1
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McShane A, Narayanan IV, Paulsen MT, Ashaka M, Blinkiewicz H, Yang NT, Magnuson B, Bedi K, Wilson TE, Ljungman M. Characterizing nascent transcription patterns of PROMPTs, eRNAs, and readthrough transcripts in the ENCODE4 deeply profiled cell lines. bioRxiv 2024:2024.04.09.588612. [PMID: 38645116 PMCID: PMC11030308 DOI: 10.1101/2024.04.09.588612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Arising as co-products of canonical gene expression, transcription-associated lincRNAs, such as promoter upstream transcripts (PROMPTs), enhancer RNAs (eRNAs), and readthrough (RT) transcripts, are often regarded as byproducts of transcription, although they may be important for the expression of nearby genes. We identified regions of nascent expression of these lincRNA in 16 human cell lines using Bru-seq techniques, and found distinctly regulated patterns of PROMPT, eRNA, and RT transcription using the diverse biochemical approaches in the ENCODE4 deeply profiled cell lines collection. Transcription of these lincRNAs was influenced by sequence-specific features and the local or 3D chromatin landscape. However, these sequence and chromatin features do not describe the full spectrum of lincRNA expression variability we identify, highlighting the complexity of their regulation. This may suggest that transcription-associated lincRNAs are not merely byproducts, but rather that the transcript itself, or the act of its transcription, is important for genomic function.
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2
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Campagne S. U1 snRNP Biogenesis Defects in Neurodegenerative Diseases. Chembiochem 2024; 25:e202300864. [PMID: 38459794 DOI: 10.1002/cbic.202300864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
The U1 small ribonucleoprotein (U1 snRNP) plays a pivotal role in the intricate process of gene expression, specifically within nuclear RNA processing. By initiating the splicing reaction and modulating 3'-end processing, U1 snRNP exerts precise control over RNA metabolism and gene expression. This ribonucleoparticle is abundantly present, and its complex biogenesis necessitates shuttling between the nuclear and cytoplasmic compartments. Over the past three decades, extensive research has illuminated the crucial connection between disrupted U snRNP biogenesis and several prominent human diseases, notably various neurodegenerative conditions. The perturbation of U1 snRNP homeostasis has been firmly established in diseases such as Spinal Muscular Atrophy, Pontocerebellar hypoplasia, and FUS-mediated Amyotrophic Lateral Sclerosis. Intriguingly, compelling evidence suggests a potential correlation in Fronto-temporal dementia and Alzheimer's disease as well. Although the U snRNP biogenesis pathway is conserved across all eukaryotic cells, neurons, in particular, appear to be highly susceptible to alterations in spliceosome homeostasis. In contrast, other cell types exhibit a greater resilience to such disturbances. This vulnerability underscores the intricate relationship between U1 snRNP dynamics and the health of neuronal cells, shedding light on potential avenues for understanding and addressing neurodegenerative disorders.
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Affiliation(s)
- Sebastien Campagne
- University of Bordeaux, INSERM U1212, CNRS UMR5320, ARNA unit 146, rue Leo Saignat, 33077, Bordeaux
- Institut Européen de Chimie et de Biologie, 2, rue Robert Escarpit, 33600, Pessac
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3
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Dudnyk K, Cai D, Shi C, Xu J, Zhou J. Sequence basis of transcription initiation in the human genome. Science 2024; 384:eadj0116. [PMID: 38662817 DOI: 10.1126/science.adj0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/28/2024] [Indexed: 05/03/2024]
Abstract
Transcription initiation is a process that is essential to ensuring the proper function of any gene, yet we still lack a unified understanding of sequence patterns and rules that explain most transcription start sites in the human genome. By predicting transcription initiation at base-pair resolution from sequences with a deep learning-inspired explainable model called Puffin, we show that a small set of simple rules can explain transcription initiation at most human promoters. We identify key sequence patterns that contribute to human promoter activity, each activating transcription with distinct position-specific effects. Furthermore, we explain the sequence basis of bidirectional transcription at promoters, identify the links between promoter sequence and gene expression variation across cell types, and explore the conservation of sequence determinants of transcription initiation across mammalian species.
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Affiliation(s)
- Kseniia Dudnyk
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Donghong Cai
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center of Excellence for Leukemia Studies (CELS), Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chenlai Shi
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Xu
- Center of Excellence for Leukemia Studies (CELS), Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jian Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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4
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Yang J, Li J, Miao L, Gao X, Sun W, Linghu S, Ren G, Peng B, Chen S, Liu Z, Wang B, Dong A, Huang D, Yuan J, Dang Y, Lai F. Transcription directionality is licensed by Integrator at active human promoters. Nat Struct Mol Biol 2024:10.1038/s41594-024-01272-z. [PMID: 38649617 DOI: 10.1038/s41594-024-01272-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/12/2024] [Indexed: 04/25/2024]
Abstract
A universal characteristic of eukaryotic transcription is that the promoter recruits RNA polymerase II (RNAPII) to produce both precursor mRNAs (pre-mRNAs) and short unstable promoter upstream transcripts (PROMPTs) toward the opposite direction. However, how the transcription machinery selects the correct direction to produce pre-mRNAs is largely unknown. Here, through multiple acute auxin-inducible degradation systems, we show that rapid depletion of an RNAPII-binding protein complex, Integrator, results in robust PROMPT accumulation throughout the genome. Interestingly, the accumulation of PROMPTs is compensated by the reduction of pre-mRNA transcripts in actively transcribed genes. Consistently, Integrator depletion alters the distribution of polymerase between the sense and antisense directions, which is marked by increased RNAPII-carboxy-terminal domain Tyr1 phosphorylation at PROMPT regions and a reduced Ser2 phosphorylation level at transcription start sites. Mechanistically, the endonuclease activity of Integrator is critical to suppress PROMPT production. Furthermore, our data indicate that the presence of U1 binding sites on nascent transcripts could counteract the cleavage activity of Integrator. In this process, the absence of robust U1 signal at most PROMPTs allows Integrator to suppress the antisense transcription and shift the transcriptional balance in favor of the sense direction.
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Affiliation(s)
- Jiao Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
- Southwest United Graduate School, Kunming, China
| | - Jingyang Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Langxi Miao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Gao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Wenhao Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Shuo Linghu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Guiping Ren
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Bangya Peng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Shunkai Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhongqi Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Bo Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Ao Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Duo Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Jinrong Yuan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China.
| | - Fan Lai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Science, Yunnan Key Laboratory of Cell Metabolism and Diseases, School of Life Sciences, Yunnan University, Kunming, China.
- Southwest United Graduate School, Kunming, China.
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5
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Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. bioRxiv 2024:2024.04.12.589208. [PMID: 38659863 PMCID: PMC11042195 DOI: 10.1101/2024.04.12.589208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and noncoding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
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Affiliation(s)
- Benjamin J. Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA USA
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6
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Palazzo AF, Qiu Y, Kang YM. mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts. RNA Biol 2024; 21:1-12. [PMID: 38091265 PMCID: PMC10732640 DOI: 10.1080/15476286.2023.2293339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
The division of the cellular space into nucleoplasm and cytoplasm promotes quality control mechanisms that prevent misprocessed mRNAs and junk RNAs from gaining access to the translational machinery. Here, we explore how properly processed mRNAs are distinguished from both misprocessed mRNAs and junk RNAs by the presence or absence of various 'identity features'.
