1
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Geisberg JV, Moqtaderi Z, Struhl K. Chromatin regulates alternative polyadenylation via the RNA polymerase II elongation rate. Proc Natl Acad Sci U S A 2024; 121:e2405827121. [PMID: 38748572 PMCID: PMC11127049 DOI: 10.1073/pnas.2405827121] [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: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
The RNA polymerase II (Pol II) elongation rate influences poly(A) site selection, with slow and fast Pol II derivatives causing upstream and downstream shifts, respectively, in poly(A) site utilization. In yeast, depletion of either of the histone chaperones FACT or Spt6 causes an upstream shift of poly(A) site use that strongly resembles the poly(A) profiles of slow Pol II mutant strains. Like slow Pol II mutant strains, FACT- and Spt6-depleted cells exhibit Pol II processivity defects, indicating that both Spt6 and FACT stimulate the Pol II elongation rate. Poly(A) profiles of some genes show atypical downstream shifts; this subset of genes overlaps well for FACT- or Spt6-depleted strains but is different from the atypical genes in Pol II speed mutant strains. In contrast, depletion of histone H3 or H4 causes a downstream shift of poly(A) sites for most genes, indicating that nucleosomes inhibit the Pol II elongation rate in vivo. Thus, chromatin-based control of the Pol II elongation rate is a potential mechanism, distinct from direct effects on the cleavage/polyadenylation machinery, to regulate alternative polyadenylation in response to genetic or environmental changes.
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Affiliation(s)
- Joseph V. Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
| | - Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA02115
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2
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Pabis K, Barardo D, Sirbu O, Selvarajoo K, Gruber J, Kennedy BK. A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence. eLife 2024; 12:RP87811. [PMID: 38567944 PMCID: PMC10990488 DOI: 10.7554/elife.87811] [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] [Indexed: 04/05/2024] Open
Abstract
Aging and senescence are characterized by pervasive transcriptional dysfunction, including increased expression of transposons and introns. Our aim was to elucidate mechanisms behind this increased expression. Most transposons are found within genes and introns, with a large minority being close to genes. This raises the possibility that transcriptional readthrough and intron retention are responsible for age-related changes in transposon expression rather than expression of autonomous transposons. To test this, we compiled public RNA-seq datasets from aged human fibroblasts, replicative and drug-induced senescence in human cells, and RNA-seq from aging mice and senescent mouse cells. Indeed, our reanalysis revealed a correlation between transposons expression, intron retention, and transcriptional readthrough across samples and within samples. Both intron retention and readthrough increased with aging or cellular senescence and these transcriptional defects were more pronounced in human samples as compared to those of mice. In support of a causal connection between readthrough and transposon expression, analysis of models showing induced transcriptional readthrough confirmed that they also show elevated transposon expression. Taken together, our data suggest that elevated transposon reads during aging seen in various RNA-seq dataset are concomitant with multiple transcriptional defects. Intron retention and transcriptional readthrough are the most likely explanation for the expression of transposable elements that lack a functional promoter.
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Affiliation(s)
- Kamil Pabis
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
| | - Diogo Barardo
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
| | - Olga Sirbu
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Kumar Selvarajoo
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of SingaporeSingaporeSingapore
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Jan Gruber
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Science Divisions, Yale-NUS CollegeSingaporeSingapore
| | - Brian K Kennedy
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
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3
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Caldas P, Luz M, Baseggio S, Andrade R, Sobral D, Grosso AR. Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features. Commun Biol 2024; 7:100. [PMID: 38225287 PMCID: PMC10789751 DOI: 10.1038/s42003-024-05779-5] [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: 03/27/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Transcription termination is a crucial step in the production of conforming mRNAs and functional proteins. Under cellular stress conditions, the transcription machinery fails to identify the termination site and continues transcribing beyond gene boundaries, a phenomenon designated as transcription readthrough. However, the prevalence and impact of this phenomenon in healthy human tissues remain unexplored. Here, we assessed transcription readthrough in almost 3000 transcriptome profiles representing 23 human tissues and found that 34% of the expressed protein-coding genes produced readthrough transcripts. The production of readthrough transcripts was restricted in genomic regions with high transcriptional activity and was associated with inefficient splicing and increased chromatin accessibility in terminal regions. In addition, we showed that these transcripts contained several binding sites for the same miRNA, unravelling a potential role as miRNA sponges. Overall, this work provides evidence that transcription readthrough is pervasive and non-stochastic, not only in abnormal conditions but also in healthy tissues. This suggests a potential role for such transcripts in modulating normal cellular functions.
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Affiliation(s)
- Paulo Caldas
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Mariana Luz
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Simone Baseggio
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Rita Andrade
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Daniel Sobral
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Ana Rita Grosso
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
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4
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Khitun A, Brion C, Moqtaderi Z, Geisberg JV, Churchman LS, Struhl K. Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs. J Biol Chem 2023; 299:105289. [PMID: 37748648 PMCID: PMC10598743 DOI: 10.1016/j.jbc.2023.105289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/01/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023] Open
Abstract
Yeast mRNAs are polyadenylated at multiple sites in their 3' untranslated regions (3' UTRs), and poly(A) site usage is regulated by the rate of transcriptional elongation by RNA polymerase II (Pol II). Slow Pol II derivatives favor upstream poly(A) sites, and fast Pol II derivatives favor downstream poly(A) sites. Transcriptional elongation and polyadenylation are linked at the nucleotide level, presumably reflecting Pol II dwell time at each residue that influences the level of polyadenylation. Here, we investigate the effect of Pol II elongation rate on pausing patterns and the relationship between Pol II pause sites and poly(A) sites within 3' UTRs. Mutations that affect Pol II elongation rate alter sequence preferences at pause sites within 3' UTRs, and pausing preferences differ between 3' UTRs and coding regions. In addition, sequences immediately flanking the pause sites show preferences that are largely independent of Pol II speed. In wild-type cells, poly(A) sites are preferentially located < 50 nucleotides upstream from Pol II pause sites, but this spatial relationship is diminished in cells harboring Pol II speed mutants. Based on a random forest classifier, Pol II pause sites are modestly predicted by the distance to poly(A) sites but are better predicted by the chromatin landscape in Pol II speed derivatives. Transcriptional regulatory proteins can influence the relationship between Pol II pausing and polyadenylation but in a manner distinct from Pol II elongation rate derivatives. These results indicate a complex relationship between Pol II pausing and polyadenylation.
