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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00723-z. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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2
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Atkinson R, Georgiou M, Yang C, Szymanska K, Lahat A, Vasconcelos EJR, Ji Y, Moya Molina M, Collin J, Queen R, Dorgau B, Watson A, Kurzawa-Akanbi M, Laws R, Saxena A, Shyan Beh C, Siachisumo C, Goertler F, Karwatka M, Davey T, Inglehearn CF, McKibbin M, Lührmann R, Steel DH, Elliott DJ, Armstrong L, Urlaub H, Ali RR, Grellscheid SN, Johnson CA, Mozaffari-Jovin S, Lako M. PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5´-splice-site selection causing tissue-specific defects. Nat Commun 2024; 15:3138. [PMID: 38605034 PMCID: PMC11009313 DOI: 10.1038/s41467-024-47253-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926 A > C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5'-splice site (5'SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5'SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches.
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Affiliation(s)
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Albert Lahat
- Department of Biosciences, Durham University, Durham, UK
| | | | - Yanlong Ji
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Marina Moya Molina
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Avril Watson
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | | | - Ross Laws
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Abhijit Saxena
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chia Shyan Beh
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | | | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Reinhard Lührmann
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David H Steel
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Henning Urlaub
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg August University of Göttingen, Göttingen, Germany
| | - Robin R Ali
- Centre for Cell and Gene Therapy, Kings College London, London, UK
| | - Sushma-Nagaraja Grellscheid
- Department of Biosciences, Durham University, Durham, UK
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Colin A Johnson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
| | - Sina Mozaffari-Jovin
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Department of Medical Genetics and Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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3
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Korchak JA, Jeffery ED, Bandyopadhyay S, Jordan BT, Lehe M, Watts EF, Fenix A, Wilhelm M, Sheynkman GM. IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. bioRxiv 2024:2024.04.01.587549. [PMID: 38617311 PMCID: PMC11014528 DOI: 10.1101/2024.04.01.587549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of pre-defined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (LR RNAseq) data to predict potential protein isoforms with prior transcript evidence. Predicted tryptic isoform-specific peptides, which are specific to individual gene product isoforms, serve as "triggers" and "targets" in the IS-PRM method, Tomahto. Using the model human stem cell line WTC11, LR RNAseq data were generated and used to inform the generation of synthetic standards for 192 isoform-specific peptides (114 isoforms from 55 genes). These synthetic "trigger" peptides were labeled with super heavy tandem mass tags (TMT) and spiked into TMT-labeled WTC11 tryptic digest, predicted to contain corresponding endogenous "target" peptides. Compared to DDA mode, Tomahto increased detectability of isoforms by 3.6-fold, resulting in the identification of five previously unannotated isoforms. Our method detected protein isoform expression for 43 out of 55 genes corresponding to 54 resolved isoforms. This LR RNA seq-informed Tomahto targeted approach, called LRP-IS-PRM, is a new modality for generating protein-level evidence of alternative isoforms - a critical first step in designing functional studies and eventually clinical assays.
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Affiliation(s)
- Jennifer A. Korchak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Erin D. Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Saikat Bandyopadhyay
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ben T. Jordan
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Micah Lehe
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Emily F. Watts
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Aidan Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
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4
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Bénitière F, Necsulea A, Duret L. Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. eLife 2024; 13:RP93629. [PMID: 38470242 DOI: 10.7554/elife.93629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that 'complex' organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this 'drift barrier' theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
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5
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Beiki H, Murdoch BM, Park CA, Kern C, Kontechy D, Becker G, Rincon G, Jiang H, Zhou H, Thorne J, Koltes JE, Michal JJ, Davenport K, Rijnkels M, Ross PJ, Hu R, Corum S, McKay S, Smith TPL, Liu W, Ma W, Zhang X, Xu X, Han X, Jiang Z, Hu ZL, Reecy JM. Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. Gigascience 2024; 13:giae019. [PMID: 38626724 PMCID: PMC11020238 DOI: 10.1093/gigascience/giae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/29/2023] [Accepted: 03/27/2024] [Indexed: 04/18/2024] Open
Abstract
BACKGROUND The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues. RESULTS A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5' untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. CONCLUSIONS These validated results show significant improvement over current bovine genome annotations.
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Affiliation(s)
- Hamid Beiki
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Brenda M Murdoch
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - Carissa A Park
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Chandlar Kern
- Department of Animal Science, Pennsylvania State University, PA 16802, USA
| | - Denise Kontechy
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - Gabrielle Becker
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | | | - Honglin Jiang
- Department of Animal and Poultry Sciences, Virginia Tech, VA 24060, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Jacob Thorne
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jennifer J Michal
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Kimberly Davenport
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - Monique Rijnkels
- Department of Veterinary Integrative Biosciences, Texas A&M University, TX 77843, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Rui Hu
- Department of Animal and Poultry Sciences, Virginia Tech, VA 24060, USA
| | - Sarah Corum
- Zoetis, Parsippany-Troy Hills, NJ 07054, USA
| | | | | | - Wansheng Liu
- Department of Animal Science, Pennsylvania State University, PA 16802, USA
| | - Wenzhi Ma
- Department of Animal Science, Pennsylvania State University, PA 16802, USA
| | - Xiaohui Zhang
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Xiaoqing Xu
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Xuelei Han
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Zhihua Jiang
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Zhi-Liang Hu
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
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6
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Malakar P, Shukla S, Mondal M, Kar RK, Siddiqui JA. The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. RNA Biol 2024; 21:1-20. [PMID: 38017665 PMCID: PMC10761143 DOI: 10.1080/15476286.2023.2286099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
The process of alternative splicing (AS) is widely deregulated in a variety of cancers. Splicing is dependent upon splicing factors. Recently, several long noncoding RNAs (lncRNAs) have been shown to regulate AS by directly/indirectly interacting with splicing factors. This review focuses on the regulation of AS by lncRNAs through their interaction with splicing factors. AS mis-regulation caused by either mutation in splicing factors or deregulated expression of splicing factors and lncRNAs has been shown to be involved in cancer development and progression, making aberrant splicing, splicing factors and lncRNA suitable targets for cancer therapy. This review also addresses some of the current approaches used to target AS, splicing factors and lncRNAs. Finally, we discuss research challenges, some of the unanswered questions in the field and provide recommendations to advance understanding of the nexus of lncRNAs, AS and splicing factors in cancer.
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Affiliation(s)
- Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Meghna Mondal
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Rajesh Kumar Kar
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
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Wang Z, Tian W, Wang D, Guo Y, Cheng Z, Zhang Y, Li X, Zhi Y, Li D, Li Z, Jiang R, Li G, Tian Y, Kang X, Li H, Dunn IC, Liu X. Comparative analyses of dynamic transcriptome profiles highlight key response genes and dominant isoforms for muscle development and growth in chicken. Genet Sel Evol 2023; 55:73. [PMID: 37872550 PMCID: PMC10591418 DOI: 10.1186/s12711-023-00849-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Modern breeding strategies have resulted in significant differences in muscle mass between indigenous chicken and specialized broiler. However, the molecular regulatory mechanisms that underlie these differences remain elusive. The aim of this study was to identify key genes and regulatory mechanisms underlying differences in breast muscle development between indigenous chicken and specialized broiler. RESULTS Two time-series RNA-sequencing profiles of breast muscles were generated from commercial Arbor Acres (AA) broiler (fast-growing) and Chinese indigenous Lushi blue-shelled-egg (LS) chicken (slow-growing) at embryonic days 10, 14, and 18, and post-hatching day 1 and weeks 1, 3, and 5. Principal component analysis of the transcriptome profiles showed that the top four principal components accounted for more than 80% of the total variance in each breed. The developmental axes between the AA and LS chicken overlapped at the embryonic stages but gradually separated at the adult stages. Integrative investigation of differentially-expressed transcripts contained in the top four principal components identified 44 genes that formed a molecular network associated with differences in breast muscle mass between the two breeds. In addition, alternative splicing analysis revealed that genes with multiple isoforms always had one dominant transcript that exhibited a significantly higher expression level than the others. Among the 44 genes, the TNFRSF6B gene, a mediator of signal transduction pathways and cell proliferation, harbored two alternative splicing isoforms, TNFRSF6B-X1 and TNFRSF6B-X2. TNFRSF6B-X1 was the dominant isoform in both breeds before the age of one week. A switching event of the dominant isoform occurred at one week of age, resulting in TNFRSF6B-X2 being the dominant isoform in AA broiler, whereas TNFRSF6B-X1 remained the dominant isoform in LS chicken. Gain-of-function assays demonstrated that both isoforms promoted the proliferation of chicken primary myoblasts, but only TNFRSF6B-X2 augmented the differentiation and intracellular protein content of chicken primary myoblasts. CONCLUSIONS For the first time, we identified several key genes and dominant isoforms that may be responsible for differences in muscle mass between slow-growing indigenous chicken and fast-growing commercial broiler. These findings provide new insights into the regulatory mechanisms underlying breast muscle development in chicken.