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Affiliation(s)
| | - Yi Qiu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yoon Mo Kang
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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7
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Russo M, Piccolo V, Polizzese D, Prosperini E, Borriero C, Polletti S, Bedin F, Marenda M, Michieletto D, Mandana GM, Rodighiero S, Cuomo A, Natoli G. Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription. Genes Dev 2023; 37:1017-1040. [PMID: 38092518 PMCID: PMC10760643 DOI: 10.1101/gad.351057.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]
Abstract
Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements. The Restrictor complex, composed of the Pol II-interacting protein WDR82 and the RNA-binding protein ZC3H4, suppresses processive transcription at thousands of extragenic sites in mammalian genomes. Restrictor-driven termination does not involve nascent RNA cleavage, and its interplay with other termination machineries is unclear. Here we show that efficient termination at Restrictor-controlled extragenic transcription units involves the recruitment of the protein phosphatase 1 (PP1) regulatory subunit PNUTS, a negative regulator of the SPT5 elongation factor, and Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent and phosphatase-dependent termination of noncoding RNAs in yeast. PNUTS and Symplekin act synergistically with, but independently from, Restrictor to dampen processive extragenic transcription. Moreover, the presence of limiting nuclear levels of Symplekin imposes a competition for its recruitment among multiple transcription termination machineries, resulting in mutual regulatory interactions. Hence, by synergizing with Restrictor, Symplekin and PNUTS enable efficient termination of processive, long-range extragenic transcription.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Danilo Polizzese
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Gaurav Madappa Mandana
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy;
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8
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Saviola AJ, Wang J, Welty R, Liu S, Vaeth K, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. bioRxiv 2023:2023.12.15.571893. [PMID: 38168357 PMCID: PMC10760170 DOI: 10.1101/2023.12.15.571893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe 2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.
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9
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Ait Said M, Bejjani F, Abdouni A, Ségéral E, Emiliani S. Premature transcription termination complex proteins PCF11 and WDR82 silence HIV-1 expression in latently infected cells. Proc Natl Acad Sci U S A 2023; 120:e2313356120. [PMID: 38015843 DOI: 10.1073/pnas.2313356120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Postintegration transcriptional silencing of HIV-1 leads to the establishment of a pool of latently infected cells. In these cells, mechanisms controlling RNA Polymerase II (RNAPII) pausing and premature transcription termination (PTT) remain to be explored. Here, we found that the cleavage and polyadenylation (CPA) factor PCF11 represses HIV-1 expression independently of the other subunits of the CPA complex or the polyadenylation signal located at the 5' LTR. We show that PCF11 interacts with the RNAPII-binding protein WDR82. Knock-down of PCF11 or WDR82 reactivated HIV-1 expression in latently infected cells. To silence HIV-1 transcription, PCF11 and WDR82 are specifically recruited at the promoter-proximal region of the provirus in an interdependent manner. Codepletion of PCF11 and WDR82 indicated that they act on the same pathway to repress HIV expression. These findings reveal PCF11/WDR82 as a PTT complex silencing HIV-1 expression in latently infected cells.
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Affiliation(s)
- Melissa Ait Said
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Fabienne Bejjani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Ahmed Abdouni
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Emmanuel Ségéral
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Stéphane Emiliani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
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10
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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11
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Polák P, Garland W, Rathore O, Schmid M, Salerno-Kochan A, Jakobsen L, Gockert M, Gerlach P, Silla T, Andersen JS, Conti E, Jensen TH. Dual agonistic and antagonistic roles of ZC3H18 provide for co-activation of distinct nuclear RNA decay pathways. Cell Rep 2023; 42:113325. [PMID: 37889751 PMCID: PMC10720265 DOI: 10.1016/j.celrep.2023.113325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/19/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the nuclear exosome targeting (NEXT) complex and the poly(A) exosome targeting (PAXT) connection. Via its association with the ARS2 and ZC3H18 proteins, NEXT/exosome is recruited to capped and short unadenylated transcripts. Conversely, PAXT/exosome is considered to target longer and adenylated substrates via their poly(A) tails. Here, mutational analysis of the core PAXT component ZFC3H1 uncovers a separate branch of the PAXT pathway, which targets short adenylated RNAs and relies on a direct ARS2-ZFC3H1 interaction. We further demonstrate that similar acidic-rich short linear motifs of ZFC3H1 and ZC3H18 compete for a common ARS2 epitope. Consequently, while promoting NEXT function, ZC3H18 antagonizes PAXT activity. We suggest that this organization of RNA decay complexes provides co-activation of NEXT and PAXT at loci with abundant production of short exosome substrates.
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Affiliation(s)
- Patrik Polák
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Om Rathore
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Piotr Gerlach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Toomas Silla
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark.
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12
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Murphy MR, Ramadei A, Doymaz A, Varriano S, Natelson D, Yu A, Aktas S, Mazzeo M, Mazzeo M, Zakusilo G, Kleiman F. Long non-coding RNA generated from CDKN1A gene by alternative polyadenylation regulates p21 expression during DNA damage response. Nucleic Acids Res 2023; 51:11911-11926. [PMID: 37870464 PMCID: PMC10681730 DOI: 10.1093/nar/gkad899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 09/21/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Alternative Polyadenylation (APA) is an emerging mechanism for dynamic changes in gene expression. Previously, we described widespread APA occurrence in introns during the DNA damage response (DDR). Here, we show that a DDR-activated APA event occurs in the first intron of CDKN1A, inducing an alternate last exon-containing lncRNA. We named this lncRNA SPUD (Selective Polyadenylation Upon DNA Damage). SPUD localizes to polysomes in the cytoplasm and is detectable as multiple isoforms in available high-throughput studies. SPUD has low abundance compared to the CDKN1A full-length isoform under non-stress conditions, and SPUD is induced in cancer and normal cells under a variety of DNA damaging conditions in part through p53. The RNA binding protein HuR binds to and promotes the stability of SPUD precursor RNA. SPUD induction increases p21 protein, but not mRNA levels, affecting p21 functions in cell-cycle, CDK2 expression and cell growth. Like CDKN1A full-length isoform, SPUD can bind two competitive p21 translational regulators, the inhibitor calreticulin and the activator CUGBP1; SPUD alters their association with CDKN1A full-length in a DDR-dependent manner, promoting CDKN1A translation. Together, these results show a new regulatory mechanism by which a lncRNA controls p21 expression post-transcriptionally, highlighting lncRNA relevance in DDR progression and cell-cycle.