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Affiliation(s)
- Alexandra Khitun
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christian Brion
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Zarmik Moqtaderi
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph V Geisberg
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Kevin Struhl
- Departments of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
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5
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Knowing when to stop: Transcription termination on protein-coding genes by eukaryotic RNAPII. Mol Cell 2023; 83:404-415. [PMID: 36634677 PMCID: PMC7614299 DOI: 10.1016/j.molcel.2022.12.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Gene expression is controlled in a dynamic and regulated manner to allow for the consistent and steady expression of some proteins as well as the rapidly changing production of other proteins. Transcription initiation has been a major focus of study because it is highly regulated. However, termination of transcription also plays an important role in controlling gene expression. Transcription termination on protein-coding genes is intimately linked with 3' end cleavage and polyadenylation of transcripts, and it generally results in the production of a mature mRNA that is exported from the nucleus. Termination on many non-coding genes can also result in the production of a mature transcript. Termination is dynamically regulated-premature termination and transcription readthrough occur in response to a number of cellular signals, and these can have varied consequences on gene expression. Here, we review eukaryotic transcription termination by RNA polymerase II (RNAPII), focusing on protein-coding genes.
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6
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Small Interfering RNAs Targeting a Chromatin-Associated RNA Induce Its Transcriptional Silencing in Human Cells. Mol Cell Biol 2022; 42:e0027122. [PMID: 36445136 PMCID: PMC9753735 DOI: 10.1128/mcb.00271-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Transcriptional gene silencing by small interfering RNAs (siRNAs) has been widely described in various species, including plants and yeast. In mammals, its extent remains somewhat debated. Previous studies showed that siRNAs targeting gene promoters could induce the silencing of the targeted promoter, although the involvement of off-target mechanisms was also suggested. Here, by using nascent RNA capture and RNA polymerase II chromatin immunoprecipitation, we show that siRNAs targeting a chromatin-associated noncoding RNA induced its transcriptional silencing. Deletion of the sequence targeted by one of these siRNAs on the two alleles by genome editing further showed that this silencing was due to base-pairing of the siRNA to the target. Moreover, by using cells with heterozygous deletion of the target sequence, we showed that only the wild-type allele, but not the deleted allele, was silenced by the siRNA, indicating that transcriptional silencing occurred only in cis. Finally, we demonstrated that both Ago1 and Ago2 are involved in this transcriptional silencing. Altogether, our data demonstrate that siRNAs targeting a chromatin-associated RNA at a distance from its promoter induce its transcriptional silencing. Our results thus extend the possible repertoire of endogenous or exogenous interfering RNAs.
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7
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Hadar S, Meller A, Saida N, Shalgi R. Stress-induced transcriptional readthrough into neighboring genes is linked to intron retention. iScience 2022; 25:105543. [PMID: 36505935 PMCID: PMC9732411 DOI: 10.1016/j.isci.2022.105543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/10/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Exposure to certain stresses leads to readthrough transcription. Using polyA-selected RNA-seq in mouse fibroblasts subjected to heat shock, oxidative, or osmotic stress, we found that readthrough transcription can proceed into proximal downstream genes, in a phenomenon previously termed "read-in." We found that read-in genes share distinctive genomic characteristics; they are GC-rich and extremely short , with genomic features conserved in human. Using ribosome profiling, we found that read-in genes show significantly reduced translation. Strikingly, read-in genes demonstrate marked intron retention, mostly in their first introns, which could not be explained solely by their short introns and GC-richness, features often associated with intron retention. Finally, we revealed H3K36me3 enrichment upstream to read-in genes. Moreover, demarcation of exon-intron junctions by H3K36me3 was absent in read-in first introns. Our data portray a relationship between read-in and intron retention, suggesting they may have co-evolved to facilitate reduced translation of read-in genes during stress.
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Affiliation(s)
- Shani Hadar
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Anatoly Meller
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Naseeb Saida
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa 31096, Israel,Corresponding author
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8
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Vijayakumar A, Park A, Steitz JA. Modulation of mRNA 3'-End Processing and Transcription Termination in Virus-Infected Cells. Front Immunol 2022; 13:828665. [PMID: 35222412 PMCID: PMC8866245 DOI: 10.3389/fimmu.2022.828665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic mRNA 3´-end processing is a multi-step process beginning with pre-mRNA transcript cleavage followed by poly(A) tail addition. Closely coupled to transcription termination, 3´-end processing is a critical step in the regulation of gene expression, and disruption of 3´-end processing is known to affect mature mRNA levels. Various viral proteins interfere with the 3´-end processing machinery, causing read-through transcription and altered levels of mature transcripts through inhibition of cleavage and polyadenylation. Thus, disruption of 3´-end processing contributes to widespread host shutoff, including suppression of the antiviral response. Additionally, observed features of read-through transcripts such as decreased polyadenylation, nuclear retention, and decreased translation suggest that viruses may utilize these mechanisms to modulate host protein production and dominate cellular machinery. The degree to which the effects of read-through transcript production are harnessed by viruses and host cells remains unclear, but existing research highlights the importance of host 3´-end processing modulation during viral infection.