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Affiliation(s)
- Zhang Wang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Dandan Wang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Yulong Guo
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Zhimin Cheng
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Yanyan Zhang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Xinyan Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Yihao Zhi
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China.
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China.
| | - Ian C Dunn
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, No. 63, Nongye Road, Zhengzhou, 450002, China.
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, 450002, China.
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8
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. Nature 2023; 622:41-47. [PMID: 37794265 PMCID: PMC10575709 DOI: 10.1038/s41586-023-06490-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/27/2023] [Indexed: 10/06/2023]
Abstract
Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, Sao Paulo, Brazil
| | | | - Francisco M De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Tempus Labs, Chicago, IL, USA
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Royston, UK
| | - Artemis G Hatzigeorgiou
- Department of Computer Science and Biomedical Informatics, Universithy of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Human Technopole, Milan, Italy.
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
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9
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Mehta P, Chattopadhyay P, Ravi V, Tarai B, Budhiraja S, Pandey R. SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing. Microbiol Spectr 2023; 11:e0135123. [PMID: 37604131 PMCID: PMC10580830 DOI: 10.1128/spectrum.01351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/16/2023] [Indexed: 08/23/2023] Open
Abstract
Like single-stranded RNA viruses, SARS-CoV-2 hijacks the host transcriptional machinery for its own replication. Numerous traditional differential gene expression-based investigations have examined the diverse clinical symptoms caused by SARS-CoV-2 infection. The virus, on the other hand, also affects the host splicing machinery, causing host transcriptional dysregulation, which can lead to diverse clinical outcomes. Hence, in this study, we performed host transcriptome sequencing of 125 hospital-admitted COVID-19 patients to understand the transcriptomic differences between the severity sub-phenotypes of mild, moderate, severe, and mortality. We performed transcript-level differential expression analysis, investigated differential isoform usage, looked at the splicing patterns within the differentially expressed transcripts (DET), and elucidated the possible genome regulatory features. Our DTE analysis showed evidence of diminished transcript length and diversity as well as altered promoter site usage in the differentially expressed protein-coding transcripts in the COVID-19 mortality patients. We also investigated the potential mechanisms driving the alternate splicing and discovered a compelling differential enrichment of repeats in the promoter region and a specific enrichment of SINE (Alu) near the splicing sites of differentially expressed transcripts. These findings suggested a repeat-mediated plausible regulation of alternative splicing as a potential modulator of COVID-19 disease severity. In this work, we emphasize the role of scarcely elucidated functional role of alternative splicing in influencing COVID-19 disease severity sub-phenotypes, clinical outcomes, and its putative mechanism. IMPORTANCE The wide range of clinical symptoms reported during the COVID-19 pandemic inherently highlights the numerous factors that influence the progression and prognosis of SARS-CoV-2 infection. While several studies have investigated the host response and discovered immunological dysregulation during severe infection, most of them have the common theme of focusing only up to the gene level. Viruses, especially RNA viruses, are renowned for hijacking the host splicing machinery for their own proliferation, which inadvertently puts pressure on the host transcriptome, exposing another side of the host response to the pathogen challenge. Therefore, in this study, we examine host response at the transcript-level to discover a transcriptional difference that culminates in differential gene-level expression. Importantly, this study highlights diminished transcript diversity and possible regulation of transcription by differentially abundant repeat elements near the promoter region and splicing sites in COVID-19 mortality patients, which together with differentially expressed isoforms hold the potential to elaborate disease severity and outcome.
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Affiliation(s)
- Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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10
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Abstract
Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced. Identifying genes in these sequences is essential to understand the biology of the species. This is challenging due to the transcriptional complexity of eukaryotic genomes, which encode hundreds of thousands of transcripts of multiple types. Among these, a small set of protein-coding mRNAs play a disproportionately large role in defining phenotypes. Due to their sequence conservation, orthology can be established, making it possible to define the universal catalog of eukaryotic protein-coding genes. This catalog should substantially contribute to uncovering the genomic events underlying the emergence of eukaryotic phenotypes. This piece briefly reviews the basics of protein-coding gene prediction, discusses challenges in finalizing annotation of the human genome, and proposes strategies for producing annotations across the eukaryotic Tree of Life. This lays the groundwork for obtaining the catalog of all genes-the Earth's code of life.
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Affiliation(s)
- Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Catalonia
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia
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11
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Chen Y, Sim A, Wan YK, Yeo K, Lee JJX, Ling MH, Love MI, Göke J. Context-aware transcript quantification from long-read RNA-seq data with Bambu. Nat Methods 2023; 20:1187-1195. [PMID: 37308696 PMCID: PMC10448944 DOI: 10.1038/s41592-023-01908-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/08/2023] [Indexed: 06/14/2023]
Abstract
Most approaches to transcript quantification rely on fixed reference annotations; however, the transcriptome is dynamic and depending on the context, such static annotations contain inactive isoforms for some genes, whereas they are incomplete for others. Here we present Bambu, a method that performs machine-learning-based transcript discovery to enable quantification specific to the context of interest using long-read RNA-sequencing. To identify novel transcripts, Bambu estimates the novel discovery rate, which replaces arbitrary per-sample thresholds with a single, interpretable, precision-calibrated parameter. Bambu retains the full-length and unique read counts, enabling accurate quantification in presence of inactive isoforms. Compared to existing methods for transcript discovery, Bambu achieves greater precision without sacrificing sensitivity. We show that context-aware annotations improve quantification for both novel and known transcripts. We apply Bambu to quantify isoforms from repetitive HERVH-LTR7 retrotransposons in human embryonic stem cells, demonstrating the ability for context-specific transcript expression analysis.
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Affiliation(s)
- Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Andre Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Keith Yeo
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Joseph Jing Xian Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Min Hao Ling
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Department of Statistics and Data Science, National University of Singapore, Singapore, Republic of Singapore.
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12
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Dalmasso B, Ghiorzo P. Long Non-Coding RNAs and Metabolic Rewiring in Pancreatic Cancer. Cancers (Basel) 2023; 15:3486. [PMID: 37444595 DOI: 10.3390/cancers15133486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Pancreatic adenocarcinoma is a highly aggressive disease with a poor prognosis. The reprogramming of energetic metabolism has long been implicated in pancreatic tumorigenesis and/or resistance to treatment. Considering that long non-coding RNA dysregulation has been described both in cancerogenesis and in the altered homeostasis of several metabolic pathways, metabolism-associated lncRNAs can contribute to pancreatic cancer evolution. The objective of this review is to assess the burden of lncRNA dysregulation in pancreatic cancer metabolic reprogramming, and its effect on this tumor's natural course and response to treatment. Therefore, we reviewed the available literature to assess whether metabolism-associated lncRNAs have been found to be differentially expressed in pancreatic cancer, as well as whether experimental evidence of their role in such pathways can be demonstrated. Specifically, we provide a comprehensive overview of lncRNAs that are implicated in hypoxia-related pathways, as well as in the reprogramming of autophagy, lipid metabolism, and amino acid metabolism. Our review gathers background material for further research on possible applications of metabolism-associated lncRNAs as diagnostic/prognostic biomarkers and/or as potential therapeutic targets in pancreatic adenocarcinoma.
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Affiliation(s)
- Bruna Dalmasso
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy
| | - Paola Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
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13
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Dolgalev G, Poverennaya E. Quantitative Analysis of Isoform Switching in Cancer. Int J Mol Sci 2023; 24:10065. [PMID: 37373214 DOI: 10.3390/ijms241210065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/26/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Over the past 8 years, multiple studies examined the phenomenon of isoform switching in human cancers and discovered that isoform switching is widespread, with hundreds to thousands of such events per cancer type. Although all of these studies used slightly different definitions of isoform switching, which in part led to a rather poor overlap of their results, they all leveraged transcript usage, a proportion of the transcript's expression in the total expression level of the parent gene, to detect isoform switching. However, how changes in transcript usage correlate with changes in transcript expression is not sufficiently explored. In this article, we adopt the most common definition of isoform switching and use a state-of-the-art tool for the analysis of differential transcript usage, SatuRn, to detect isoform switching events in 12 cancer types. We analyze the detected events in terms of changes in transcript usage and the relationship between transcript usage and transcript expression on a global scale. The results of our analysis suggest that the relationship between changes in transcript usage and changes in transcript expression is far from straightforward, and that such quantitative information can be effectively used for prioritizing isoform switching events for downstream analyses.
