had active transcription and were relevant to tissue-specific functions. In addition, other non-coding tissue-specific peaks were involved in both physical activity and the morphogenesis of neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands our current understanding of epigenetic regulation in mammalian tissues and organ development, which can benefit both economic trait improvement and improve the biomedical usage of pigs.
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Affiliation(s)
- Jingyi Bai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziyu Chen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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150
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Mbebi AJ, Nikoloski Z. Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection. PLoS Comput Biol 2023; 19:e1010832. [PMID: 37523414 PMCID: PMC10414675 DOI: 10.1371/journal.pcbi.1010832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/10/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Despite extensive research efforts, reconstruction of gene regulatory networks (GRNs) from transcriptomics data remains a pressing challenge in systems biology. While non-linear approaches for reconstruction of GRNs show improved performance over simpler alternatives, we do not yet have understanding if joint modelling of multiple target genes may improve performance, even under linearity assumptions. To address this problem, we propose two novel approaches that cast the GRN reconstruction problem as a blend between regularized multivariate regression and graphical models that combine the L2,1-norm with classical regularization techniques. We used data and networks from the DREAM5 challenge to show that the proposed models provide consistently good performance in comparison to contenders whose performance varies with data sets from simulation and experiments from model unicellular organisms Escherichia coli and Saccharomyces cerevisiae. Since the models' formulation facilitates the prediction of master regulators, we also used the resulting findings to identify master regulators over all data sets as well as their plasticity across different environments. Our results demonstrate that the identified master regulators are in line with experimental evidence from the model bacterium E. coli. Together, our study demonstrates that simultaneous modelling of several target genes results in improved inference of GRNs and can be used as an alternative in different applications.
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Affiliation(s)
- Alain J. Mbebi
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Germany
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Germany
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