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Affiliation(s)
- Aarthi Vijayakumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Annsea Park
- Department of Immunobiology, Yale University, New Haven, CT, United States
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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9
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Rosa-Mercado NA, Steitz JA. Who let the DoGs out? - biogenesis of stress-induced readthrough transcripts. Trends Biochem Sci 2022; 47:206-217. [PMID: 34489151 PMCID: PMC8840951 DOI: 10.1016/j.tibs.2021.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/27/2021] [Accepted: 08/10/2021] [Indexed: 01/22/2023]
Abstract
Readthrough transcription caused by inefficient 3'-end cleavage of nascent mRNAs has emerged as a hallmark of the mammalian cellular stress response and results in the production of long noncoding RNAs known as downstream-of-gene (DoG)-containing transcripts. DoGs arise from around 10% of human protein-coding genes and are retained in the nucleus. They are produced minutes after cell exposure to stress and can be detected hours after stress removal. However, their biogenesis and the role(s) that DoGs or their production play in the cellular stress response are incompletely understood. We discuss findings that implicate host and viral proteins in the mechanisms underlying DoG production, as well as the transcriptional landscapes that accompany DoG induction under different stress conditions.
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Affiliation(s)
- Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA.
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10
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Abstract
Transcription termination is a critical stage for the production of legitimate mRNAs, and consequently functional proteins. However, the transcription machinery can ignore the stop signs and continue elongating beyond gene boundaries, invading downstream neighboring genes. Such phenomenon, designated transcription readthrough, can trigger the expression of pseudogenes usually silenced or lacking the proper regulatory signals. Due to the sequence similarity to parental genes, readthrough transcribed pseudogenes can regulate relevant protein-coding genes and impact biological functions. Here, we describe a computational pipeline that employs already existent bioinformatic tools to detect readthrough transcribed pseudogenes from expression profiles. We also unveil that combining strand-specific transcriptome data and epigenetic profiles can enhance and corroborate the results. By applying such approach to renal cancer biopsies, we show that pseudogenes can be readthrough transcribed as part of unspliced transcripts or processed RNA chimeras. Overall, our pipeline allows us to scrutinize transcriptome profiles to detect a diversity of readthrough events leading to expression of pseudogenes.
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11
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Muniz L, Nicolas E, Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J 2021; 40:e105740. [PMID: 34254686 PMCID: PMC8327950 DOI: 10.15252/embj.2020105740] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co‐transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read‐through transcripts. RNA Pol II speed itself is regulated in response to intra‐ and extra‐cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co‐transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.
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Affiliation(s)
- Lisa Muniz
- MCD, Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Estelle Nicolas
- MCD, Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Didier Trouche
- MCD, Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
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12
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Jochems F, Thijssen B, De Conti G, Jansen R, Pogacar Z, Groot K, Wang L, Schepers A, Wang C, Jin H, Beijersbergen RL, Leite de Oliveira R, Wessels LFA, Bernards R. The Cancer SENESCopedia: A delineation of cancer cell senescence. Cell Rep 2021; 36:109441. [PMID: 34320349 PMCID: PMC8333195 DOI: 10.1016/j.celrep.2021.109441] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
Cellular senescence is characterized as a stable proliferation arrest that can be triggered by multiple stresses. Most knowledge about senescent cells is obtained from studies in primary cells. However, senescence features may be different in cancer cells, since the pathways that are involved in senescence induction are often deregulated in cancer. We report here a comprehensive analysis of the transcriptome and senolytic responses in a panel of 13 cancer cell lines rendered senescent by two distinct compounds. We show that in cancer cells, the response to senolytic agents and the composition of the senescence-associated secretory phenotype are more influenced by the cell of origin than by the senescence trigger. Using machine learning, we establish the SENCAN gene expression classifier for the detection of senescence in cancer cell samples. The expression profiles and senescence classifier are available as an interactive online Cancer SENESCopedia. Senescent cancer cells respond differently to senolytic ABT-263 SASP expression in cancer is heterogeneous and influenced by cell origin The SENCAN classifier detects cancer cell senescence in vitro The Cancer SENESCopedia contains transcriptome data from 37 senescence models
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Affiliation(s)
- Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Robin Jansen
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Arnout Schepers
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Cun Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Haojie Jin
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, The NKI Robotics and Screening Center, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands; Faculty of EEMCS, Delft University of Technology, Delft, the Netherlands.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 Amsterdam, the Netherlands.
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13
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Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM. Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biol 2021; 22:136. [PMID: 33952325 PMCID: PMC8097831 DOI: 10.1186/s13059-021-02350-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes almost any genomic context. Currently, the source and function of most RNAs originating from intergenic regions in the human genome remain unclear. RESULTS We hypothesize that many intergenic RNAs can be ascribed to the presence of as-yet unannotated genes or the "fuzzy" transcription of known genes that extends beyond the annotated boundaries. To elucidate the contributions of these two sources, we assemble a dataset of more than 2.5 billion publicly available RNA-seq reads across 5 human cell lines and multiple cellular compartments to annotate transcriptional units in the human genome. About 80% of transcripts from unannotated intergenic regions can be attributed to the fuzzy transcription of existing genes; the remaining transcripts originate mainly from putative long non-coding RNA loci that are rarely spliced. We validate the transcriptional activity of these intergenic RNAs using independent measurements, including transcriptional start sites, chromatin signatures, and genomic occupancies of RNA polymerase II in various phosphorylation states. We also analyze the nuclear localization and sensitivities of intergenic transcripts to nucleases to illustrate that they tend to be rapidly degraded either on-chromatin by XRN2 or off-chromatin by the exosome. CONCLUSIONS We provide a curated atlas of intergenic RNAs that distinguishes between alternative processing of well-annotated genes from independent transcriptional units based on the combined analysis of chromatin signatures, nuclear RNA localization, and degradation pathways.
