1
|
Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A. Post-transcriptional splicing can occur in a slow-moving zone around the gene. eLife 2024; 12:RP91357. [PMID: 38577979 PMCID: PMC10997330 DOI: 10.7554/elife.91357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single-molecule RNA FISH, expansion microscopy, and live-cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription-site-proximal zone through which RNA move more slowly than in the nucleoplasm. Full-length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.
Collapse
Affiliation(s)
- Allison Coté
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Aoife O'Farrell
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Ian Dardani
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Margaret Dunagin
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Chris Coté
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Yihan Wan
- School of Life Sciences, Westlake UniversityHangzhouChina
| | - Sareh Bayatpour
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Heather L Drexler
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Katherine A Alexander
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Fei Chen
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Asmamaw T Wassie
- Department of Cell and Molecular Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Rohan Patel
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Kenneth Pham
- Department of Cell and Molecular Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Edward S Boyden
- Departments of Biological Engineering and Brain and Cognitive Sciences, Media Lab and McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Shelly Berger
- Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | | | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Arjun Raj
- Department of Bioengineering, University of PennsylvaniaPhiladelphiaUnited States
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| |
Collapse
|
2
|
Shenasa H, Bentley DL. Pre-mRNA splicing and its cotranscriptional connections. Trends Genet 2023; 39:672-685. [PMID: 37236814 PMCID: PMC10524715 DOI: 10.1016/j.tig.2023.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Transcription of eukaryotic genes by RNA polymerase II (Pol II) yields RNA precursors containing introns that must be spliced out and the flanking exons ligated together. Splicing is catalyzed by a dynamic ribonucleoprotein complex called the spliceosome. Recent evidence has shown that a large fraction of splicing occurs cotranscriptionally as the RNA chain is extruded from Pol II at speeds of up to 5 kb/minute. Splicing is more efficient when it is tethered to the transcription elongation complex, and this linkage permits functional coupling of splicing with transcription. We discuss recent progress that has uncovered a network of connections that link splicing to transcript elongation and other cotranscriptional RNA processing events.
Collapse
Affiliation(s)
- Hossein Shenasa
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
| |
Collapse
|
3
|
Bielewicz D, Dolata J, Bajczyk M, Szewc L, Gulanicz T, Bhat SS, Karlik A, Jozwiak M, Jarmolowski A, Szweykowska-Kulinska Z. Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes. PLANT & CELL PHYSIOLOGY 2023; 64:571-582. [PMID: 37040378 DOI: 10.1093/pcp/pcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 06/16/2023]
Abstract
Hyponastic Leaves 1 (HYL1) [also known as Double-stranded RNA-Binding protein 1 (DRB1)] is a double-stranded RNA-binding protein involved in microRNA (miRNA) processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by the Dicer-Like 1 protein. In this work, we report a novel function of the HYL1 protein in the transcription of miRNA (MIR) genes. HYL1 colocalizes with RNA polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that the HYL1 protein interacts with many transcription factors. Finally, we show that the action of HYL1 is not limited to MIR genes and impacts the expression of many other genes, a majority of which are involved in plastid organization. These discoveries indicate HYL1 as an additional player in gene regulation at the transcriptional level, independent of its role in miRNA biogenesis.
Collapse
Affiliation(s)
- Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Advanced Technologies, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun 87-100, Poland
| | - Susheel S Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Anna Karlik
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Monika Jozwiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| |
Collapse
|
4
|
Magnuson B, Bedi K, Narayanan IV, Bartkowiak B, Blinkiewicz H, Paulsen MT, Greenleaf A, Ljungman M. CDK12 regulates co-transcriptional splicing and RNA turnover in human cells. iScience 2022; 25:105030. [PMID: 36111258 PMCID: PMC9468413 DOI: 10.1016/j.isci.2022.105030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/13/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
The cyclin-dependent kinase CDK12 has garnered interest as a cancer therapeutic target as DNA damage response genes are particularly suppressed by loss of CDK12 activity. In this study, we assessed the acute effects of CDK12 inhibition on transcription and RNA processing using nascent RNA Bru-seq and BruChase-seq. Acute transcriptional changes were overall small after CDK12 inhibition but over 600 genes showed intragenic premature termination, including DNA repair and cell cycle genes. Furthermore, many genes showed reduced transcriptional readthrough past the end of genes in the absence of CDK12 activity. RNA turnover was dramatically affected by CDK12 inhibition and importantly, caused increased degradation of many transcripts from DNA damage response genes. We also show that co-transcriptional splicing was suppressed by CDK12 inhibition. Taken together, these studies reveal the roles of CDK12 in regulating transcription elongation, transcription termination, co-transcriptional splicing, and RNA turnover. Over 600 genes showed prematurely terminated transcription when CDK12 was inhibited CDK12 promotes transcriptional readthrough past transcription end sites (TESs) CDK12 promotes splicing and affects transcript stability
Collapse
Affiliation(s)
- Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karan Bedi
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Bartlomiej Bartkowiak
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hailey Blinkiewicz
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T. Paulsen
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arno Greenleaf
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mats Ljungman
- Rogel Cancer Center and Center for RNA Biomedicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Radiation Oncology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author
| |
Collapse
|
5
|
Le P, Ahmed N, Yeo GW. Illuminating RNA biology through imaging. Nat Cell Biol 2022; 24:815-824. [PMID: 35697782 PMCID: PMC11132331 DOI: 10.1038/s41556-022-00933-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/06/2022] [Indexed: 12/14/2022]
Abstract
RNA processing plays a central role in accurately transmitting genetic information into functional RNA and protein regulators. To fully appreciate the RNA life-cycle, tools to observe RNA with high spatial and temporal resolution are critical. Here we review recent advances in RNA imaging and highlight how they will propel the field of RNA biology. We discuss current trends in RNA imaging and their potential to elucidate unanswered questions in RNA biology.
