1
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Agrawal S, Buyan A, Severin J, Koido M, Alam T, Abugessaisa I, Chang HY, Dostie J, Itoh M, Kere J, Kondo N, Li Y, Makeev VJ, Mendez M, Okazaki Y, Ramilowski JA, Sigorskikh AI, Strug LJ, Yagi K, Yasuzawa K, Yip CW, Hon CC, Hoffman MM, Terao C, Kulakovskiy IV, Kasukawa T, Shin JW, Carninci P, de Hoon MJL. Annotation of nuclear lncRNAs based on chromatin interactions. PLoS One 2024; 19:e0295971. [PMID: 38709794 PMCID: PMC11073715 DOI: 10.1371/journal.pone.0295971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/02/2023] [Indexed: 05/08/2024] Open
Abstract
The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.
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Affiliation(s)
- Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Andrey Buyan
- Autosome.org, Russia
- FANTOM Consortium, Dolgoprudny, Russia
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Howard Y. Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California, United States of America
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yunjing Li
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | | | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jordan A. Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | | | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Ontario, Canada
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michael M. Hoffman
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jay W. Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
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2
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Yoshida M, Kwon AT, Qin XY, Nishimura H, Maeda S, Miyamoto Y, Yoshida Y, Hoshino Y, Suzuki H. Transcriptome analysis of long non-coding RNAs in Mycobacterium avium complex-infected macrophages. Front Immunol 2024; 15:1374437. [PMID: 38711507 PMCID: PMC11070510 DOI: 10.3389/fimmu.2024.1374437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/28/2024] [Indexed: 05/08/2024] Open
Abstract
Mycobacterium avium complex (MAC) is a non-tuberculous mycobacterium widely distributed in the environment. Even though MAC infection is increasing in older women and immunocompromised patients, to our knowledge there has been no comprehensive analysis of the MAC-infected host-cell transcriptome-and particularly of long non-coding RNAs (lncRNAs). By using in vitro-cultured primary mouse bone-marrow-derived macrophages (BMDMs) and Cap analysis of gene expression, we analyzed the transcriptional and kinetic landscape of macrophage genes, with a focus on lncRNAs, during MAC infection. MAC infection of macrophages induced the expression of immune/inflammatory response genes and other genes similar to those involved in M1 macrophage activation, consistent with previous reports, although Nos2 (M1 activation) and Arg1 (M2 activation) had distinct expression profiles. We identified 31 upregulated and 30 downregulated lncRNA promoters corresponding respectively to 18 and 26 lncRNAs. Upregulated lncRNAs were clustered into two groups-early and late upregulated-predicted to be associated with immune activation and the immune response to infection, respectively. Furthermore, an Ingenuity Pathway Analysis revealed canonical pathways and upstream transcription regulators associated with differentially expressed lncRNAs. Several differentially expressed lncRNAs reported elsewhere underwent expressional changes upon M1 or M2 preactivation and subsequent MAC infection. Finally, we showed that expressional change of lncRNAs in MAC-infected BMDMs was mediated by toll-like receptor 2, although there may be other mechanisms that sense MAC infection. We identified differentially expressed lncRNAs in MAC-infected BMDMs, revealing diverse features that imply the distinct roles of these lncRNAs in MAC infection and macrophage polarization.
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Affiliation(s)
- Mitsunori Yoshida
- Department of Mycobacteriology, National Institute of Infectious Diseases, Higashi-Murayama, Tokyo, Japan
| | - Andrew Taejun Kwon
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Xian-Yang Qin
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hajime Nishimura
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shiori Maeda
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yuji Miyamoto
- Department of Mycobacteriology, National Institute of Infectious Diseases, Higashi-Murayama, Tokyo, Japan
| | - Yasuhiro Yoshida
- Department of Immunology and Parasitology, University of Occupational and Environmental Health, Kita-Kyushu, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, National Institute of Infectious Diseases, Higashi-Murayama, Tokyo, Japan
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
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3
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Kawakami K, Maeda SI, Tanimoto Y, Shimizu M, Kato H. A budding yeast CAGE dataset comprising two cell types. Genes Genet Syst 2024; 99:n/a. [PMID: 38447993 DOI: 10.1266/ggs.24-00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying chromatin regulation with high-resolution genome-wide analyses. Since newly generated genome-wide data are often compared with publicly available datasets, expanding our dataset repertoire will be beneficial for the field. Information on transcription start sites (TSSs) determined at base pair resolution is essential for elucidating mechanisms of transcription and related chromatin regulation, yet no datasets that cover two different cell types are available. Here, we present a CAGE (cap analysis of gene expression) dataset for a-cells and α-cells grown in defined and rich media. Cell type-specific genes were differentially expressed as expected, ensuring the reliability of the data. Some of the differentially expressed TSSs were medium-specific or detected due to unrecognized chromosome rearrangement. By comparing the CAGE data with a high-resolution nucleosome map, major TSSs were primarily found in +1 nucleosomes, with a peak approximately 30 bp from the promoter-proximal end of the nucleosome. The dataset is available at DDBJ/GEA.
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Affiliation(s)
- Kei Kawakami
- Department of Life Sciences, Shimane University School of Medicine
| | - Shin-Ichi Maeda
- Department of Life Sciences, Shimane University School of Medicine
| | - Yoshiko Tanimoto
- Department of Life Sciences, Shimane University School of Medicine
| | | | - Hiroaki Kato
- Department of Life Sciences, Shimane University School of Medicine
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4
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Camellato BR, Brosh R, Ashe HJ, Maurano MT, Boeke JD. Synthetic reversed sequences reveal default genomic states. Nature 2024; 628:373-380. [PMID: 38448583 PMCID: PMC11006607 DOI: 10.1038/s41586-024-07128-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'1-4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in 'default genomic states' between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.
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Affiliation(s)
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York, NY, USA.
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5
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Abugessaisa I, Manabe RI, Kawashima T, Tagami M, Takahashi C, Okazaki Y, Bandinelli S, Kasukawa T, Ferrucci L. OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults. GeroScience 2024; 46:2063-2081. [PMID: 37817005 PMCID: PMC10828349 DOI: 10.1007/s11357-023-00961-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/24/2023] [Indexed: 10/12/2023] Open
Abstract
While some old adults stay healthy and non-frail up to late in life, others experience multimorbidity and frailty often accompanied by a pro-inflammatory state. The underlying molecular mechanisms for those differences are still obscure. Here, we used gene expression analysis to understand the molecular underpinning between non-frail and frail individuals in old age. Twenty-four adults (50% non-frail and 50% frail) from InCHIANTI study were included. Total RNA extracted from whole blood was analyzed by Cap Analysis of Gene Expression (CAGE). CAGE identified transcription start site (TSS) and active enhancer regions. We identified a set of differentially expressed (DE) TSS and enhancer between non-frail and frail and male and female participants. Several DE TSSs were annotated as lncRNA (XIST and TTTY14) and antisense RNAs (ZFX-AS1 and OVCH1 Antisense RNA 1). The promoter region chr6:366,786,54-366,787,97;+ was DE and overlapping the longevity CDKN1A gene. GWAS-LD enrichment analysis identifies overlapping LD-blocks with the DE regions with reported traits in GWAS catalog (isovolumetric relaxation time and urinary tract infection frequency). Furthermore, we used weighted gene co-expression network analysis (WGCNA) to identify changes of gene expression associated with clinical traits and identify key gene modules. We performed functional enrichment analysis of the gene modules with significant trait/module correlation. One gene module is showing a very distinct pattern in hub genes. Glycogen Phosphorylase L (PYGL) was the top ranked hub gene between non-frail and frail. We predicted transcription factor binding sites (TFBS) and motif activity. TF involved in age-related pathways (e.g., FOXO3 and MYC) shows different expression patterns between non-frail and frail participants. Expanding the study of OVCH1 Antisense RNA 1 and PYGL may help understand the mechanisms leading to loss of homeostasis that ultimately causes frailty.
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Affiliation(s)
- Imad Abugessaisa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Ri-Ichiroh Manabe
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Tsugumi Kawashima
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Michihira Tagami
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Chitose Takahashi
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yasushi Okazaki
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Stefania Bandinelli
- Azienda USL Toscana Centro, InCHIANTI, Villa Margherita, Primo piano Viale Michelangelo, 41, 50125, Firenze, Italy
| | - Takeya Kasukawa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD, 21225, USA
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6
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Peng Y, Huang Q, Liu D, Kong S, Kamada R, Ozato K, Zhang Y, Zhu J. A single-cell genomic strategy for alternative transcript start sites identification. Biotechnol J 2024; 19:e2300516. [PMID: 38472100 DOI: 10.1002/biot.202300516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. We report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-β stimulated mouse embryonic fibroblasts (MEFs). The data clearly discriminate two IFN-β stimulated MEFs. Moreover, our results indicate 81% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on Cap-Analysis Gene Expression (CAGE) (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future.
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Affiliation(s)
- Yanling Peng
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qitong Huang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Danli Liu
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Siyuan Kong
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Yubo Zhang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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7
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Valdivia-Francia F, Sendoel A. No country for old methods: New tools for studying microproteins. iScience 2024; 27:108972. [PMID: 38333695 PMCID: PMC10850755 DOI: 10.1016/j.isci.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.