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14
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 295] [Impact Index Per Article: 295.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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15
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. ArXiv 2023:arXiv:2303.13996v1. [PMID: 36994150 PMCID: PMC10055485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, São Paulo, SP, Brasil
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Francisco M. De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA; Tempus Labs, Inc., Chicago, IL
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Da Vinci Building. Melbourn Science Park, Royston UK SG8 6HB
| | - Artemis G. Hatzigeorgiou
- Universithy of Thessaly, Department of Computer Science and Biomedical Informatics, Lamia, Greece; Hellenic Pasteur Institute, Athens, Greece
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, D04 V1W8 Dublin, Ireland; Conway Institute of Biomedical and Biomolecular Research, University College Dublin, D04 V1W8 Dublin, Ireland; Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Terence D. Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama Kanagawa 230-0045 Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ales Varabyou
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A. Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010 Vic Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Human Technopole, via Rita Levi Montalcini 1, Milan 20157 Italy
| | - Steven L. Salzberg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
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16
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Vaquero-Garcia J, Aicher JK, Jewell S, Gazzara MR, Radens CM, Jha A, Norton SS, Lahens NF, Grant GR, Barash Y. RNA splicing analysis using heterogeneous and large RNA-seq datasets. Nat Commun 2023; 14:1230. [PMID: 36869033 PMCID: PMC9984406 DOI: 10.1038/s41467-023-36585-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/06/2023] [Indexed: 03/05/2023] Open
Abstract
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit increased variability compared to biological replicates, and involve thousands of unannotated splice variants resulting in increased transcriptome complexity. We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we assess the advantages of MAJIQ v2 compared to existing methods. We then apply MAJIQ v2 package to analyze differential splicing across 2,335 samples from 13 brain subregions, demonstrating its ability to offer insights into brain subregion-specific splicing regulation.
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Affiliation(s)
| | - Joseph K Aicher
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - San Jewell
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew R Gazzara
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Caleb M Radens
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Anupama Jha
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott S Norton
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory R Grant
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yoseph Barash
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA.
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17
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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18
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Mukherjee SB, Mukherjee S, Detroja R, Frenkel-Morgenstern M. The landscape of differential splicing and transcript alternations in severe COVID-19 infection. FEBS J 2023. [PMID: 36628954 DOI: 10.1111/febs.16723] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/25/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Viral infections can modulate the widespread alternations of cellular splicing, favouring viral replication within the host cells by overcoming host immune responses. However, how SARS-CoV-2 induces host cell differential splicing and affects the landscape of transcript alternation in severe COVID-19 infection remains elusive. Understanding the differential splicing and transcript alternations in severe COVID-19 infection may improve our molecular insights into the SARS-CoV-2 pathogenesis. In this study, we analysed the publicly available blood and lung transcriptome data of severe COVID-19 patients, blood transcriptome data of recovered COVID-19 patients at 12-, 16- and 24-week postinfection and healthy controls. We identified a significant transcript isoform switching in the individual blood and lung RNA-seq data of severe COVID-19-infected patients and 25 common genes that alter their transcript isoform in both blood and lung samples. Altered transcripts show significant loss of the open reading frame, functional domains and switch from coding to noncoding transcript, impacting normal cellular functions. Furthermore, we identified the expression of several novel recurrent chimeric transcripts in the blood samples from severe COVID-19 patients. Moreover, the analysis of the isoform switching into blood samples from recovered COVID-19 patients highlights that there is no significant isoform switching in 16- and 24-week postinfection, and the levels of expressed chimeric transcripts are reduced. This finding emphasizes that SARS-CoV-2 severe infection induces widespread splicing in the host cells, which could help the virus alter the host immune responses and facilitate the viral replication within the host and the efficient translation of viral proteins.
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Affiliation(s)
- Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rajesh Detroja
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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19
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Tung KF, Lin WC. TEx-MST: tissue expression profiles of MANE select transcripts. Database (Oxford) 2022; 2022:6726258. [PMID: 36170113 PMCID: PMC9518666 DOI: 10.1093/database/baac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 12/05/2022]
Abstract
Recently, a new reference transcript dataset [Matched Annotation from the NCBI and EMBL-EBI (MANE) select] was released by NCBI and EMBL-EBI to make available a new unified representative transcript for human protein-coding genes. While the main purpose of MANE project is to provide a harmonized gene and transcript information standard, there is no explicit tissue expression information about these MANE select transcripts. In this report, we tried to provide useful expression profiles of MANE select transcripts in various normal human tissues to allow further interrogation of their molecular modulations and functional significance. We obtained the new V9 transcript expression dataset from the Genotype-Tissue Expression (GTEx) web portal. This new GTEx dataset, based on a long-read sequencing platform, affords better assessment of the expression of alternative spliced transcripts. This tissue expression profiles of MANE select transcripts (TEx-MST) database not only provides the basic information of MANE select transcripts but also tissue expression profiles on alternative transcripts in protein-coding genes. Users can initiate the interrogation by gene symbol searches or by browsing the MANE genes with various criteria (such as genome locations or expression rankings). We further utilized the GENCODE biotype feature to identify the top-ranked protein-coding transcripts by choosing the most expressed protein-coding transcripts from GTEx datasets (both V8 and V9 datasets). In summary, there are 18 083 genes matched between MANE and GTEx. Among them, 13 245 MANE select transcripts matched with the top-ranked protein-coding transcripts in GTEx V9 dataset, which underlined the dominate expression of MANE select transcripts. This TEx-MST web bioinformatic database provides a visualized user interface for the normal tissue expression patterns of MANE select transcripts using the newly released GTEx dataset. Database URL: TEx-MST is available at https://texmst.ibms.sinica.edu.tw/
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Affiliation(s)
- Kuo-Feng Tung
- Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan, R.O.C
| | - Wen-chang Lin
- Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan, R.O.C
- Institute of Biomedical Informatics, National Yang-Ming Chiao Tung University , Taipei 112, Taiwan, R.O.C
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20
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Pozo F, Rodriguez JM, Martínez Gómez L, Vázquez J, Tress ML. APPRIS principal isoforms and MANE Select transcripts define reference splice variants. Bioinformatics 2022; 38:ii89-ii94. [PMID: 36124785 PMCID: PMC9486585 DOI: 10.1093/bioinformatics/btac473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Selecting the splice variant that best represents a coding gene is a crucial first step in many experimental analyses, and vital for mapping clinically relevant variants. This study compares the longest isoforms, MANE Select transcripts, APPRIS principal isoforms, and expression data, and aims to determine which method is best for selecting biological important reference splice variants for large-scale analyses. RESULTS Proteomics analyses and human genetic variation data suggest that most coding genes have a single main protein isoform. We show that APPRIS principal isoforms and MANE Select transcripts best describe these main cellular isoforms, and find that using the longest splice variant as the representative is a poor strategy. Exons unique to the longest splice isoforms are not under selective pressure, and so are unlikely to be functionally relevant. Expression data are also a poor means of selecting the main splice variant. APPRIS principal and MANE Select exons are under purifying selection, while exons specific to alternative transcripts are not. There are MANE and APPRIS representatives for almost 95% of genes, and where they agree they are particularly effective, coinciding with the main proteomics isoform for over 98.2% of genes. AVAILABILITY AND IMPLEMENTATION APPRIS principal isoforms for human, mouse and other model species can be downloaded from the APPRIS database (https://appris.bioinfo.cnio.es), GENCODE genes (https://www.gencodegenes.org/) and the Ensembl website (https://www.ensembl.org). MANE Select transcripts for the human reference set are available from the Ensembl, GENCODE and RefSeq databases (https://www.ncbi.nlm.nih.gov/refseq/). Lists of splice variants where MANE and APPRIS coincide are available from the APPRIS database. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - José Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Laura Martínez Gómez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Jesús Vázquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain,CIBER de Investigaciones Cardiovasculares (CIBERCV), 28029 Madrid, Spain
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21
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Xia W, Jiang H, Guo H, Liu Y, Gou X. Integrated gene co-expression network analysis reveals unique developmental processes of Aurelia aurita. Gene X 2022; 840:146733. [PMID: 35863715 DOI: 10.1016/j.gene.2022.146733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 06/15/2022] [Accepted: 07/08/2022] [Indexed: 11/04/2022] Open
Abstract
The typical life cycle of the moon jellyfish (Aurelia aurita) includes the planula, polyp, strobila, ephyra, and medusa developmental stages. These stages exhibit huge differences in both external morphology and internal physiological functions. However, the gene co-expression network involved in these post-embryonic developmental processes has not been studied yet. Here, based on 15 RNA sequencing samples covering all five stages of the A. aurita life cycle, we systematically analyzed the gene co-expression network and obtained 35 relevant modules. Furthermore, we identified the highly correlated modules and hub genes for each stage. These hub genes are implicated to play important roles in the developmental processes of A. aurita, which should help improve our understanding of the jellyfish life cycle.
