1
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Xi S, Nguyen T, Murray S, Lorenz P, Mellor J. Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes. Yeast 2024; 41:222-241. [PMID: 38433440 DOI: 10.1002/yea.3931] [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: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Genomes from yeast to humans are subject to pervasive transcription. A single round of pervasive transcription is sufficient to alter local chromatin conformation, nucleosome dynamics and gene expression, but is hard to distinguish from background signals. Size fractionated native elongating transcript sequencing (sfNET-Seq) was developed to precisely map nascent transcripts independent of expression levels. RNAPII-associated nascent transcripts are fractionation into different size ranges before library construction. When anchored to the transcription start sites (TSS) of annotated genes, the combined pattern of the output metagenes gives the expected reference pattern. Bioinformatic pattern matching to the reference pattern identified 9542 transcription units in Saccharomyces cerevisiae, of which 47% are coding and 53% are noncoding. In total, 3113 (33%) are unannotated noncoding transcription units. Anchoring all transcription units to the TSS or polyadenylation site (PAS) of annotated genes reveals distinctive architectures of linked pairs of divergent transcripts approximately 200nt apart. The Reb1 transcription factor is enriched 30nt downstream of the PAS only when an upstream (TSS -60nt with respect to PAS) noncoding transcription unit co-occurs with a downstream (TSS +150nt) coding transcription unit and acts to limit levels of upstream antisense transcripts. The potential for extensive transcriptional interference is evident from low abundance unannotated transcription units with variable TSS (median -240nt) initiating within a 500nt window upstream of, and transcribing over, the promoters of protein-coding genes. This study confirms a highly interleaved yeast genome with different types of transcription units altering the chromatin landscape in distinctive ways, with the potential to exert extensive regulatory control.
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Affiliation(s)
- Shidong Xi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Tania Nguyen
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Struan Murray
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Phil Lorenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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2
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Meydan S, Barros GC, Simões V, Harley L, Cizubu BK, Guydosh NR, Silva GM. The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress. Cell Rep 2023; 42:113359. [PMID: 37917585 PMCID: PMC10755677 DOI: 10.1016/j.celrep.2023.113359] [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: 03/16/2023] [Revised: 07/26/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Oxidative stress causes K63-linked ubiquitination of ribosomes by the E2 ubiquitin conjugase Rad6. How Rad6-mediated ubiquitination of ribosomes affects translation, however, is unclear. We therefore perform Ribo-seq and Disome-seq in Saccharomyces cerevisiae and show that oxidative stress causes ribosome pausing at specific amino acid motifs, which also leads to ribosome collisions. However, these redox-pausing signatures are lost in the absence of Rad6 and do not depend on the ribosome-associated quality control (RQC) pathway. We also show that Rad6 is needed to inhibit overall translation in response to oxidative stress and that its deletion leads to increased expression of antioxidant genes. Finally, we observe that the lack of Rad6 leads to changes during translation that affect activation of the integrated stress response (ISR) pathway. Our results provide a high-resolution picture of the gene expression changes during oxidative stress and unravel an additional stress response pathway affecting translation elongation.
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Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Postdoctoral Research Associate Training Fellowship, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20982, USA
| | | | - Vanessa Simões
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Lana Harley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA.
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3
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Wacholder A, Parikh SB, Coelho NC, Acar O, Houghton C, Chou L, Carvunis AR. A vast evolutionarily transient translatome contributes to phenotype and fitness. Cell Syst 2023; 14:363-381.e8. [PMID: 37164009 PMCID: PMC10348077 DOI: 10.1016/j.cels.2023.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/30/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Translation is the process by which ribosomes synthesize proteins. Ribosome profiling recently revealed that many short sequences previously thought to be noncoding are pervasively translated. To identify protein-coding genes in this noncanonical translatome, we combine an integrative framework for extremely sensitive ribosome profiling analysis, iRibo, with high-powered selection inferences tailored for short sequences. We construct a reference translatome for Saccharomyces cerevisiae comprising 5,400 canonical and almost 19,000 noncanonical translated elements. Only 14 noncanonical elements were evolving under detectable purifying selection. A representative subset of translated elements lacking signatures of selection demonstrated involvement in processes including DNA repair, stress response, and post-transcriptional regulation. Our results suggest that most translated elements are not conserved protein-coding genes and contribute to genotype-phenotype relationships through fast-evolving molecular mechanisms.
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Affiliation(s)
- Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Saurin Bipin Parikh
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Integrative Systems Biology Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Nelson Castilho Coelho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Omer Acar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt PhD Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Carly Houghton
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Joint CMU-Pitt PhD Program in Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lin Chou
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Integrative Systems Biology Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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4
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Gvozdenov Z. Genome-Wide Mapping of 5' Isoforms with 5'-Seq. Curr Protoc 2023; 3:e750. [PMID: 37084173 DOI: 10.1002/cpz1.750] [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] [Indexed: 04/22/2023]
Abstract
The transcriptome is far more complex than previously assumed. Transcripts from the same gene can differ in terms of transcription start site, transcription end site, or pattern of splicing, and growing evidence supports the functional importance of these distinct transcript isoforms. Easily identifying these isoforms experimentally via library construction and high-throughput sequencing is crucial. Current library construction methods for identifying transcription start sites (5' transcript isoforms) involve large number of steps and (expensive) reagents, utilization of cDNA intermediates for adapter ligation, and are less suitable for studying low-abundance isoforms. Here, I describe a quick protocol for the generation of sequencing libraries to define capped 5' isoforms (5'-Seq) of various abundances in yeast and suggest a 5' isoform data analysis pipeline. The protocol relies on the utilization of a dephosphorylation-decapping method (oligo-capping) to generate a sequencing library from mRNA fragments and is a simplification of previously published 5' isoform protocols in terms of the handling steps, time, and cost. This method is exemplified using Saccharomyces cerevisiae mRNA, but it can be applied to various cellular conditions to study the effects of 5' transcript isoforms on transcriptional and/or translational regulation. © 2023 Wiley Periodicals LLC. Basic Protocol: Construction of a DNA sequencing library from capped 5' isoforms Support Protocol: Sequencing data analysis.
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Affiliation(s)
- Zlata Gvozdenov
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts
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5
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Carter JA, Strömich L, Peacey M, Chapin SR, Velten L, Steinmetz LM, Brors B, Pinto S, Meyer HV. Transcriptomic diversity in human medullary thymic epithelial cells. Nat Commun 2022; 13:4296. [PMID: 35918316 PMCID: PMC9345899 DOI: 10.1038/s41467-022-31750-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
The induction of central T cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs). This promiscuous gene expression (pGE) drives mTEC transcriptomic diversity, with non-canonical transcript initiation, alternative splicing, and expression of endogenous retroelements (EREs) representing important but incompletely understood contributors. Here we map the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5' cap and RNA sequencing. Both mTEC populations show high splicing entropy, potentially driven by the expression of peripheral splicing factors. During mTEC maturation, rates of global transcript mis-initiation increase and EREs enriched in long terminal repeat retrotransposons are up-regulated, the latter often found in proximity to differentially expressed genes. As a resource, we provide an interactive public interface for exploring mTEC transcriptomic diversity. Our findings therefore help construct a map of transcriptomic diversity in the healthy human thymus and may ultimately facilitate the identification of those epitopes which contribute to autoimmunity and immune recognition of tumor antigens.