Collapse
Affiliation(s)
- Phuong Le
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Noorsher Ahmed
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
6
|
Dumbović G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun 2021; 12:3308. [PMID: 34083519 PMCID: PMC8175569 DOI: 10.1038/s41467-021-23221-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The spatial partitioning of the transcriptome in the cell is an important form of gene-expression regulation. Here, we address how intron retention influences the spatio-temporal dynamics of transcripts from two clinically relevant genes: TERT (Telomerase Reverse Transcriptase) pre-mRNA and TUG1 (Taurine-Upregulated Gene 1) lncRNA. Single molecule RNA FISH reveals that nuclear TERT transcripts uniformly and robustly retain specific introns. Our data suggest that the splicing of TERT retained introns occurs during mitosis. In contrast, TUG1 has a bimodal distribution of fully spliced cytoplasmic and intron-retained nuclear transcripts. We further test the functionality of intron-retention events using RNA-targeting thiomorpholino antisense oligonucleotides to block intron excision. We show that intron retention is the driving force for the nuclear compartmentalization of these RNAs. For both RNAs, altering this splicing-driven subcellular distribution has significant effects on cell viability. Together, these findings show that stable retention of specific introns can orchestrate spatial compartmentalization of these RNAs within the cell. This process reveals that modulating RNA localization via targeted intron retention can be utilized for RNA-based therapies.
Collapse
Affiliation(s)
- Gabrijela Dumbović
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | | | - Heera K Langner
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Michael Smallegan
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Josep Biayna
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
| | - Evan P Hass
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Katarzyna Jastrzebska
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | | | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Marvin H Caruthers
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
| |
Collapse
|
7
|
Bedi K, Magnuson BR, Narayanan I, Paulsen M, Wilson TE, Ljungman M. Co-transcriptional splicing efficiencies differ within genes and between cell types. RNA (NEW YORK, N.Y.) 2021; 27:rna.078662.120. [PMID: 33975916 PMCID: PMC8208053 DOI: 10.1261/rna.078662.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/05/2021] [Indexed: 06/01/2023]
Abstract
Pre-mRNA splicing is carried out by the spliceosome and involves splice site recognition, removal of introns, and ligation of exons. Components of the spliceosome have been shown to interact with the elongating RNA polymerase II (RNAPII) which is thought to allow splicing to occur concurrently with transcription. However, little is known about the regulation and efficiency of co-transcriptional splicing in human cells. In this study, we used Bru-seq and BruChase-seq to determine the co-transcriptional splicing efficiencies of 17,000 introns expressed across 6 human cell lines. We found that less than half of all introns across these 6 cell lines were co-transcriptionally spliced. Splicing efficiencies for individual introns showed variations across cell lines, suggesting that splicing may be regulated in a cell-type specific manner. Moreover, the splicing efficiency of introns varied within genes. The efficiency of co-transcriptional splicing did not correlate with gene length, intron position, splice site strengths, or the intron/neighboring exons GC content. However, we identified binding signals from multiple RNA binding proteins (RBPs) that correlated with splicing efficiency, including core spliceosomal machinery components-such as SF3B4, U2AF1 and U2AF2 showing higher binding signals in poorly spliced introns. In addition, multiple RBPs, such as BUD13, PUM1 and SND1, showed preferential binding in exons that flank introns with high splicing efficiencies. The nascent RNA splicing patterns presented here across multiple cell types add to our understanding of the complexity in RNA splicing, wherein RNA-binding proteins may play important roles in determining splicing outcomes in a cell type- and intron-specific manner.
Collapse
|
8
|
Zhu J, Zhao H, Kong F, Liu B, Liu M, Dong Z. Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf. FRONTIERS IN PLANT SCIENCE 2021; 12:649634. [PMID: 33897737 PMCID: PMC8063115 DOI: 10.3389/fpls.2021.649634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/02/2021] [Indexed: 05/13/2023]
Abstract
Transcription is the first step of central dogma, in which the genetic information stored in DNA is copied into RNA. In addition to mature RNA sequencing (RNA-seq), high-throughput nascent RNA assays have been established and applied to provide detailed transcriptional information. Here, we present the profiling of nascent RNA from trifoliate leaves and shoot apices of soybean. In combination with nascent RNA (chromatin-bound RNA, CB RNA) and RNA-seq, we found that introns were largely spliced cotranscriptionally. Although alternative splicing (AS) was mainly determined at nascent RNA biogenesis, differential AS between the leaf and shoot apex at the mature RNA level did not correlate well with cotranscriptional differential AS. Overall, RNA abundance was moderately correlated between nascent RNA and mature RNA within each tissue, but the fold changes between the leaf and shoot apex were highly correlated. Thousands of novel transcripts (mainly non-coding RNA) were detected by CB RNA-seq, including the overlap of natural antisense RNA with two important genes controlling soybean reproductive development, FT2a and Dt1. Taken together, we demonstrated the adoption of CB RNA-seq in soybean, which may shed light on gene expression regulation of important agronomic traits in leguminous crops.
Collapse
Affiliation(s)
- Jiafu Zhu
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fanjiang Kong
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Min Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
- *Correspondence: Min Liu,
| | - Zhicheng Dong
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
- Zhicheng Dong,
| |
Collapse
|
9
|
Li S, Wang Y, Zhao Y, Zhao X, Chen X, Gong Z. Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs. MOLECULAR PLANT 2020; 13:266-277. [PMID: 31759129 PMCID: PMC8034514 DOI: 10.1016/j.molp.2019.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 05/20/2023]
Abstract
RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription. However, co-transcriptional splicing has not yet been explored in plants. Here, we built transcriptomes of nascent chromatin RNAs in Arabidopsis thaliana and showed that nearly all introns undergo co-transcriptional splicing, which occurs with higher efficiency for introns in protein-coding genes than for those in noncoding RNAs. Total intron number and intron position are two predominant features that correlate with co-transcriptional splicing efficiency, and introns with alternative 5' or 3' splice sites are less efficiently spliced. Furthermore, we found that mutations in genes encoding trans-acting proteins lead to more introns with increased splicing defects in nascent RNAs than in mature RNAs, and that introns with increased splicing defects in mature RNAs are inefficiently spliced at the co-transcriptional level. Collectively, our results not only uncovered widespread co-transcriptional splicing in Arabidopsis but also identified features that may affect or be affected by co-transcriptional splicing efficiency.