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Affiliation(s)
| | - Julian Zagalak
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Jan Attig
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, Gower Street, London, WC1E 6BT, UK
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
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14
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O’Connor NJ, Bordoy AE, Chatterjee A. Engineering Transcriptional Interference through RNA Polymerase Processivity Control. ACS Synth Biol 2021; 10:737-748. [PMID: 33710852 DOI: 10.1021/acssynbio.0c00534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Antisense transcription is widespread in all kingdoms of life and has been shown to influence gene expression through transcriptional interference (TI), a phenomenon in which one transcriptional process negatively influences another in cis. The processivity, or uninterrupted transcription, of an RNA polymerase (RNAP) is closely tied to levels of antisense transcription in bacterial genomes, but its influence on TI, while likely important, is not well-characterized. Here, we show that TI can be tuned through processivity control via three distinct antitermination strategies: the antibiotic bicyclomycin, phage protein Psu, and ribosome-RNAP coupling. We apply these methods toward TI and tune ribosome-RNAP coupling to produce 38-fold transcription-level gene repression due to both RNAP collisions and antisense RNA interference. We then couple protein roadblock and TI to design minimal genetic NAND and NOR logic gates. Together, these results show the importance of processivity control for strong TI and demonstrate TI's potential for synthetic biology.
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Affiliation(s)
- Nolan J. O’Connor
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Antoni E. Bordoy
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Antimicrobial Regeneration Consortium, Boulder, Colorado 80301, United States
- Sachi Bioworks, Inc., Boulder, Colorado 80301, United States
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15
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Mullani N, Porozhan Y, Mangelinck A, Rachez C, Costallat M, Batsché E, Goodhardt M, Cenci G, Mann C, Muchardt C. Reduced RNA turnover as a driver of cellular senescence. Life Sci Alliance 2021; 4:4/3/e202000809. [PMID: 33446491 PMCID: PMC7812316 DOI: 10.26508/lsa.202000809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
RNAs originating from transcription upstream and downstream of genes accumulate in the cytoplasm of a subset of senescent cells, suggesting an RNA alternative to cytoplasmic DNA in the triggering of senescence. Accumulation of senescent cells is an important contributor to chronic inflammation upon aging. The inflammatory phenotype of senescent cells was previously shown to be driven by cytoplasmic DNA. Here, we propose that cytoplasmic double-stranded RNA has a similar effect. We find that several cell types driven into senescence by different routes share an accumulation of long promoter RNAs and 3′ gene extensions rich in retrotransposon sequences. Accordingly, these cells display increased expression of genes involved in response to double stranded RNA of viral origin downstream of the interferon pathway. The RNA accumulation is associated with evidence of reduced RNA turnover, including in some cases, reduced expression of RNA exosome subunits. Reciprocally, depletion of RNA exosome subunit EXOSC3 accelerated expression of multiple senescence markers. A senescence-like RNA accumulation was also observed in cells exposed to oxidative stress, an important trigger of cellular senescence. Altogether, we propose that in a subset of senescent cells, repeat-containing transcripts stabilized by oxidative stress or reduced RNA exosome activity participate in driving and maintaining the permanent inflammatory state characterizing cellular senescence.
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Affiliation(s)
- Nowsheen Mullani
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France.,Sorbonne Université, Ecole Doctorale "Complexité du Vivant" (ED515), Paris, France
| | - Yevheniia Porozhan
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Adèle Mangelinck
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christophe Rachez
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Mickael Costallat
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Eric Batsché
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Michele Goodhardt
- Institut National de la Santé et de la Recherche Médicale (INSERM) U976, Institut de Recherche Saint Louis, Université de Paris, Paris, France
| | - Giovanni Cenci
- Dipartimento Biologia e Biotecnologie "C. Darwin," SAPIENZA Università di Roma, Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Carl Mann
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christian Muchardt
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
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16
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Reimer KA, Mimoso CA, Adelman K, Neugebauer KM. Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis. Mol Cell 2021; 81:998-1012.e7. [PMID: 33440169 DOI: 10.1016/j.molcel.2020.12.018] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
Pre-mRNA processing steps are tightly coordinated with transcription in many organisms. To determine how co-transcriptional splicing is integrated with transcription elongation and 3' end formation in mammalian cells, we performed long-read sequencing of individual nascent RNAs and precision run-on sequencing (PRO-seq) during mouse erythropoiesis. Splicing was not accompanied by transcriptional pausing and was detected when RNA polymerase II (Pol II) was within 75-300 nucleotides of 3' splice sites (3'SSs), often during transcription of the downstream exon. Interestingly, several hundred introns displayed abundant splicing intermediates, suggesting that splicing delays can take place between the two catalytic steps. Overall, splicing efficiencies were correlated among introns within the same transcript, and intron retention was associated with inefficient 3' end cleavage. Remarkably, a thalassemia patient-derived mutation introducing a cryptic 3'SS improved both splicing and 3' end cleavage of individual β-globin transcripts, demonstrating functional coupling between the two co-transcriptional processes as a determinant of productive gene output.
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Affiliation(s)
- Kirsten A Reimer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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17
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The aging proteostasis decline: From nematode to human. Exp Cell Res 2021; 399:112474. [PMID: 33434530 PMCID: PMC7868887 DOI: 10.1016/j.yexcr.2021.112474] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 02/08/2023]
Abstract
The aging proteostasis decline manifests in a failure of aging cells and organisms to properly respond to proteotoxic challenges. This proteostasis collapse has long been considered a hallmark of aging in nematodes, and has recently been shown to occur also in human cells upon entry to senescence, opening the way to exploring the phenomenon in the broader context of human aging. Cellular senescence is part of the normal human physiology of aging, with senescent cell accumulation as a prominent feature of aged tissues. Being highly resistant to cell death, senescent cells, as they accumulate, become pro-inflammatory and promote disease. Here we discuss the causes of human senescence proteostasis decline, in view of the current literature on nematodes, on the one hand, and senescence, on the other hand. We review two major aspects of the phenomenon: (1) the decline in transcriptional activation of stress-response pathways, and (2) impairments in proteasome function. We further outline potential underlying mechanisms of transcriptional proteostasis decline, focusing on reduced chromatin dynamics and compromised nuclear integrity. Finally, we discuss potential strategies for reinforcing proteostasis as a means to improve organismal health and address the relationship to senolytics.