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Affiliation(s)
- Fabiola Valdivia-Francia
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
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8
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Seki M, Kuze Y, Zhang X, Kurotani KI, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y. An improved method for the highly specific detection of transcription start sites. Nucleic Acids Res 2024; 52:e7. [PMID: 37994784 PMCID: PMC10810191 DOI: 10.1093/nar/gkad1116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Precise detection of the transcriptional start site (TSS) is a key for characterizing transcriptional regulation of genes and for annotation of newly sequenced genomes. Here, we describe the development of an improved method, designated 'TSS-seq2.' This method is an iterative improvement of TSS-seq, a previously published enzymatic cap-structure conversion method to detect TSSs in base sequences. By modifying the original procedure, including by introducing split ligation at the key cap-selection step, the yield and the accuracy of the reaction has been substantially improved. For example, TSS-seq2 can be conducted using as little as 5 ng of total RNA with an overall accuracy of 96%; this yield a less-biased and more precise detection of TSS. We then applied TSS-seq2 for TSS analysis of four plant species that had not yet been analyzed by any previous TSS method.
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Affiliation(s)
- Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yuta Kuze
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Xiang Zhang
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Nagoya, Japan
| | - Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Ibaraki, Japan
| | - Satoko Yoshida
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Sumio Sugano
- Institute of Kashiwa-no-ha Omics Gate, Chiba, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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9
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Wragg JW, White PL, Hadzhiev Y, Wanigasooriya K, Stodolna A, Tee L, Barros-Silva JD, Beggs AD, Müller F. Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism. Nat Struct Mol Biol 2023; 30:1970-1984. [PMID: 37996663 PMCID: PMC10716046 DOI: 10.1038/s41594-023-01156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/19/2023] [Indexed: 11/25/2023]
Abstract
Global changes in transcriptional regulation and RNA metabolism are crucial features of cancer development. However, little is known about the role of the core promoter in defining transcript identity and post-transcriptional fates, a potentially crucial layer of transcriptional regulation in cancer. In this study, we use CAGE-seq analysis to uncover widespread use of dual-initiation promoters in which non-canonical, first-base-cytosine (C) transcription initiation occurs alongside first-base-purine initiation across 59 human cancers and healthy tissues. C-initiation is often followed by a 5' terminal oligopyrimidine (5'TOP) sequence, dramatically increasing the range of genes potentially subjected to 5'TOP-associated post-transcriptional regulation. We show selective, dynamic switching between purine and C-initiation site usage, indicating transcription initiation-level regulation in cancers. We additionally detail global metabolic changes in C-initiation transcripts that mark differentiation status, proliferative capacity, radiosensitivity, and response to irradiation and to PI3K-Akt-mTOR and DNA damage pathway-targeted radiosensitization therapies in colorectal cancer organoids and cancer cell lines and tissues.
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Affiliation(s)
- Joseph W Wragg
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Paige-Louise White
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Kasun Wanigasooriya
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Surgery, University Hospitals Birmingham National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Agata Stodolna
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Louise Tee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joao D Barros-Silva
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew D Beggs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Department of Surgery, University Hospitals Birmingham National Health Service (NHS) Foundation Trust, Birmingham, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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10
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Cimen I, Natarelli L, Abedi Kichi Z, Henderson JM, Farina FM, Briem E, Aslani M, Megens RTA, Jansen Y, Mann-Fallenbuchel E, Gencer S, Duchêne J, Nazari-Jahantigh M, van der Vorst EPC, Enard W, Döring Y, Schober A, Santovito D, Weber C. Targeting a cell-specific microRNA repressor of CXCR4 ameliorates atherosclerosis in mice. Sci Transl Med 2023; 15:eadf3357. [PMID: 37910599 DOI: 10.1126/scitranslmed.adf3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
The CXC chemokine receptor 4 (CXCR4) in endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) is crucial for vascular integrity. The atheroprotective functions of CXCR4 in vascular cells may be counteracted by atherogenic functions in other nonvascular cell types. Thus, strategies for cell-specifically augmenting CXCR4 function in vascular cells are crucial if this receptor is to be useful as a therapeutic target in treating atherosclerosis and other vascular disorders. Here, we identified miR-206-3p as a vascular-specific CXCR4 repressor and exploited a target-site blocker (CXCR4-TSB) that disrupted the interaction of miR-206-3p with CXCR4 in vitro and in vivo. In vitro, CXCR4-TSB enhanced CXCR4 expression in human and murine ECs and VSMCs to modulate cell viability, proliferation, and migration. Systemic administration of CXCR4-TSB in Apoe-deficient mice enhanced Cxcr4 expression in ECs and VSMCs in the walls of blood vessels, reduced vascular permeability and monocyte adhesion to endothelium, and attenuated the development of diet-induced atherosclerosis. CXCR4-TSB also increased CXCR4 expression in B cells, corroborating its atheroprotective role in this cell type. Analyses of human atherosclerotic plaque specimens revealed a decrease in CXCR4 and an increase in miR-206-3p expression in advanced compared with early lesions, supporting a role for the miR-206-3p-CXCR4 interaction in human disease. Disrupting the miR-206-3p-CXCR4 interaction in a cell-specific manner with target-site blockers is a potential therapeutic approach that could be used to treat atherosclerosis and other vascular diseases.
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Affiliation(s)
- Ismail Cimen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Lucia Natarelli
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Zahra Abedi Kichi
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - James M Henderson
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Floriana M Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Eva Briem
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 85152 Planegg-Martinsried, Germany
| | - Maria Aslani
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biomedical Engineering, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6200 MD Maastricht, Netherlands
| | - Yvonne Jansen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Elizabeth Mann-Fallenbuchel
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Selin Gencer
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Johan Duchêne
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Maliheh Nazari-Jahantigh
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Emiel P C van der Vorst
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, 52074 Aachen, Germany
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, 52062 Aachen, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 85152 Planegg-Martinsried, Germany
| | - Yvonne Döring
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Angiology, Swiss Cardiovascular Center, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland
| | - Andreas Schober
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Institute of Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council (CNR), 20090 Milan, Italy
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, 80336 Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6229 HX Maastricht, Netherlands
- Munich Cluster for Systems Neurology (SyNergy), 81337 Munich, Germany
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11
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Vijjamarri AK, Gupta N, Onu C, Niu X, Zhang F, Kumar R, Lin Z, Greenberg M, Hinnebusch AG. mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability. Nucleic Acids Res 2023; 51:9314-9336. [PMID: 37439347 PMCID: PMC10516646 DOI: 10.1093/nar/gkad584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/17/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023] Open
Abstract
We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1Δ and pat1Δ mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in wild-type cells. These mRNAs show both reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.
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Affiliation(s)
- Anil Kumar Vijjamarri
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neha Gupta
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Xiao Niu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Fan Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rakesh Kumar
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Wang J, Chew BLA, Lai Y, Dong H, Xu L, Liu Y, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome. Nat Protoc 2023; 18:2671-2698. [PMID: 37567932 DOI: 10.1038/s41596-023-00857-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/26/2023] [Indexed: 08/13/2023]
Abstract
Chemical modifications of transcripts with a 5' cap occur in all organisms and function in many aspects of RNA metabolism. To facilitate analysis of RNA caps, we developed a systems-level mass spectrometry-based technique, CapQuant, for accurate and sensitive quantification of the cap epitranscriptome. The protocol includes the addition of stable isotope-labeled cap nucleotides (CNs) to RNA, enzymatic hydrolysis of endogenous RNA to release CNs, and off-line enrichment of CNs by ion-pairing high-pressure liquid chromatography, followed by a 17 min chromatography-coupled tandem quadrupole mass spectrometry run for the identification and quantification of individual CNs. The total time required for the protocol can be up to 7 d. In this approach, 26 CNs can be quantified in eukaryotic poly(A)-tailed RNA, bacterial total RNA and viral RNA. This protocol can be modified to analyze other types of RNA and RNA from in vitro sources. CapQuant stands out from other methods in terms of superior specificity, sensitivity and accuracy, and it is not limited to individual caps nor does it require radiolabeling. Thanks to its unique capability of accurately and sensitively quantifying RNA caps on a systems level, CapQuant can reveal both the RNA cap landscape and the transcription start site distribution of capped RNA in a broad range of settings.
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Affiliation(s)
- Jin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
- Institute of Biomedical Sciences, Inner Mongolia University, Hohhot, China.
| | - Bing Liang Alvin Chew
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
| | - Yong Lai
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Luang Xu
- Cancer Science Institute of Singapore, Singapore, Singapore
- School of Life Science and Technology, Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yu Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, People's Republic of China
| | - Xin-Yuan Fu
- Cancer Science Institute of Singapore, Singapore, Singapore
- Generos Pharmaceutical Co. Ltd, Hangzhou, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Pharmacology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
- GlaxoSmithKline, Rockville, MD, USA
| | - Timothy K Lu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Synthetic Biology Center, Departments of Biological Engineering and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Senti Bio, San Francisco, CA, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
- Dept. of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Tounosu N, Sesoko K, Hori K, Shimojima M, Ohta H. Cis-regulatory elements and transcription factors related to auxin signaling in the streptophyte algae Klebsormidium nitens. Sci Rep 2023; 13:9635. [PMID: 37322074 PMCID: PMC10272232 DOI: 10.1038/s41598-023-36500-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
The phytohormone auxin affects numerous processes in land plants. The central auxin signaling machinery, called the nuclear auxin pathway, is mediated by its pivotal receptor named TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB). The nuclear auxin pathway is widely conserved in land plants, but auxin also accumulates in various algae. Although auxin affects the growth of several algae, the components that mediate auxin signaling have not been identified. We previously reported that exogenous auxin suppresses cell proliferation in the Klebsormidium nitens that is a member of streptophyte algae, a paraphyletic group sharing the common ancestor with land plants. Although K. nitens lacks TIR1/AFB, auxin affects the expression of numerous genes. Thus, elucidation of the mechanism of auxin-inducible gene expression in K. nitens would provide important insights into the evolution of auxin signaling. Here, we show that some motifs are enriched in the promoter sequences of auxin-inducible genes in K. nitens. We also found that the transcription factor KnRAV activates several auxin-inducible genes and directly binds the promoter of KnLBD1, a representative auxin-inducible gene. We propose that KnRAV has the potential to regulate auxin-responsive gene expression in K. nitens.