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Affiliation(s)
- Michael R Murphy
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Anthony Ramadei
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Ahmet Doymaz
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Sophia Varriano
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Devorah M Natelson
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Amy Yu
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Sera Aktas
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Marie Mazzeo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Michael Mazzeo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - George Zakusilo
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
| | - Frida E Kleiman
- Chemistry Department, Hunter College, The City University of New York, New York, NY 10021, USA
- Biology Program, The Graduate Center, The City University of New York, New York, NY 10016, USA
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13
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Contreras X, Depierre D, Akkawi C, Srbic M, Helsmoortel M, Nogaret M, LeHars M, Salifou K, Heurteau A, Cuvier O, Kiernan R. PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs. Nat Commun 2023; 14:6745. [PMID: 37875486 PMCID: PMC10598014 DOI: 10.1038/s41467-023-42620-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/17/2023] [Indexed: 10/26/2023] Open
Abstract
Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we identify additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma (PAPγ) associates with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM27 and PAPγ shows that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolishes recruitment of PAXT subunits including PAPγ to TSSs and concomitantly increases the abundance of PROMPTs at the same sites. Moreover, PAPγ, as well as MTR4 and ZFC3H1, is implicated in the polyadenylation of PROMPTs. Our results thus provide key insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
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Affiliation(s)
- Xavier Contreras
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - David Depierre
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Charbel Akkawi
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marina Srbic
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Marion Helsmoortel
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Maguelone Nogaret
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Matthieu LeHars
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Kader Salifou
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France
| | - Alexandre Heurteau
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Olivier Cuvier
- Center of Integrative Biology (CBI-CNRS), Molecular, Cellular and Developmental Biology (MCD Unit), University of Toulouse, 31000, Toulouse, France
| | - Rosemary Kiernan
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, Montpellier, France.
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14
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Ntini E, Budach S, Vang Ørom UA, Marsico A. Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs. Cell Syst 2023; 14:906-922.e6. [PMID: 37857083 DOI: 10.1016/j.cels.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in gene expression regulation in cis. Although enriched in the cell chromatin fraction, to what degree this defines their regulatory potential remains unclear. Furthermore, the factors underlying lncRNA chromatin tethering, as well as the molecular basis of efficient lncRNA chromatin dissociation and its impact on enhancer activity and target gene expression, remain to be resolved. Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. By incorporating genomic, transcriptomic, and epigenetic metrics, as well as RNA-binding protein propensities, in machine learning models, we identify features that define transcript groups of different chromatin dissociation dynamics. Notably, lncRNAs transcribed from enhancers display reduced chromatin retention, suggesting that, in addition to splicing, their chromatin dissociation may shape enhancer activity.
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Affiliation(s)
- Evgenia Ntini
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Institute of Molecular Biology and Biotechnology, IMBB-FORTH, 70013 Heraklio, Greece.
| | - Stefan Budach
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany
| | - Ulf A Vang Ørom
- Aarhus University, Department of Molecular Biology and Genetics, 8000 Aarhus, Denmark
| | - Annalisa Marsico
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Computational Health Center, Helmholtz Center Munich, Munich, Germany.
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15
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Mcdonald BR, Picard C, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. bioRxiv 2023:2023.09.25.559415. [PMID: 37808859 PMCID: PMC10557634 DOI: 10.1101/2023.09.25.559415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating ("nascent") transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many "distal" elements in plants initiate tissue-specific stable transcripts and are likely bone fide promoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer "enhancers" or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.
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Affiliation(s)
- Bayley R. Mcdonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Colette Picard
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ian M. Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Marina I. Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | | | - Steven E. Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sascha H. Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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16
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Myburgh MW, Schwerdtfeger KS, Cripwell RA, van Zyl WH, Viljoen-Bloom M. Promoters and introns as key drivers for enhanced gene expression in Saccharomyces cerevisiae. Adv Appl Microbiol 2023; 124:1-29. [PMID: 37597945 DOI: 10.1016/bs.aambs.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
The transcription of genes in the yeast Saccharomyces cerevisiae is governed by multiple layers of regulatory elements and proteins, cooperating to ensure optimum expression of the final protein product based on the cellular requirements. Promoters have always been regarded as the most important determinant of gene transcription, but introns also play a key role in the expression of intron-encoding genes. Some introns can enhance transcription when introduced either promoter-proximal or embedded in the open reading frame of genes. However, the outcome is seldom predictable, with some introns increasing or decreasing transcription depending on the promoter and reporter gene employed. This chapter provides an overview of the general structure and function of promoters and introns and how they may cooperate during transcription to allow intron-mediated enhancement of gene expression. Since S. cerevisiae is a suitable host for recombinant protein production on a commercial level, stronger and more controllable promoters are in high demand. Enhanced gene expression can be achieved via promoter engineering, which may include introns that increase the efficacy of recombinant expression cassettes. Different models for the role of introns in transcription are briefly discussed to show how these intervening sequences can actively interact with the transcription machinery. Furthermore, recent examples of improved protein production via the introduction of promoter-proximal introns are highlighted to showcase the potential value of intron-mediated enhancement of gene expression.
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Affiliation(s)
| | | | - Rosemary Anne Cripwell
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, South Africa
| | - Willem Heber van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, South Africa.
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17
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Abstract
Transcription initiation is an essential process for ensuring proper function of any gene, however, a unified understanding of sequence patterns and rules that determine transcription initiation sites in human genome remains elusive. By explaining transcription initiation at basepair resolution from sequence with a deep learning-inspired explainable modeling approach, here we show that simple rules can explain the vast majority of human promoters. We identified key sequence patterns that contribute to human promoter function, each activating transcription with a distinct position-specific effect curve that likely reflects its mechanism of promoting transcription initiation. Most of these position-specific effects have not been previously characterized, and we verified them using experimental perturbations of transcription factors and sequences. We revealed the sequence basis of bidirectional transcription at promoters and links between promoter selectivity and gene expression variation across cell types. Additionally, by analyzing 241 mammalian genomes and mouse transcription initiation site data, we showed that the sequence determinants are conserved across mammalian species. Taken together, we provide a unified model of the sequence basis of transcription initiation at the basepair level that is broadly applicable across mammalian species, and shed new light on basic questions related to promoter sequence and function.
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Affiliation(s)
- Kseniia Dudnyk
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center; Dallas, Texas, United States of America
| | - Chenlai Shi
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center; Dallas, Texas, United States of America
| | - Jian Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center; Dallas, Texas, United States of America
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18
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Tokunaga M, Imamura T. Emerging concepts involving inhibitory and activating RNA functionalization towards the understanding of microcephaly phenotypes and brain diseases in humans. Front Cell Dev Biol 2023; 11:1168072. [PMID: 37408531 PMCID: PMC10318543 DOI: 10.3389/fcell.2023.1168072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
Microcephaly is characterized as a small head circumference, and is often accompanied by developmental disorders. Several candidate risk genes for this disease have been described, and mutations in non-coding regions are occasionally found in patients with microcephaly. Various non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), SINEUPs, telomerase RNA component (TERC), and promoter-associated lncRNAs (pancRNAs) are now being characterized. These ncRNAs regulate gene expression, enzyme activity, telomere length, and chromatin structure through RNA binding proteins (RBPs)-RNA interaction. Elucidating the potential roles of ncRNA-protein coordination in microcephaly pathogenesis might contribute to its prevention or recovery. Here, we introduce several syndromes whose clinical features include microcephaly. In particular, we focus on syndromes for which ncRNAs or genes that interact with ncRNAs may play roles. We discuss the possibility that the huge ncRNA field will provide possible new therapeutic approaches for microcephaly and also reveal clues about the factors enabling the evolutionary acquisition of the human-specific "large brain."