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Affiliation(s)
- Jason A. Carter
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA ,grid.36425.360000 0001 2216 9681Medical Scientist Training Program, Stony Brook University, Stony Brook, NY USA ,grid.34477.330000000122986657Department of Surgery, University of Washington, Seattle, WA USA
| | - Léonie Strömich
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany ,grid.7445.20000 0001 2113 8111Present Address: Imperial College London, London, UK
| | - Matthew Peacey
- grid.225279.90000 0004 0387 3667School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Sarah R. Chapin
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Lars Velten
- grid.473715.30000 0004 6475 7299Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lars M. Steinmetz
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Genome Technology Center, Palo Alto, CA USA
| | - Benedikt Brors
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany
| | - Sheena Pinto
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany
| | - Hannah V. Meyer
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
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6
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Tresenrider A, Chia M, van Werven FJ, Ünal E. Long undecoded transcript isoform (LUTI) detection in meiotic budding yeast by direct RNA and transcript leader sequencing. STAR Protoc 2022; 3:101145. [PMID: 35169715 PMCID: PMC8829799 DOI: 10.1016/j.xpro.2022.101145] [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] [Indexed: 01/07/2023] Open
Abstract
LUTIs (Long Undecoded Transcript Isoforms) are 5'-extended and poorly translated mRNAs that can downregulate transcription from promoters more proximal to a gene's coding sequence (CDS). In this protocol, polyA RNA is extracted from budding yeast cells undergoing highly synchronized meiosis. Using a combination of long-read direct RNA sequencing and transcript leader sequencing (TL-seq), meiosis-specific LUTIs are systematically identified. Following identification, TL-seq is used to quantify the abundance of both LUTI and the more canonical gene-proximal (PROX) transcripts. For complete details on the use and execution of this protocol, please refer to Tresenrider et al. (2021).
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Affiliation(s)
- Amy Tresenrider
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Genome Sciences, Foege Hall, University of Washington, Seattle, WA 98105, USA
| | - Minghao Chia
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | | | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley, Berkeley, CA 94720, USA
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7
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Niederer RO, Rojas-Duran MF, Zinshteyn B, Gilbert WV. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation. Cell Syst 2022; 13:256-264.e3. [PMID: 35041803 PMCID: PMC8930539 DOI: 10.1016/j.cels.2021.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/15/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022]
Abstract
Translational control shapes the proteome in normal and pathophysiological conditions. Current high-throughput approaches reveal large differences in mRNA-specific translation activity but cannot identify the causative mRNA features. We developed direct analysis of ribosome targeting (DART) and used it to dissect regulatory elements within 5' untranslated regions that confer 1,000-fold differences in ribosome recruitment in biochemically accessible cell lysates. Using DART, we determined a functional role for most alternative 5' UTR isoforms expressed in yeast, revealed a general mode of increased translation via direct binding to a core translation factor, and identified numerous translational control elements including C-rich silencers that are sufficient to repress translation both in vitro and in vivo. DART enables systematic assessment of the translational regulatory potential of 5' UTR variants, whether native or disease-associated, and will facilitate engineering of mRNAs for optimized protein production in various systems.
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Affiliation(s)
- Rachel O Niederer
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA
| | - Maria F Rojas-Duran
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA
| | - Boris Zinshteyn
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA.
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8
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Li B, Marques S, Wang J, Pelechano V. Using TIF-Seq2 to investigate association between 5´ and 3´mRNA ends. Methods Enzymol 2021; 655:85-118. [PMID: 34183135 DOI: 10.1016/bs.mie.2021.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The development of high-throughput technologies has revealed pervasive transcription in all genomes that have been investigated so far. This has uncovered a highly interleaved transcriptome organization involving thousands of overlapping coding and non-coding RNA isoforms that challenge our traditional definitions of genes and functional regions of the genome. In this chapter, we discuss the application of an improved Transcript Isoform Sequencing approach (TIF-Seq2) able to concurrently determine the start and end sites of individual RNA molecules. We exemplify its use for the investigation of the human transcriptome and show how it is especially well suited to discriminate between overlapping molecules and accurately define their boundaries.
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Affiliation(s)
- Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
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9
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Chia M, Li C, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol 2021; 22:34. [PMID: 33446241 PMCID: PMC7807719 DOI: 10.1186/s13059-020-02245-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms. RESULTS Cell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription. CONCLUSIONS The integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.
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Affiliation(s)
- Minghao Chia
- The Francis Crick Institute, London, UK
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Cai Li
- The Francis Crick Institute, London, UK
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicente Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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10
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Gowthaman U, García-Pichardo D, Jin Y, Schwarz I, Marquardt S. DNA Processing in the Context of Noncoding Transcription. Trends Biochem Sci 2020; 45:1009-1021. [DOI: 10.1016/j.tibs.2020.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/17/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022]
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11
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Wang J, Li B, Marques S, Steinmetz LM, Wei W, Pelechano V. TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes. Nucleic Acids Res 2020; 48:e104. [PMID: 32816037 PMCID: PMC7544212 DOI: 10.1093/nar/gkaa691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/17/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic transcriptomes are complex, involving thousands of overlapping transcripts. The interleaved nature of the transcriptomes limits our ability to identify regulatory regions, and in some cases can lead to misinterpretation of gene expression. To improve the understanding of the overlapping transcriptomes, we have developed an optimized method, TIF-Seq2, able to sequence simultaneously the 5' and 3' ends of individual RNA molecules at single-nucleotide resolution. We investigated the transcriptome of a well characterized human cell line (K562) and identified thousands of unannotated transcript isoforms. By focusing on transcripts which are challenging to be investigated with RNA-Seq, we accurately defined boundaries of lowly expressed unannotated and read-through transcripts putatively encoding fusion genes. We validated our results by targeted long-read sequencing and standard RNA-Seq for chronic myeloid leukaemia patient samples. Taking the advantage of TIF-Seq2, we explored transcription regulation among overlapping units and investigated their crosstalk. We show that most overlapping upstream transcripts use poly(A) sites within the first 2 kb of the downstream transcription units. Our work shows that, by paring the 5' and 3' end of each RNA, TIF-Seq2 can improve the annotation of complex genomes, facilitate accurate assignment of promoters to genes and easily identify transcriptionally fused genes.