Collapse
Affiliation(s)
- Shaofang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China.
| | - Yuan Wang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yonghui Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Plant Phenomics Research Center, Nanjing Agricultural University, Nanjing 210018, China
| | - Xinjie Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| |
Collapse
|
10
|
Zhu D, Mao F, Tian Y, Lin X, Gu L, Gu H, Qu LJ, Wu Y, Wu Z. The Features and Regulation of Co-transcriptional Splicing in Arabidopsis. MOLECULAR PLANT 2020; 13:278-294. [PMID: 31760161 DOI: 10.1016/j.molp.2019.11.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/29/2019] [Accepted: 11/15/2019] [Indexed: 05/20/2023]
Abstract
Precursor mRNA (pre-mRNA) splicing is essential for gene expression in most eukaryotic organisms. Previous studies from mammals, Drosophila, and yeast show that the majority of splicing events occurs co-transcriptionally. In plants, however, the features of co-transcriptional splicing (CTS) and its regulation still remain largely unknown. Here, we used chromatin-bound RNA sequencing to study CTS in Arabidopsis thaliana. We found that CTS is widespread in Arabidopsis seedlings, with a large proportion of alternative splicing events determined co-transcriptionally. CTS efficiency correlated with gene expression level, the chromatin landscape and, most surprisingly, the number of introns and exons of individual genes, but is independent of gene length. In combination with enhanced crosslinking and immunoprecipitation sequencing analysis, we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding, frequently to exonic sequences. Notably, this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level, not at the mRNA level. RZ-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated introns. We propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons, introns, and splicing factors. Our work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.
Collapse
Affiliation(s)
- Danling Zhu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fei Mao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Yuanchun Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Xiaoya Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China.
| | - Zhe Wu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
| |
Collapse
|
11
|
Maita H, Nakagawa S. What is the switch for coupling transcription and splicing? RNA Polymerase II C‐terminal domain phosphorylation, phase separation and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1574. [DOI: 10.1002/wrna.1574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 01/12/2023]
Affiliation(s)
- Hiroshi Maita
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan
| |
Collapse
|
12
|
Neugebauer KM. Nascent RNA and the Coordination of Splicing with Transcription. Cold Spring Harb Perspect Biol 2019; 11:11/8/a032227. [PMID: 31371351 DOI: 10.1101/cshperspect.a032227] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other processing events during its synthesis. This review discusses the development of three major methods that enable us to track the conversion of precursor messenger RNA (pre-mRNA) to messenger RNA (mRNA) products in vivo: live-cell imaging, metabolic labeling of RNA, and RNA-seq of purified nascent RNA. These approaches are complementary, addressing distinct issues of transcription rates and intron lifetimes alongside spatial information regarding the gene position of Pol II at which spliceosomes act. The findings will be placed in the context of active transcription units, each of which-because of the presence of nascent RNA, Pol II, and features of the chromatin environment-will recruit a potentially gene-specific constellation of RNA binding proteins and processing machineries.
Collapse
Affiliation(s)
- Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| |
Collapse
|
13
|
Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
Collapse
Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| |
Collapse
|
14
|
Carrocci TJ, Neugebauer KM. Pre-mRNA Splicing in the Nuclear Landscape. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 84:11-20. [PMID: 32493763 PMCID: PMC7384967 DOI: 10.1101/sqb.2019.84.040402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Eukaryotic gene expression requires the cumulative activity of multiple molecular machines to synthesize and process newly transcribed pre-messenger RNA. Introns, the noncoding regions in pre-mRNA, must be removed by the spliceosome, which assembles on the pre-mRNA as it is transcribed by RNA polymerase II (Pol II). The assembly and activity of the spliceosome can be modulated by features including the speed of transcription elongation, chromatin, post-translational modifications of Pol II and histone tails, and other RNA processing events like 5'-end capping. Here, we review recent work that has revealed cooperation and coordination among co-transcriptional processing events and speculate on new avenues of research. We anticipate new mechanistic insights capable of unraveling the relative contribution of coupled processing to gene expression.
Collapse
Affiliation(s)
- Tucker J Carrocci
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| |
Collapse
|
15
|
Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis. PLoS Genet 2018; 14:e1007761. [PMID: 30365503 PMCID: PMC6221363 DOI: 10.1371/journal.pgen.1007761] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/07/2018] [Accepted: 10/12/2018] [Indexed: 11/27/2022] Open
Abstract
Nuclear genes of euglenids and marine diplonemids harbor atypical, nonconventional introns which are not observed in the genomes of other eukaryotes. Nonconventional introns do not have the conserved borders characteristic for spliceosomal introns or the sequence complementary to U1 snRNA at the 5' end. They form a stable secondary structure bringing together both exon/intron junctions, nevertheless, this conformation does not resemble the form of self-splicing or tRNA introns. In the genes studied so far, frequent nonconventional introns insertions at new positions have been observed, whereas conventional introns have been either found at the conserved positions, or simply lost. In this work, we examined the order of intron removal from Euglena gracilis transcripts of the tubA and gapC genes, which contain two types of introns: nonconventional and spliceosomal. The relative order of intron excision was compared for pairs of introns belonging to different types. Furthermore, intermediate products of splicing were analyzed using the PacBio Next Generation Sequencing system. The analysis led to the main conclusion that nonconventional introns are removed in a rapid way but later than spliceosomal introns. Moreover, the observed accumulation of transcripts with conventional introns removed and nonconventional present may suggest the existence of a time gap between the two types of splicing. The existence of conventional spliceosomal introns in genes of eukaryotic organisms is a well-known theorem. However, genes of the unicellular algae group, euglenids, contain also another type of introns, so-called nonconventional ones. They lack canonical borders, a feature most characteristic for conventional introns and form a stable secondary structure bringing together their ends. Along with the increasing popularity of whole genome studies, nonconventional introns were also disclosed in the genes of other protists, diplonemids. In this study we were particularly interested which introns–conventional or nonconventional–are removed earlier from euglenids’ pre-mRNA. To track this process we analyzed transcripts of the two Euglena gracilis genes. The relative order of intron excision was compared for pairs of introns belonging to different types. We also surveyed thousands of intermediate products of splicing using the Next-Generation Sequencing system. Summarizing the results of both experiments, we proved that spliceosomal introns are removed at an earlier stage of pre-mRNA maturation than nonconventional ones.