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18
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Deb S, Felix DA, Koch P, Deb MK, Szafranski K, Buder K, Sannai M, Groth M, Kirkpatrick J, Pietsch S, Gollowitzer A, Groß A, Riemenschneider P, Koeberle A, González‐Estévez C, Rudolph KL. Tnfaip2/exoc3-driven lipid metabolism is essential for stem cell differentiation and organ homeostasis. EMBO Rep 2021; 22:e49328. [PMID: 33300287 PMCID: PMC7788457 DOI: 10.15252/embr.201949328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 01/07/2023] Open
Abstract
Lipid metabolism influences stem cell maintenance and differentiation but genetic factors that control these processes remain to be delineated. Here, we identify Tnfaip2 as an inhibitor of reprogramming of mouse fibroblasts into induced pluripotent stem cells. Tnfaip2 knockout impairs differentiation of embryonic stem cells (ESCs), and knockdown of the planarian para-ortholog, Smed-exoc3, abrogates in vivo tissue homeostasis and regeneration-processes that are driven by somatic stem cells. When stimulated to differentiate, Tnfaip2-deficient ESCs fail to induce synthesis of cellular triacylglycerol (TAG) and lipid droplets (LD) coinciding with reduced expression of vimentin (Vim)-a known inducer of LD formation. Smed-exoc3 depletion also causes a strong reduction of TAGs in planarians. The study shows that Tnfaip2 acts epistatically with and upstream of Vim in impairing cellular reprogramming. Supplementing palmitic acid (PA) and palmitoyl-L-carnitine (the mobilized form of PA) restores the differentiation capacity of Tnfaip2-deficient ESCs and organ maintenance in Smed-exoc3-depleted planarians. Together, these results identify a novel role of Tnfaip2 and exoc3 in controlling lipid metabolism, which is essential for ESC differentiation and planarian organ maintenance.
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Affiliation(s)
- Sarmistha Deb
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Daniel A Felix
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Philipp Koch
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | | | - Karol Szafranski
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Katrin Buder
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Mara Sannai
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Marco Groth
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | | | - Stefan Pietsch
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - André Gollowitzer
- Institute of PharmacyFriedrich‐Schiller‐UniversityJenaGermany
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Alexander Groß
- Institute of Medical Systems BiologyUlm UniversityUlmGermany
| | | | - Andreas Koeberle
- Institute of PharmacyFriedrich‐Schiller‐UniversityJenaGermany
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | | | - Karl Lenhard Rudolph
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
- University Hospital JenaFriedrich Schiller UniversityJenaGermany
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19
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Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Mol Cell 2021; 81:502-513.e4. [PMID: 33400923 DOI: 10.1016/j.molcel.2020.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/11/2020] [Accepted: 11/30/2020] [Indexed: 02/04/2023]
Abstract
Stress-induced readthrough transcription results in the synthesis of downstream-of-gene (DoG)-containing transcripts. The mechanisms underlying DoG formation during cellular stress remain unknown. Nascent transcription profiles during DoG induction in human cell lines using TT-TimeLapse sequencing revealed widespread transcriptional repression upon hyperosmotic stress. Yet, DoGs are produced regardless of the transcriptional level of their upstream genes. ChIP sequencing confirmed that stress-induced redistribution of RNA polymerase (Pol) II correlates with the transcriptional output of genes. Stress-induced alterations in the Pol II interactome are observed by mass spectrometry. While certain cleavage and polyadenylation factors remain Pol II associated, Integrator complex subunits dissociate from Pol II under stress leading to a genome-wide loss of Integrator on DNA. Depleting the catalytic subunit of Integrator using siRNAs induces hundreds of readthrough transcripts, whose parental genes partially overlap those of stress-induced DoGs. Our results provide insights into the mechanisms underlying DoG production and how Integrator activity influences DoG transcription.
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20
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Ávila-López PA, Guerrero G, Nuñez-Martínez HN, Peralta-Alvarez CA, Hernández-Montes G, Álvarez-Hilario LG, Herrera-Goepfert R, Albores-Saavedra J, Villegas-Sepúlveda N, Cedillo-Barrón L, Montes-Gómez AE, Vargas M, Schnoor M, Recillas-Targa F, Hernández-Rivas R. H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma. Oncogene 2021; 40:2065-2080. [PMID: 33627784 PMCID: PMC7979544 DOI: 10.1038/s41388-021-01664-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 12/11/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most intractable and devastating malignant tumors. Epigenetic modifications such as DNA methylation and histone modification regulate tumor initiation and progression. However, the contribution of histone variants in PDAC is unknown. Here, we demonstrated that the histone variant H2A.Z is highly expressed in PDAC cell lines and PDAC patients and that its overexpression correlates with poor prognosis. Moreover, all three H2A.Z isoforms (H2A.Z.1, H2A.Z.2.1, and H2A.Z.2.2) are highly expressed in PDAC cell lines and PDAC patients. Knockdown of these H2A.Z isoforms in PDAC cell lines induces a senescent phenotype, cell cycle arrest in phase G2/M, increased expression of cyclin-dependent kinase inhibitor CDKN2A/p16, SA-β-galactosidase activity and interleukin 8 production. Transcriptome analysis of H2A.Z-depleted PDAC cells showed altered gene expression in fatty acid biosynthesis pathways and those that regulate cell cycle and DNA damage repair. Importantly, depletion of H2A.Z isoforms reduces the tumor size in a mouse xenograft model in vivo and sensitizes PDAC cells to gemcitabine. Overexpression of H2A.Z.1 and H2A.Z.2.1 more than H2A.Z.2.2 partially restores the oncogenic phenotype. Therefore, our data suggest that overexpression of H2A.Z isoforms enables cells to overcome the oncoprotective barrier associated with senescence, favoring PDAC tumor grow and chemoresistance. These results make H2A.Z a potential candidate as a diagnostic biomarker and therapeutic target for PDAC.