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Affiliation(s)
- Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Sueli Marques
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Center for Biomedical Informatics, Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden
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12
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Ng PC, Wong ED, MacPherson KA, Aleksander S, Argasinska J, Dunn B, Nash RS, Skrzypek MS, Gondwe F, Jha S, Karra K, Weng S, Miyasato S, Simison M, Engel SR, Cherry JM. Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res 2020; 48:D743-D748. [PMID: 31612944 PMCID: PMC7061941 DOI: 10.1093/nar/gkz892] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.
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Affiliation(s)
- Patrick C Ng
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Edith D Wong
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | | | - Suzi Aleksander
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Joanna Argasinska
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Barbara Dunn
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Robert S Nash
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Marek S Skrzypek
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Felix Gondwe
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Sagar Jha
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Shuai Weng
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Matt Simison
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Palo Alto, CA 94304-5477, USA
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13
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Thomas QA, Ard R, Liu J, Li B, Wang J, Pelechano V, Marquardt S. Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis. Nat Commun 2020; 11:2589. [PMID: 32444691 PMCID: PMC7244574 DOI: 10.1038/s41467-020-16390-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/29/2020] [Indexed: 01/22/2023] Open
Abstract
RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that ~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.
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Affiliation(s)
- Quentin Angelo Thomas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ryan Ard
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jinghan Liu
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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14
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Ye C, Lin J, Li QQ. Discovery of alternative polyadenylation dynamics from single cell types. Comput Struct Biotechnol J 2020; 18:1012-1019. [PMID: 32382395 PMCID: PMC7200215 DOI: 10.1016/j.csbj.2020.04.009] [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: 02/20/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative polyadenylation (APA) occurs in the process of mRNA maturation by adding a poly(A) tail at different locations, resulting increased diversity of mRNA isoforms and contributing to the complexity of gene regulatory network. Benefit from the development of high-throughput sequencing technologies, we could now delineate APA profiles of transcriptomes at an unprecedented pace. Especially the single cell RNA sequencing (scRNA-seq) technologies provide us opportunities to interrogate biological details of diverse and rare cell types. Despite increasing evidence showing that APA is involved in the cell type-specific regulation and function, efficient and specific laboratory methods for capturing poly(A) sites at single cell resolution are underdeveloped to date. In this review, we summarize existing experimental and computational methods for the identification of APA dynamics from diverse single cell types. A future perspective is also provided.
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Affiliation(s)
- Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
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15
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McMillan J, Lu Z, Rodriguez JS, Ahn TH, Lin Z. YeasTSS: an integrative web database of yeast transcription start sites. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5479513. [PMID: 31032841 PMCID: PMC6484093 DOI: 10.1093/database/baz048] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/04/2019] [Accepted: 03/25/2019] [Indexed: 12/22/2022]
Abstract
The transcription initiation landscape of eukaryotic genes is complex and highly dynamic. In eukaryotes, genes can generate multiple transcript variants that differ in 5' boundaries due to usages of alternative transcription start sites (TSSs), and the abundance of transcript isoforms are highly variable. Due to a large number and complexity of the TSSs, it is not feasible to depict details of transcript initiation landscape of all genes using text-format genome annotation files. Therefore, it is necessary to provide data visualization of TSSs to represent quantitative TSS maps and the core promoters (CPs). In addition, the selection and activity of TSSs are influenced by various factors, such as transcription factors, chromatin remodeling and histone modifications. Thus, integration and visualization of functional genomic data related to these features could provide a better understanding of the gene promoter architecture and regulatory mechanism of transcription initiation. Yeast species play important roles for the research and human society, yet no database provides visualization and integration of functional genomic data in yeast. Here, we generated quantitative TSS maps for 12 important yeast species, inferred their CPs and built a public database, YeasTSS (www.yeastss.org). YeasTSS was designed as a central portal for visualization and integration of the TSS maps, CPs and functional genomic data related to transcription initiation in yeast. YeasTSS is expected to benefit the research community and public education for improving genome annotation, studies of promoter structure, regulated control of transcription initiation and inferring gene regulatory network.
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Affiliation(s)
- Jonathan McMillan
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Parks College of Engineering, Aviation and Technology, Program in Computer Engineering, Saint Louis University, St. Louis, MO, USA
| | - Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Judith S Rodriguez
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO, USA
| | - Tae-Hyuk Ahn
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO, USA.,Department of Computer Sciences, Saint Louis University, St. Louis, MO, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO, USA
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16
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Gao Y, Xi F, zhang H, Liu X, Wang H, zhao L, Reddy AS, Gu L. Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190204151746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The advent of the Single-Molecule Real-time (SMRT) Isoform Sequencing
(Iso-Seq) has paved the way to obtain longer full-length transcripts. This method was found to
be much superior in identifying full-length splice variants and other post-transcriptional events as
compared to the Next Generation Sequencing (NGS)-based short read sequencing (RNA-Seq).
Several different bioinformatics tools to analyze the Iso-Seq data have been developed and some
of them are still being refined to address different aspects of transcriptome complexity. However, a
comprehensive summary of the available tools and their utility is still lacking.
Objective:
Here, we summarized the existing Iso-Seq analysis tools and presented an integrated
bioinformatics pipeline for Iso-Seq analysis, which overcomes the limitations of NGS and generates
long contiguous Full-Length Non-Chimeric (FLNC) reads for the analysis of posttranscriptional
events.
Results:
In this review, we summarized recent applications of Iso-Seq in plants, which include improved
genome annotations, identification of novel genes and lncRNAs, identification of fulllength
splice isoforms, detection of novel Alternative Splicing (AS) and Alternative Polyadenylation
(APA) events. In addition, we also discussed the bioinformatics pipeline for comprehensive
Iso-Seq data analysis, including how to reduce the error rate in the reads and how to identify and
quantify post-transcriptional events. Furthermore, the visualization approach of Iso-Seq was discussed
as well. Finally, we discussed methods to combine Iso-Seq data with RNA-Seq for transcriptome
quantification.
Conclusion:
Overall, this review demonstrates that the Iso-Seq is pivotal for analyzing transcriptome
complexity and this new method offers unprecedented opportunities to comprehensively understand
transcripts diversity.
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Affiliation(s)
- Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangzhen zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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17
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Nadal-Ribelles M, Islam S, Wei W, Latorre P, Nguyen M, de Nadal E, Posas F, Steinmetz LM. Yeast Single-cell RNA-seq, Cell by Cell and Step by Step. Bio Protoc 2019; 9:e3359. [PMID: 33654857 DOI: 10.21769/bioprotoc.3359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 11/02/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) has become an established method for uncovering the intrinsic complexity within populations. Even within seemingly homogenous populations of isogenic yeast cells, there is a high degree of heterogeneity that originates from a compact and pervasively transcribed genome. Research with microorganisms such as yeast represents a major challenge for single-cell transcriptomics, due to their small size, rigid cell wall, and low RNA content per cell. Because of these technical challenges, yeast-specific scRNA-seq methodologies have recently started to appear, each one of them relying on different cell-isolation and library-preparation methods. Consequently, each approach harbors unique strengths and weaknesses that need to be considered. We have recently developed a yeast single-cell RNA-seq protocol (yscRNA-seq), which is inexpensive, high-throughput and easy-to-implement, tailored to the unique needs of yeast. yscRNA-seq provides a unique platform that combines single-cell phenotyping via index sorting with the incorporation of unique molecule identifiers on transcripts that allows to digitally count the number of molecules in a strand- and isoform-specific manner. Here, we provide a detailed, step-by-step description of the experimental and computational steps of yscRNA-seq protocol. This protocol will ease the implementation of yscRNA-seq in other laboratories and provide guidelines for the development of novel technologies.