Collapse
|
16
|
Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
Collapse
Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
| |
Collapse
|
17
|
Beta RAA, Balatsos NAA. Tales around the clock: Poly(A) tails in circadian gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1484. [PMID: 29911349 DOI: 10.1002/wrna.1484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/15/2018] [Accepted: 04/20/2018] [Indexed: 11/07/2022]
Abstract
Circadian rhythms are ubiquitous time-keeping processes in eukaryotes with a period of ~24 hr. Light is perhaps the main environmental cue (zeitgeber) that affects several aspects of physiology and behaviour, such as sleep/wake cycles, orientation of birds and bees, and leaf movements in plants. Temperature can serve as the main zeitgeber in the absence of light cycles, even though it does not lead to rhythmicity through the same mechanism as light. Additional cues include feeding patterns, humidity, and social rhythms. At the molecular level, a master oscillator orchestrates circadian rhythms and organizes molecular clocks located in most cells. The generation of the 24 hr molecular clock is based on transcriptional regulation, as it drives intrinsic rhythmic changes based on interlocked transcription/translation feedback loops that synchronize expression of genes. Thus, processes and factors that determine rhythmic gene expression are important to understand circadian rhythms. Among these, the poly(A) tails of RNAs play key roles in their stability, translational efficiency and degradation. In this article, we summarize current knowledge and discuss perspectives on the role and significance of poly(A) tails and associating factors in the context of the circadian clock. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > 3' End Processing.
Collapse
Affiliation(s)
- Rafailia A A Beta
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| |
Collapse
|
18
|
Galganski L, Urbanek MO, Krzyzosiak WJ. Nuclear speckles: molecular organization, biological function and role in disease. Nucleic Acids Res 2017; 45:10350-10368. [PMID: 28977640 PMCID: PMC5737799 DOI: 10.1093/nar/gkx759] [Citation(s) in RCA: 298] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022] Open
Abstract
The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Further studies on transcription and mRNA maturation and export revealed a more general role for splicing speckles in RNA metabolism. Here, we discuss the functional implications of the localization of numerous proteins crucial for epigenetic regulation, chromatin organization, DNA repair and RNA modification to nuclear speckles. We highlight recent advances suggesting that NSs facilitate integrated regulation of gene expression. In addition, we consider the influence of abundant regulatory and signaling proteins, i.e. protein kinases and proteins involved in protein ubiquitination, phosphoinositide signaling and nucleoskeletal organization, on pre-mRNA synthesis and maturation. While many of these regulatory proteins act within NSs, direct evidence for mRNA metabolism events occurring in NSs is still lacking. NSs contribute to numerous human diseases, including cancers and viral infections. In addition, recent data have demonstrated close relationships between these structures and the development of neurological disorders.
Collapse
Affiliation(s)
- Lukasz Galganski
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
19
|
Neves LT, Douglass S, Spreafico R, Venkataramanan S, Kress TL, Johnson TL. The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae. Genes Dev 2017; 31:702-717. [PMID: 28446598 PMCID: PMC5411710 DOI: 10.1101/gad.295188.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/27/2017] [Indexed: 01/01/2023]
Abstract
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation. Here we show that splicing of intron-containing genes in cells lacking H2A.Z is impaired, particularly under suboptimal splicing conditions. Cells lacking H2A.Z are especially dependent on a functional U2 snRNP (small nuclear RNA [snRNA] plus associated proteins), as H2A.Z shows extensive genetic interactions with U2 snRNP-associated proteins, and RNA sequencing (RNA-seq) reveals that introns with nonconsensus branch points are particularly sensitive to H2A.Z loss. Consistently, H2A.Z promotes efficient spliceosomal rearrangements involving the U2 snRNP, as H2A.Z loss results in persistent U2 snRNP association and decreased recruitment of downstream snRNPs to nascent RNA. H2A.Z impairs transcription elongation, suggesting that spliceosome rearrangements are tied to H2A.Z's role in elongation. Depletion of disassembly factor Prp43 suppresses H2A.Z-mediated splice defects, indicating that, in the absence of H2A.Z, stalled spliceosomes are disassembled, and unspliced RNAs are released. Together, these data demonstrate that H2A.Z is required for efficient pre-mRNA splicing and indicate a role for H2A.Z in coordinating the kinetics of transcription elongation and splicing.
Collapse
Affiliation(s)
- Lauren T Neves
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA.,Graduate Program in Molecular Biology Interdepartmental Program, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Stephen Douglass
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Srivats Venkataramanan
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA
| | - Tracy L Kress
- Department of Biology, The College of New Jersey, Ewing, New Jersey 08628, USA
| | - Tracy L Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA.,Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
| |
Collapse
|
20
|
Björk P, Wieslander L. Integration of mRNP formation and export. Cell Mol Life Sci 2017; 74:2875-2897. [PMID: 28314893 PMCID: PMC5501912 DOI: 10.1007/s00018-017-2503-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022]
Abstract
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA–protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs. After release from the gene, the mRNPs move by diffusion within the interchromatin compartment, making up pools of mRNPs. Here, splicing and polyadenylation can be completed and the mRNPs recruit the major export receptor NXF1. Export competent mRNPs interact with the nuclear pore complex, leading to export, concomitant with compositional and conformational changes of the mRNPs. We summarize the integrated nuclear processes involved in the formation and export of mRNPs.
Collapse
Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| |
Collapse
|
21
|
Abstract
Transcription and splicing are fundamental steps in gene expression. These processes have been studied intensively over the past four decades, and very recent findings are challenging some of the formerly established ideas. In particular, splicing was shown to occur much faster than previously thought, with the first spliced products observed as soon as splice junctions emerge from RNA polymerase II (Pol II). Splicing was also found coupled to a specific phosphorylation pattern of Pol II carboxyl-terminal domain (CTD), suggesting a new layer of complexity in the CTD code. Moreover, phosphorylation of the CTD may be scarcer than expected, and other post-translational modifications of the CTD are emerging with unanticipated roles in gene expression regulation.