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Affiliation(s)
- Wangxiao Xia
- Shaanxi Key Laboratory of Brain Disorders,Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China
| | - Hui Jiang
- College of Life Science, Hainan Normal University, Haikou 571158, China
| | - Huifang Guo
- Shaanxi Key Laboratory of Infection and Immune Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an 710021, China
| | - Yaowen Liu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650231, China.
| | - Xingchun Gou
- Shaanxi Key Laboratory of Brain Disorders,Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China.
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22
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Liu J, Chen S, Liu M, Chen Y, Fan W, Lee S, Xiao H, Kudrna D, Li Z, Chen X, Peng Y, Tian K, Zhang B, Wing RA, Zhang J, Wang X. Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max. Int J Mol Sci 2022; 23:7371. [PMID: 35806374 PMCID: PMC9266934 DOI: 10.3390/ijms23137371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/25/2022] [Accepted: 06/29/2022] [Indexed: 02/04/2023] Open
Abstract
Alternative splicing (AS) is a ubiquitous phenomenon among eukaryotic intron-containing genes, which greatly contributes to transcriptome and proteome diversity. Here we performed the isoform sequencing (Iso-Seq) of soybean underground tissues inoculated and uninoculated with Rhizobium and obtained 200,681 full-length transcripts covering 26,183 gene loci. It was found that 80.78% of the multi-exon loci produced more than one splicing variant. Comprehensive analysis of these identified 7874 differentially splicing events with highly diverse splicing patterns during nodule development, especially in defense and transport-related processes. We further profiled genes with differential isoform usage and revealed that 2008 multi-isoform loci underwent stage-specific or simultaneous major isoform switches after Rhizobium inoculation, indicating that AS is a vital way to regulate nodule development. Moreover, we took the lead in identifying 1563 high-confidence long non-coding RNAs (lncRNAs) in soybean, and 157 of them are differentially expressed during nodule development. Therefore, our study uncovers the landscape of AS during the soybean-Rhizobium interaction and provides systematic transcriptomic data for future study of multiple novel directions in soybean.
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Affiliation(s)
- Jing Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Shengcai Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Min Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
| | - Yimian Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Wei Fan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Han Xiao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Zixin Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
| | - Xu Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Yaqi Peng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Kewei Tian
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (S.C.); (M.L.); (Y.C.); (W.F.); (Z.L.); (X.C.); (K.T.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Bao Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; (S.L.); (D.K.); (R.A.W.); (J.Z.)
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuelu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China; (H.X.); (Y.P.); (B.Z.)
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Kwiatkowski M, Hotze M, Schumacher J, Asif AR, Pittol JMR, Brenig B, Ramljak S, Zischler H, Herlyn H. Protein speciation is likely to increase the chance of proteins to be determined in 2‐DE/MS. Electrophoresis 2022; 43:1203-1214. [DOI: 10.1002/elps.202000393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 11/30/2021] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Marcel Kwiatkowski
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | - Madlen Hotze
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | | | - Abdul R. Asif
- Department of Clinical Chemistry/UMG‐Laboratories University Medical Center Göttingen Germany
| | - Jose Miguel Ramos Pittol
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | - Bertram Brenig
- Department of Molecular Biology of Livestock Institute of Veterinary Medicine University of Göttingen Göttingen Germany
| | | | - Hans Zischler
- Institute of Organismic and Molecular Evolution, Anthropology University of Mainz Mainz Germany
| | - Holger Herlyn
- Institute of Organismic and Molecular Evolution, Anthropology University of Mainz Mainz Germany
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24
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Plawgo K, Raczynska KD. Context-Dependent Regulation of Gene Expression by Non-Canonical Small RNAs. Noncoding RNA 2022; 8:29. [PMID: 35645336 PMCID: PMC9149963 DOI: 10.3390/ncrna8030029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
In recent functional genomics studies, a large number of non-coding RNAs have been identified. It has become increasingly apparent that noncoding RNAs are crucial players in a wide range of cellular and physiological functions. They have been shown to modulate gene expression on different levels, including transcription, post-transcriptional processing, and translation. This review aims to highlight the diverse mechanisms of the regulation of gene expression by small noncoding RNAs in different conditions and different types of human cells. For this purpose, various cellular functions of microRNAs (miRNAs), circular RNAs (circRNAs), snoRNA-derived small RNAs (sdRNAs) and tRNA-derived fragments (tRFs) will be exemplified, with particular emphasis on the diversity of their occurrence and on the effects on gene expression in different stress conditions and diseased cell types. The synthesis and effect on gene expression of these noncoding RNAs varies in different cell types and may depend on environmental conditions such as different stresses. Moreover, noncoding RNAs play important roles in many diseases, including cancer, neurodegenerative disorders, and viral infections.
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25
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Tung KF, Pan CY, Lin WC. Dominant transcript expression profiles of human protein-coding genes interrogated with GTEx dataset. Sci Rep 2022; 12:6969. [PMID: 35484179 DOI: 10.1038/s41598-022-10619-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/11/2022] [Indexed: 12/27/2022] Open
Abstract
The discovery and quantification of mRNA transcripts using short-read next-generation sequencing (NGS) data is a complicated task. There are far more alternative mRNA transcripts expressed by human genes than can be identified from NGS transcriptome data and various bioinformatic pipelines, while the numbers of annotated human protein-coding genes has gradually declined in recent years. It is essential to learn more about the thorough tissue expression profiles of alternative transcripts in order to obtain their molecular modulations and actual functional significance. In this report, we present a bioinformatic database for interrogating the representative tissue of human protein-coding transcripts. The database allows researchers to visually explore the top-ranked transcript expression profiles in particular tissue types. Most transcripts of protein-coding genes were found to have certain tissue expression patterns. This observation demonstrated that many alternative transcripts were particularly modulated in different cell types. This user-friendly tool visually represents transcript expression profiles in a tissue-specific manner. Identification of tissue specific protein-coding genes and transcripts is a substantial advance towards interpreting their biological functions and further functional genomics studies.
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26
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Abstract
The production of functional mature RNA transcripts from genes undergoes various pre-transcriptional regulation and post-transcriptional modifications. Accumulating studies demonstrated that gene transcription carries out in tissue and cancer type-dependent ways. However, RNA transcript-level specificity analysis in large-scale transcriptomics data across different normal tissue and cancer types is lacking. We applied reference-based de novo transcript assembly and quantification of 27,741 samples across 33 cancer types, 29 tissue types, and 25 cancer cell line types. We totally identified 231,836 specific RNA transcripts (SRTs) across various tissue and cancer types, most of which are found independent of specific genes. Almost half of tumor SRTs are also tissue-specific but in different tissues. Furthermore, we found that 10 ~ 20% of tumor SRTs in most tumor types were testis-specific. The SRT database (SRTdb) was constructed based on these resources. Taking liver cancer as an example, we showed how SRTdb resource is utilized to optimize the identification of RNA transcripts for more precision diagnosis of particular cancers. Our results provide a useful resource for exploring transcript specificity across various cancer and tissue types, and boost the precision medicine for tumor patients.
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Affiliation(s)
- Qili Shi
- Fudan University Shanghai Cancer Center and Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Teng Liu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China.,Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, Taizhou, 318000, China
| | - Wei Hu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620, China.