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19
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Estell C, Davidson L, Eaton JD, Kimura H, Gold VAM, West S. A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription. Mol Cell 2023:S1097-2765(23)00385-4. [PMID: 37329883 DOI: 10.1016/j.molcel.2023.05.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The transcriptional termination of unstable non-coding RNAs (ncRNAs) is poorly understood compared to coding transcripts. We recently identified ZC3H4-WDR82 ("restrictor") as restricting human ncRNA transcription, but how it does this is unknown. Here, we show that ZC3H4 additionally associates with ARS2 and the nuclear exosome targeting complex. The domains of ZC3H4 that contact ARS2 and WDR82 are required for ncRNA restriction, suggesting their presence in a functional complex. Consistently, ZC3H4, WDR82, and ARS2 co-transcriptionally control an overlapping population of ncRNAs. ZC3H4 is proximal to the negative elongation factor, PNUTS, which we show enables restrictor function and is required to terminate the transcription of all major RNA polymerase II transcript classes. In contrast to short ncRNAs, longer protein-coding transcription is supported by U1 snRNA, which shields transcripts from restrictor and PNUTS at hundreds of genes. These data provide important insights into the mechanism and control of transcription by restrictor and PNUTS.
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Affiliation(s)
- Chris Estell
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Lee Davidson
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Joshua D Eaton
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Hiroshi Kimura
- Cell Biology Centre, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Steven West
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom.
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20
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Mimoso CA, Adelman K. U1 snRNP increases RNA Pol II elongation rate to enable synthesis of long genes. Mol Cell 2023; 83:1264-1279.e10. [PMID: 36965480 PMCID: PMC10135401 DOI: 10.1016/j.molcel.2023.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/06/2023] [Accepted: 02/28/2023] [Indexed: 03/27/2023]
Abstract
The expansion of introns within mammalian genomes poses a challenge for the production of full-length messenger RNAs (mRNAs), with increasing evidence that these long AT-rich sequences present obstacles to transcription. Here, we investigate RNA polymerase II (RNAPII) elongation at high resolution in mammalian cells and demonstrate that RNAPII transcribes faster across introns. Moreover, we find that this acceleration requires the association of U1 snRNP (U1) with the elongation complex at 5' splice sites. The role of U1 to stimulate elongation rate through introns reduces the frequency of both premature termination and transcriptional arrest, thereby dramatically increasing RNA production. We further show that changes in RNAPII elongation rate due to AT content and U1 binding explain previous reports of pausing or termination at splice junctions and the edge of CpG islands. We propose that U1-mediated acceleration of elongation has evolved to mitigate the risks that long AT-rich introns pose to transcript completion.
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Affiliation(s)
- 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; Ludwig Center at Harvard, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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21
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Gorbea Colón JJ, Palao L, Chen SF, Kim HJ, Snyder L, Chang YW, Tsai KL, Murakami K. Structural basis of a transcription pre-initiation complex on a divergent promoter. Mol Cell 2023; 83:574-588.e11. [PMID: 36731470 PMCID: PMC10162435 DOI: 10.1016/j.molcel.2023.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/28/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
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Affiliation(s)
- Jose J Gorbea Colón
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Center for Genome Integrity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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22
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Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. A CpG island-encoded mechanism protects genes from premature transcription termination. Nat Commun 2023; 14:726. [PMID: 36759609 PMCID: PMC9911701 DOI: 10.1038/s41467-023-36236-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
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Affiliation(s)
- Amy L Hughes
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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23
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Arunima A, van Schaik EJ, Samuel JE. The emerging roles of long non-coding RNA in host immune response and intracellular bacterial infections. Front Cell Infect Microbiol 2023; 13:1160198. [PMID: 37153158 PMCID: PMC10160451 DOI: 10.3389/fcimb.2023.1160198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/07/2023] [Indexed: 05/09/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) are evolutionarily conserved classes of non-coding regulatory transcripts of > 200 nucleotides in length. They modulate several transcriptional and post-transcriptional events in the organism. Depending on their cellular localization and interactions, they regulate chromatin function and assembly; and alter the stability and translation of cytoplasmic mRNAs. Although their proposed range of functionality remains controversial, there is increasing research evidence that lncRNAs play a regulatory role in the activation, differentiation and development of immune signaling cascades; microbiome development; and in diseases such as neuronal and cardiovascular disorders; cancer; and pathogenic infections. This review discusses the functional roles of different lncRNAs in regulation of host immune responses, signaling pathways during host-microbe interaction and infection caused by obligate intracellular bacterial pathogens. The study of lncRNAs is assuming significance as it could be exploited for development of alternative therapeutic strategies for the treatment of severe and chronic pathogenic infections caused by Mycobacterium, Chlamydia and Rickettsia infections, as well as commensal colonization. Finally, this review summarizes the translational potential of lncRNA research in development of diagnostic and prognostic tools for human diseases.
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24
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An NA, Zhang J, Mo F, Luan X, Tian L, Shen QS, Li X, Li C, Zhou F, Zhang B, Ji M, Qi J, Zhou WZ, Ding W, Chen JY, Yu J, Zhang L, Shu S, Hu B, Li CY. De novo genes with an lncRNA origin encode unique human brain developmental functionality. Nat Ecol Evol 2023; 7:264-278. [PMID: 36593289 PMCID: PMC9911349 DOI: 10.1038/s41559-022-01925-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 10/04/2022] [Indexed: 01/03/2023]
Abstract
Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA-mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.
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Affiliation(s)
- Ni A. An
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Zhang
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Fan Mo
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xuke Luan
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Lu Tian
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiangshang Li
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chunqiong Li
- grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, China
| | - Fanqi Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Boya Zhang
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Mingjun Ji
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jianhuan Qi
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Zhen Zhou
- grid.415105.40000 0004 9430 5605State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wanqiu Ding
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia-Yu Chen
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jia Yu
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Li Zhang
- grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, China
| | - Shaokun Shu
- grid.11135.370000 0001 2256 9319Peking University International Cancer Institute, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China. .,Chinese Institute for Brain Research, Beijing, China.
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25
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Fujiwara N, Shigemoto M, Hirayama M, Fujita KI, Seno S, Matsuda H, Nagahama M, Masuda S. MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus. Nucleic Acids Res 2022; 50:8779-8806. [PMID: 35902094 PMCID: PMC9410898 DOI: 10.1093/nar/gkac559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/10/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Recent in vitro reconstitution analyses have proven that the physical interaction between the exosome core and MTR4 helicase, which promotes the exosome activity, is maintained by either MPP6 or RRP6. However, knowledge regarding the function of MPP6 with respect to in vivo exosome activity remains scarce. Here, we demonstrate a facilitative function of MPP6 that composes a specific part of MTR4-dependent substrate decay by the human exosome. Using RNA polymerase II-transcribed poly(A)+ substrate accumulation as an indicator of a perturbed exosome, we found functional redundancy between RRP6 and MPP6 in the decay of these poly(A)+ transcripts. MTR4 binding to the exosome core via MPP6 was essential for MPP6 to exert its redundancy with RRP6. However, at least for the decay of our identified exosome substrates, MTR4 recruitment by MPP6 was not functionally equivalent to recruitment by RRP6. Genome-wide classification of substrates based on their sensitivity to each exosome component revealed that MPP6 deals with a specific range of substrates and highlights the importance of MTR4 for their decay. Considering recent findings of competitive binding to the exosome between auxiliary complexes, our results suggest that the MPP6-incorporated MTR4-exosome complex is one of the multiple alternative complexes rather than the prevailing one.