Collapse
Affiliation(s)
- Noélia Custódio
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| | - Maria Carmo-Fonseca
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| |
Collapse
|
22
|
Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins. Gene 2016; 587:107-19. [PMID: 27154819 DOI: 10.1016/j.gene.2016.04.057] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 04/30/2016] [Indexed: 01/04/2023]
Abstract
Alternative pre-mRNA splicing provides a source of vast protein diversity by removing non-coding sequences (introns) and accurately linking different exonic regions in the correct reading frame. The regulation of alternative splicing is essential for various cellular functions in both pathological and physiological conditions. In eukaryotic cells, this process is commonly used to increase proteomic diversity and to control gene expression either co- or post-transcriptionally. Alternative splicing occurs within a megadalton-sized, multi-component machine consisting of RNA and proteins; during the splicing process, this complex undergoes dynamic changes via RNA-RNA, protein-protein and RNA-protein interactions. Co-transcriptional splicing functionally integrates the transcriptional machinery, thereby enabling the two processes to influence one another, whereas post-transcriptional splicing facilitates the coupling of RNA splicing with post-splicing events. This review addresses the structural aspects of spliceosomes and the mechanistic implications of their stepwise assembly on the regulation of pre-mRNA splicing. Moreover, the role of phosphorylation-based, signal-induced changes in the regulation of the splicing process is demonstrated.
Collapse
|
23
|
Björk P, Persson JO, Wieslander L. Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo. J Cell Biol 2016; 211:63-75. [PMID: 26459599 PMCID: PMC4602041 DOI: 10.1083/jcb.201412017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The exon junction core complex associates with Balbiani ring (BR) premRNPs during transcription and in relation to splicing, whereas the export factor NXF1 is recruited in the interchromatin, and BR mRNPs become export competent only after passage through the interchromatin. Eukaryotic gene expression requires the ordered association of numerous factors with precursor messenger RNAs (premRNAs)/messenger RNAs (mRNAs) to achieve efficiency and regulation. Here, we use the Balbiani ring (BR) genes to demonstrate the temporal and spatial association of the exon junction complex (EJC) core with gene-specific endogenous premRNAs and mRNAs. The EJC core components bind cotranscriptionally to BR premRNAs during or very rapidly after splicing. The EJC core does not recruit the nonsense-mediated decay mediaters UPF2 and UPF3 until the BR messenger RNA protein complexes (mRNPs) enter the interchromatin. Even though several known adapters for the export factor NXF1 become part of BR mRNPs already at the gene, NXF1 binds to BR mRNPs only in the interchromatin. In steady state, a subset of the BR mRNPs in the interchromatin binds NXF1, UPF2, and UPF3. This binding appears to occur stochastically, and the efficiency approximately equals synthesis and export of the BR mRNPs. Our data provide unique in vivo information on how export competent eukaryotic mRNPs are formed.
Collapse
Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jan-Olov Persson
- Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|
24
|
Herrero Ó, Planelló R, Morcillo G. The ribosome biogenesis pathway as an early target of benzyl butyl phthalate (BBP) toxicity in Chironomus riparius larvae. CHEMOSPHERE 2016; 144:1874-1884. [PMID: 26539713 DOI: 10.1016/j.chemosphere.2015.10.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/14/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
Butyl benzyl phthalate (BBP) is a ubiquitous contaminant whose presence in the environment is expected for decades, since it has been extensively used worldwide as a plasticizer in the polyvinyl chloride (PVC) industry and the manufacturing of many other products. In the present study, the interaction of BBP with the ribosome biogenesis pathway and the general transcriptional profile of Chironomus riparius aquatic larvae were investigated by means of changes in the rDNA activity (through the study of the internal transcribed spacer 2, ITS2) and variations in the expression profile of ribosomal protein genes (rpL4, rpL11, and rpL13) after acute 24-h and 48-h exposures to a wide range of BBP doses. Furthermore, cytogenetic assays were conducted to evaluate the transcriptional activity of polytene chromosomes from salivary gland cells, with special attention to the nucleolus and the Balbiani rings (BRs) of chromosome IV. BBP caused a dose and time-dependent toxicity in most of the selected biomarkers, with a general depletion in the gene expression levels and the activity of BR2 after 48-h treatments. At the same time, decondensation and activation of some centromeres took place, while the activity of nucleolus remained unaltered. Withdrawal of the xenobiotic allowed the larvae to reach control levels in the case of rpL4 and rpL13 genes, which were previously slightly downregulated in 24-h tests. These data provide the first evidence on the interaction of BBP with the ribosome synthesis pathways, which results in a significant impairment of the functional activity of ribosomal protein genes. Thus, the depletion of ribosomes would be a long-term effect of BBP-induced cellular damage. These findings may have important implications for understanding the adverse biological effects of BBP in C. riparius, since they provide new sensitive biomarkers of BBP exposure and highlight the suitability of this organism for ecotoxicological risk assessment, especially in aquatic ecosystems.
Collapse
Affiliation(s)
- Óscar Herrero
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040 Madrid, Spain.
| | - Rosario Planelló
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040 Madrid, Spain.
| | - Gloria Morcillo
- Grupo de Biología y Toxicología Ambiental, Facultad de Ciencias, Universidad Nacional de Educación a Distancia, UNED, Paseo de la Senda del Rey 9, 28040 Madrid, Spain.
| |
Collapse
|
25
|
Björk P, Wieslander L. The Balbiani Ring Story: Synthesis, Assembly, Processing, and Transport of Specific Messenger RNA-Protein Complexes. Annu Rev Biochem 2015; 84:65-92. [PMID: 26034888 DOI: 10.1146/annurev-biochem-060614-034150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic gene expression is the result of the integrated action of multimolecular machineries. These machineries associate with gene transcripts, often already nascent precursor messenger RNAs (pre-mRNAs). They rebuild the transcript and convey properties allowing the processed transcript, the mRNA, to be exported to the cytoplasm, quality controlled, stored, translated, and degraded. To understand these integrated processes, one must understand the temporal and spatial aspects of the fate of the gene transcripts in relation to interacting molecular machineries. Improved methodology is necessary to study gene expression in vivo for endogenous genes. A complementary approach is to study biological systems that provide exceptional experimental possibilities. We describe such a system, the Balbiani ring (BR) genes in polytene cells in the dipteran Chironomus tentans. The BR genes, along with their pre-mRNA-protein complexes (pre-mRNPs) and mRNA-protein complexes (mRNPs), allow the visualization of intact cell nuclei and enable analyses of where and when different molecular machineries associate with and act on the BR pre-mRNAs and mRNAs.