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Affiliation(s)
- P. A. Ávila-López
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - G. Guerrero
- grid.9486.30000 0001 2159 0001Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - H. N. Nuñez-Martínez
- grid.9486.30000 0001 2159 0001Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - C. A. Peralta-Alvarez
- grid.9486.30000 0001 2159 0001Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - G. Hernández-Montes
- grid.9486.30000 0001 2159 0001Coordinación de la Investigación Científica, Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - L. G. Álvarez-Hilario
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - R. Herrera-Goepfert
- grid.419167.c0000 0004 1777 1207Departamento de Patología, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - J. Albores-Saavedra
- Departamento de Patología, Medica Sur Clínica y Fundación, Ciudad de México, Mexico
| | - N. Villegas-Sepúlveda
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - L. Cedillo-Barrón
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - A. E. Montes-Gómez
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - M. Vargas
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - M. Schnoor
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - F. Recillas-Targa
- grid.9486.30000 0001 2159 0001Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - R. Hernández-Rivas
- grid.418275.d0000 0001 2165 8782Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
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21
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Vidal AF. Read-through circular RNAs reveal the plasticity of RNA processing mechanisms in human cells. RNA Biol 2020; 17:1823-1826. [PMID: 32783578 PMCID: PMC7714478 DOI: 10.1080/15476286.2020.1805233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
In the human genome, there are several genes whose primary transcripts are both canonically and non-canonically spliced to generate mRNAs and RNA circles, respectively. These RNA circles are a novel class of long non-coding RNAs that became known as circular RNAs (circRNAs). Recently, a new type of circRNA was discovered and called read-through circRNAs (rt-circRNAs). They are hybrid circles that include coding exons from two adjacent and similarly oriented genes. The function of rt-circRNAs, as well as the impact of read-through transcription in our transcriptome, remains to be elucidated. Although we have just begun to scratch it, here I discussed some insights that these fascinating circRNAs are already giving us about the plasticity of RNA processing in our cells.
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Affiliation(s)
- Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Brazil
- Graduate Program of Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
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22
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Biggs H, Parthasarathy P, Gavryushkina A, Gardner PP. ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6013764. [PMID: 33258967 PMCID: PMC7706182 DOI: 10.1093/database/baaa105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/13/2020] [Accepted: 11/12/2020] [Indexed: 11/22/2022]
Abstract
Variants within the non-coding genome are frequently associated with phenotypes in genome-wide association studies. These non-coding regions may be involved in the regulation of gene expression, encode functional non-coding RNAs, or influence splicing and other cellular functions. We have curated a list of characterized non-coding human genome variants based on the published evidence that indicates phenotypic consequences of the variation. In order to minimize annotation errors, two curators have independently verified the supporting evidence for pathogenicity of each non-coding variant in the published literature. The database consists of 721 non-coding variants linked to the published literature describing the evidence of functional consequences. We have also sampled 7228 covariate-matched benign controls, that have a population frequency of over 5%, from the single nucleotide polymorphism database (dbSNP151) database. These were sampled controlling for potential confounding factors such as linkage with pathogenic variants, annotation type (untranslated region, intron, intergenic, etc.) and variant type (substitution or indel). The dataset presented here represents a curated repository, with a potential use for the training or evaluation of algorithms used in the prediction of non-coding variant functionality. Database URL: https://github.com/Gardner-BinfLab/ncVarDB.
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Affiliation(s)
- Harry Biggs
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Padmini Parthasarathy
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Alexandra Gavryushkina
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Paul P Gardner
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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23
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Muniz L, Lazorthes S, Delmas M, Ouvrard J, Aguirrebengoa M, Trouche D, Nicolas E. Circular ANRIL isoforms switch from repressors to activators of p15/CDKN2B expression during RAF1 oncogene-induced senescence. RNA Biol 2020; 18:404-420. [PMID: 32862732 PMCID: PMC7951966 DOI: 10.1080/15476286.2020.1812910] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Long non-coding RNAs (ncRNAs) are major regulators of gene expression and cell fate. The INK4 locus encodes the tumour suppressor proteins p15INK4b, p16INK4a and p14ARF required for cell cycle arrest and whose expression increases during senescence. ANRIL is a ncRNA antisense to the p15 gene. In proliferative cells, ANRIL prevents senescence by repressing INK4 genes through the recruitment of Polycomb-group proteins. In models of replicative and RASval12 oncogene-induced senescence (OIS), the expression of ANRIL and Polycomb proteins decreases, thus allowing INK4 derepression. Here, we found in a model of RAF1 OIS that ANRIL expression rather increases, due in particular to an increased stability. This led us to search for circular ANRIL isoforms, as circular RNAs are rather stable species. We found that the expression of two circular ANRIL increases in several OIS models (RAF1, MEK1 and BRAF). In proliferative cells, they repress p15 expression, while in RAF1 OIS, they promote full induction of p15, p16 and p14ARF expression. Further analysis of one of these circular ANRIL shows that it interacts with Polycomb proteins and decreases EZH2 Polycomb protein localization and H3K27me3 at the p15 and p16 promoters, respectively. We propose that changes in the ratio between Polycomb proteins and circular ANRIL isoforms allow these isoforms to switch from repressors of p15 gene to activators of all INK4 genes in RAF1 OIS. Our data reveal that regulation of ANRIL expression depends on the senescence inducer and underline the importance of circular ANRIL in the regulation of INK4 gene expression and senescence.