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Affiliation(s)
- Naoko Fujiwara
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Maki Shigemoto
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Mizuki Hirayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Ken-Ichi Fujita
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan.,Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Seiji Masuda
- Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto 606-8502, Japan.,Department of Food Science and Nutrition, Faculty of Agriculture Kindai University, Nara, Nara 631-8505, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Nara 631-8505, Japan.,Antiaging center, Kindai University, Higashiosaka, Osaka 577-8502, Japan
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26
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Wu M, Schmid M, Jensen T, Sandelin A. Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting. NAR Genom Bioinform 2022; 4:lqac071. [PMID: 36128426 PMCID: PMC9477074 DOI: 10.1093/nargab/lqac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 11/15/2022] Open
Abstract
The RNA exosome degrades transcripts in the nucleoplasm of mammalian cells. Its substrate specificity is mediated by two adaptors: the ‘nuclear exosome targeting (NEXT)’ complex and the ‘poly(A) exosome targeting (PAXT)’ connection. Previous studies have revealed some DNA/RNA elements that differ between the two pathways, but how informative these features are for distinguishing pathway targeting, or whether additional genomic features that are informative for such classifications exist, is unknown. Here, we leverage the wealth of available genomic data and develop machine learning models that predict exosome targets and subsequently rank the features the models use by their predictive power. As expected, features around transcript end sites were most predictive; specifically, the lack of canonical 3′ end processing was highly predictive of NEXT targets. Other associated features, such as promoter-proximal G/C content and 5′ splice sites, were informative, but only for distinguishing NEXT and not PAXT targets. Finally, we discovered predictive features not previously associated with exosome targeting, in particular RNA helicase DDX3X binding sites. Overall, our results demonstrate that nucleoplasmic exosome targeting is to a large degree predictable, and our approach can assess the predictive power of previously known and new features in an unbiased way.
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Affiliation(s)
- Mengjun Wu
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen , Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , 171 65 Solna , Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University , Universitetsbyen 81, Aarhus , DK-8000, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University , Universitetsbyen 81, Aarhus , DK-8000, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen , Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
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27
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Abstract
Transcriptome-wide interrogation of eukaryotic genomes has unveiled the pervasive nature of RNA polymerase II transcription. Virtually, any DNA region with an accessible chromatin structure can be transcribed, resulting in a mass production of noncoding RNAs (ncRNAs) with the potential of interfering with gene expression programs. Budding yeast has proved to be a powerful model organism to understand the mechanisms at play to control pervasive transcription and overcome the risks of hazardous disruption of cellular functions. In this review, we focus on the actors and strategies yeasts employ to govern ncRNA production, and we discuss recent findings highlighting the dangers of losing control over pervasive transcription.
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Affiliation(s)
- Tommaso Villa
- Institut Jacques Monod CNRS, Université de Paris Cité France
| | - Odil Porrua
- Institut Jacques Monod CNRS, Université de Paris Cité France
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28
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Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles. RNA 2022; 28:878-894. [PMID: 35351812 PMCID: PMC9074902 DOI: 10.1261/rna.079104.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/12/2022] [Indexed: 05/22/2023]
Abstract
Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.
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Affiliation(s)
- Eliza S Lee
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Harrison W Smith
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Eric J Wolf
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Aysegul Guvenek
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Yifan E Wang
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Bin Tian
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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29
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Vlaming H, Mimoso CA, Field AR, Martin BJE, Adelman K. Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential. Nat Struct Mol Biol 2022; 29:613-20. [PMID: 35681023 DOI: 10.1038/s41594-022-00785-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 04/28/2022] [Indexed: 01/07/2023]
Abstract
Precise regulation of transcription by RNA polymerase II (RNAPII) is critical for organismal growth and development. However, what determines whether an engaged RNAPII will synthesize a full-length transcript or terminate prematurely is poorly understood. Notably, RNAPII is far more susceptible to termination when transcribing non-coding RNAs than when synthesizing protein-coding mRNAs, but the mechanisms underlying this are unclear. To investigate the impact of transcribed sequence on elongation potential, we developed a method to screen the effects of thousands of INtegrated Sequences on Expression of RNA and Translation using high-throughput sequencing (INSERT-seq). We found that higher AT content in non-coding RNAs, rather than specific sequence motifs, drives RNAPII termination. Further, we demonstrate that 5' splice sites autonomously stimulate processive transcription, even in the absence of polyadenylation signals. Our results reveal a potent role for the transcribed sequence in dictating gene output and demonstrate the power of INSERT-seq toward illuminating these contributions.
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30
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Wan L, Li W, Meng Y, Hou Y, Chen M, Xu B. Inflammatory Immune-Associated eRNA: Mechanisms, Functions and Therapeutic Prospects. Front Immunol 2022; 13:849451. [PMID: 35514959 PMCID: PMC9063412 DOI: 10.3389/fimmu.2022.849451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of multiple high-throughput sequencing technologies has made it possible to explore the critical roles and mechanisms of functional enhancers and enhancer RNAs (eRNAs). The inflammatory immune response, as a fundamental pathological process in infectious diseases, cancers and immune disorders, coordinates the balance between the internal and external environment of the organism. It has been shown that both active enhancers and intranuclear eRNAs are preferentially expressed over inflammation-related genes in response to inflammatory stimuli, suggesting that enhancer transcription events and their products influence the expression and function of inflammatory genes. Therefore, in this review, we summarize and discuss the relevant inflammatory roles and regulatory mechanisms of eRNAs in inflammatory immune cells, non-inflammatory immune cells, inflammatory immune diseases and tumors, and explore the potential therapeutic effects of enhancer inhibitors affecting eRNA production for diseases with inflammatory immune responses.
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Affiliation(s)
- Lilin Wan
- Medical School, Southeast University, Nanjing, China
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Wenchao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Yuan Meng
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics and Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
- Department of Urology, Nanjing Lishui District People’s Hospital, Zhongda Hospital, Southeast University, Nanjing, China
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31
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Abstract
Omics-based technologies, which have developed rapidly over the last few decades, have generated increasing evidence demonstrating pervasive divergent transcription from RNA polymerase II (Pol II) promoters of eukaryotic genome, and indeed have raised considerable discussion as to their potential physiopathological function. Unlike many other long non-coding RNAs (lncRNAs), promoter antisense RNAs (PAS RNAs) were initially considered to be merely passive transcription by-products of active promoters. However, recent studies have begun to reveal their critical importance in a broad spectrum of biological processes. In this Review, I summarize recent technological advances that enable accurate detection of PAS RNA and discuss the mechanisms of PAS RNA biogenesis emphasizing the functional importance of its structure enabling the diverse functions of PAS RNA in transcription and chromatin regulation.