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Affiliation(s)
- Noriaki Tounosu
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Kanami Sesoko
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Koichi Hori
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-65, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
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14
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Conlon FL, Arnold AP. Sex chromosome mechanisms in cardiac development and disease. NATURE CARDIOVASCULAR RESEARCH 2023; 2:340-350. [PMID: 37808586 PMCID: PMC10558115 DOI: 10.1038/s44161-023-00256-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/13/2023] [Indexed: 10/10/2023]
Abstract
Many human diseases, including cardiovascular disease, show differences between men and women in pathology and treatment outcomes. In the case of cardiac disease, sex differences are exemplified by differences in the frequency of specific types of congenital and adult-onset heart disease. Clinical studies have suggested that gonadal hormones are a factor in sex bias. However, recent research has shown that gene and protein networks under non-hormonal control also account for cardiac sex differences. In this review, we describe the sex chromosome pathways that lead to sex differences in the development and function of the heart and highlight how these findings affect future care and treatment of cardiac disease.
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Affiliation(s)
- Frank L Conlon
- Departments of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, CA, 90095, USA
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15
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Hayashi T, Kishi M, Takamochi K, Hosoya M, Kohsaka S, Kishikawa S, Ura A, Sano K, Sasahara N, Suehara Y, Takahashi F, Saito T, Suzuki K, Yao T. Expression of paired box 9 defines an aggressive subset of lung adenocarcinoma preferentially occurring in smokers. Histopathology 2023; 82:672-683. [PMID: 36527228 DOI: 10.1111/his.14853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
AIMS A distinct subset of lung adenocarcinomas (LADs), arising from a series of peripheral lung cells defined as the terminal respiratory unit (TRU), is characterised by thyroid transcription factor 1 (TTF-1) expression. The clinical relevance of transcription factors (TFs) other than TTF-1 remains unknown in LAD and was explored in the present study. METHODS AND RESULTS Seventy-one LAD samples were subjected to high-throughput transcriptome screening of LAD using cap analysis gene expression (CAGE) sequencing data; CAGE provides genome-wide expression levels of the transcription start sites (TSSs). In total, 1083 invasive LAD samples were subjected to immunohistochemical examination for paired box 9 (PAX9) and TTF-1 expression levels. PAX9 is an endoderm development-associated TF that most strongly and inversely correlates with the expression of TTF-1 TSS subsets. Immunohistochemically, PAX9 expression was restricted to the nuclei of ciliated epithelial and basal cells in the bronchi and bronchioles and the nuclei of epithelial cells of the bronchial glands; moreover, PAX9 expression was observed in 304 LADs (28%). PAX9-positive LADs were significantly associated with heavy smoking, non-lepidic subtype, EGFR wild-type tumours and PD-L1 expression (all P < 0.0001). All these characteristics were opposite to those of TRU-type LADs with TTF-1 expression. PAX9 expression was an independent prognostic factor for decreased overall survival (P = 0.022). CONCLUSIONS Our results revealed that PAX9 expression defines an aggressive subset of LADs preferentially occurring in smokers that may arise from bronchial or bronchiolar cells.
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Affiliation(s)
- Takuo Hayashi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Monami Kishi
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Masaki Hosoya
- Department of Medical Oncology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Chuo-ku, Tokyo
| | - Satsuki Kishikawa
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Ayako Ura
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Kei Sano
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo.,Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Noriko Sasahara
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Yoshiyuki Suehara
- Department of Medicine for Orthopaedics and Motor Organ, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Kenji Suzuki
- Department of General Thoracic Surgery, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
| | - Takashi Yao
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo
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16
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Kanamori K, Suina K, Shukuya T, Takahashi F, Hayashi T, Hara K, Saito T, Mitsuishi Y, Shimamura SS, Winardi W, Tajima K, Ko R, Mimori T, Asao T, Itoh M, Kawaji H, Suehara Y, Takamochi K, Suzuki K, Takahashi K. CALML5 is a novel diagnostic marker for differentiating thymic squamous cell carcinoma from type B3 thymoma. Thorac Cancer 2023; 14:1089-1097. [PMID: 36924358 PMCID: PMC10125782 DOI: 10.1111/1759-7714.14853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Thymic squamous cell carcinoma and type B3 thymoma are primary neoplasms of the anterior mediastinum that are sometimes difficult to differentiate from one another histologically. However, only a few immunohistochemical markers are available for the differential diagnosis. The purpose of this study was to discover a novel marker for differentiating between thymic squamous cell carcinoma and type B3 thymoma. METHODS We used histological samples of thymic carcinomas (n = 26) and type B3 thymomas (n = 38) which were resected between 1986 and 2017. To search for candidates of differential markers, gene expression levels were evaluated in samples using promoter analysis by cap analysis of gene expression (CAGE) sequencing. RESULTS Promoter level expression of CALML5 genes was significantly higher in thymic carcinomas than in type B3 thymomas. We further validated the results of the CAGE analysis in all 26 thymic carcinomas and 38 type B3 thymomas by immunohistochemistry (IHC). CALML5 was strongly expressed in the cytoplasm in 19 of 26 cases with thymic carcinoma, whereas positivity at the protein level was shown in two of 38 type B3 thymomas. Thus, the sensitivity (73.1%) and specificity (94.7%) of CALML5 as markers for immunohistochemical diagnosis of thymic carcinoma were extremely high. CONCLUSION We identified CALML5 as a potential marker for differentiating thymic squamous cell carcinoma from type B3 thymoma. It is assumed that future clinical use of CALML5 may improve the diagnostic accuracy of differentiating between these two diseases.
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Affiliation(s)
- Koichiro Kanamori
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kentaro Suina
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Takehito Shukuya
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kieko Hara
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Yoichiro Mitsuishi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Shoko Sonobe Shimamura
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Wira Winardi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Ken Tajima
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Ryo Ko
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Tomoyasu Mimori
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Tetsuhiko Asao
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan.,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yoshiyuki Suehara
- Department of Orthopedic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kenji Suzuki
- Department of General Thoracic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
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17
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Vijjamarri AK, Niu X, Vandermeulen MD, Onu C, Zhang F, Qiu H, Gupta N, Gaikwad S, Greenberg ML, Cullen PJ, Lin Z, Hinnebusch AG. Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522830. [PMID: 36711592 PMCID: PMC9881900 DOI: 10.1101/2023.01.05.522830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, in coupling codon non-optimality to enhanced degradation, and as a translational repressor, but its functions in cells are incompletely understood. RNA-Seq analyses coupled with CAGE sequencing of all capped mRNAs revealed increased abundance of hundreds of mRNAs in dcp2 Δ cells that appears to result directly from impaired decapping rather than elevated transcription, which was confirmed by ChIP-Seq analysis of RNA Polymerase II occupancies genome-wide. Interestingly, only a subset of mRNAs requires Dhh1 for targeting by Dcp2, and also generally requires the other decapping activators Pat1, Lsm2, Edc3 or Scd6; whereas most of the remaining transcripts utilize NMD factors for Dcp2-mediated turnover. Neither inefficient translation initiation nor stalled elongation appears to be a major driver of Dhh1-enhanced mRNA degradation. Surprisingly, ribosome profiling revealed that dcp2 Δ confers widespread changes in relative TEs that generally favor well-translated mRNAs. Because ribosome biogenesis is reduced while capped mRNA abundance is increased by dcp2 Δ, we propose that an increased ratio of mRNA to ribosomes increases competition among mRNAs for limiting ribosomes to favor efficiently translated mRNAs in dcp2 Δ cells. Interestingly, genes involved in respiration or utilization of alternative carbon or nitrogen sources are derepressed, and both mitochondrial function and cell filamentation (a strategy for nutrient foraging) are elevated by dcp2 Δ, suggesting that mRNA decapping sculpts gene expression post-transcriptionally to fine-tune metabolic pathways and morphological transitions according to nutrient availability.
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Affiliation(s)
- Anil Kumar Vijjamarri
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Xiao Niu
- Department of Biology, Saint Louis University, St. Louis, MO
| | | | - Chisom Onu
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Fan Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Hongfang Qiu
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Neha Gupta
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Swati Gaikwad
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | | | - Paul J Cullen
- Department of Biological Sciences, State University of Buffalo, Buffalo, NY
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Alan G Hinnebusch
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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18
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Weber R, Ghoshdastider U, Spies D, Duré C, Valdivia-Francia F, Forny M, Ormiston M, Renz PF, Taborsky D, Yigit M, Bernasconi M, Yamahachi H, Sendoel A. Monitoring the 5'UTR landscape reveals isoform switches to drive translational efficiencies in cancer. Oncogene 2023; 42:638-650. [PMID: 36550360 PMCID: PMC9957725 DOI: 10.1038/s41388-022-02578-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5' and 3' untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. Focusing on squamous cell carcinomas, we show that a small cohort of genes with alternative 5'UTR isoforms exhibit overall increased translational efficiencies and are enriched in ribosomal proteins and splicing factors. By combining polysome fractionations and CAGE-seq, we further characterize two of these UTR isoform genes with identical coding sequences and demonstrate that the underlying transcription start site heterogeneity frequently results in 5' terminal oligopyrimidine (TOP) and pyrimidine-rich translational element (PRTE) motif switches to drive mTORC1-dependent translation of the mRNA. Genome-wide, we show that highly translated squamous cell carcinoma transcripts switch towards increased use of 5'TOP and PRTE motifs, have generally shorter 5'UTRs and expose decreased RNA secondary structures. Notably, we found that the two 5'TOP motif-containing, but not the TOP-less, RPL21 transcript isoforms strongly correlated with overall survival in human head and neck squamous cell carcinoma patients. Our findings warrant isoform-specific analyses in human cancer datasets and suggest that switching between 5'UTR isoforms is an elegant and simple way to alter protein synthesis rates, set their sensitivity to the mTORC1-dependent nutrient-sensing pathway and direct the translational potential of an mRNA by the precise 5'UTR sequence.