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27
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Bogias KJ, Pederson SM, Leemaqz S, Smith MD, McAninch D, Jankovic-Karasoulos T, McCullough D, Wan Q, Bianco-Miotto T, Breen J, Roberts CT. Placental Transcription Profiling in 6-23 Weeks' Gestation Reveals Differential Transcript Usage in Early Development. Int J Mol Sci 2022; 23:ijms23094506. [PMID: 35562897 PMCID: PMC9105363 DOI: 10.3390/ijms23094506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
The human placenta is a rapidly developing transient organ that is key to pregnancy success. Early development of the conceptus occurs in a low oxygen environment before oxygenated maternal blood begins to flow into the placenta at ~10-12 weeks' gestation. This process is likely to substantially affect overall placental gene expression. Transcript variability underlying gene expression has yet to be profiled. In this study, accurate transcript expression profiles were identified for 84 human placental chorionic villus tissue samples collected across 6-23 weeks' gestation. Differential gene expression (DGE), differential transcript expression (DTE) and differential transcript usage (DTU) between 6-10 weeks' and 11-23 weeks' gestation groups were assessed. In total, 229 genes had significant DTE yet no significant DGE. Integration of DGE and DTE analyses found that differential expression patterns of individual transcripts were commonly masked upon aggregation to the gene-level. Of the 611 genes that exhibited DTU, 534 had no significant DGE or DTE. The four most significant DTU genes ADAM10, VMP1, GPR126, and ASAH1, were associated with hypoxia-responsive pathways. Transcript usage is a likely regulatory mechanism in early placentation. Identification of functional roles will facilitate new insight in understanding the origins of pregnancy complications.
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Affiliation(s)
- Konstantinos J. Bogias
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Stephen M. Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Shalem Leemaqz
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Melanie D. Smith
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Dale McAninch
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
| | - Tanja Jankovic-Karasoulos
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Dylan McCullough
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Qianhui Wan
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute (Adelaide Office), Adelaide, SA 5000, Australia;
- College of Health & Medicine, Australian National University, Canberra, ACT 2600, Australia
| | - Claire T. Roberts
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
- Correspondence:
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Muniz MMM, Fonseca LFS, Dos Santos Silva DB, Magalhães AFB, Ferro JA, Chardulo LAL, Baldi F, Cánovas A, de Albuquerque LG. Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle. Funct Integr Genomics 2022. [PMID: 35305194 DOI: 10.1007/s10142-022-00844-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/04/2022]
Abstract
The aim of this study was to identify mRNA isoforms and small genetic variants that may be affecting marbling and beef color in Nellore cattle. Longissimus thoracis muscle samples from 20 bulls with different phenotypes (out of 80 bulls set) for marbling (moderate (n = 10) and low (n = 10) groups) and beef color (desirable (n = 10) and undesirable (n = 9) group) traits were used to perform transcriptomic analysis using RNA sequencing. Fourteen and 15 mRNA isoforms were detected as differentially expressed (DE) (P-value ≤ 0.001) between divergent groups for marbling and meat color traits, respectively. Some of those DE mRNA isoforms have shown sites of splicing modified by small structural variants as single nucleotide variant (SNV), insertion, and/or deletion. Enrichment analysis identified metabolic pathways, such as O2/CO2 exchange in erythrocytes, tyrosine biosynthesis, and phenylalanine degradation. The results obtained suggest potential key regulatory genes associated with these economically important traits for the beef industry and for the consumer.
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Bai Y, Wang M, Zhao J, Bai H, Zhang X, Wang J, Ke Q, Qu A, Pu F, Zheng W, Zhou T, Xu P. Comparative transcriptome analysis reveals immunoregulation mechanism of lncRNA-mRNA in gill and skin of large yellow croaker (Larimichthys crocea) in response to Cryptocaryon irritans infection. BMC Genomics 2022; 23:206. [PMID: 35287569 DOI: 10.1186/s12864-022-08431-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Background Cryptocaryonosis caused by Cryptocaryon irritans is one of the major diseases of large yellow croaker (Larimichthys crocea), which lead to massive economic losses annually to the aquaculture industry of L. crocea. Although there have been some studies on the pathogenesis for cryptocaryonosis, little is known about the innate defense mechanism of different immune organs of large yellow croaker. Results In order to analyze the roles of long non-coding RNAs and genes specifically expressed between immune organs during the infection of C. irritans, in this study, by comparing transcriptome data from different tissues of L. crocea, we identified tissue-specific transcripts in the gills and skin, including 507 DE lncRNAs and 1592 DEGs identified in the gills, and 110 DE lncRNAs and 1160 DEGs identified in the skin. Furthermore, we constructed transcriptome co-expression profiles of L. crocea gill and skin, including 7,503 long noncoding RNAs (lncRNAs) and 23,172 protein-coding genes. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the DEGs and the target genes of the DE lncRNAs in the gill were specifically enriched in several pathways related to immune such as HIF-1 signaling pathway. The target genes of DE lncRNAs and DEGs in the skin are specifically enriched in the complement and coagulation cascade pathways. Protein–protein interaction (PPI) network analysis identified 3 hub genes including NFKBIA, TNFAIP3 and CEBPB, and 5 important DE lncRNAs including MSTRG.24134.4, MSTRG.3038.5, MSTRG.27019.3, MSTRG.26559.1, and MSTRG.10983.1. The expression patterns of 6 randomly selected differentially expressed immune-related genes were validated using the quantitative real-time PCR method. Conclusions In short, our study is helpful to explore the potential interplay between lncRNAs and protein coding genes in different tissues of L. crocea post C. irritans and the molecular mechanism of pathogenesis for cryptocaryonosis. Highlights Skin and gills are important sources of pro-inflammatory molecules,
and their gene expression patterns are tissue-specific after C. irritans infection. 15 DEGs and 5 DE
lncRNAs were identified as hub regulatory elements after C. irritans infection The HIF-1 signaling
pathway and the complement and coagulation cascade pathway may be key
tissue-specific regulatory pathways in gills and skin, respectively.
Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08431-w.
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Zenere A, Rundquist O, Gustafsson M, Altafini C. Multi-omics protein-coding units as massively parallel Bayesian networks: empirical validation of causality structure. iScience 2022; 25:104048. [PMID: 35355520 PMCID: PMC8958332 DOI: 10.1016/j.isci.2022.104048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/17/2022] [Accepted: 03/08/2022] [Indexed: 11/29/2022] Open
Abstract
In this article we use high-throughput epigenomics, transcriptomics, and proteomics data to construct fine-graded models of the “protein-coding units” gathering all transcript isoforms and chromatin accessibility peaks associated with more than 4000 genes in humans. Each protein-coding unit has the structure of a directed acyclic graph (DAG) and can be represented as a Bayesian network. The factorization of the joint probability distribution induced by the DAGs imposes a number of conditional independence relationships among the variables forming a protein-coding unit, corresponding to the missing edges in the DAGs. We show that a large fraction of these conditional independencies are indeed verified by the data. Factors driving this verification appear to be the structural and functional annotation of the transcript isoforms, as well as a notion of structural balance (or frustration-free) of the corresponding sample correlation graph, which naturally leads to reduction of correlation (and hence to independence) upon conditioning. Protein coding unit: DAG associated with epigenetic and gene information of a protein DAGs correspond to Bayesian networks Edge absence on a DAG corresponds to conditional independence Multi-omics data (ATAC-seq, RNA-seq and mass-spec) are used for DAG validation
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Hao W, Yang Z, Sun Y, Li J, Zhang D, Liu D, Yang X. Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents. Biomolecules 2022; 12:biom12020154. [PMID: 35204660 PMCID: PMC8961525 DOI: 10.3390/biom12020154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition.
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Affiliation(s)
- Wanjun Hao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Zewei Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Yuanlu Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Jiaxin Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
| | - Dongjie Zhang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
- Correspondence: (D.L.); (X.Y.); Tel.: +86-451-8667-7458 (D.L.); +86-451-5519-1738 (X.Y.)
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (W.H.); (Z.Y.); (Y.S.); (J.L.)
- Correspondence: (D.L.); (X.Y.); Tel.: +86-451-8667-7458 (D.L.); +86-451-5519-1738 (X.Y.)
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Rodriguez JM, Pozo F, Cerdán-Vélez D, Di Domenico T, Vázquez J, Tress M. APPRIS: selecting functionally important isoforms. Nucleic Acids Res 2022; 50:D54-D59. [PMID: 34755885 PMCID: PMC8728124 DOI: 10.1093/nar/gkab1058] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/20/2022] Open
Abstract
APPRIS (https://appris.bioinfo.cnio.es) is a well-established database housing annotations for protein isoforms for a range of species. APPRIS selects principal isoforms based on protein structure and function features and on cross-species conservation. Most coding genes produce a single main protein isoform and the principal isoforms chosen by the APPRIS database best represent this main cellular isoform. Human genetic data, experimental protein evidence and the distribution of clinical variants all support the relevance of APPRIS principal isoforms. APPRIS annotations and principal isoforms have now been expanded to 10 model organisms. In this paper we highlight the most recent updates to the database. APPRIS annotations have been generated for two new species, cow and chicken, the protein structural information has been augmented with reliable models from the EMBL-EBI AlphaFold database, and we have substantially expanded the confirmatory proteomics evidence available for the human genome. The most significant change in APPRIS has been the implementation of TRIFID functional isoform scores. TRIFID functional scores are assigned to all splice isoforms, and APPRIS uses the TRIFID functional scores and proteomics evidence to determine principal isoforms when core methods cannot.