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Affiliation(s)
- Fan Yang
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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32
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Rouvière JO, Lykke-Andersen S, Jensen TH. Control of non-productive RNA polymerase II transcription via its early termination in metazoans. Biochem Soc Trans 2022:BST20201140. [PMID: 35166324 DOI: 10.1042/BST20201140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Transcription establishes the universal first step of gene expression where RNA is produced by a DNA-dependent RNA polymerase. The most versatile of eukaryotic RNA polymerases, RNA polymerase II (Pol II), transcribes a broad range of DNA including protein-coding and a variety of non-coding transcription units. Although Pol II can be configured as a durable enzyme capable of transcribing hundreds of kilobases, there is reliable evidence of widespread abortive Pol II transcription termination shortly after initiation, which is often followed by rapid degradation of the associated RNA. The molecular details underlying this phenomenon are still vague but likely reflect the action of quality control mechanisms on the early Pol II complex. Here, we summarize current knowledge of how and when such promoter-proximal quality control is asserted on metazoan Pol II.
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33
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Nojima T, Proudfoot NJ. Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 2022; 23:389-406. [DOI: 10.1038/s41580-021-00447-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
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34
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Tan JY, Marques AC. The activity of human enhancers is modulated by the splicing of their associated lncRNAs. PLoS Comput Biol 2022; 18:e1009722. [PMID: 35015755 PMCID: PMC8803168 DOI: 10.1371/journal.pcbi.1009722] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/31/2022] [Accepted: 12/05/2021] [Indexed: 11/19/2022] Open
Abstract
Pervasive enhancer transcription is at the origin of more than half of all long noncoding RNAs in humans. Transcription of enhancer-associated long noncoding RNAs (elncRNA) contribute to their cognate enhancer activity and gene expression regulation in cis. Recently, splicing of elncRNAs was shown to be associated with elevated enhancer activity. However, whether splicing of elncRNA transcripts is a mere consequence of accessibility at highly active enhancers or if elncRNA splicing directly impacts enhancer function, remains unanswered. We analysed genetically driven changes in elncRNA splicing, in humans, to address this outstanding question. We showed that splicing related motifs within multi-exonic elncRNAs evolved under selective constraints during human evolution, suggesting the processing of these transcripts is unlikely to have resulted from transcription across spurious splice sites. Using a genome-wide and unbiased approach, we used nucleotide variants as independent genetic factors to directly assess the causal relationship that underpin elncRNA splicing and their cognate enhancer activity. We found that the splicing of most elncRNAs is associated with changes in chromatin signatures at cognate enhancers and target mRNA expression. We provide evidence that efficient and conserved processing of enhancer-associated elncRNAs contributes to enhancer activity. Most, if not all, active enhancers are transcribed, giving rise to a plethora of transcripts, including enhancer-associated long noncoding RNAs (elncRNAs). Changes in elncRNA levels impacts cognate enhancer activity. Recently splicing of elncRNA has also been found to associate with enhancer activity. Whether this associations reflects a contribution of elncRNA splicing to increased enhancer activity or else is simply the consequence of increased chromatin accessibility that promotes transcriptional elongation and allows for spurious splicing events remains unknown. We show that natural selection has acted, at the species and population level, to preserve DNA elements required for frequent and efficient elncRNA splicing Importantly, using a genome-wide and unbiased statistical population genomics approach, we demonstrate that elncRNA splicing is associated with cognate enhancer function, contributing to chromatin status and enhancer activity. Our results provides strong evidence that efficient elncRNA splicing contributes to enhancer activity genome-wide.
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Affiliation(s)
- Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- * E-mail: (JYT); (ACM)
| | - Ana Claudia Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- * E-mail: (JYT); (ACM)
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35
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Ogami K, Suzuki HI. Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function. Int J Mol Sci 2021; 22:13401. [PMID: 34948199 PMCID: PMC8707817 DOI: 10.3390/ijms222413401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.
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Affiliation(s)
- Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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36
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Gowthaman U, Ivanov M, Schwarz I, Patel HP, Müller NA, García‐Pichardo D, Lenstra TL, Marquardt S. The Hda1 histone deacetylase limits divergent non-coding transcription and restricts transcription initiation frequency. EMBO J 2021; 40:e108903. [PMID: 34661296 PMCID: PMC8634119 DOI: 10.15252/embj.2021108903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 09/28/2021] [Indexed: 01/01/2023] Open
Abstract
Nucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA and a divergent non-coding (DNC) transcript of unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. Using high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements, we identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC transcription. Nascent transcription profiling showed a genome-wide role of Hda1C in repression of DNC transcription. Live-cell imaging of transcription revealed that mutations in the Hda3 subunit increased the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC transcription regions, supporting DNC transcription repression by histone deacetylation. Our data support the interpretation that DNC transcription results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.
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Affiliation(s)
- Uthra Gowthaman
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Maxim Ivanov
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Isabel Schwarz
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Heta P Patel
- Division of Gene RegulationThe Netherlands Cancer Institute (NKI)Oncode InstituteAmsterdamThe Netherlands
| | - Niels A Müller
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Present address:
Thünen Institute of Forest GeneticsGrosshansdorfGermany
| | - Desiré García‐Pichardo
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Tineke L Lenstra
- Division of Gene RegulationThe Netherlands Cancer Institute (NKI)Oncode InstituteAmsterdamThe Netherlands
| | - Sebastian Marquardt
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
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37
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Abstract
The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies demonstrating binding of TFIIB to both the 5’ and 3’ ends of genes in a diverse set of eukaryotes strongly suggested a rather unexpected role of the factor in termination. TFIIB indeed plays a role in termination of transcription. TFIIB occupancy of the 3’ end is possibly due to its interaction with the termination factors residing there. Interaction of the promoter-bound TFIIB with factors occupying the 3’ end of a gene may be the basis of transcription-dependent gene looping. The proximity of the terminator-bound factors with the promoter in a gene loop has the potential to terminate promoter-initiated upstream anti-sense transcription thereby conferring promoter directionality. TFIIB, therefore, is emerging as a factor with pleiotropic roles in the transcription cycle. This could be the reason for preferential targeting of TFIIB by viruses. Further studies are needed to understand the critical role of TFIIB in viral pathogenesis in the context of its newly identified roles in termination, gene looping and promoter directionality.
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38
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Syed KM, Hon CC. Heterogeneity among enhancer RNAs: origins, consequences and perspectives. Essays Biochem 2021; 65:709-21. [PMID: 34414426 DOI: 10.1042/EBC20200064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs transcribed from distal cis-regulatory elements (i.e. enhancers), which are stereotyped as short, rarely spliced and unstable. In fact, a non-negligible fraction of eRNAs seems to be longer, spliced and more stable, and their cognate enhancers are epigenomically and functionally distinguishable from typical enhancers. In this review, we first summarized the genomic and molecular origins underlying the observed heterogeneity among eRNAs. Then, we discussed how their heterogeneous properties (e.g. stability) affect the modes of interaction with their regulatory partners, from promiscuous cis-interactions to specific trans-interactions. Finally, we highlighted the existence of a seemingly continuous spectrum of eRNA properties and its implications in the genomic origins of non-coding RNA genes from an evolutionary perspective.