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Affiliation(s)
- Mariona Nadal-Ribelles
- Department of Genetics, Stanford University, School of Medicine, California, USA.,Stanford Genome Technology Center, Stanford University, California, USA.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Cell Signaling Research Group, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Saiful Islam
- Department of Genetics, Stanford University, School of Medicine, California, USA.,Stanford Genome Technology Center, Stanford University, California, USA
| | - Wu Wei
- Department of Genetics, Stanford University, School of Medicine, California, USA.,Stanford Genome Technology Center, Stanford University, California, USA.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pablo Latorre
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Cell Signaling Research Group, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Michelle Nguyen
- Department of Genetics, Stanford University, School of Medicine, California, USA.,Stanford Genome Technology Center, Stanford University, California, USA
| | - Eulàlia de Nadal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Cell Signaling Research Group, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesc Posas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Cell Signaling Research Group, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lars M Steinmetz
- Department of Genetics, Stanford University, School of Medicine, California, USA.,Stanford Genome Technology Center, Stanford University, California, USA.,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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18
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Abstract
Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3' end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3' ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.
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19
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Jiang F, Zhang J, Liu Q, Liu X, Wang H, He J, Kang L. Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts. RNA Biol 2019; 16:950-959. [PMID: 30982421 PMCID: PMC6546357 DOI: 10.1080/15476286.2019.1602437] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
The large genome of the migratory locust (Locusta migratoria) genome accumulates massive amount of accumulated transposable elements (TEs), which show intrinsic transcriptional activities. Hampering the ability to precisely determine full-length RNA transcript sequences are exonized TEs, which produce numerous highly similar fragments that are difficult to resolve using short-read sequencing technology. Here, we applied a 5'-Cap capturing method using Nanopore long-read direct RNA sequencing to characterize full-length transcripts in their native RNA form and to analyze the TE exonization pattern in the locust transcriptome. Our results revealed the widespread establishment of TE exonization and a substantial contribution of TEs to RNA splicing in the locust transcriptome. The results of the transcriptomic spectrum influenced by Piwi expression indicated that TE-derived sequences were the main targets of Piwi-mediated repression. Furthermore, our study showed that Piwi expression regulates the length of RNA transcripts containing TE-derived sequences, creating an alternative UTR usage. Overall, our results reveal the transcriptomic characteristics of TE exonization in the species characterized by large and repetitive genomes.
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Affiliation(s)
- Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Qing Liu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huimin Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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20
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Lu Z, Lin Z. Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. Genome Res 2019; 29:1198-1210. [PMID: 31076411 PMCID: PMC6633255 DOI: 10.1101/gr.245456.118] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Transcription initiation is finely regulated to ensure proper expression and function of genes. The regulated transcription initiation in response to various environmental stimuli in a classic model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start sites (TSSs) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions using no-amplification nontagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. We mapped ∼1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of the budding yeast. The comprehensive TSS maps allowed us to identify core promoters for ∼96% verified protein-coding genes. We corrected misannotation of translation start codon for 122 genes and suggested an alternative start codon for 57 genes. We found that 56% of yeast genes are controlled by multiple core promoters, and alternative core promoter usage by a gene is widespread in response to changing environments. Most core promoter shifts are coupled with altered gene expression, indicating that alternative core promoter usage might play an important role in controlling gene transcriptional activities. Based on their activities in responding to environmental cues, we divided core promoters into constitutive class (55%) and inducible class (45%). The two classes of core promoters display distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, our study improved the annotation of the yeast genome and demonstrated a much more pervasive and dynamic nature of transcription initiation in yeast than previously recognized.
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Affiliation(s)
- Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, Missouri 63104, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, Missouri 63104, USA
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21
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Nadal-Ribelles M, Islam S, Wei W, Latorre P, Nguyen M, de Nadal E, Posas F, Steinmetz LM. Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations. Nat Microbiol 2019; 4:683-692. [PMID: 30718850 PMCID: PMC6433287 DOI: 10.1038/s41564-018-0346-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/07/2018] [Indexed: 12/19/2022]
Abstract
Single-cell RNA-seq has revealed extensive cellular heterogeneity within
many organisms, but few methods have been developed for microbial clonal
populations. The yeast genome displays unusually dense transcript spacing, with
interleaved and overlapping transcription from both strands, resulting in a
minuscule but complex pool of RNA protected by a resilient cell wall. Here, we
have developed a sensitive, scalable, and inexpensive yeast single-cell RNA-seq
(yscRNA-seq) method that digitally counts transcript start sites in a strand-
and isoform-specific manner. YscRNA-seq detects the expression of low-abundant,
non-coding RNAs, and at least half of the protein-coding genome in each cell.
Within clonal cells, we observed a negative correlation for the expression of
sense/antisense pairs, while paralogs and divergent transcripts co-express.
Combining yscRNA-seq with index sorting, we uncovered a linear relationship
between cell size and RNA content. Although we detected an average of
~3.5 molecules/gene, the number of expressed isoforms are restricted at
the single-cell level. Remarkably, the expression of metabolic genes is highly
variable, while their stochastic expression primes cells for increased fitness
towards the corresponding environmental challenge. These findings suggest that
functional transcript diversity acts as a mechanism for providing a selective
advantage to individual cells within otherwise transcriptionally heterogeneous
populations.
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Affiliation(s)
- Mariona Nadal-Ribelles
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA.,Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Saiful Islam
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
| | - Wu Wei
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pablo Latorre
- Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Michelle Nguyen
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA.,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA
| | - Eulàlia de Nadal
- Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group. Departament de Ciències Experimentals i de la Salut., Universitat Pompeu Fabra , Barcelona, Spain.,Cell Signaling. Institute for Research in Biomedicine. Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lars M Steinmetz
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, USA. .,Stanford Genome Technology Center, Stanford University, Stanford, CA, USA. .,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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22
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Wang HLV, Chekanova JA. An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK! Methods Mol Biol 2019; 1933:1-30. [PMID: 30945176 PMCID: PMC6684206 DOI: 10.1007/978-1-4939-9045-0_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The discovery of pervasive transcription in eukaryotic genomes provided one of many surprising (and perhaps most surprising) findings of the genomic era and led to the uncovering of a large number of previously unstudied transcriptional events. This pervasive transcription leads to the production of large numbers of noncoding RNAs (ncRNAs) and thus opened the window to study these diverse, abundant transcripts of unclear relevance and unknown function. Since that discovery, recent advances in high-throughput sequencing technologies have identified a large collection of ncRNAs, from microRNAs to long noncoding RNAs (lncRNAs). Subsequent discoveries have shown that many lncRNAs play important roles in various eukaryotic processes; these discoveries have profoundly altered our understanding of the regulation of eukaryotic gene expression. Although the identification of ncRNAs has become a standard experimental approach, the functional characterization of these diverse ncRNAs remains a major challenge. In this chapter, we highlight recent progress in the methods to identify lncRNAs and the techniques to study the molecular function of these lncRNAs and the application of these techniques to the study of plant lncRNAs.