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Affiliation(s)
- Jose Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Fernando Pozo
- Bioinformatics Institute, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Daniel Cerdán-Vélez
- Bioinformatics Institute, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Tomás Di Domenico
- Bioinformatics Institute, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Jesús Vázquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Michael L Tress
- Bioinformatics Institute, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
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Reixachs-Solé M, Eyras E. Uncovering the impacts of alternative splicing on the proteome with current omics techniques. Wiley Interdiscip Rev RNA 2022; 13:e1707. [PMID: 34979593 PMCID: PMC9542554 DOI: 10.1002/wrna.1707] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
The high‐throughput sequencing of cellular RNAs has underscored a broad effect of isoform diversification through alternative splicing on the transcriptome. Moreover, the differential production of transcript isoforms from gene loci has been recognized as a critical mechanism in cell differentiation, organismal development, and disease. Yet, the extent of the impact of alternative splicing on protein production and cellular function remains a matter of debate. Multiple experimental and computational approaches have been developed in recent years to address this question. These studies have unveiled how molecular changes at different steps in the RNA processing pathway can lead to differences in protein production and have functional effects. New and emerging experimental technologies open exciting new opportunities to develop new methods to fully establish the connection between messenger RNA expression and protein production and to further investigate how RNA variation impacts the proteome and cell function. This article is categorized under:RNA Processing > Splicing Regulation/Alternative Splicing Translation > Regulation RNA Evolution and Genomics > Computational Analyses of RNA
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Affiliation(s)
- Marina Reixachs-Solé
- The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.,EMBL Australia Partner Laboratory Network and the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eduardo Eyras
- The John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.,EMBL Australia Partner Laboratory Network and the Australian National University, Canberra, Australian Capital Territory, Australia.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain.,Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
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Karakulak T, Moch H, von Mering C, Kahraman A. Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies. Front Mol Biosci 2021; 8:726902. [PMID: 34888349 PMCID: PMC8650491 DOI: 10.3389/fmolb.2021.726902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/01/2021] [Indexed: 12/03/2022] Open
Abstract
Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances in sequencing technologies and analysis methods led to new insights into the extent and functional impact of disturbed alternative splicing events. In this review, we give a brief overview of the molecular mechanisms driving alternative splicing, highlight the function of alternative splicing in healthy tissues and describe how alternative splicing is disrupted in cancer. We summarize current available computational tools for analyzing differential transcript usage, isoform switching events, and the pathogenic impact of cancer-specific splicing events. Finally, the strategies of three recent pan-cancer studies on isoform switching events are compared. Their methodological similarities and discrepancies are highlighted and lessons learned from the comparison are listed. We hope that our assessment will lead to new and more robust methods for cancer-specific transcript detection and help to produce more accurate functional impact predictions of isoform switching events.
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Affiliation(s)
- Tülay Karakulak
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abdullah Kahraman
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Tian L, Jabbari JS, Thijssen R, Gouil Q, Amarasinghe SL, Voogd O, Kariyawasam H, Du MRM, Schuster J, Wang C, Su S, Dong X, Law CW, Lucattini A, Prawer YDJ, Collar-Fernández C, Chung JD, Naim T, Chan A, Ly CH, Lynch GS, Ryall JG, Anttila CJA, Peng H, Anderson MA, Flensburg C, Majewski I, Roberts AW, Huang DCS, Clark MB, Ritchie ME. Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing. Genome Biol 2021; 22:310. [PMID: 34763716 PMCID: PMC8582192 DOI: 10.1186/s13059-021-02525-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity.
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Affiliation(s)
- Luyi Tian
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
| | - Jafar S Jabbari
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Rachel Thijssen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Quentin Gouil
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Shanika L Amarasinghe
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Oliver Voogd
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Hasaru Kariyawasam
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Mei R M Du
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jakob Schuster
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Changqing Wang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Shian Su
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Xueyi Dong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Charity W Law
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Alexis Lucattini
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Yair David Joseph Prawer
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC, Australia
| | | | - Jin D Chung
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Timur Naim
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Audrey Chan
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Chi Hai Ly
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Present address: Department of Neurology, Stanford University, Stanford, CA, USA
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - James G Ryall
- Centre for Muscle Research, Department of Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Present address: VOW, North Parramatta, NSW, Australia
| | - Casey J A Anttila
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Hongke Peng
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Mary Ann Anderson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Christoffer Flensburg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Ian Majewski
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew W Roberts
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
- Victorian Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Michael B Clark
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
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Arora D, Park JE, Lim D, Choi BH, Cho IC, Srikanth K, Kim J, Park W. Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig. BMC Genomics 2021; 22:801. [PMID: 34743693 PMCID: PMC8573883 DOI: 10.1186/s12864-021-08123-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. RESULTS A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. CONCLUSIONS In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.
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Affiliation(s)
- Devender Arora
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 63242, Jeju, Korea
| | - Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea
- Department of Animal Science, Cornell University, NY, 14853, Ithaca, USA
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, 05029, Seoul, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, 55365, Wanju, Republic of Korea.
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Olivieri JE, Dehghannasiri R, Wang PL, Jang S, de Morree A, Tan SY, Ming J, Ruohao Wu A, Quake SR, Krasnow MA, Salzman J. RNA splicing programs define tissue compartments and cell types at single-cell resolution. eLife 2021; 10:e70692. [PMID: 34515025 PMCID: PMC8563012 DOI: 10.7554/elife.70692] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/10/2021] [Indexed: 02/05/2023] Open
Abstract
The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in >110K cells from 12 human tissues. Using 10X Chromium data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes MYL6 and RPS24. These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable based on gene expression, illustrated by subpopulation-specific splicing of classical monocytes involving an ultraconserved exon in SAT1. Together, this analysis of differential splicing across multiple organs establishes that splicing is regulated cell-type-specifically.
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Affiliation(s)
- Julia Eve Olivieri
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Roozbeh Dehghannasiri
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Peter L Wang
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - SoRi Jang
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of MedicineStanfordUnited States
| | - Serena Y Tan
- Department of Pathology, Stanford University Medical CenterStanfordUnited States
| | - Jingsi Ming
- Academy for Statistics and Interdisciplinary Sciences, Faculty of Economics and Management,East China Normal UniversityShanghaiChina
- Department of Mathematics, The Hong Kong University of Science and TechnologyHong KongChina
| | - Angela Ruohao Wu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and TechnologyHong KongChina
| | - Stephen R Quake
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Mark A Krasnow
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Julia Salzman
- Department of Biomedical Data Science, Stanford UniversityStanfordUnited States
- Department of Biochemistry, Stanford UniversityStanfordUnited States
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38
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De Paoli-Iseppi R, Gleeson J, Clark MB. Isoform Age - Splice Isoform Profiling Using Long-Read Technologies. Front Mol Biosci 2021; 8:711733. [PMID: 34409069 PMCID: PMC8364947 DOI: 10.3389/fmolb.2021.711733] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/19/2021] [Indexed: 01/12/2023] Open
Abstract
Alternative splicing (AS) of RNA is a key mechanism that results in the expression of multiple transcript isoforms from single genes and leads to an increase in the complexity of both the transcriptome and proteome. Regulation of AS is critical for the correct functioning of many biological pathways, while disruption of AS can be directly pathogenic in diseases such as cancer or cause risk for complex disorders. Current short-read sequencing technologies achieve high read depth but are limited in their ability to resolve complex isoforms. In this review we examine how long-read sequencing (LRS) technologies can address this challenge by covering the entire RNA sequence in a single read and thereby distinguish isoform changes that could impact RNA regulation or protein function. Coupling LRS with technologies such as single cell sequencing, targeted sequencing and spatial transcriptomics is producing a rapidly expanding suite of technological approaches to profile alternative splicing at the isoform level with unprecedented detail. In addition, integrating LRS with genotype now allows the impact of genetic variation on isoform expression to be determined. Recent results demonstrate the potential of these techniques to elucidate the landscape of splicing, including in tissues such as the brain where AS is particularly prevalent. Finally, we also discuss how AS can impact protein function, potentially leading to novel therapeutic targets for a range of diseases.