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An B, Kameda T, Imamura T. The evolutionary acquisition and mode of functions of promoter-associated non-coding RNAs (pancRNAs) for mammalian development. Essays Biochem 2021:EBC20200143. [PMID: 34328174 DOI: 10.1042/EBC20200143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence has shown that many long non-coding RNAs (lncRNAs) are involved in gene regulation in a variety of ways such as transcriptional, post-transcriptional and epigenetic regulation. Promoter-associated non-coding RNAs (pancRNAs), which are categorized into the most abundant single-copy lncRNA biotype, play vital regulatory roles in finely tuning cellular specification at the epigenomic level. In short, pancRNAs can directly or indirectly regulate downstream genes to participate in the development of organisms in a cell-specific manner. In this review, we will introduce the evolutionarily acquired characteristics of pancRNAs as determined by comparative epigenomics and elaborate on the research progress on pancRNA-involving processes in mammalian embryonic development, including neural differentiation.
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40
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Leader Y, Lev Maor G, Sorek M, Shayevitch R, Hussein M, Hameiri O, Tammer L, Zonszain J, Keydar I, Hollander D, Meshorer E, Ast G. The upstream 5' splice site remains associated to the transcription machinery during intron synthesis. Nat Commun 2021; 12:4545. [PMID: 34315864 DOI: 10.1038/s41467-021-24774-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/02/2021] [Indexed: 12/28/2022] Open
Abstract
In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF along with other proteins. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns in human cells, we discovered that the nascent 5′ splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. This association functionally corresponds with splicing outcome, involves bona fide 5′ splice sites and cryptic intronic sites, and occurs transcriptome-wide. Overall, our findings reveal that the upstream 5′ splice sites remain attached to the transcriptional machinery during intron synthesis and are thus brought into proximity of the 3′ splice sites; potentially mediating the rapid splicing of long introns. We know that most splicing reactions take place co-transcriptionally, but how the transcription machinery facilitate splicing of introns is unknown. Here the authors show that the 5′ splice site remains associated with the transcription machinery during intron synthesis through U1 snRNP, providing a basis for the rapid splicing reaction of introns.
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41
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Campagne S, de Vries T, Malard F, Afanasyev P, Dorn G, Dedic E, Kohlbrecher J, Boehringer D, Cléry A, Allain FHT. An in vitro reconstituted U1 snRNP allows the study of the disordered regions of the particle and the interactions with proteins and ligands. Nucleic Acids Res 2021; 49:e63. [PMID: 33677607 PMCID: PMC8216277 DOI: 10.1093/nar/gkab135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022] Open
Abstract
U1 small nuclear ribonucleoparticle (U1 snRNP) plays a central role during RNA processing. Previous structures of U1 snRNP revealed how the ribonucleoparticle is organized and recognizes the pre-mRNA substrate at the exon–intron junction. As with many other ribonucleoparticles involved in RNA metabolism, U1 snRNP contains extensions made of low complexity sequences. Here, we developed a protocol to reconstitute U1 snRNP in vitro using mostly full-length components in order to perform liquid-state NMR spectroscopy. The accuracy of the reconstitution was validated by probing the shape and structure of the particle by SANS and cryo-EM. Using an NMR spectroscopy-based approach, we probed, for the first time, the U1 snRNP tails at atomic detail and our results confirm their high degree of flexibility. We also monitored the labile interaction between the splicing factor PTBP1 and U1 snRNP and validated the U1 snRNA stem loop 4 as a binding site for the splicing regulator on the ribonucleoparticle. Altogether, we developed a method to probe the intrinsically disordered regions of U1 snRNP and map the interactions controlling splicing regulation. This approach could be used to get insights into the molecular mechanisms of alternative splicing and screen for potential RNA therapeutics.
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Affiliation(s)
- Sébastien Campagne
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Tebbe de Vries
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Florian Malard
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Emil Dedic
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | | | - Daniel Boehringer
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Antoine Cléry
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Biochemistry, Department of Biology, ETH Zurich, Hönggerbergring 64, CH-8093 Zürich, Switzerland
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42
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Zeng X, Park SJ, Nakai K. Characterizing Promoter and Enhancer Sequences by a Deep Learning Method. Front Genet 2021; 12:681259. [PMID: 34211503 PMCID: PMC8239401 DOI: 10.3389/fgene.2021.681259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
Promoters and enhancers are well-known regulatory elements modulating gene expression. As confirmed by high-throughput sequencing technologies, these regulatory elements are bidirectionally transcribed. That is, promoters produce stable mRNA in the sense direction and unstable RNA in the antisense direction, while enhancers transcribe unstable RNA in both directions. Although it is thought that enhancers and promoters share a similar architecture of transcription start sites (TSSs), how the transcriptional machinery distinctly uses these genomic regions as promoters or enhancers remains unclear. To address this issue, we developed a deep learning (DL) method by utilizing a convolutional neural network (CNN) and the saliency algorithm. In comparison with other classifiers, our CNN presented higher predictive performance, suggesting the overarching importance of the high-order sequence features, captured by the CNN. Moreover, our method revealed that there are substantial sequence differences between the enhancers and promoters. Remarkably, the 20–120 bp downstream regions from the center of bidirectional TSSs seemed to contribute to the RNA stability. These regions in promoters tend to have a larger number of guanines and cytosines compared to those in enhancers, and this feature contributed to the classification of the regulatory elements. Our CNN-based method can capture the complex TSS architectures. We found that the genomic regions around TSSs for promoters and enhancers contribute to RNA stability and show GC-biased characteristics as a critical determinant for promoter TSSs.
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Affiliation(s)
- Xin Zeng
- Department of Computational Biology and Medical Science, The University of Tokyo, Kashiwa, Japan
| | - Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Science, The University of Tokyo, Kashiwa, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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43
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Lubelsky Y, Zuckerman B, Ulitsky I. High-resolution mapping of function and protein binding in an RNA nuclear enrichment sequence. EMBO J 2021; 40:e106357. [PMID: 33938020 PMCID: PMC8204871 DOI: 10.15252/embj.2020106357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 03/14/2021] [Accepted: 03/24/2021] [Indexed: 01/04/2023] Open
Abstract
The functions of long RNAs, including mRNAs and long noncoding RNAs (lncRNAs), critically depend on their subcellular localization. The identity of the sequences that dictate subcellular localization and their high-resolution anatomy remain largely unknown. We used a suite of massively parallel RNA assays and libraries containing thousands of sequence variants to pinpoint the functional features within the SIRLOIN element, which dictates nuclear enrichment through hnRNPK recruitment. In addition, we profiled the endogenous SIRLOIN RNA-nucleoprotein complex and identified the nuclear RNA-binding proteins SLTM and SNRNP70 as novel SIRLOIN binders. Taken together, using massively parallel assays, we identified the features that dictate binding of hnRNPK, SLTM, and SNRNP70 to SIRLOIN and found that these factors are jointly required for SIRLOIN activity. Our study thus provides a roadmap for high-throughput dissection of functional sequence elements in long RNAs.