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Affiliation(s)
- Lisa Muniz
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sandra Lazorthes
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Maxime Delmas
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Ouvrard
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marion Aguirrebengoa
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Didier Trouche
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Estelle Nicolas
- LBCMCP, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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24
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Roth SJ, Heinz S, Benner C. ARTDeco: automatic readthrough transcription detection. BMC Bioinformatics 2020; 21:214. [PMID: 32456667 PMCID: PMC7249449 DOI: 10.1186/s12859-020-03551-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription past the 3' end of genes, which can result in novel transcripts, changes in epigenetic states and altered 3D genome structure. RESULTS We developed Automatic Readthrough Transcription Detection (ARTDeco), a tool to detect and analyze multiple features of readthrough transcription from RNA-seq and other next-generation sequencing (NGS) assays that profile transcriptional activity. ARTDeco robustly quantifies the global severity of readthrough phenotypes, and reliably identifies individual genes that fail to terminate (readthrough genes), are aberrantly transcribed due to upstream termination failure (read-in genes), and novel transcripts created as a result of readthrough (downstream of gene or DoG transcripts). We used ARTDeco to characterize readthrough transcription observed during influenza A virus (IAV) infection, validating its specificity and sensitivity by comparing its performance in samples infected with a mutant virus that fails to block transcription termination. We verify ARTDeco's ability to detect readthrough as well as identify read-in genes from different experimental assays across multiple experimental systems with known defects in transcriptional termination, and show how these results can be leveraged to improve the interpretation of gene expression and downstream analysis. Applying ARTDeco to a gene expression data set from IAV-infected monocytes from different donors, we find strong evidence that read-in gene-associated expression quantitative trait loci (eQTLs) likely regulate genes upstream of read-in genes. This indicates that taking readthrough transcription into account is important for the interpretation of eQTLs in systems where transcription termination is blocked. CONCLUSIONS ARTDeco aids researchers investigating readthrough transcription in a variety of systems and contexts.
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Affiliation(s)
- Samuel J Roth
- Bioinformatics and Systems Biology Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA.
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Lamaa A, Humbert J, Aguirrebengoa M, Cheng X, Nicolas E, Côté J, Trouche D. Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation. eLife 2020; 9:53375. [PMID: 32109204 PMCID: PMC7048395 DOI: 10.7554/elife.53375] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is encoded by two genes expressing two isoforms, H2A.Z.1 and H2A.Z.2 differing by three amino acids. Here, we undertook an integrated analysis of their functions in gene expression using endogenously-tagged proteins. RNA-Seq analysis in untransformed cells showed that they can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner. Furthermore, they have similar or antagonistic function depending on genes. H2A.Z.1 and H2A.Z.2 can replace each other at Transcription Start Sites, providing a molecular explanation for this interplay. Mass spectrometry analysis showed that H2A.Z.1 and H2A.Z.2 have specific interactors, which can mediate their functional antagonism. Our data indicate that the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important to regulate specific gene expression, providing an additional layer of complexity to the control of gene expression by histone variants.
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Affiliation(s)
- Assala Lamaa
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Marion Aguirrebengoa
- BigA Core Facility, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Estelle Nicolas
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center and Oncology Division of CHU de Québec-Université Laval Research Center, Quebec, Canada
| | - Didier Trouche
- LBCMCP, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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Bordoy AE, O’Connor NJ, Chatterjee A. Construction of Two-Input Logic Gates Using Transcriptional Interference. ACS Synth Biol 2019; 8:2428-2441. [PMID: 31532632 DOI: 10.1021/acssynbio.9b00321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Transcriptional interference (TI) has been shown to regulate gene expression at the DNA level via different molecular mechanisms. The obstacles present on the DNA that a transcribing RNA polymerase might encounter, for example, a DNA-bound protein or another RNA polymerase, can result in TI causing termination of transcription, thus reducing gene expression. However, the potential of TI as a new strategy to engineer complex gene expression modules has not been fully explored yet. Here we created a series of two-input genetic devices that use the presence of a roadblocking protein to control gene expression and analyzed their behaviors using both experimental and mathematical modeling approaches. We explored how multiple characteristics affect the response of genetic devices engineered to act like either AND, OR, or single input logic gates. We show that the dissociation constant of the roadblocking protein, inducer activation of promoter and operator sites, and distance between tandem promoters tune gate behavior. This work highlights the potential of rationally creating different types of genetic responses using the same transcription factors in subtly different genetic architectures.
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Melnick M, Gonzales P, Cabral J, Allen MA, Dowell RD, Link CD. Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA. PLoS One 2019; 14:e0206715. [PMID: 30958820 PMCID: PMC6453478 DOI: 10.1371/journal.pone.0206715] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/25/2019] [Indexed: 12/14/2022] Open
Abstract
We observed that heat shock of Caenorhabditis elegans leads to the formation of nuclear double-stranded RNA (dsRNA) foci, detectable with a dsRNA-specific monoclonal antibody. These foci significantly overlap with nuclear HSF-1 granules. To investigate the molecular mechanism(s) underlying dsRNA foci formation, we used RNA-seq to globally characterize total RNA and immunoprecipitated dsRNA from control and heat shocked worms. We find a subset of both sense and antisense transcripts enriched in the dsRNA pool by heat shock overlap with dsRNA transcripts enriched by deletion of tdp-1, which encodes the C. elegans ortholog of TDP-43. Interestingly, transcripts involved in translation are over-represented in the dsRNAs induced by either heat shock or deletion of tdp-1. Also enriched in the dsRNA transcripts are sequences downstream of annotated genes (DoGs), which we globally quantified with a new algorithm. To validate these observations, we used fluorescence in situ hybridization (FISH) to confirm both antisense and downstream of gene transcription for eif-3.B, one of the affected loci we identified.