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Affiliation(s)
- Hsiao-Lin V Wang
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
- Present address: Department of Biology, Emory University, Atlanta, GA, USA
| | - Julia A Chekanova
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China.
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23
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Abstract
Single-cell RNAseq and alternative splicing studies have recently become two of the most prominent applications of RNAseq. However, the combination of both is still challenging, and few research efforts have been dedicated to the intersection between them. Cell-level insight on isoform expression is required to fully understand the biology of alternative splicing, but it is still an open question to what extent isoform expression analysis at the single-cell level is actually feasible. Here, we establish a set of four conditions that are required for a successful single-cell-level isoform study and evaluate how these conditions are met by these technologies in published research.
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Affiliation(s)
- Ángeles Arzalluz-Luque
- Genomics of Gene Expression Laboratory, Centro de Investigación Principe Felipe (CIPF), 46012, Valencia, Spain
| | - Ana Conesa
- Genomics of Gene Expression Laboratory, Centro de Investigación Principe Felipe (CIPF), 46012, Valencia, Spain.
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA.
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24
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Blighe K, DeDionisio L, Christie KA, Chawes B, Shareef S, Kakouli-Duarte T, Chao-Shern C, Harding V, Kelly RS, Castellano L, Stebbing J, Lasky-Su JA, Nesbit MA, Moore CBT. Gene editing in the context of an increasingly complex genome. BMC Genomics 2018; 19:595. [PMID: 30086710 PMCID: PMC6081867 DOI: 10.1186/s12864-018-4963-8] [Citation(s) in RCA: 8] [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] [Received: 06/26/2017] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
The reporting of the first draft of the human genome in 2000 brought with it much hope for the future in what was felt as a paradigm shift toward improved health outcomes. Indeed, we have now mapped the majority of variation across human populations with landmark projects such as 1000 Genomes; in cancer, we have catalogued mutations across the primary carcinomas; whilst, for other diseases, we have identified the genetic variants with strongest association. Despite this, we are still awaiting the genetic revolution in healthcare to materialise and translate itself into the health benefits for which we had hoped. A major problem we face relates to our underestimation of the complexity of the genome, and that of biological mechanisms, generally. Fixation on DNA sequence alone and a 'rigid' mode of thinking about the genome has meant that the folding and structure of the DNA molecule -and how these relate to regulation- have been underappreciated. Projects like ENCODE have additionally taught us that regulation at the level of RNA is just as important as that at the spatiotemporal level of chromatin.In this review, we chart the course of the major advances in the biomedical sciences in the era pre- and post the release of the first draft sequence of the human genome, taking a focus on technology and how its development has influenced these. We additionally focus on gene editing via CRISPR/Cas9 as a key technique, in particular its use in the context of complex biological mechanisms. Our aim is to shift the mode of thinking about the genome to that which encompasses a greater appreciation of the folding of the DNA molecule, DNA- RNA/protein interactions, and how these regulate expression and elaborate disease mechanisms.Through the composition of our work, we recognise that technological improvement is conducive to a greater understanding of biological processes and life within the cell. We believe we now have the technology at our disposal that permits a better understanding of disease mechanisms, achievable through integrative data analyses. Finally, only with greater understanding of disease mechanisms can techniques such as gene editing be faithfully conducted.
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Affiliation(s)
- K Blighe
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA.
- Department of Cancer Studies and Molecular Medicine, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK.
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, WC1E 6DD, London, UK.
| | - L DeDionisio
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - K A Christie
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - B Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - S Shareef
- University of Raparin, Ranya, Kurdistan Region, Iraq
| | - T Kakouli-Duarte
- Institute of Technology Carlow, Department of Science and Health, Kilkenny Road, Carlow, Ireland
| | - C Chao-Shern
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
- Avellino Laboratories, Menlo Park, CA, 94025, USA
| | - V Harding
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - R S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - L Castellano
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- JMS Building, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - J Stebbing
- Imperial College London, Division of Cancer, Department of Surgery and Cancer, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - J A Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, USA
| | - M A Nesbit
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK
| | - C B T Moore
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK.
- Avellino Laboratories, Menlo Park, CA, 94025, USA.
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25
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Miller D, Brandt N, Gresham D. Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen. PLoS Genet 2018; 14:e1007406. [PMID: 29782489 PMCID: PMC5983874 DOI: 10.1371/journal.pgen.1007406] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/01/2018] [Accepted: 05/09/2018] [Indexed: 01/20/2023] Open
Abstract
Cellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeast Saccharomyces cerevisiae during a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming of the transcriptome. To explore the molecular basis of destabilization we implemented a SortSeq approach to screen the pooled deletion collection library for trans factors that mediate rapid GAP1 mRNA repression. We combined low-input multiplexed Barcode sequencing with branched-DNA single-molecule mRNA FISH and Fluorescence-activated cell sorting (BFF) to identify the Lsm1-7p/Pat1p complex and general mRNA decay machinery as important for GAP1 mRNA clearance. We also find that the decapping modulators EDC3 and SCD6, translation factor eIF4G2, and the 5' UTR of GAP1 are factors that mediate rapid repression of GAP1 mRNA, suggesting that translational control may impact the post-transcriptional fate of mRNAs in response to environmental changes.
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Affiliation(s)
- Darach Miller
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Nathan Brandt
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- * E-mail:
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26
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Le Scornet A, Redder P. Post-transcriptional control of virulence gene expression in Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:734-741. [PMID: 29705591 DOI: 10.1016/j.bbagrm.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 12/12/2022]
Abstract
Opportunistic pathogens have to be ready to change life-style whenever the occasion arises, and therefore need to keep tight control over the expression of their virulence factors. Doubly so for commensal bacteria, such as Staphylococcus aureus, which should avoid harming their hosts when they are in a state of peaceful co-existence. S. aureus carries very few sigma factors to help define the transcriptional programs, but instead uses a plethora of small RNA molecules and RNA-RNA interactions to regulate gene expression post-transcriptionally. The endoribonucleases RNase III and RNase Y contribute to this regulatory diversity, and provide a link to RNA-decay and intra-cellular spatiotemporal control of expression. In this review we describe some of these post-transcriptional mechanisms as well as some of the novel transcriptomic approaches that have been used to find and to study them.