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Affiliation(s)
- Yoav Lubelsky
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Binyamin Zuckerman
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Igor Ulitsky
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
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44
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Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC, Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH; FANTOM consortium. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 2021; 12:3297. [PMID: 34078885 DOI: 10.1038/s41467-021-23143-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
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45
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Shkurin A, Hughes TR. Known sequence features can explain half of all human gene ends. NAR Genom Bioinform 2021; 3:lqab042. [PMID: 34104882 PMCID: PMC8176999 DOI: 10.1093/nargab/lqab042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/14/2021] [Accepted: 05/10/2021] [Indexed: 11/15/2022] Open
Abstract
Cleavage and polyadenylation (CPA) sites define eukaryotic gene ends. CPA sites are associated with five key sequence recognition elements: the upstream UGUA, the polyadenylation signal (PAS), and U-rich sequences; the CA/UA dinucleotide where cleavage occurs; and GU-rich downstream elements (DSEs). Currently, it is not clear whether these sequences are sufficient to delineate CPA sites. Additionally, numerous other sequences and factors have been described, often in the context of promoting alternative CPA sites and preventing cryptic CPA site usage. Here, we dissect the contributions of individual sequence features to CPA using standard discriminative models. We show that models comprised only of the five primary CPA sequence features give highest probability scores to constitutive CPA sites at the ends of coding genes, relative to the entire pre-mRNA sequence, for 41% of all human genes. U1-hybridizing sequences provide a small boost in performance. The addition of all known RBP RNA binding motifs to the model, however, increases this figure to 49%, and suggests an involvement of both known and suspected CPA regulators as well as potential new factors in delineating constitutive CPA sites. To our knowledge, this high effectiveness of established features to predict human gene ends has not previously been documented.
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Affiliation(s)
- Aleksei Shkurin
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, Toronto, ON M5S 3E1, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, Toronto, ON M5S 3E1, Canada
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46
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Cai Z, So BR, Dreyfuss G. Comprehensive RNP profiling in cells identifies U1 snRNP complexes with cleavage and polyadenylation factors active in telescripting. Methods Enzymol 2021; 655:325-347. [PMID: 34183128 DOI: 10.1016/bs.mie.2021.04.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Full-length transcription in the majority of protein-coding and other genes transcribed by RNA polymerase II in complex eukaryotes requires U1 snRNP (U1) to co-transcriptionally suppress transcription-terminating premature 3'-end cleavage and polyadenylation (PCPA) from cryptic polyadenylation signals (PASs). This U1 activity, termed telescripting, requires U1 to base-pair with the nascent RNA and inhibit usage of a downstream PAS. Here we describe experimental methods to determine the mechanism of U1 telescripting, involving mapping of U1 and CPA factors (CPAFs) binding locations in relation to PCPA sites, and identify U1 and CPAFs interactomes. The methods which utilizes rapid reversible protein-RNA and protein-protein chemical crosslinking, immunoprecipitations (XLIPs) of components of interest, and RNA-seq and quantitative proteomic mass spectrometry, captured U1-CPAFs complexes in cells, providing important insights into telescripting mechanism. XLIP profiling can be used for comprehensive molecular definition of diverse RNPs.
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Affiliation(s)
- Zhiqiang Cai
- Department of Biochemistry and Biophysics, School of Medicine, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Byung Ran So
- Department of Biochemistry and Biophysics, School of Medicine, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Gideon Dreyfuss
- Department of Biochemistry and Biophysics, School of Medicine, Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, United States.
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47
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Shen H, Yang M, Li S, Zhang J, Peng B, Wang C, Chang Z, Ong J, Du P. Mouse totipotent stem cells captured and maintained through spliceosomal repression. Cell 2021; 184:2843-2859.e20. [PMID: 33991488 DOI: 10.1016/j.cell.2021.04.020] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 02/15/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022]
Abstract
Since establishment of the first embryonic stem cells (ESCs), in vitro culture of totipotent cells functionally and molecularly comparable with in vivo blastomeres with embryonic and extraembryonic developmental potential has been a challenge. Here we report that spliceosomal repression in mouse ESCs drives a pluripotent-to-totipotent state transition. Using the splicing inhibitor pladienolide B, we achieve stable in vitro culture of totipotent ESCs comparable at molecular levels with 2- and 4-cell blastomeres, which we call totipotent blastomere-like cells (TBLCs). Mouse chimeric assays combined with single-cell RNA sequencing (scRNA-seq) demonstrate that TBLCs have a robust bidirectional developmental capability to generate multiple embryonic and extraembryonic cell lineages. Mechanically, spliceosomal repression causes widespread splicing inhibition of pluripotent genes, whereas totipotent genes, which contain few short introns, are efficiently spliced and transcriptionally activated. Our study provides a means for capturing and maintaining totipotent stem cells.
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Affiliation(s)
- Hui Shen
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Min Yang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shiyu Li
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jing Zhang
- School of Life Sciences, Tsinghua University, Beijing 100871, China
| | - Bing Peng
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chunhui Wang
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zai Chang
- School of Life Sciences, Tsinghua University, Beijing 100871, China
| | - Jennie Ong
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
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48
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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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49
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Roberts BS, Partridge EC, Moyers BA, Agarwal V, Newberry KM, Martin BK, Shendure J, Myers RM, Cooper GM. Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands. Genome Res 2021; 31:866-876. [PMID: 33879525 PMCID: PMC8092006 DOI: 10.1101/gr.270751.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/18/2021] [Indexed: 11/24/2022]
Abstract
Massively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human genomes. An aspect of MPRAs that is not typically the focus of analysis is their intrinsic ability to differentiate activity levels for a given sequence element when placed in both of its possible orientations relative to the reporter construct. Here, we describe pervasive strand asymmetry of MPRA signals in data sets from multiple reporter configurations in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that function related to endogenous transcription is driving the phenomenon. Similarly, we find that within Alu mobile element insertions, strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes and is more pronounced in less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and show its prediction from sequence alone. We see some evidence for RNA stabilization and transcriptional activation mechanisms and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry is a pervasive and reproducible feature in MPRA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
| | | | - Bryan A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Vikram Agarwal
- Calico Life Sciences LLC, South San Francisco, California 94080, USA
| | | | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, Seattle, Washington 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
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50
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Austenaa LMI, Piccolo V, Russo M, Prosperini E, Polletti S, Polizzese D, Ghisletti S, Barozzi I, Diaferia GR, Natoli G. A first exon termination checkpoint preferentially suppresses extragenic transcription. Nat Struct Mol Biol 2021; 28:337-46. [PMID: 33767452 DOI: 10.1038/s41594-021-00572-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023]
Abstract
Interactions between the splicing machinery and RNA polymerase II increase protein-coding gene transcription. Similarly, exons and splicing signals of enhancer-generated long noncoding RNAs (elncRNAs) augment enhancer activity. However, elncRNAs are inefficiently spliced, suggesting that, compared with protein-coding genes, they contain qualitatively different exons with a limited ability to drive splicing. We show here that the inefficiently spliced first exons of elncRNAs as well as promoter-antisense long noncoding RNAs (pa-lncRNAs) in human and mouse cells trigger a transcription termination checkpoint that requires WDR82, an RNA polymerase II-binding protein, and its RNA-binding partner of previously unknown function, ZC3H4. We propose that the first exons of elncRNAs and pa-lncRNAs are an intrinsic component of a regulatory mechanism that, on the one hand, maximizes the activity of these cis-regulatory elements by recruiting the splicing machinery and, on the other, contains elements that suppress pervasive extragenic transcription.
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