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Affiliation(s)
- Ramona Weber
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - Umesh Ghoshdastider
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - Daniel Spies
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - Clara Duré
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Fabiola Valdivia-Francia
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Merima Forny
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - Mark Ormiston
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - Peter F. Renz
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - David Taborsky
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Merve Yigit
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Martino Bernasconi
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - Homare Yamahachi
- grid.7400.30000 0004 1937 0650Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952 Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Wagistrasse 12, CH-8952, Schlieren-Zurich, Switzerland.
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19
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Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. Cell Rep 2022; 41:111893. [PMID: 36577377 DOI: 10.1016/j.celrep.2022.111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/30/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further reveals cis- and trans-interacting partners as potential primary targets. Additionally, cell-type enrichment analysis identifies lncRNAs associated with pluripotency, while the knockdown of LINC02595, CATG00000090305.1, and RP11-148B6.2 modulates colony formation of iPSCs. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit a consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights that molecular phenotyping is more comprehensive in revealing affected pathways.
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Affiliation(s)
- Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Anika V Prabhu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Callum Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yan Jun Lan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, QC, Canada
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Wing Hin Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Xufeng Shu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Human Technopole, via Rita Levi Montalcini 1, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.
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20
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Makhnovskii PA, Gusev OA, Bokov RO, Gazizova GR, Vepkhvadze TF, Lysenko EA, Vinogradova OL, Kolpakov FA, Popov DV. Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle. Hum Genomics 2022; 16:24. [PMID: 35869513 PMCID: PMC9308330 DOI: 10.1186/s40246-022-00399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 07/14/2022] [Indexed: 11/18/2022] Open
Abstract
Background More than half of human protein-coding genes have an alternative transcription start site (TSS). We aimed to investigate the contribution of alternative TSSs to the acute-stress-induced transcriptome response in human tissue (skeletal muscle) using the cap analysis of gene expression approach. TSSs were examined at baseline and during recovery after acute stress (a cycling exercise). Results We identified 44,680 CAGE TSS clusters (including 3764 first defined) belonging to 12,268 genes and annotated for the first time 290 TSSs belonging to 163 genes. The transcriptome dynamically changes during the first hours after acute stress; the change in the expression of 10% of genes was associated with the activation of alternative TSSs, indicating differential TSSs usage. The majority of the alternative TSSs do not increase proteome complexity suggesting that the function of thousands of alternative TSSs is associated with the fine regulation of mRNA isoform expression from a gene due to the transcription factor-specific activation of various alternative TSSs. We identified individual muscle promoter regions for each TSS using muscle open chromatin data (ATAC-seq and DNase-seq). Then, using the positional weight matrix approach we predicted time course activation of “classic” transcription factors involved in response of skeletal muscle to contractile activity, as well as diversity of less/un-investigated factors. Conclusions Transcriptome response induced by acute stress related to activation of the alternative TSSs indicates that differential TSSs usage is an essential mechanism of fine regulation of gene response to stress stimulus. A comprehensive resource of accurate TSSs and individual promoter regions for each TSS in muscle was created. This resource together with the positional weight matrix approach can be used to accurate prediction of TFs in any gene(s) of interest involved in the response to various stimuli, interventions or pathological conditions in human skeletal muscle. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00399-8.
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21
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Ueno D, Yamasaki S, Sadakiyo Y, Teruyama T, Demura T, Kato K. Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes. J Biosci Bioeng 2022; 134:450-461. [PMID: 36137896 DOI: 10.1016/j.jbiosc.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 10/14/2022]
Abstract
RNA degradation is one of the critical steps for control of gene expression, and endonucleolytic cleavage-dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the Cap analysis of gene expression (CAGE) method. Although uncapped cleavage sites are widespread in eukaryotes, comparatively little information has been obtained about these sites using CAGE-based degradome analysis. Previously, we developed the truncated RNA-end sequencing (TREseq) method in plant species and used it to acquire comprehensive information about uncapped cleavage sites; we observed G-rich sequences near cleavage sites. However, it remains unclear whether this finding is general to other eukaryotes. In this study, we conducted TREseq analyses in fruit flies (Drosophila melanogaster) and budding yeast (Saccharomyces cerevisiae). The results revealed specific sequence features related to RNA cleavage in D. melanogaster and S. cerevisiae that were similar to sequence patterns in Arabidopsis thaliana. Although previous studies suggest that ribosome movements are important for determining cleavage position, feature selection using a random forest classifier showed that sequences around cleavage sites were major determinant for cleaved or uncleaved sites. Together, our results suggest that sequence features around cleavage sites are critical for determining cleavage position, and that sequence-specific endonucleolytic cleavage-dependent RNA degradation is highly conserved across eukaryotes.
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Affiliation(s)
- Daishin Ueno
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shotaro Yamasaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yuta Sadakiyo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Takumi Teruyama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Ko Kato
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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22
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de Hoon M, Bonetti A, Plessy C, Ando Y, Hon CC, Ishizu Y, Itoh M, Kato S, Lin D, Maekawa S, Murata M, Nishiyori H, Shin JW, Stolte J, Suzuki AM, Tagami M, Takahashi H, Thongjuea S, Forrest ARR, Hayashizaki Y, Kere J, Carninci P. Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs. Genome Res 2022; 32:gr.276647.122. [PMID: 35961773 PMCID: PMC9528987 DOI: 10.1101/gr.276647.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/09/2022] [Indexed: 12/03/2022]
Abstract
In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs. Transcription initiation peaks associated with genes in the sense direction have a strong preference to produce either long or short capped RNAs, with one out of six peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs have highly specific 3' ends, typically overlapping splice sites. Enhancers also preferentially generate either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Enhancers producing either short or long capped RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.
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Affiliation(s)
- Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshinari Ando
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuri Ishizu
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Sachi Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Dongyan Lin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Mila, Montreal, Quebec H2S 3H1, Canada
| | - Sho Maekawa
- RIKEN Omics Science Center (OSC), Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138632, Singapore
| | - Jens Stolte
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ana Maria Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hazuki Takahashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Kanagawa 230-0045, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki 00290, Finland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Human Technopole, Milan 20157, Italy
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23
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Schon MA, Lutzmayer S, Hofmann F, Nodine MD. Bookend: precise transcript reconstruction with end-guided assembly. Genome Biol 2022; 23:143. [PMID: 35768836 PMCID: PMC9245221 DOI: 10.1186/s13059-022-02700-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/05/2022] [Indexed: 12/29/2022] Open
Abstract
We developed Bookend, a package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. We demonstrate that correct identification of transcript start and end sites is essential for precise full-length transcript assembly. Utilization of end-labeled reads present in full-length single-cell RNA-seq datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis thaliana, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells, can produce reference-quality end-to-end transcript annotations.
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Affiliation(s)
- Michael A Schon
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708, PB, The Netherlands. .,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
| | - Stefan Lutzmayer
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Falko Hofmann
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Michael D Nodine
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, 6708, PB, The Netherlands. .,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
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24
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Nagano M, Hu B, Yokobayashi S, Yamamura A, Umemura F, Coradin M, Ohta H, Yabuta Y, Ishikura Y, Okamoto I, Ikeda H, Kawahira N, Nosaka Y, Shimizu S, Kojima Y, Mizuta K, Kasahara T, Imoto Y, Meehan K, Stocsits R, Wutz G, Hiraoka Y, Murakawa Y, Yamamoto T, Tachibana K, Peters JM, Mirny LA, Garcia BA, Majewski J, Saitou M. Nucleome programming is required for the foundation of totipotency in mammalian germline development. EMBO J 2022; 41:e110600. [PMID: 35703121 DOI: 10.15252/embj.2022110600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres-an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.
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Affiliation(s)
- Masahiro Nagano
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Bo Hu
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Shihori Yokobayashi
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Akitoshi Yamamura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumiya Umemura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mariel Coradin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Hiroshi Ohta
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukiko Ishikura
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ikuhiro Okamoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroki Ikeda
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Department of Embryology, Nara Medical University, Nara, Japan
| | - Naofumi Kawahira
- Department of Molecular Cell Developmental Biology, School of Life Science, University of California, Los Angeles, CA, USA.,Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yoshiaki Nosaka
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sakura Shimizu
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoji Kojima
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ken Mizuta
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoko Kasahara
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yusuke Imoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Killian Meehan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Roman Stocsits
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Yasuaki Hiraoka
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yasuhiro Murakawa
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takuya Yamamoto
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project, Kyoto, Japan
| | - Kikue Tachibana
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.,Department of Totipotency, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jan-Michel Peters
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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25
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Kageyama Y, Nakamura M, Igari Y, Yamaguchi S, Oguchi A, Murakawa Y, Hattori Y, Sasano Y. Expression of matrix metalloproteinase-3 and -10 is up-regulated in the periodontal tissues of aged mice. J Periodontal Res 2022; 57:733-741. [PMID: 35502585 PMCID: PMC9542255 DOI: 10.1111/jre.12996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 04/05/2022] [Accepted: 04/17/2022] [Indexed: 12/12/2022]
Abstract
Objective The present study was designed to investigate the whole transcriptome of periodontal tissues of both young and aged mice to identify the characteristic up‐regulation of protease genes with aging and to localize their translated protein products in the periodontal tissues. Background The metzincin protease superfamily is composed of matrix metalloproteinases (MMPs), a disintegrin and metalloproteinases, and a disintegrin and metalloproteinases with thrombospondin motifs. Up‐regulation of these extracellular matrix‐degrading proteases has been implicated in senescence of tissues and organs, including the skin. However, few studies have investigated the expression profiles of these proteases and potential involvement in aging of periodontal tissues. Methods Periodontal tissues with the surrounding mandibular bones were collected from 50‐ and 10‐week‐old mice. Total RNA was extracted from the periodontal tissue and analyzed by cap analysis of gene expression (CAGE) to identify differentially expressed genes encoding the metzincin proteases. Furthermore, quantitative real‐time polymerase chain reaction (qRT‐PCR) was performed to validate the CAGE results, and the phenotypic expression of proteases involved in aging was localized via immunohistochemical analysis. Results The CAGE results showed that the expression levels of MMP‐3, ‐10, and ‐12 were up‐regulated at 50 weeks. Subsequent qRT‐PCR analysis showed that the gene expression levels of MMP‐3 and ‐10 were significantly increased with age. MMP‐10 immunoreactivity was localized exclusively in the cementum and alveolar bone adjacent to the periodontal ligament and was stronger and broader in aged mice than young mice. MMP‐3 immunoreactivity was localized in the periodontal ligaments at both 10 and 50 weeks. Conclusion In the present study, we demonstrated that the expression of MMP‐3 and ‐10 increased with aging and identified their characteristic localizations in aged periodontal tissues.