Collapse
Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
| | | |
Collapse
|
26
|
Sudo R, Sato F, Azechi T, Wachi H. MiR-29-mediated elastin down-regulation contributes to inorganic phosphorus-induced osteoblastic differentiation in vascular smooth muscle cells. Genes Cells 2015; 20:1077-87. [DOI: 10.1111/gtc.12311] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/28/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Ryo Sudo
- Department of Tissue Regeneration; Hoshi University School of Pharmacy and Pharmaceutical Sciences; 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| | - Fumiaki Sato
- Department of Analytical Pathophysiology; Hoshi University School of Pharmacy and Pharmaceutical Sciences; 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| | - Takuya Azechi
- Department of Tissue Regeneration; Hoshi University School of Pharmacy and Pharmaceutical Sciences; 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| | - Hiroshi Wachi
- Department of Tissue Regeneration; Hoshi University School of Pharmacy and Pharmaceutical Sciences; 2-4-41 Ebara Shinagawa-ku Tokyo 142-8501 Japan
| |
Collapse
|
27
|
Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system. Mech Dev 2015; 138 Pt 2:133-140. [PMID: 26277563 DOI: 10.1016/j.mod.2015.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/05/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
Homeotic genes are aligned on the chromosome in the order of the segments that they specify along the antero-posterior axis of the fly. In general the genes affecting the more posterior segments repress the more anterior genes, a phenomenon known as "posterior dominance". There is however a noticeable exception to this rule in the central nervous system of Drosophila melanogaster where the posterior Abd-B gene does not repress the immediately more anterior abd-A gene. Instead, abd-A repression is accomplished by a 92 kb-long ncRNA (the iab-8ncRNA) that is transcribed from the large inter-genic region between abd-A and Abd-B. This iab-8ncRNA encodes a microRNA to repress abd-A and also a second redundant repression mechanism acting in cis and thought to be transcriptional interference with the abd-A promoter. Using in situ hybridization, a previous work suggested that the iab8ncRNA transcript forms discrete foci restricted to the nuclear periphery and that this localization may be important for its function. In order to better characterize the intra-cellular localization of the iab-8ncRNA we used the MS2-MCP system, which allows fluorescent labeling of RNA in cells and relies on the interaction between GFP-tagged MS2 coat protein (MCP-GFP) and MS2 RNA stem loops. Our results indicate that the large foci seen in previous studies correspond to the site of iab8ncRNA transcription and that the foci seen may simply be an indication of the level of transcription at the locus. We find no evidence to suggest that this localization is important for its function on abd-A repression. We discuss the idea that the iab-8ncRNA may be a relic of a more general ancient mechanism of posterior dominance during the emergence of the hox clusters that was mediated by transcriptional interference.
Collapse
|
28
|
Abstract
mRNA localisation coupled to translational regulation provides an important means of dictating when and where proteins function in a variety of model systems. This mechanism is particularly relevant in polarised or migrating cells. Although many of the models for how this is achieved were first proposed over 20 years ago, some of the molecular details are still poorly understood. Nevertheless, advanced imaging, biochemical and computational approaches have started to shed light on the cis-acting localisation signals and trans-acting factors that dictate the final destination of localised transcripts. In this Cell Science at a Glance article and accompanying poster, we provide an overview of mRNA localisation, from transcription to degradation, focusing on the microtubule-dependent active transport and anchoring mechanism, which we will use to explain the general paradigm. However, it is clear that there are diverse ways in which mRNAs become localised and target protein expression, and we highlight some of the similarities and differences between these mechanisms.
Collapse
Affiliation(s)
- Richard M Parton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alexander Davidson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| |
Collapse
|
29
|
Boutz PL, Bhutkar A, Sharp PA. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Genes Dev 2015; 29:63-80. [PMID: 25561496 PMCID: PMC4281565 DOI: 10.1101/gad.247361.114] [Citation(s) in RCA: 285] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts. Boutz et al. identified thousands of these “detained” introns (DIs) in human and mouse cell lines as well as the adult mouse liver. Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs, altering transcript pools of >300 genes. Srsf4 regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as “detained” introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs—including those in Mdm4, a negative regulator of p53—was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression.
Collapse
Affiliation(s)
- Paul L Boutz
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Arjun Bhutkar
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Phillip A Sharp
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
30
|
Rino J, Martin RM, Carvalho C, de Jesus AC, Carmo-Fonseca M. Single-Molecule Imaging of RNA Splicing in Live Cells. Methods Enzymol 2015; 558:571-585. [PMID: 26068754 DOI: 10.1016/bs.mie.2015.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Expression of genetic information in eukaryotes involves a series of interconnected processes that ultimately determine the quality and amount of proteins in the cell. Many individual steps in gene expression are kinetically coupled, but tools are lacking to determine how temporal relationships between chemical reactions contribute to the output of the final gene product. Here, we describe a strategy that permits direct measurements of intron dynamics in single pre-mRNA molecules in live cells. This approach reveals that splicing can occur much faster than previously proposed and opens new avenues for studying how kinetic mechanisms impact on RNA biogenesis.
Collapse
Affiliation(s)
- José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Robert M Martin
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Célia Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana C de Jesus
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
| |
Collapse
|
31
|
Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L. The Chironomus tentans genome sequence and the organization of the Balbiani ring genes. BMC Genomics 2014; 15:819. [PMID: 25261295 PMCID: PMC4192438 DOI: 10.1186/1471-2164-15-819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/22/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes. RESULTS The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations. CONCLUSIONS We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.