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Affiliation(s)
- Marko Melnick
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Patrick Gonzales
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Joseph Cabral
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
| | - Mary A. Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Robin D. Dowell
- BioFrontiers Institute and Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Christopher D. Link
- Integrative Physiology, University of Colorado, Boulder, Colorado, United States of America
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
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28
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Epigenetic Regulation by lncRNAs: An Overview Focused on UCA1 in Colorectal Cancer. Cancers (Basel) 2018; 10:cancers10110440. [PMID: 30441811 PMCID: PMC6266399 DOI: 10.3390/cancers10110440] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancers have become the second leading cause of cancer-related deaths. In particular, acquired chemoresistance and metastatic lesions occurring in colorectal cancer are a major challenge for chemotherapy treatment. Accumulating evidence shows that long non-coding (lncRNAs) are involved in the initiation, progression, and metastasis of cancer. We here discuss the epigenetic mechanisms through which lncRNAs regulate gene expression in cancer cells. In the second part of this review, we focus on the role of lncRNA Urothelial Cancer Associated 1 (UCA1) to integrate research in different types of cancer in order to decipher its putative function and mechanism of regulation in colorectal cancer cells. UCA1 is highly expressed in cancer cells and mediates transcriptional regulation on an epigenetic level through the interaction with chromatin modifiers, by direct regulation via chromatin looping and/or by sponging the action of a diversity of miRNAs. Furthermore, we discuss the role of UCA1 in the regulation of cell cycle progression and its relation to chemoresistance in colorectal cancer cells.
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Affiliation(s)
- Bernadette Neve
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
| | - Nicolas Jonckheere
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
| | - Audrey Vincent
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
| | - Isabelle Van Seuningen
- Inserm UMR-S 1172, Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer (JPArc), Team "Mucins, Epithelial Differentiation and Carcinogenesis"; University Lille; CHU Lille,59045, Lille CEDEX, France.
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29
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Wiesel Y, Sabath N, Shalgi R. DoGFinder: a software for the discovery and quantification of readthrough transcripts from RNA-seq. BMC Genomics 2018; 19:597. [PMID: 30089468 PMCID: PMC6083495 DOI: 10.1186/s12864-018-4983-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023] Open
Abstract
Background Recent studies have described a widespread induction of transcriptional readthrough as a consequence of various stress conditions in mammalian cells. This novel phenomenon, initially identified from analysis of RNA-seq data, suggests intriguing new levels of gene expression regulation. However, the mechanism underlying naturally occurring transcriptional readthrough, as well as its regulatory consequences, still remain elusive. Furthermore, the readthrough response to stress has thus far not been investigated outside of mammalian species, and the occurrence of readthrough in many physiological and disease conditions remains to be explored. Results To facilitate a wider investigation into transcriptional readthrough, we created the DoGFinder software package, for the streamlined identification and quantification of readthrough transcripts, also known as DoGs (Downstream of Gene-containing transcripts), from any RNA-seq dataset. Using DoGFinder, we explore the dependence of DoG discovery potential on RNA-seq library depth, and show that stress-induced readthrough induction discovery is robust to sequencing depth, and input parameter settings. We further demonstrate the use of the DoGFinder software package on a new publically available RNA-seq dataset, and discover DoG induction in human PME cells following hypoxia – a previously unknown readthrough inducing stress type. Conclusions DoGFinder will enable users to explore, in a few simple steps, the readthrough phenomenon in any condition and organism. DoGFinder is freely available at https://github.com/shalgilab/DoGFinder. Electronic supplementary material The online version of this article (10.1186/s12864-018-4983-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuval Wiesel
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Niv Sabath
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 31096, Israel.
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30
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Sabath N, Vilborg A, Steitz JA, Shalgi R. Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal. Hum Genomics 2018; 12:32. [PMID: 29945683 PMCID: PMC6020437 DOI: 10.1186/s40246-018-0164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/11/2018] [Indexed: 11/18/2022] Open
Abstract
Naturally occurring stress-induced transcriptional readthrough is a recently discovered phenomenon, in which stress conditions lead to dramatic induction of long transcripts as a result of transcription termination failure. In 2015, we reported the induction of such downstream of gene (DoG) containing transcripts upon osmotic stress in human cells, while others observed similar transcripts in virus-infected and cancer cells. Using the rigorous methodology Cap-Seq, we demonstrated that DoGs result from transcriptional readthrough, not de novo initiation. More recently, we presented a genome-wide comparison of NIH3T3 mouse cells subjected to osmotic, heat, and oxidative stress and concluded that massive induction of transcriptional readthrough is a hallmark of the mammalian stress response. In their recent letter, Huang and Liu in contrast claim that DoG transcripts result from novel transcription initiation near the ends of genes. Their conclusions rest on analyses of a publicly available transcription start site (TSS-Seq) dataset from unstressed NIH3T3 cells. Here, we present evidence that this dataset identifies not only true transcription start sites, TSSs, but also 5′-ends of numerous snoRNAs, which are generally processed from introns in mammalian cells. We show that failure to recognize these erroneous assignments in the TSS-Seq dataset, as well as ignoring published Cap-Seq data on TSS mapping during osmotic stress, have led to misinterpretation by Huang and Liu. We conclude that, contrary to the claims made by Huang and Liu, TSS-Seq reads near gene ends cannot explain the existence of DoGs, nor their stress-mediated induction. Rather it is, as we originally demonstrated, transcriptional readthrough that leads to the formation of DoGs.
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Affiliation(s)
- Niv Sabath
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096, Haifa, Israel
| | - Anna Vilborg
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT, 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT, 06536, USA
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096, Haifa, Israel.
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31
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Herzel L, Straube K, Neugebauer KM. Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome Res 2018; 28:1008-1019. [PMID: 29903723 PMCID: PMC6028129 DOI: 10.1101/gr.232025.117] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/24/2018] [Indexed: 12/13/2022]
Abstract
Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe. Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2, the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3′ end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation.
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Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Korinna Straube
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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