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Affiliation(s)
| | | | - Michael B. Clark
- Centre for Stem Cell Systems, Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, Australia
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39
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Zea DJ, Laskina S, Baudin A, Richard H, Laine E. Assessing conservation of alternative splicing with evolutionary splicing graphs. Genome Res 2021; 31:1462-1473. [PMID: 34266979 PMCID: PMC8327911 DOI: 10.1101/gr.274696.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Understanding how protein function has evolved and diversified is of great importance for human genetics and medicine. Here, we tackle the problem of describing the whole transcript variability observed in several species by generalizing the definition of splicing graph. We provide a practical solution to construct parsimonious evolutionary splicing graphs where each node is a minimal transcript building block defined across species. We show a clear link between the functional relevance, tissue regulation, and conservation of alternative transcripts on a set of 50 genes. By scaling up to the whole human protein-coding genome, we identify a few thousand genes where alternative splicing modulates the number and composition of pseudorepeats. We have implemented our approach in ThorAxe, an efficient, versatile, robust, and freely available computational tool.
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Affiliation(s)
- Diego Javier Zea
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Sofya Laskina
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany
| | - Alexis Baudin
- Sorbonne Université, CNRS, LIP6, F-75005 Paris, France
| | - Hugues Richard
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353 Berlin, Germany
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
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40
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Pozo F, Martinez-Gomez L, Walsh TA, Rodriguez JM, Di Domenico T, Abascal F, Vazquez J, Tress ML. Assessing the functional relevance of splice isoforms. NAR Genom Bioinform 2021; 3:lqab044. [PMID: 34046593 PMCID: PMC8140736 DOI: 10.1093/nargab/lqab044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/22/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing of messenger RNA can generate an array of mature transcripts, but it is not clear how many go on to produce functionally relevant protein isoforms. There is only limited evidence for alternative proteins in proteomics analyses and data from population genetic variation studies indicate that most alternative exons are evolving neutrally. Determining which transcripts produce biologically important isoforms is key to understanding isoform function and to interpreting the real impact of somatic mutations and germline variations. Here we have developed a method, TRIFID, to classify the functional importance of splice isoforms. TRIFID was trained on isoforms detected in large-scale proteomics analyses and distinguishes these biologically important splice isoforms with high confidence. Isoforms predicted as functionally important by the algorithm had measurable cross species conservation and significantly fewer broken functional domains. Additionally, exons that code for these functionally important protein isoforms are under purifying selection, while exons from low scoring transcripts largely appear to be evolving neutrally. TRIFID has been developed for the human genome, but it could in principle be applied to other well-annotated species. We believe that this method will generate valuable insights into the cellular importance of alternative splicing.
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Affiliation(s)
- Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Laura Martinez-Gomez
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Thomas A Walsh
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - José Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Tomas Di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Federico Abascal
- Somatic Evolution Group, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Jesús Vazquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Michael L Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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41
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Lee VV, Judd LM, Jex AR, Holt KE, Tonkin CJ, Ralph SA. Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites. mSystems 2021; 6:e01081-20. [PMID: 33688018 DOI: 10.1128/mSystems.01081-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterized in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic features, such as the high AU content of Plasmodium RNA, but also the limitations of short-read sequencing in deciphering complex splicing events. In this study, we utilized the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum. We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or nearly full-length transcripts with comparable quantification to Illumina sequencing. By comparing these data with available gene models, we find widespread alternative splicing, particularly intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic diversity, rather than expanding proteomic diversity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This study highlights a strategy in using long-read sequencing to understand splicing events at the whole-transcript level and has implications in the future interpretation of transcriptome sequencing studies. IMPORTANCE We have used a novel nanopore sequencing technology to directly analyze parasite transcriptomes. The very long reads of this technology reveal the full-length genes of the parasites that cause malaria and toxoplasmosis. Gene transcripts must be processed in a process called splicing before they can be translated to protein. Our analysis reveals that these parasites very frequently only partially process their gene products, in a manner that departs dramatically from their human hosts.
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42
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Liu X, Andrews MV, Skinner JP, Johanson TM, Chong MMW. A comparison of alternative mRNA splicing in the CD4 and CD8 T cell lineages. Mol Immunol 2021; 133:53-62. [PMID: 33631555 DOI: 10.1016/j.molimm.2021.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/05/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
T cells can be subdivided into a number of different subsets that are defined by their distinct functions. While the specialization of different T cell subsets is partly achieved by the expression of specific genes, the overall transcriptional profiles of all T cells appear very similar. Alternative mRNA splicing is a mechanism that facilitates greater transcript/protein diversity from a limited number of genes, which may contribute to the functional specialization of distinct T cell subsets. In this study we employ a combination of short-read and long-read sequencing technologies to compare alternative mRNA splicing between the CD4 and CD8 T cell lineages. While long-read technology was effective at assembling full-length alternatively spliced transcripts, the low sequencing depth did not facilitate accurate quantitation. On the other hand, short-read technology was ineffective at assembling full-length transcripts but was highly accurate for quantifying expression. We show that integrating long-read and short-read data together achieves a more complete view of transcriptomic diversity. We found that while the overall usage of transcript isoforms was very similar between the CD4 and CD8 lineages, there were numerous alternative spliced mRNA isoforms that were preferentially used by one lineage over the other. These alternative spliced isoforms included ones with different exon usage, exon exclusion or intron inclusion, all of which are expected to significantly alter the protein sequence.
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Affiliation(s)
- Xin Liu
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Matthew V Andrews
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Jarrod P Skinner
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Timothy M Johanson
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Mark M W Chong
- St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; Department of Medicine (St Vincent's), The University of Melbourne, Fitzroy, Victoria, Australia.
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43
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Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain PL, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation. Mol Syst Biol 2021; 16:e9170. [PMID: 32175694 PMCID: PMC7073818 DOI: 10.15252/msb.20199170] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post‐translational turnover, we devised a strategy combining pulse stable isotope‐labeled amino acids in cells (pSILAC), data‐independent acquisition mass spectrometry (DIA‐MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and isoform groups. We demonstrated our approach by the genome‐wide correlation analysis between mRNA amounts and protein degradation across different strains of HeLa cells that harbor a high grade of gene dosage variation. The dataset revealed that specific biological processes, cellular organelles, spatial compartments of organelles, and individual protein isoforms of the same genes could have distinctive degradation rate. The protein degradation diversity thus dissects the corresponding buffering or concerting protein turnover control across cancer cell lines. The data further indicate that specific mRNA splicing events such as intron retention significantly impact the protein abundance levels. Our findings support the tight association between transcriptome variability and proteostasis and provide a methodological foundation for studying functional protein degradation.
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Affiliation(s)
- Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.,Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Max Frank
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | | | - Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Pierre-Luc Germain
- Institute for Neuroscience, D-HEST, ETH Zurich, Zurich, Switzerland.,Statistical Bioinformatics Lab, DMLS, University of Zürich, Zurich, Switzerland
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
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44
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Abstract
All aspects of each protein existence in the eukaryotic cells, starting from the pre-translation events, through translation, multiple different post-translational modifications, functional life and eventual proteostatic removal after loss of functionality and changes in physico-chemical properties, can be collectively called the proteodynamics. With aging, passing of time as well as accumulating effects of exposures, interactions and wearing-off lead to problems at each of the above mentioned stages, eventually leading to general malfunction of the proteome. This work briefly reviews and summarizes current knowledge concerning this important topic.
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Affiliation(s)
- Jacek M Witkowski
- Department of Pathophysiology, Medical University of Gdańsk, Gdańsk, Poland.
| | - Ewa Bryl
- Department of Pathology and Experimental Rheumatology, Medical University of Gdańsk, Gdańsk, Poland
| | - Tamas Fulop
- Research Center on Aging, Graduate Program in Immunology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, Canada
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45
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Harnett D, Meerdink E, Calviello L, Sydow D, Ohler U. Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant. Methods Mol Biol 2021; 2252:331-46. [PMID: 33765284 DOI: 10.1007/978-1-0716-1150-0_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ribosome profiling, or Ribo-seq, provides precise information about the position of actively translating ribosomes. It can be used to identify open reading frames (ORFs) that are translated in a given sample. The RiboTaper pipeline, and the ORFquant R package, leverages the periodic distribution of such ribosomes along the ORF to perform a statistically robust test for translation which is insensitive to aperiodic noise and provides a statistically robust measure of translation. In addition to accounting for complex loci with overlapping ORFs, ORFquant is also able to use Ribo-seq as a tool for distinguishing actively translated transcripts from non-translated ones, within a given gene locus.