Collapse
Affiliation(s)
- Alexey Kutsenko
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Thomas Svensson
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Björn Nystedt
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE 752 37 Uppsala, Sweden
| | - Joakim Lundeberg
- />Science for Life Laboratory, KTH, Royal Institute of Technology, Science for Life Laboratory, SE 171 65 Solna, Sweden
| | - Petra Björk
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Erik Sonnhammer
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
- />Department of Biochemistry and Biophysics, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Stefania Giacomello
- />Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE 171 21 Solna, Sweden
| | - Neus Visa
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Lars Wieslander
- />Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| |
Collapse
|
32
|
Batsché E, Ameyar-Zazoua M. The influence of Argonaute proteins on alternative RNA splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:141-56. [DOI: 10.1002/wrna.1264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 07/28/2014] [Accepted: 07/31/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Eric Batsché
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
| | - Maya Ameyar-Zazoua
- Institut Pasteur, Dpt Biologie du Développement et Cellules Souches; Unité de Régulation Epigénétique; 75015 Paris France
- URA2578; CNRS
- Laboratoire Epigénétique et Destin Cellulaire, CNRS UMR7216; Université Paris Diderot, Cité Sorbonne Paris; Paris France
| |
Collapse
|
33
|
Björk P, Wieslander L. Mechanisms of mRNA export. Semin Cell Dev Biol 2014; 32:47-54. [PMID: 24813364 DOI: 10.1016/j.semcdb.2014.04.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/17/2014] [Indexed: 02/02/2023]
Abstract
Release of properly processed and assembled mRNPs from the actively transcribing genes, movement of the mRNPs through the interchromatin and interaction with the Nuclear Pore Complexes, leading to cytoplasmic export, are essential steps of eukaryotic gene expression. Here, we review these intranuclear gene expression steps.
Collapse
Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
| |
Collapse
|
34
|
Maslon MM, Heras SR, Bellora N, Eyras E, Cáceres JF. The translational landscape of the splicing factor SRSF1 and its role in mitosis. eLife 2014; 3:e02028. [PMID: 24842991 PMCID: PMC4027812 DOI: 10.7554/elife.02028] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/21/2014] [Indexed: 12/19/2022] Open
Abstract
The shuttling Serine/Arginine rich (SR) protein SRSF1 (previously known as SF2/ASF) is a splicing regulator that also activates translation in the cytoplasm. In order to dissect the gene network that is translationally regulated by SRSF1, we performed a high-throughput deep sequencing analysis of polysomal fractions in cells overexpressing SRSF1. We identified approximately 1,500 mRNAs that are translational targets of SRSF1. These include mRNAs encoding proteins involved in cell cycle regulation, such as spindle, kinetochore and M phase proteins, which are essential for accurate chromosome segregation. Indeed, we show that translational activity of SRSF1 is required for normal mitotic progression. Furthermore, we found that mRNAs that display alternative splicing changes upon SRSF1 overexpression are also its translational targets; strongly suggesting that SRSF1 couples pre-mRNA splicing and translation. These data provide insights on the complex role of SRSF1 in the control of gene expression at multiple levels and its implications in cancer.
Collapse
Affiliation(s)
- Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sara R Heras
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Nicolas Bellora
- Computational Genomics Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduardo Eyras
- Computational Genomics Group, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
35
|
Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet 2014; 15:163-75. [PMID: 24514444 DOI: 10.1038/nrg3662] [Citation(s) in RCA: 546] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maturation of mRNA precursors often occurs simultaneously with their synthesis by RNA polymerase II (Pol II). The co-transcriptional nature of mRNA processing has permitted the evolution of coupling mechanisms that coordinate transcription with mRNA capping, splicing, editing and 3' end formation. Recent experiments using sophisticated new methods for analysis of nascent RNA have provided important insights into the relative amount of co-transcriptional and post-transcriptional processing, the relationship between mRNA elongation and processing, and the role of the Pol II carboxy-terminal domain (CTD) in regulating these processes.
Collapse
Affiliation(s)
- David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, MS8101, PO BOX 6511, Aurora, Colorado 80045, USA
| |
Collapse
|
36
|
Abstract
Since it became clear that intervening sequences or introns are spliced out from precursor pre-mRNA molecules in the nucleus before mature mRNAs are exported to the cytoplasm, questions were raised about the timing of splicing. Does splicing start while RNA polymerase II is still transcribing? Is splicing a slow or a fast process? Is timing important to control the splicing reaction? Although our understanding on the mechanism and function of splicing is largely based on data obtained using biochemical and large-scale "omic" approaches, microscopy has been instrumental to address questions related to timing. Experiments done with the electron microscope paved the way to the discovery of splicing and provided unequivocal evidence that splicing can occur co-transcriptionally. More recently, live-cell microscopy introduced a technical breakthrough that allows real-time visualization of splicing dynamics. We discuss here some of the microscopy advances that provided the basis for the current conceptual view of the splicing process and we outline a most recent development that permits direct measurement, in living cells, of the time it takes to synthesize and excise an intron from individual pre-mRNA molecules.
Collapse
Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisboa, Portugal
| | - Tomas Kirchhausen
- Departments of Cell Biology and Pediatrics; Harvard Medical School and Program in Molecular and Cellular Medicine at Boston Children's Hospital; Boston, MA USA
| |
Collapse
|
37
|
Zaghlool A, Ameur A, Cavelier L, Feuk L. Splicing in the human brain. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 116:95-125. [PMID: 25172473 DOI: 10.1016/b978-0-12-801105-8.00005-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It has become increasingly clear over the past decade that RNA has important functions in human cells beyond its role as an intermediate translator of DNA to protein. It is now known that RNA plays highly specific roles in pathways involved in regulatory, structural, and catalytic functions. The complexity of RNA production and regulation has become evident with the advent of high-throughput methods to study the transcriptome. Deep sequencing has revealed an enormous diversity of RNA types and transcript isoforms in human cells. The transcriptome of the human brain is particularly interesting as it contains more expressed genes than other tissues and also displays an extreme diversity of transcript isoforms, indicating that highly complex regulatory pathways are present in the brain. Several of these regulatory proteins are now identified, including RNA-binding proteins that are neuron specific. RNA-binding proteins also play important roles in regulating the splicing process and the temporal and spatial isoform production. While significant progress has been made in understanding the human transcriptome, many questions still remain regarding the basic mechanisms of splicing and subcellular localization of RNA. A long-standing question is to what extent the splicing of pre-mRNA is cotranscriptional and posttranscriptional, respectively. Recent data, including studies of the human brain, indicate that splicing is primarily cotranscriptional in human cells. This chapter describes the current understanding of splicing and splicing regulation in the human brain and discusses the recent global sequence-based analyses of transcription and splicing.