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Affiliation(s)
- Yoko Kageyama
- Division of Aging and Geriatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Megumi Nakamura
- Division of Craniofacial Development and Tissue Biology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Yohei Igari
- Division of Aging and Geriatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoshi Yamaguchi
- Division of Aging and Geriatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Yoshinori Hattori
- Division of Aging and Geriatric Dentistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Yasuyuki Sasano
- Division of Craniofacial Development and Tissue Biology, Tohoku University Graduate School of Dentistry, Sendai, Japan
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26
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Ueno D, Yamasaki S, Kato K. Methods for detecting RNA degradation intermediates in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 318:111241. [PMID: 35351296 DOI: 10.1016/j.plantsci.2022.111241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/12/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
RNA degradation is an important process for controlling gene expression and is mediated by decapping / deadenylation-dependent or endonucleolytic cleavage-dependent RNA degradation mechanisms. High-throughput sequencing of RNA degradation intermediates was initially developed in Arabidopsis thaliana and similar RNA degradome sequencing methods were conducted in other eukaryotes. However, interpreting results obtained by these sequencing methods is fragmented, and an overview is needed. Here we review the findings and limitations of these sequencing methods and discuss the missing experiments needed to understand RNA degradation intermediates accurately. This review provides direction for future research on RNA degradation and is a reference for RNA degradome studies in other species.
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Affiliation(s)
- Daishin Ueno
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shotaro Yamasaki
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Ko Kato
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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27
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Vuoristo S, Bhagat S, Hydén-Granskog C, Yoshihara M, Gawriyski L, Jouhilahti EM, Ranga V, Tamirat M, Huhtala M, Kirjanov I, Nykänen S, Krjutškov K, Damdimopoulos A, Weltner J, Hashimoto K, Recher G, Ezer S, Paluoja P, Paloviita P, Takegami Y, Kanemaru A, Lundin K, Airenne TT, Otonkoski T, Tapanainen JS, Kawaji H, Murakawa Y, Bürglin TR, Varjosalo M, Johnson MS, Tuuri T, Katayama S, Kere J. DUX4 is a multifunctional factor priming human embryonic genome activation. iScience 2022; 25:104137. [PMID: 35402882 PMCID: PMC8990217 DOI: 10.1016/j.isci.2022.104137] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/04/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Double homeobox 4 (DUX4) is expressed at the early pre-implantation stage in human embryos. Here we show that induced human DUX4 expression substantially alters the chromatin accessibility of non-coding DNA and activates thousands of newly identified transcribed enhancer-like regions, preferentially located within ERVL-MaLR repeat elements. CRISPR activation of transcribed enhancers by C-terminal DUX4 motifs results in the increased expression of target embryonic genome activation (EGA) genes ZSCAN4 and KHDC1P1. We show that DUX4 is markedly enriched in human zygotes, followed by intense nuclear DUX4 localization preceding and coinciding with minor EGA. DUX4 knockdown in human zygotes led to changes in the EGA transcriptome but did not terminate the embryos. We also show that the DUX4 protein interacts with the Mediator complex via the C-terminal KIX binding motif. Our findings contribute to the understanding of DUX4 as a regulator of the non-coding genome.
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Affiliation(s)
- Sanna Vuoristo
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
| | | | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden
| | - Lisa Gawriyski
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Vipin Ranga
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mahlet Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mikko Huhtala
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Ida Kirjanov
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Sonja Nykänen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Competence Centre for Health Technologies, 51010 Tartu, Estonia.,University of Tartu, Department of Obstetrics and Gynecology, Institute of Clinical Medicine, 50406 Tartu, Estonia
| | | | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Gaëlle Recher
- Laboratoire Photonique Numérique et Nanosciences, CNRS, Institut d'Optique Graduate School, University of Bordeaux, UMR 5298, 33400 Bordeaux, France
| | - Sini Ezer
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Priit Paluoja
- Competence Centre for Health Technologies, 51010 Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50090 Tartu, Estonia.,University of Helsinki, Doctoral Program in Population Health, 00014 Helsinki, Finland
| | - Pauliina Paloviita
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | | | | | - Karolina Lundin
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Tomi T Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Children's Hospital, Helsinki University Central Hospital, 00290
| | - Juha S Tapanainen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland.,Oulu University Hospital, 90220 Oulu, Finland
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan.,IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Thomas R Bürglin
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
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28
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Pospiech K, Orzechowska M, Nowakowska M, Anusewicz D, Płuciennik E, Kośla K, Bednarek AK. TGFα-EGFR pathway in breast carcinogenesis, association with WWOX expression and estrogen activation. J Appl Genet 2022; 63:339-359. [PMID: 35290621 PMCID: PMC8979909 DOI: 10.1007/s13353-022-00690-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022]
Abstract
WWOX is a tumor-suppressive steroid dehydrogenase, which relationship with hormone receptors was shown both in animal models and breast cancer patients. Herein, through nAnT-iCAGE high-throughput gene expression profiling, we studied the interplay of estrogen receptors and the WWOX in breast cancer cell lines (MCF7, T47D, MDA-MB-231, BT20) under estrogen stimulation and either introduction of the WWOX gene by retroviral transfection (MDA-MB-231, T47D) or silenced with shRNA (MCF7, BT20). Additionally, we evaluated the consequent biological characteristics by proliferation, apoptosis, invasion, and adhesion assays. TGFα-EGFR signaling was found to be significantly affected in all examined breast cancer cell lines in response to estrogen and strongly associated with the level of WWOX expression, especially in ER-positive MCF7 cells. Under the influence of 17β-estradiol presence, biological characteristics of the cell lines were also delineated. The study revealed modulation of adhesion, invasion, and apoptosis. The obtained results point at a complex role of the WWOX gene in the carcinogenesis of the breast tissue, which seems to be closely related to the presence of estrogen α and/or β receptors.
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Affiliation(s)
- Karolina Pospiech
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | | | - Magdalena Nowakowska
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | - Dorota Anusewicz
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Kośla
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland.
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29
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Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency. Proc Natl Acad Sci U S A 2022; 119:2117226119. [PMID: 35217614 PMCID: PMC8892498 DOI: 10.1073/pnas.2117226119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 01/15/2023] Open
Abstract
Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of mammalian genes, we identified five homeobox (Hox) gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. An analysis of published cap analysis of gene expression sequencing (CAGE-seq) data and generated CAGE-seq data for messenger RNAs (mRNAs) from mouse somites revealed that the 5' leaders of Hox mRNAs of interest contain conserved uORFs, are generally much shorter than reported, and lack previously proposed internal ribosome entry site elements. We show that the conserved uORFs inhibit Hox reporter expression and that altering the stringency of start codon selection by overexpressing eIF1 or eIF5 modulates the expression of Hox reporters. We also show that modifying ribosome homeostasis by depleting a large ribosomal subunit protein or treating cells with sublethal concentrations of puromycin leads to lower stringency of start codon selection. Thus, altering global translation can confer gene-specific effects through altered start codon selection stringency.
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30
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Dahale S, Ruiz-Orera J, Silhavy J, Hübner N, van Heesch S, Pravenec M, Atanur SS. Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension. Life Sci Alliance 2022; 5:5/4/e202101234. [PMID: 34996843 PMCID: PMC8742872 DOI: 10.26508/lsa.202101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
The role of alternative promoter usage in tissue-specific gene expression has been well established; however, its role in complex diseases is poorly understood. We performed cap analysis of gene expression (CAGE) sequencing from the left ventricle of a rat model of hypertension, the spontaneously hypertensive rat (SHR), and a normotensive strain, Brown Norway to understand the role of alternative promoter usage in complex disease. We identified 26,560 CAGE-defined transcription start sites in the rat left ventricle, including 1,970 novel cardiac transcription start sites. We identified 28 genes with alternative promoter usage between SHR and Brown Norway, which could lead to protein isoforms differing at the amino terminus between two strains and 475 promoter switching events altering the length of the 5' UTR. We found that the shift in Insr promoter usage was significantly associated with insulin levels and blood pressure within a panel of HXB/BXH recombinant inbred rat strains, suggesting that hyperinsulinemia due to insulin resistance might lead to hypertension in SHR. Our study provides a preliminary evidence of alternative promoter usage in complex diseases.