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Affiliation(s)
- Alexandre Le Scornet
- LMGM, Centre de Biologie Integrative, Paul Sabatier University, 118, Route de Narbonne, 31062 Toulouse, France
| | - Peter Redder
- LMGM, Centre de Biologie Integrative, Paul Sabatier University, 118, Route de Narbonne, 31062 Toulouse, France.
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27
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Candelli T, Challal D, Briand JB, Boulay J, Porrua O, Colin J, Libri D. High-resolution transcription maps reveal the widespread impact of roadblock termination in yeast. EMBO J 2018; 37:embj.201797490. [PMID: 29351914 DOI: 10.15252/embj.201797490] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 01/04/2023] Open
Abstract
Transcription termination delimits transcription units but also plays important roles in limiting pervasive transcription. We have previously shown that transcription termination occurs when elongating RNA polymerase II (RNAPII) collides with the DNA-bound general transcription factor Reb1. We demonstrate here that many different DNA-binding proteins can induce termination by a similar roadblock (RB) mechanism. We generated high-resolution transcription maps by the direct detection of RNAPII upon nuclear depletion of two essential RB factors or when the canonical termination pathways for coding and non-coding RNAs are defective. We show that RB termination occurs genomewide and functions independently of (and redundantly with) the main transcription termination pathways. We provide evidence that transcriptional readthrough at canonical terminators is a significant source of pervasive transcription, which is controlled to a large extent by RB termination. Finally, we demonstrate the occurrence of RB termination around centromeres and tRNA genes, which we suggest shields these regions from RNAPII to preserve their functional integrity.
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Affiliation(s)
- Tito Candelli
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France.,Ecole doctorale Structure et Dynamique des Systèmes Vivants, Université Paris Saclay, Gif sur Yvette, France
| | - Drice Challal
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France.,Ecole doctorale Structure et Dynamique des Systèmes Vivants, Université Paris Saclay, Gif sur Yvette, France
| | - Jean-Baptiste Briand
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France.,Ecole doctorale Structure et Dynamique des Systèmes Vivants, Université Paris Saclay, Gif sur Yvette, France
| | - Jocelyne Boulay
- Institut de Biologie Intégrative de la Cellule (I2BC), CNRS, UMR 9198, Univ Paris-Saclay, Centre Energie Atomique, Gif sur Yvette, France
| | - Odil Porrua
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France
| | - Jessie Colin
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, CNRS, UMR 7592, Univ Paris Diderot, Paris, France
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28
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Soares LM, He PC, Chun Y, Suh H, Kim T, Buratowski S. Determinants of Histone H3K4 Methylation Patterns. Mol Cell 2017; 68:773-785.e6. [PMID: 29129639 DOI: 10.1016/j.molcel.2017.10.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 08/23/2017] [Accepted: 10/12/2017] [Indexed: 11/28/2022]
Abstract
Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene expression. This methylation "gradient" is thought to result from preferential binding of the H3K4 methyltransferase Set1/complex associated with Set1 (COMPASS) to promoter-proximal RNA polymerase II. However, other studies have suggested that location-specific cues allosterically activate Set1. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments show that H3K4 methylation patterns on active genes are not universal or fixed and change in response to both transcription elongation rate and frequency as well as reduced COMPASS activity. Fusing Set1 to RNA polymerase II results in H3K4me2 throughout transcribed regions and similarly extended H3K4me3 on highly transcribed genes. Tethered Set1 still requires histone H2B ubiquitylation for activity. These results show that higher-level methylations reflect not only Set1/COMPASS recruitment but also multiple rounds of transcription. This model provides a simple explanation for non-canonical methylation patterns at some loci or in certain COMPASS mutants.
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Affiliation(s)
- Luis M Soares
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - P Cody He
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hyunsuk Suh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - TaeSoo Kim
- Department of Life Science, Ewha Womans University, Seoul 03760, Korea
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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29
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Afik S, Bartok O, Artyomov MN, Shishkin AA, Kadri S, Hanan M, Zhu X, Garber M, Kadener S. Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic Acids Res 2017; 45:e95. [PMID: 28335028 PMCID: PMC5499799 DOI: 10.1093/nar/gkx133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 02/15/2017] [Indexed: 01/19/2023] Open
Abstract
Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5΄- and 3΄-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods. We applied our methodology to study the impact of temperature on the Drosophila melanogaster head transcriptome. We found hundreds of previously unidentified TSS and PAS which revealed two interesting phenomena: first, genes with multiple PASs tend to harbor a motif near the most proximal PAS, which likely represents a new cleavage and polyadenylation signal. Second, motif analysis of promoters of genes affected by temperature suggested that boundary element association factor of 32 kDa (BEAF-32) and DREF mediates a transcriptional program at warm temperatures, a result we validated in a fly line where beaf-32 is downregulated. These results demonstrate the utility of a high-throughput platform for complete experimental and computational analysis of mRNA-ends to improve gene annotation.
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Affiliation(s)
- Shaked Afik
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Osnat Bartok
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alexander A Shishkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sabah Kadri
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Mor Hanan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Xiaopeng Zhu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
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30
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Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PLoS Genet 2017; 13:e1006863. [PMID: 28665995 PMCID: PMC5513554 DOI: 10.1371/journal.pgen.1006863] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 07/17/2017] [Accepted: 06/10/2017] [Indexed: 01/04/2023] Open
Abstract
Transcriptome studies on eukaryotic cells have revealed an unexpected abundance and diversity of noncoding RNAs synthesized by RNA polymerase II (Pol II), some of which influence the expression of protein-coding genes. Yet, much less is known about biogenesis of Pol II non-coding RNA than mRNAs. In the budding yeast Saccharomyces cerevisiae, initiation of non-coding transcripts by Pol II appears to be similar to that of mRNAs, but a distinct pathway is utilized for termination of most non-coding RNAs: the Sen1-dependent or “NNS” pathway. Here, we examine the effect on the S. cerevisiae transcriptome of conditional mutations in the genes encoding six different essential proteins that influence Sen1-dependent termination: Sen1, Nrd1, Nab3, Ssu72, Rpb11, and Hrp1. We observe surprisingly diverse effects on transcript abundance for the different proteins that cannot be explained simply by differing severity of the mutations. Rather, we infer from our results that termination of Pol II transcription of non-coding RNA genes is subject to complex combinatorial control that likely involves proteins beyond those studied here. Furthermore, we identify new targets and functions of Sen1-dependent termination, including a role in repression of meiotic genes in vegetative cells. In combination with other recent whole-genome studies on termination of non-coding RNAs, our results provide promising directions for further investigation. The information stored in the DNA of a cell’s chromosomes is transmitted to the rest of the cell by transcribing the DNA into RNA copies or “transcripts”. The fidelity of this process, and thus the health of the cell, depends critically on the proper function of proteins that direct transcription. Since hundreds of genes, each specifying a unique RNA transcript, are arranged in tandem along each chromosome, the beginning and end of each gene must be marked in the DNA sequence. Although encoded in DNA, the signal for terminating an RNA transcript is usually recognized in the transcript itself. We examined the genome-wide functional targets of six proteins implicated in transcription termination by identifying transcripts whose structure or abundance is altered by a mutation that compromises the activity of each protein. For a small minority of transcripts, a mutation in any of the six proteins disrupts termination. Much more commonly, a transcript is affected by a mutation in only one or a few of the six proteins, revealing the varying extent to which the proteins cooperate with one another. We discovered affected transcripts that were not known to be controlled by any of the six proteins, including a cohort of genes required for meiosis.