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46
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Abdel-Salam EM, Faisal M, Alatar AA, Qahtan AA, Alam P. Genome-wide transcriptome variation landscape in Ruta chalepensis organs revealed potential genes responsible for rutin biosynthesis. J Biotechnol 2020; 325:43-56. [PMID: 33271156 DOI: 10.1016/j.jbiotec.2020.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/15/2020] [Accepted: 11/28/2020] [Indexed: 12/17/2022]
Abstract
Ruta chalepensis L., most commonly known as 'fringed rue,' is an excellent and valuable bioactive plant that produces a range of complex flavonoids, of which rutin is the major compound present in this plant of great pharmaceutical and medicinal significance. The present study is a pioneering attempt to examine the changes in the transcriptomic landscape of leaf, stem, and root tissues and correlate this with rutin quantity in each tissue in order to identify the candidate genes responsible for rutin biosynthesis and to increase genomic resources in fringed rue. Comparative transcriptome sequencing of leaves, stems and roots were performed using the NovaSeq 6000 platform. The de novo transcriptome assembly generated 254,685 transcripts representing 154,018 genes with GC content of 42.60 % and N50 of 2280 bp. Searching assembled transcripts against UniRef90 and SwissProt databases annotated 79.7 % of them as protein coding. The leaf tissues had the highest rutin content followed by stems and roots. Several differentially expressed genes and transcripts relating to rutin biosynthesis were identified in leaves comparing with roots or stems comparing with roots. All the genes known to be involved in rutin biosynthesis showed up-regulation in leaves as compared with roots. These results were confirmed by gene ontology (GO) and pathway enrichment analyses. Up-regulated genes in leaves as compared with roots enriched GO terms with relation to rutin biosynthesis e.g. action of flavonol synthase, biosynthetic mechanism of malonyl-CoA, and action of monooxygenase. Phylogenetic analysis of the rhamnosyltransferase (RT) gene showed that it was highly homologues with RT sequence from Citrus species and all were located in the same clade. This transcriptomic dataset will serve as an important public resource for future genomics and transcriptomic studies in R. chalepensis and will act as a benchmark for the identification and genetic modification of genes involved in the biosynthesis of secondary metabolites.
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Affiliation(s)
- Eslam M Abdel-Salam
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohammad Faisal
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Abdulrahman A Alatar
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ahmed A Qahtan
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Perwez Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
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47
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Wang ZY, Leushkin E, Liechti A, Ovchinnikova S, Mößinger K, Brüning T, Rummel C, Grützner F, Cardoso-Moreira M, Janich P, Gatfield D, Diagouraga B, de Massy B, Gill ME, Peters AHFM, Anders S, Kaessmann H. Transcriptome and translatome co-evolution in mammals. Nature 2020; 588:642-7. [PMID: 33177713 DOI: 10.1038/s41586-020-2899-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Gene expression programs define shared and species-specific phenotypes, but their evolution remains largely uncharacterized beyond the transcriptome layer1. Here we report an analysis of the co-evolution of translatomes and transcriptomes using ribosome-profling and matched RNA-sequencing data for three organs (brain, liver and testis) in fve mammals (human, macaque, mouse, opossum and platypus) and a bird (chicken). Our within-species analyses reveal that translational regulation is widespread in the diferent organs, in particular across the spermatogenic cell types of the testis. The between-species divergence in gene expression is around 20% lower at the translatome layer than at the transcriptome layer owing to extensive buffering between the expression layers, which especially preserved old, essential and housekeeping genes. Translational upregulation specifcally counterbalanced global dosage reductions during the evolution of sex chromosomes and the efects of meiotic sex-chromosome inactivation during spermatogenesis. Despite the overall prevalence of bufering, some genes evolved faster at the translatome layer—potentially indicating adaptive changes in expression; testis tissue shows the highest fraction of such genes. Further analyses incorporating mass spectrometry proteomics data establish that the co-evolution of transcriptomes and translatomes is refected at the proteome layer. Together, our work uncovers co-evolutionary patterns and associated selective forces across the expression layers, and provides a resource for understanding their interplay in mammalian organs.
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48
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Rehman A, Atif RM, Qayyum A, Du X, Hinze L, Azhar MT. Genome-wide identification and characterization of HSP70 gene family in four species of cotton. Genomics 2020; 112:4442-4453. [DOI: 10.1016/j.ygeno.2020.07.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 12/26/2022]
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49
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Saengboonmee C, Phoomak C, Supabphol S, Covington KR, Hampton O, Wongkham C, Gibbs RA, Umezawa K, Seubwai W, Gingras MC, Wongkham S. NF-κB and STAT3 co-operation enhances high glucose induced aggressiveness of cholangiocarcinoma cells. Life Sci 2020; 262:118548. [PMID: 33038372 DOI: 10.1016/j.lfs.2020.118548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
AIMS The present report aimed to investigate the underlying genes and pathways of high glucose driving cholangiocarcinoma (CCA) aggressiveness. MAIN METHODS We screened and compared the gene expression profiles obtained by RNA sequencing, of CCA cells cultured in high and normal glucose. Results from the transcriptomic analysis were confirmed in additional cell lines using in vitro migration-invasion assay, Western blotting and immunocytofluorescence. KEY FINDINGS Data indicated that high glucose increased the expression of interleukin-1β (IL-1β), an upstream regulator of nuclear factor-κB (NF-κB) pathway, through the nuclear localization of NF-κB. High glucose-induced NF-κB increased the migration and invasion of CCA cells and the expression of downstream NF-κB targeted genes associated with aggressiveness, including interleukin-6, a potent triggering signal of the signal transducer and activator of transcription 3 (STAT3) pathway. Such effects were reversed by inhibiting NF-κB nuclear translocation which additionally reduced the phosphorylation of STAT3 at Y705. SIGNIFICANCE These results indicate that NF-κB is activated by high glucose and they suggest that NF-κB interaction with STAT3 enhances CCA aggressiveness. Therefore, targeting multiple pathways such as STAT3 and NF-κB might improve CCA treatment outcome especially in condition such as hyperglycemia.
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50
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Rodriguez JM, Pozo F, di Domenico T, Vazquez J, Tress ML. An analysis of tissue-specific alternative splicing at the protein level. PLoS Comput Biol 2020; 16:e1008287. [PMID: 33017396 PMCID: PMC7561204 DOI: 10.1371/journal.pcbi.1008287] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/15/2020] [Accepted: 08/25/2020] [Indexed: 01/09/2023] Open
Abstract
The role of alternative splicing is one of the great unanswered questions in cellular biology. There is strong evidence for alternative splicing at the transcript level, and transcriptomics experiments show that many splice events are tissue specific. It has been suggested that alternative splicing evolved in order to remodel tissue-specific protein-protein networks. Here we investigated the evidence for tissue-specific splicing among splice isoforms detected in a large-scale proteomics analysis. Although the data supporting alternative splicing is limited at the protein level, clear patterns emerged among the small numbers of alternative splice events that we could detect in the proteomics data. More than a third of these splice events were tissue-specific and most were ancient: over 95% of splice events that were tissue-specific in both proteomics and RNAseq analyses evolved prior to the ancestors of lobe-finned fish, at least 400 million years ago. By way of contrast, three in four alternative exons in the human gene set arose in the primate lineage, so our results cannot be extrapolated to the whole genome. Tissue-specific alternative protein forms in the proteomics analysis were particularly abundant in nervous and muscle tissues and their genes had roles related to the cytoskeleton and either the structure of muscle fibres or cell-cell connections. Our results suggest that this conserved tissue-specific alternative splicing may have played a role in the development of the vertebrate brain and heart. We manually curated a set of 255 splice events detected in a large-scale tissue-based proteomics experiment and found that more than a third had evidence of significant tissue-specific differences. Events that were significantly tissue-specific at the protein level were highly conserved; almost 75% evolved over 400 million years ago. The tissues in which we found most evidence for tissue-specific splicing were nervous tissues and cardiac tissues. Genes with tissue-specific events in these two tissues had functions related to important cellular structures in brain and heart tissues. These splice events may have been essential for the development of vertebrate heart and muscle. However, our data set may not be representative of alternative exons as a whole. We found that most tissue specific splicing was strongly conserved, but just 5% of annotated alternative exons in the human gene set are ancient. More than three quarters of alternative exons are primate-derived. Although the analysis does not provide a definitive answer to the question of the functional role of alternative splicing, our results do indicate that alternative splice variants may have played a significant part in the evolution of brain and heart tissues in vertebrates.
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Affiliation(s)
- Jose Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle Melchor Fernandez, Madrid, Spain
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
| | - Tomas di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
| | - Jesus Vazquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle Melchor Fernandez, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Michael L. Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
- * E-mail:
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