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Affiliation(s)
- Sonal Dahale
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK.,Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Charité -Universitätsmedizin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | | | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Santosh S Atanur
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK .,The National Institute for Health Research, Imperial Biomedical Research Centre, ITMAT Data Science Group, Imperial College London, London, UK
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31
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2223-2235. [DOI: 10.1093/hmg/ddac023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/11/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
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32
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Abstract
Transcription start site (TSS) usage is a critical factor in the regulation of gene expression. A number of methods for global TSS mapping have been developed, but barriers of expense, technical difficulty, time, and/or cost have limited their broader adoption. To address these issues, we developed Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq). Requiring only three enzymatic steps with intervening bead cleanups, a STRIPE-seq library can be prepared from as little as 50 ng total RNA in ~5 h at a cost of ~$12 (US). In addition to profiling TSS usage, STRIPE-seq provides information on transcript levels that can be used for differential expression analysis. Thanks to its simplicity and low cost, we envision that STRIPE-seq could be employed by any molecular biology laboratory interested in profiling transcription initiation.
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Affiliation(s)
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN, USA.
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.
- eGenesis, Inc., Cambridge, MA, USA.
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33
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Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res 2021; 32:162-174. [PMID: 34815308 PMCID: PMC8744680 DOI: 10.1101/gr.275784.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the other RNA polymerases that also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq, which comprehensively identifies TSS for both Pol II and non-Pol II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5' m7G caps and 5' triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol II TSSs that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSSs associated with Pol III transcripts that have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and noncoding RNA concurrently and enables the classification of epigenetic profiles associated with Pol II and non-Pol II TSS.
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Affiliation(s)
- Bo Yan
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Ira Schildkraut
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
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Lu Z, Berry K, Hu Z, Zhan Y, Ahn TH, Lin Z. TSSr: an R package for comprehensive analyses of TSS sequencing data. NAR Genom Bioinform 2021; 3:lqab108. [PMID: 34805991 PMCID: PMC8598296 DOI: 10.1093/nargab/lqab108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/05/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription initiation is regulated in a highly organized fashion to ensure proper cellular functions. Accurate identification of transcription start sites (TSSs) and quantitative characterization of transcription initiation activities are fundamental steps for studies of regulated transcriptions and core promoter structures. Several high-throughput techniques have been developed to sequence the very 5'end of RNA transcripts (TSS sequencing) on the genome scale. Bioinformatics tools are essential for processing, analysis, and visualization of TSS sequencing data. Here, we present TSSr, an R package that provides rich functions for mapping TSS and characterizations of structures and activities of core promoters based on all types of TSS sequencing data. Specifically, TSSr implements several newly developed algorithms for accurately identifying TSSs from mapped sequencing reads and inference of core promoters, which are a prerequisite for subsequent functional analyses of TSS data. Furthermore, TSSr also enables users to export various types of TSS data that can be visualized by genome browser for inspection of promoter activities in association with other genomic features, and to generate publication-ready TSS graphs. These user-friendly features could greatly facilitate studies of transcription initiation based on TSS sequencing data. The source code and detailed documentations of TSSr can be freely accessed at https://github.com/Linlab-slu/TSSr.
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Affiliation(s)
- Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Keenan Berry
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Zhenbin Hu
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Yu Zhan
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Tae-Hyuk Ahn
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
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Chiba Y, Yoshizaki K, Tian T, Miyazaki K, Martin D, Saito K, Yamada A, Fukumoto S. Integration of Single-Cell RNA- and CAGE-seq Reveals Tooth-Enriched Genes. J Dent Res 2021; 101:220345211049785. [PMID: 34806461 PMCID: PMC9052834 DOI: 10.1177/00220345211049785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Organ development is dictated by the regulation of genes preferentially expressed in tissues or cell types. Gene expression profiling and identification of specific genes in organs can provide insights into organogenesis. Therefore, genome-wide analysis is a powerful tool for clarifying the mechanisms of development during organogenesis as well as tooth development. Single-cell RNA sequencing (scRNA-seq) is a suitable tool for unraveling the gene expression profile of dental cells. Using scRNA-seq, we can obtain a large pool of information on gene expression; however, identification of functional genes, which are key molecules for tooth development, via this approach remains challenging. In the present study, we performed cap analysis of gene expression sequence (CAGE-seq) using mouse tooth germ to identify the genes preferentially expressed in teeth. The CAGE-seq counts short reads at the 5'-end of transcripts; therefore, this method can quantify the amount of transcripts without bias related to the transcript length. We hypothesized that this CAGE data set would be of great help for further understanding a gene expression profile through scRNA-seq. We aimed to identify the important genes involved in tooth development via bioinformatics analyses, using a combination of scRNA-seq and CAGE-seq. We obtained the scRNA-seq data set of 12,212 cells from postnatal day 1 mouse molars and the CAGE-seq data set from postnatal day 1 molars. scRNA-seq analysis revealed the spatiotemporal expression of cell type-specific genes, and CAGE-seq helped determine whether these genes are preferentially expressed in tooth or ubiquitously. Furthermore, we identified candidate genes as novel tooth-enriched and dental cell type-specific markers. Our results show that the integration of scRNA-seq and CAGE-seq highlights the genes important for tooth development among numerous gene expression profiles. These findings should contribute to resolving the mechanism of tooth development and establishing the basis for tooth regeneration in the future.
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Affiliation(s)
- Y. Chiba
- Section of Oral Medicine for
Children, Division of Oral Health, Growth and Development, Faculty of Dental
Science, Kyushu University, Fukuoka, Japan
| | - K. Yoshizaki
- Section of Orthodontics and
Dentofacial Orthopedics, Division of Oral Health, Growth and Development,
Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - T. Tian
- Section of Orthodontics and
Dentofacial Orthopedics, Division of Oral Health, Growth and Development,
Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - K. Miyazaki
- Section of Orthodontics and
Dentofacial Orthopedics, Division of Oral Health, Growth and Development,
Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - D. Martin
- Genomics and Computational
Biology Core, National Institute on Deafness and Other Communication
Disorders, National Institute of Dental and Craniofacial Research, National
Institutes of Health, Bethesda, MD, USA
| | - Genomics and Computational Biology Core
- Genomics and Computational
Biology Core, National Institute on Deafness and Other Communication
Disorders, National Institute of Dental and Craniofacial Research, National
Institutes of Health, Bethesda, MD, USA
| | - K. Saito
- Division of Pediatric Dentistry,
Department of Community Social Dentistry, Graduate School of Dentistry,
Tohoku University, Sendai, Japan
| | - A. Yamada
- Division of Pediatric Dentistry,
Department of Community Social Dentistry, Graduate School of Dentistry,
Tohoku University, Sendai, Japan
| | - S. Fukumoto
- Section of Oral Medicine for
Children, Division of Oral Health, Growth and Development, Faculty of Dental
Science, Kyushu University, Fukuoka, Japan
- Division of Pediatric Dentistry,
Department of Community Social Dentistry, Graduate School of Dentistry,
Tohoku University, Sendai, Japan
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Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle. Commun Biol 2021; 4:1290. [PMID: 34782710 PMCID: PMC8592991 DOI: 10.1038/s42003-021-02819-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
Mice enter an active hypometabolic state, called daily torpor when they experience a lowered caloric intake under cold ambient temperature. During torpor, the oxygen consumption rate in some animals drops to less than 30% of the normal rate without harming the body. This safe but severe reduction in metabolism is attractive for various clinical applications; however, the mechanism and molecules involved are unclear. Therefore, here we systematically analyzed the gene expression landscape on the level of the RNA transcription start sites in mouse skeletal muscles under various metabolic states to identify torpor-specific transcribed regulatory patterns. We analyzed the soleus muscles from 38 mice in torpid and non-torpid conditions and identified 287 torpor-specific promoters out of 12,862 detected promoters. Furthermore, we found that the transcription factor ATF3 is highly expressed during torpor deprivation and its binding motif is enriched in torpor-specific promoters. Atf3 was also highly expressed in the heart and brown adipose tissue during torpor and systemically knocking out Atf3 affected the torpor phenotype. Our results demonstrate that mouse torpor combined with powerful genetic tools is useful for studying active hypometabolism.
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Hale AE, Moorman NJ. The Ends Dictate the Means: Promoter Switching in Herpesvirus Gene Expression. Annu Rev Virol 2021; 8:201-218. [PMID: 34129370 DOI: 10.1146/annurev-virology-091919-072841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Herpesvirus gene expression is dynamic and complex, with distinct complements of viral genes expressed at specific times in different infection contexts. These complex patterns of viral gene expression arise in part from the integration of multiple cellular and viral signals that affect the transcription of viral genes. The use of alternative promoters provides an increased level of control, allowing different promoters to direct the transcription of the same gene in response to distinct temporal and contextual cues. While once considered rare, herpesvirus alternative promoter usage was recently found to be far more pervasive and impactful than previously thought. Here we review several examples of promoter switching in herpesviruses and discuss the functional consequences on the transcriptional and post-transcriptional regulation of viral gene expression.
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Affiliation(s)
- Andrew E Hale
- Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
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Shaw PJ, Piriyapongsa J, Kaewprommal P, Wongsombat C, Chaosrikul C, Teeravajanadet K, Boonbangyang M, Uthaipibull C, Kamchonwongpaisan S, Tongsima S. Identifying transcript 5' capped ends in Plasmodium falciparum. PeerJ 2021; 9:e11983. [PMID: 34527439 PMCID: PMC8401752 DOI: 10.7717/peerj.11983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Background The genome of the human malaria parasite Plasmodium falciparum is poorly annotated, in particular, the 5' capped ends of its mRNA transcripts. New approaches are needed to fully catalog P. falciparum transcripts for understanding gene function and regulation in this organism. Methods We developed a transcriptomic method based on next-generation sequencing of complementary DNA (cDNA) enriched for full-length fragments using eIF4E, a 5' cap-binding protein, and an unenriched control. DNA sequencing adapter was added after enrichment of full-length cDNA using two different ligation protocols. From the mapped sequence reads, enrichment scores were calculated for all transcribed nucleotides and used to calculate P-values of 5' capped nucleotide enrichment. Sensitivity and accuracy were increased by combining P-values from replicate experiments. Data were obtained for P. falciparum ring, trophozoite and schizont stages of intra-erythrocytic development. Results 5' capped nucleotide signals were mapped to 17,961 non-overlapping P. falciparum genomic intervals. Analysis of the dominant 5' capped nucleotide in these genomic intervals revealed the presence of two groups with distinctive epigenetic features and sequence patterns. A total of 4,512 transcripts were annotated as 5' capped based on the correspondence of 5' end with 5' capped nucleotide annotated from full-length cDNA data. Discussion The presence of two groups of 5' capped nucleotides suggests that alternative mechanisms may exist for producing 5' capped transcript ends in P. falciparum. The 5' capped transcripts that are antisense, outside of, or partially overlapping coding regions may be important regulators of gene function in P. falciparum.