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Affiliation(s)
- Xin Chen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Kunal Poorey
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Melissa N. Carver
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Ulrika Müller
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
- * E-mail: (DAB); (DTA)
| | - David A. Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail: (DAB); (DTA)
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31
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Baejen C, Andreani J, Torkler P, Battaglia S, Schwalb B, Lidschreiber M, Maier KC, Boltendahl A, Rus P, Esslinger S, Söding J, Cramer P. Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes. Mol Cell 2017; 66:38-49.e6. [PMID: 28318822 DOI: 10.1016/j.molcel.2017.02.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/06/2016] [Accepted: 02/09/2017] [Indexed: 01/09/2023]
Abstract
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3'-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3'-transition in budding yeast. We find that the 3'-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the "torpedo" exonuclease Rat1 (XRN2 in human). The Rat1-interacting factor Rai1 contributes to RNA degradation downstream of the pA site. Defects in the 3'-transition can result in increased transcription at downstream genes.
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Affiliation(s)
- Carlo Baejen
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jessica Andreani
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Phillipp Torkler
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sofia Battaglia
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bjoern Schwalb
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Karolinska Institutet, Department of Biosciences and Nutrition, Center for Innovative Medicine and Science for Life Laboratory, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden
| | - Kerstin C Maier
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrea Boltendahl
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Petra Rus
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stephanie Esslinger
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Johannes Söding
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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32
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Kryuchkova-Mostacci N, Robinson-Rechavi M. Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs. PLoS Comput Biol 2016; 12:e1005274. [PMID: 28030541 PMCID: PMC5193323 DOI: 10.1371/journal.pcbi.1005274] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/26/2016] [Indexed: 11/18/2022] Open
Abstract
The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.
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Affiliation(s)
- Nadezda Kryuchkova-Mostacci
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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33
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Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet 2016; 48:984-94. [PMID: 27455346 PMCID: PMC5008441 DOI: 10.1038/ng.3616] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/14/2016] [Indexed: 12/11/2022]
Abstract
Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here we found that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but owing to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provide a framework with which evolution shapes transcriptomes.
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Affiliation(s)
- Yun Chen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Athma A Pai
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jan Herudek
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michal Lubas
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Nicola Meola
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Aino I Järvelin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vicent Pelechano
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Palo Alto, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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34
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Thompson MK, Rojas-Duran MF, Gangaramani P, Gilbert WV. The ribosomal protein Asc1/RACK1 is required for efficient translation of short mRNAs. eLife 2016; 5. [PMID: 27117520 PMCID: PMC4848094 DOI: 10.7554/elife.11154] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/21/2016] [Indexed: 02/06/2023] Open
Abstract
Translation is a core cellular process carried out by a highly conserved macromolecular machine, the ribosome. There has been remarkable evolutionary adaptation of this machine through the addition of eukaryote-specific ribosomal proteins whose individual effects on ribosome function are largely unknown. Here we show that eukaryote-specific Asc1/RACK1 is required for efficient translation of mRNAs with short open reading frames that show greater than average translational efficiency in diverse eukaryotes. ASC1 mutants in S. cerevisiae display compromised translation of specific functional groups, including cytoplasmic and mitochondrial ribosomal proteins, and display cellular phenotypes consistent with their gene-specific translation defects. Asc1-sensitive mRNAs are preferentially associated with the translational ‘closed loop’ complex comprised of eIF4E, eIF4G, and Pab1, and depletion of eIF4G mimics the translational defects of ASC1 mutants. Together our results reveal a role for Asc1/RACK1 in a length-dependent initiation mechanism optimized for efficient translation of genes with important housekeeping functions. DOI:http://dx.doi.org/10.7554/eLife.11154.001 Ribosomes are structures within cells that are responsible for making proteins. Molecules called messenger RNAs (or mRNAs), which contain genetic information derived from the DNA of a gene, pass through ribosomes that then “translate” that information to build proteins. Although all living cells contain ribosomes, the protein building blocks that make up the structure of the ribosome are not the same in all species. Furthermore, the exact roles that each building block plays during translation are not known. The ribosomes of plants, animals, and budding yeast contain the same protein, known as Asc1 in budding yeast and RACK1 in plants and animals. Thompson et al. have now explored the role of Asc1 in yeast cells by measuring translation in the absence of Asc1 using a technique called ribosome footprint profiling. This analysis revealed that cells lacking Asc1 translate fewer short mRNA molecules than normal cells. Short mRNAs encode small proteins that tend to play important ‘housekeeping’ roles in the cell — by forming the structural building blocks of ribosomes, for example. It has been observed previously that short mRNAs are translated at a higher rate than longer mRNAs on average, although the reasons behind this bias are still mysterious. The findings of Thompson et al. suggest that the ribosome itself may discriminate between short and long mRNAs and that the Asc1 protein is involved in calibrating the ribosome’s preference for short mRNAs. Cells need differing amounts of small proteins in different growth conditions. It will therefore be interesting to investigate whether mRNA length discrimination can be regulated by Asc1 and/or other components of the ribosome to tune gene expression to the environment. DOI:http://dx.doi.org/10.7554/eLife.11154.002
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Affiliation(s)
- Mary K Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Maria F Rojas-Duran
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Paritosh Gangaramani
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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35
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Pelechano V, Wei W, Steinmetz LM. Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics. Nat Protoc 2016; 11:359-76. [PMID: 26820793 DOI: 10.1038/nprot.2016.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Co-translational mRNA degradation is a widespread process in which 5'-3' exonucleolytic degradation follows the last translating ribosome, thus producing an in vivo ribosomal footprint that delimits the 5' position of the mRNA molecule within the ribosome. To study this degradation process and ribosome dynamics, we developed 5PSeq, which is a method that profiles the genome-wide abundance of mRNA degradation intermediates by virtue of their 5'-phosphorylated (5'P) ends. The approach involves targeted ligation of an oligonucleotide to the 5'P end of mRNA degradation intermediates, followed by depletion of rRNA molecules, reverse transcription of 5'P mRNAs and Illumina high-throughput sequencing. 5PSeq can identify translational pauses at rare codons that are often masked when using alternative methods. This approach can be applied to previously extracted RNA samples, and it is straightforward and does not require polyribosome purification or in vitro RNA footprinting. The protocol we describe here can be applied to Saccharomyces cerevisiae and potentially to other eukaryotic organisms. Three days are required to generate 5PSeq libraries.
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Affiliation(s)
- Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Wu Wei
- Stanford Genome Technology Center, Palo Alto, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Palo Alto, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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36
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Mellor J, Woloszczuk R, Howe FS. The Interleaved Genome. Trends Genet 2016; 32:57-71. [DOI: 10.1016/j.tig.2015.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/29/2015] [Accepted: 10/23/2015] [Indexed: 12/25/2022]
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37
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Geisberg JV, Moqtaderi Z. Genome-Wide Study of mRNA Isoform Half-Lives. Methods Mol Biol 2015; 1358:317-23. [PMID: 26463393 DOI: 10.1007/978-1-4939-3067-8_20] [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: 02/23/2023]
Abstract
In eukaryotes, RNA polymerase II-driven transcription and processing results in the formation of numerous mRNA 3' isoforms that for any given gene may differ from one another by as little as a single nucleotide. These 3' isoforms can vary in physical properties that may affect their function and stability. Here, we outline a systematic framework to measure individual mRNA 3' isoform half-lives on a genome-wide level in S. cerevisiae. Our approach utilizes the Anchor-Away system to sequester RNA polymerase II (Pol II) in the cytoplasm followed by direct single-molecule RNA sequencing to generate a highly detailed view of 3' isoform stability under most physiological conditions without many of the adverse effects associated with commonly used alternative approaches.
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Affiliation(s)
- Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
| | - Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
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38
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Yu NYL, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y, Uhlén M, Daub CO. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res 2015; 43:6787-98. [PMID: 26117540 PMCID: PMC4538815 DOI: 10.1093/nar/gkv608] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/20/2022] Open
Abstract
Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5'-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes.
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Affiliation(s)
- Nancy Yiu-Lin Yu
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
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39
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Pelechano V, Wei W, Steinmetz LM. Widespread Co-translational RNA Decay Reveals Ribosome Dynamics. Cell 2015; 161:1400-12. [PMID: 26046441 DOI: 10.1016/j.cell.2015.05.008] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/25/2015] [Accepted: 04/20/2015] [Indexed: 12/19/2022]
Abstract
It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and conserved process affecting most genes, where 5'-3' transcript degradation follows the last translating ribosome, producing an in vivo ribosomal footprint. By sequencing the ends of 5' phosphorylated mRNA degradation intermediates, we obtain a genome-wide drug-free measurement of ribosome dynamics. We identify general translation termination pauses in both normal and stress conditions. In addition, we describe novel codon-specific ribosomal pausing sites in response to oxidative stress that are dependent on the RNase Rny1. Our approach is simple and straightforward and does not require the use of translational inhibitors or in vitro RNA footprinting that can alter ribosome protection patterns.
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Affiliation(s)
- Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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40
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Abstract
Viral genomes harbor a variety of unusual translational phenomena that allow them to pack coding information more densely and evade host restriction mechanisms imposed by the cellular translational apparatus. Annotating translated sequences within these genomes thus poses particular challenges, but identifying the full complement of proteins encoded by a virus is critical for understanding its life cycle and defining the epitopes it presents for immune surveillance. Ribosome profiling is an emerging technique for global analysis of translation that offers direct and experimental annotation of viral genomes. Ribosome profiling has been applied to two herpesvirus genomes, those of human cytomegalovirus and Kaposi's sarcoma-associated herpesvirus, revealing translated sequences within presumptive long noncoding RNAs and identifying other micropeptides. Synthesis of these proteins has been confirmed by mass spectrometry and by identifying T cell responses following infection. Ribosome profiling in other viruses will likely expand further our understanding of viral gene regulation and the proteome.
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Affiliation(s)
- Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720;
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41
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de Nadal E, Posas F. Osmostress-induced gene expression--a model to understand how stress-activated protein kinases (SAPKs) regulate transcription. FEBS J 2015; 282:3275-85. [PMID: 25996081 PMCID: PMC4744689 DOI: 10.1111/febs.13323] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/27/2015] [Accepted: 05/18/2015] [Indexed: 01/18/2023]
Abstract
Adaptation is essential for maximizing cell survival and for cell fitness in response to sudden changes in the environment. Several aspects of cell physiology change during adaptation. Major changes in gene expression are associated with cell exposure to environmental changes, and several aspects of mRNA biogenesis appear to be targeted by signaling pathways upon stress. Exhaustive reviews have been written regarding adaptation to stress and regulation of gene expression. In this review, using osmostress in yeast as a prototypical case study, we highlight those aspects of regulation of gene induction that are general to various environmental stresses as well as mechanistic aspects that are potentially conserved from yeast to mammals.
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Affiliation(s)
- Eulàlia de Nadal
- Cell Signaling Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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42
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Chabbert CD, Adjalley SH, Klaus B, Fritsch ES, Gupta I, Pelechano V, Steinmetz LM. A high-throughput ChIP-Seq for large-scale chromatin studies. Mol Syst Biol 2015; 11:777. [PMID: 25583149 PMCID: PMC4332152 DOI: 10.15252/msb.20145776] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We present a modified approach of chromatin immuno-precipitation followed by sequencing (ChIP-Seq), which relies on the direct ligation of molecular barcodes to chromatin fragments, thereby permitting experimental scale-up. With Bar-ChIP now enabling the concurrent profiling of multiple DNA–protein interactions, we report the simultaneous generation of 90 ChIP-Seq datasets without any robotic instrumentation. We demonstrate that application of Bar-ChIP to a panel of Saccharomyces cerevisiae chromatin-associated mutants provides a rapid and accurate genome-wide overview of their chromatin status. Additionally, we validate the utility of this technology to derive novel biological insights by identifying a role for the Rpd3S complex in maintaining H3K14 hypo-acetylation in gene bodies. We also report an association between the presence of intragenic H3K4 tri-methylation and the emergence of cryptic transcription in a Set2 mutant. Finally, we uncover a crosstalk between H3K14 acetylation and H3K4 methylation in this mutant. These results show that Bar-ChIP enables biological discovery through rapid chromatin profiling at single-nucleosome resolution for various conditions and protein modifications at once.
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Affiliation(s)
| | - Sophie H Adjalley
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Bernd Klaus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Emilie S Fritsch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Ishaan Gupta
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vicent Pelechano
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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43
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Abstract
Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology.
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Affiliation(s)
- Fred D Mast
- Seattle Biomedical Research Institute, Seattle, WA 98109 Institute for Systems Biology, Seattle, WA 98109
| | - Alexander V Ratushny
- Seattle Biomedical Research Institute, Seattle, WA 98109 Institute for Systems Biology, Seattle, WA 98109
| | - John D Aitchison
- Seattle Biomedical Research Institute, Seattle, WA 98109 Institute for Systems Biology, Seattle, WA 98109
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