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Affiliation(s)
- Philip J Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Jittima Piriyapongsa
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Pavita Kaewprommal
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chayaphat Wongsombat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chadapohn Chaosrikul
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Krirkwit Teeravajanadet
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Manon Boonbangyang
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chairat Uthaipibull
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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39
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Ducoli L, Agrawal S, Hon CC, Ramilowski JA, Sibler E, Tagami M, Itoh M, Kondo N, Abugessaisa I, Hasegawa A, Kasukawa T, Suzuki H, Carninci P, Shin JW, de Hoon MJL, Detmar M. The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background. BMC Genom Data 2021; 22:33. [PMID: 34521352 PMCID: PMC8439024 DOI: 10.1186/s12863-021-00992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/29/2021] [Indexed: 11/18/2022] Open
Abstract
Background The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism’s physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner. Results To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background. Conclusion In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00992-1.
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Affiliation(s)
- Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Eliane Sibler
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan.,Human Technopole, Via Cristina Belgioioso 171, 20157, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
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Guerrini MM, Oguchi A, Suzuki A, Murakawa Y. Cap analysis of gene expression (CAGE) and noncoding regulatory elements. Semin Immunopathol 2021; 44:127-136. [PMID: 34468849 DOI: 10.1007/s00281-021-00886-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/13/2021] [Indexed: 01/06/2023]
Abstract
Cap analysis of gene expression (CAGE) was developed to detect the 5' end of RNA. Trapping of the RNA 5'-cap structure enables the enrichment and selective sequencing of complete transcripts. Upscaled high-throughput versions of CAGE have enabled the genome-wide identification of transcription start sites, including transcriptionally active promoters and enhancers. CAGE sequencing can be exploited to draw comprehensive maps of active genomic regulatory elements in a cell type- and activation-specific manner. The cells of the immune system are among the best candidates to be analyzed in humans, since they are easily accessible. In this review, we discuss how CAGE data are instrumental for integrative analyses with quantitative trait loci and omics data, and their usefulness in the mechanistic interpretation of the effects of genetic variations over the entire human genome. Integrating CAGE data with the currently available omics information will contribute to better understanding of the genome-wide association study variants that lie outside of annotated genes, deepening our knowledge on human diseases, and enabling the targeted design of more specific therapeutic interventions.
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Affiliation(s)
- Matteo Maurizio Guerrini
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
| | - Akiko Oguchi
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy
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41
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A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions. Methods Mol Biol 2021. [PMID: 34382181 DOI: 10.1007/978-1-0716-1597-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Knowledge in gene transcription and chromatin regulation has been intensely studied for decades, but thanks to next-generation sequencing (NGS) techniques there has been a major leap forward in the last few years. Historically, identification of specific enhancer elements has led to the identification of master transcription factors (TFs) in the 1990s. Genetic and biochemical experiments have identified the key regulators controlling RNA polymerase II (RNAPII) transcription and structurally analyses have elucidated detailed mechanisms. NGS and the development of chromatin immunoprecipitation (ChIP) have accelerated the gain of knowledge in the recent years. By now, we have a dazzling wealth of techniques that are currently used to put gene expression into a genome-wide context. This book is an attempt to assemble useful protocols for many researchers within and nearby research areas. In general, these innovative techniques focus on enhancer and promoter studies. The techniques should also be of interest for related fields such as DNA repair and replication.
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Kikuchi Y, Tokita S, Hirama T, Kochin V, Nakatsugawa M, Shinkawa T, Hirohashi Y, Tsukahara T, Hata F, Takemasa I, Sato N, Kanaseki T, Torigoe T. CD8 + T-cell Immune Surveillance against a Tumor Antigen Encoded by the Oncogenic Long Noncoding RNA PVT1. Cancer Immunol Res 2021; 9:1342-1353. [PMID: 34433589 DOI: 10.1158/2326-6066.cir-20-0964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/11/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022]
Abstract
CD8+ T cells recognize peptides displayed by HLA class I molecules on cell surfaces, monitoring pathologic conditions such as cancer. Advances in proteogenomic analysis of HLA ligandomes have demonstrated that cells present a subset of cryptic peptides derived from noncoding regions of the genome; however, the roles of cryptic HLA ligands in tumor immunity remain unknown. In the current study, we comprehensively and quantitatively investigated the HLA class I ligandome of a set of human colorectal cancer and matched normal tissues, showing that cryptic translation products accounted for approximately 5% of the HLA class I ligandome. We also found that a peptide encoded by the long noncoding RNA (lncRNA) PVT1 was predominantly enriched in multiple colorectal cancer tissues. The PVT1 gene is located downstream of the MYC gene in the genome and is aberrantly overexpressed across a variety of cancers, reflecting its oncogenic property. The PVT1 peptide was recognized by patient CD8+ tumor-infiltrating lymphocytes, as well as peripheral blood mononuclear cells, suggesting the presence of patient immune surveillance. Our findings show that peptides can be translated from lncRNAs and presented by HLA class I and that cancer patient T cells are capable of sensing aberrations in noncoding regions of the genome.
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Affiliation(s)
- Yasuhiro Kikuchi
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Tomomi Hirama
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Vitaly Kochin
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Department of Immunology, Nagoya University, Nagoya, Japan
| | - Munehide Nakatsugawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Department of Pathology, Tokyo Medical University Hachioji Medical Center, Hachioji, Tokyo, Japan
| | - Tomoyo Shinkawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | | | | | | | - Ichiro Takemasa
- Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Sapporo Dohto Hospital, Sapporo, Japan
| | - Takayuki Kanaseki
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.
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Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling. Genome Res 2021; 31:1680-1692. [PMID: 34330790 PMCID: PMC8415375 DOI: 10.1101/gr.275684.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
Abstract
We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus. We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were located near gene bodies, and temporal patterns of eRNA expression tended to parallel those of nearby genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays was associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are available at Echinobase, the public database of information related to echinoderm genomics.
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44
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Yamamoto K, Suzuki A, Guerrini MM. Functional genetics for studying the human immune system. Int Immunol 2021; 33:647-651. [PMID: 34313763 DOI: 10.1093/intimm/dxab046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/27/2021] [Indexed: 12/21/2022] Open
Abstract
Although small numbers of immune-mediated diseases are inherited due to rare genetic mutations, most are multifactorial diseases caused by multiple elements including genetic and environmental factors. In the case of autoimmune diseases, many disease-susceptibility genes, including several in the major histocompatibility gene complex, have been reported, and over the past 10 years, genome-wide association studies (GWAS) have been used to analyze disease-susceptibility loci in representative diseases. Furthermore, many disease susceptibility variants have been found to be related to gene expression levels. The expression of genes involved in disease pathogenesis is often cell type-specific, and this is closely related to epigenome alterations. Genomic information is present even before the onset of a disease and has a clear causal relationship to the disease (i.e., the outcome). Therefore, it is important to establish functional genetics in human immunology to understand the pathogenesis of diseases using these pieces of information. We can then apply these results to drug discovery. Here, we will review these issues, especially focusing on autoimmune diseases, and discuss current and future directions of human immune system research.
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Affiliation(s)
- Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Matteo Maurizio Guerrini
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Varshney A, Kyono Y, Elangovan VR, Wang C, Erdos MR, Narisu N, Albanus RD, Orchard P, Stitzel ML, Collins FS, Kitzman JO, Parker SCJ. A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures. Diabetes 2021; 70:1581-1591. [PMID: 33849996 PMCID: PMC8336006 DOI: 10.2337/db20-1087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/09/2021] [Indexed: 12/21/2022]
Abstract
Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ∼20% of which are islet specific and occur mostly distal to known gene TSS. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validated the transcriptional enhancer activity for 2,279 of 3,378 (∼68%) tested islet CAGE elements (5% false discovery rate). TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting active enhancers at GWAS loci.
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Affiliation(s)
- Arushi Varshney
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Yasuhiro Kyono
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | - Collin Wang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Peter Orchard
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
| | | | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jacob O Kitzman
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Stephen C J Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
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Sano K, Hayashi T, Suehara Y, Hosoya M, Takamochi K, Kohsaka S, Kishikawa S, Kishi M, Saito S, Takahashi F, Kaneko K, Suzuki K, Yao T, Ishijima M, Saito T. Transcription start site-level expression of thyroid transcription factor 1 isoforms in lung adenocarcinoma and its clinicopathological significance. J Pathol Clin Res 2021; 7:361-374. [PMID: 34014042 PMCID: PMC8185369 DOI: 10.1002/cjp2.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
There are multiple transcription start sites (TSSs) in agreement with multiple transcript variants encoding different isoforms of NKX2-1/TTF-1 (thyroid transcription factor 1); however, the clinicopathological significance of each transcript isoform of NKX2-1/TTF-1 in lung adenocarcinoma (LAD) is unknown. Herein, TSS-level expression of NKX2-1/TTF-1 isoforms was evaluated in 71 LADs using bioinformatic analysis of cap analysis of gene expression (CAGE)-sequencing data, which provides genome-wide expression levels of the 5'-untranslated regions and the TSSs of different isoforms. Results of CAGE were further validated in 664 LADs using in situ hybridisation. Fourteen of 17 TSSs in NKX2-1/TTF-1 (80% of known TSSs in FANTOM5, an atlas of mammalian promoters) were identified in LADs, including TSSs 1-13 and 15; four isoforms of NKX2-1/TTF-1 transcripts (NKX2-1_001, NKX2-1_002, NKX2-1_004, and NKX2-1_005) were expressed in LADs, although NKX2-1_005 did not contain a homeodomain. Among those, six TSSs regulated NKX2-1_004 and NKX2-1_005, both of which contain exon 1. LADs with low expression of isoforms from TSS region 11 regulating exon 1 were significantly associated with poor prognosis in the CAGE data set. In the validation set, 62 tumours (9.3%) showed no expression of NKX2-1/TTF-1 exon 1; such tumours were significantly associated with older age, EGFR wild-type tumours, and poor prognosis. In contrast, 94 tumours, including 22 of 30 pulmonary invasive mucinous adenocarcinomas (IMAs) exhibited exon 1 expression without immunohistochemical TTF-1 protein expression. Furthermore, IMAs commonly exhibited higher exon 1 expression relative to that of exon 4/5, which contained a homeodomain in comparison with EGFR-mutated LADs. These transcriptome and clinicopathological results reveal that LAD use at least 80% of NKX2-1 TSSs and expression of the NKX2-1/TTF-1 transcript isoform without exon 1 (NKX2-1_004 and NKX2-1_005) defines a distinct subset of LAD characterised by aggressive behaviour in elder patients. Moreover, usage of alternative TSSs regions regulating NKX2-1_005 may occur in subsets of LADs.
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Affiliation(s)
- Kei Sano
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
- Department of Medicine for Orthopaedics and Motor OrganJuntendo University Graduate School of MedicineTokyoJapan
| | - Takuo Hayashi
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Yoshiyuki Suehara
- Department of Medicine for Orthopaedics and Motor OrganJuntendo University Graduate School of MedicineTokyoJapan
| | - Masaki Hosoya
- Department of Medical OncologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Kazuya Takamochi
- Department of General Thoracic SurgeryJuntendo University Graduate School of MedicineTokyoJapan
| | - Shinji Kohsaka
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Satsuki Kishikawa
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Monami Kishi
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Satomi Saito
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Fumiyuki Takahashi
- Department of Respiratory MedicineJuntendo University Graduate School of MedicineTokyoJapan
| | - Kazuo Kaneko
- Department of Medicine for Orthopaedics and Motor OrganJuntendo University Graduate School of MedicineTokyoJapan
| | - Kenji Suzuki
- Department of General Thoracic SurgeryJuntendo University Graduate School of MedicineTokyoJapan
| | - Takashi Yao
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Muneaki Ishijima
- Department of Medicine for Orthopaedics and Motor OrganJuntendo University Graduate School of MedicineTokyoJapan
| | - Tsuyoshi Saito
- Department of Human PathologyJuntendo University Graduate School of MedicineTokyoJapan
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Hata T, Satoh S, Takada N, Matsuo M, Obokata J. Kozak Sequence Acts as a Negative Regulator for De Novo Transcription Initiation of Newborn Coding Sequences in the Plant Genome. Mol Biol Evol 2021; 38:2791-2803. [PMID: 33705557 PMCID: PMC8233501 DOI: 10.1093/molbev/msab069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells. The systematic characterization of the LUC-TSSs revealed that 80% of them occurred under the influence of endogenous promoters, while the remainder underwent de novo activation in the intergenic regions, starting from pyrimidine-purine dinucleotides. These de novo TSSs obeyed unexpected rules; they predominantly occurred ∼100 bp upstream of the LUC inserts and did not overlap with Kozak-containing putative open reading frames (ORFs). These features were the output of the immediate responses to the sequence insertions, rather than a bias in the screening of the LUC gene function. Regarding the wild-type genic TSSs, they appeared to have evolved to lack any ORFs in their vicinities. Therefore, the repulsion by the de novo TSSs of Kozak-containing ORFs described above might be the first selection gate for the occurrence and evolution of TSSs in the plant genome. Based on these results, we characterized the de novo type of TSS identified in the plant genome and discuss its significance in genome evolution.
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Affiliation(s)
- Takayuki Hata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto, Japan
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto, Japan
| | - Naoto Takada
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka, Japan
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Pintus SS, Akberdin IR, Yevshin I, Makhnovskii P, Tyapkina O, Nigmetzyanov I, Nurullin L, Devyatiyarov R, Shagimardanova E, Popov D, Kolpakov FA, Gusev O, Gazizova GR. Genome-Wide Atlas of Promoter Expression Reveals Contribution of Transcribed Regulatory Elements to Genetic Control of Disuse-Mediated Atrophy of Skeletal Muscle. BIOLOGY 2021; 10:biology10060557. [PMID: 34203013 PMCID: PMC8235325 DOI: 10.3390/biology10060557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/05/2022]
Abstract
Simple Summary The genetic process underlying the control of skeletal muscle homeostasis is a key factor in methods that develop technologies to prevent age and immobility-driven atrophy. In the current paper, using advanced methods for the whole-genome profiling of transcription starting sites in fast and slow muscle in rats, we developed an integrative database of transcribed regulatory elements. Employing methods of comparative transcriptomics, we demonstrate that cis-regulatory elements are actively involved in the control of atrophy and recovery, and that the differential use of promoters and enhancers is the one of the key mechanisms that distinguishes between specific processes in slow and fast skeletal muscles. Abstract The prevention of muscle atrophy carries with it clinical significance for the control of increased morbidity and mortality following physical inactivity. While major transcriptional events associated with muscle atrophy-recovery processes are the subject of active research on the gene level, the contribution of non-coding regulatory elements and alternative promoter usage is a major source for both the production of alternative protein products and new insights into the activity of transcription factors. We used the cap-analysis of gene expression (CAGE) to create a genome-wide atlas of promoter-level transcription in fast (m. EDL) and slow (m. soleus) muscles in rats that were subjected to hindlimb unloading and subsequent recovery. We found that the genetic regulation of the atrophy-recovery cycle in two types of muscle is mediated by different pathways, including a unique set of non-coding transcribed regulatory elements. We showed that the activation of “shadow” enhancers is tightly linked to specific stages of atrophy and recovery dynamics, with the largest number of specific regulatory elements being transcriptionally active in the muscles on the first day of recovery after a week of disuse. The developed comprehensive database of transcription of regulatory elements will further stimulate research on the gene regulation of muscle homeostasis in mammals.
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Affiliation(s)
- Sergey S. Pintus
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
| | - Ilya R. Akberdin
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ivan Yevshin
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
| | - Pavel Makhnovskii
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow 123007, Russia; (P.M.); (D.P.)
| | - Oksana Tyapkina
- Kazan Institute of Biochemistry and Biophysics FRC Kazan Scientific Center of RAS, 420007 Kazan, Russia; (O.T.); (L.N.)
- Department of Biology, Kazan State Medical University, 420012 Kazan, Russia
| | - Islam Nigmetzyanov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
| | - Leniz Nurullin
- Kazan Institute of Biochemistry and Biophysics FRC Kazan Scientific Center of RAS, 420007 Kazan, Russia; (O.T.); (L.N.)
- Department of Biology, Kazan State Medical University, 420012 Kazan, Russia
| | - Ruslan Devyatiyarov
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
| | - Elena Shagimardanova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
| | - Daniil Popov
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow 123007, Russia; (P.M.); (D.P.)
| | - Fedor A. Kolpakov
- Laboratory of Bioinformatics, Federal Research Center for Information and Computational Technologies, 630090 Novosibirsk, Russia
- Department of Computational Biology, Scientific Center for Information Technologies and Artificial Intelligence, Sirius University of Science and Technology, 354340 Sochi, Russia
- BIOSOFT.RU LLC, 630058 Novosibirsk, Russia; (S.S.P.); (I.R.A.); (I.Y.)
- Correspondence: or (F.A.K.); (O.G.); (G.R.G.)
| | - Oleg Gusev
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
- RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- Department of Functional Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Correspondence: or (F.A.K.); (O.G.); (G.R.G.)
| | - Guzel R. Gazizova
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420009 Kazan, Russia; (I.N.); (R.D.); (E.S.)
- Correspondence: or (F.A.K.); (O.G.); (G.R.G.)
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 2021; 12:3297. [PMID: 34078885 PMCID: PMC8172540 DOI: 10.1038/s41467-021-23143-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
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Sun W, Modica S, Dong H, Wolfrum C. Plasticity and heterogeneity of thermogenic adipose tissue. Nat Metab 2021; 3:751-761. [PMID: 34158657 DOI: 10.1038/s42255-021-00417-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022]
Abstract
The perception of adipose tissue, both in the scientific community and in the general population, has changed dramatically in the past 20 years. While adipose tissue was thought for a long time to be a rather simple lipid storage entity, it is now recognized as a highly heterogeneous organ and a critical regulator of systemic metabolism, composed of many different subtypes of cells, with important endocrine functions. Additionally, adipose tissue is nowadays recognized to contribute to energy turnover, due to the presence of specialized thermogenic adipocytes, which can be found in many adipose depots. This review discusses the unprecedented insights that we have gained into the heterogeneity of thermogenic adipocytes and their respective precursors due to the technical developments in single-cell and nucleus technologies. These methodological advances have increased our understanding of how adipose tissue catabolic function is influenced by developmental and intercellular communication events.
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Affiliation(s)
- Wenfei Sun
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Salvatore Modica
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Hua Dong
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Christian Wolfrum
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland.
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