Collapse
Affiliation(s)
- Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Uppsala University Hospital, Uppsala, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
38
|
Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL. Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA (NEW YORK, N.Y.) 2013; 19:811-27. [PMID: 23616639 PMCID: PMC3683915 DOI: 10.1261/rna.039081.113] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/13/2013] [Indexed: 05/26/2023]
Abstract
The expression of eukaryotic mRNAs is achieved though an intricate series of molecular processes that provide many steps for regulating the production of a final gene product. However, the relationships between individual steps in mRNA biosynthesis and the rates at which they occur are poorly understood. By applying RNA-seq to chromatin-associated and soluble nucleoplasmic fractions of RNA from Lipid A-stimulated macrophages, we examined the timing of exon ligation and transcript release from chromatin relative to the induction of transcription. We find that for a subset of genes in the Lipid A response, the ligation of certain exon pairs is delayed relative to the synthesis of the complete transcript. In contrast, 3' end cleavage and polyadenylation occur rapidly once transcription extends through the cleavage site. Our data indicate that these transcripts with delayed splicing are not released from the chromatin fraction until all the introns have been excised. These unusual kinetics result in a chromatin-associated pool of completely transcribed and 3'-processed transcripts that are not yet fully spliced. We also find that long introns containing repressed exons that will be excluded from the final mRNA are excised particularly slowly relative to other introns in a transcript. These results indicate that the kinetics of splicing and transcript release contribute to the timing of expression for multiple genes of the inflammatory response.
Collapse
Affiliation(s)
- Amy Pandya-Jones
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Dev M. Bhatt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
| | - Ann-Jay Tong
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Stephen T. Smale
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
| | - Douglas L. Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90025, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90025, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90025, USA
| |
Collapse
|
39
|
Brugiolo M, Herzel L, Neugebauer KM. Counting on co-transcriptional splicing. F1000PRIME REPORTS 2013; 5:9. [PMID: 23638305 PMCID: PMC3619158 DOI: 10.12703/p5-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Splicing is the removal of intron sequences from pre-mRNA by the spliceosome. Researchers working in multiple model organisms – notably yeast, insects and mammalian cells – have shown that pre-mRNA can be spliced during the process of transcription (i.e. co-transcriptionally), as well as after transcription termination (i.e. post-transcriptionally). Co-transcriptional splicing does not assume that transcription and splicing machineries are mechanistically coupled, yet it raises this possibility. Early studies were based on a limited number of genes, which were often chosen because of their experimental accessibility. Since 2010, eight studies have used global datasets as counting tools, in order to quantify co-transcriptional intron removal. The consensus view, based on four organisms, is that the majority of splicing events take place co-transcriptionally in most cells and tissues. Here, we discuss the nature of the various global datasets and how bioinformatic analyses were conducted. Considering the broad differences in experimental approach and analysis, the level of agreement on the prevalence of co-transcriptional splicing is remarkable.
Collapse
|
40
|
Schor IE, Gómez Acuña LI, Kornblihtt AR. Coupling between transcription and alternative splicing. Cancer Treat Res 2013; 158:1-24. [PMID: 24222352 DOI: 10.1007/978-3-642-31659-3_1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The scenario of alternative splicing regulation is far more complex than the classical picture of a pre-mRNA being processed post-transcriptionally in more than one way. Introns are efficiently removed while transcripts are still being synthesized, supporting the idea of a co-transcriptional regulation of alternative splicing. Evidence of a functional coupling between splicing and transcription has recently emerged as it was observed that properties of one process may affect the outcome of the other. Co-transcriptionality is thought to improve splicing efficiency and kinetics by directing the nascent pre-mRNA into proper spliceosome assembly and favoring splicing factor recruitment. Two models have been proposed to explain the coupling of transcription and alternative splicing: in the recruitment model, promoters and pol II status affect the recruitment to the transcribing gene of splicing factors or bifunctional factors acting on both transcription and splicing; in the kinetic model, differences in the elongation rate of pol II would determine the timing in which splicing sites are presented, and thus the outcome of alternative splicing decisions. In the later model, chromatin structure has emerged as a key regulator. Although definitive evidence for transcriptionally coupled alternative splicing alterations in tumor development or cancer pathogenesis is still missing, many alternative splicing events altered in cancer might be subject to transcription-splicing coupling regulation.
Collapse
Affiliation(s)
- Ignacio E Schor
- Laboratorio de Fisiologia y Biologia Molecular, Departmento de Fisiologia, Biologia Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, PAB. II, 20 Piso, Buenos Aires, 1428, Argentina
| | | | | |
Collapse
|
41
|
Khodor YL, Menet JS, Tolan M, Rosbash M. Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA (NEW YORK, N.Y.) 2012; 18:2174-86. [PMID: 23097425 PMCID: PMC3504670 DOI: 10.1261/rna.034090.112] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Spliceosome assembly and/or splicing of a nascent transcript may be crucial for proper isoform expression and gene regulation in higher eukaryotes. We recently showed that cotranscriptional splicing occurs efficiently in Drosophila, but there are not comparable genome-wide nascent splicing data from mammals. To provide this comparison, we analyze a recently generated, high-throughput sequencing data set of mouse liver nascent RNA, originally studied for circadian transcriptional regulation. Cotranscriptional splicing is approximately twofold less efficient in mouse liver than in Drosophila, i.e., nascent intron levels relative to exon levels are ∼0.55 in mouse versus 0.25 in the fly. An additional difference between species is that only mouse cotranscriptional splicing is optimal when 5'-exon length is between 50 and 500 bp, and intron length does not correlate with splicing efficiency, consistent with exon definition. A similar analysis of intron and exon length dependence in the fly is more consistent with intron definition. Contrasted with these differences are many similarities between the two systems: Alternatively annotated introns are less efficiently spliced cotranscriptionally than constitutive introns, and introns of single-intron genes are less efficiently spliced than introns from multi-intron genes. The most striking common feature is intron position: Cotranscriptional splicing is much more efficient when introns are far from the 3' ends of their genes. Additionally, absolute gene length correlates positively with cotranscriptional splicing efficiency independently of intron location and position, in flies as well as in mice. The gene length and distance effects indicate that more "nascent time" gives rise to greater cotranscriptional splicing efficiency in both systems.
Collapse
Affiliation(s)
- Yevgenia L. Khodor
- Howard Hughes Medical Institute and National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Jerome S. Menet
- Howard Hughes Medical Institute and National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael Tolan
- Howard Hughes Medical Institute and National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
- Corresponding authorE-mail
| |
Collapse
|
42
|
Girard C, Will CL, Peng J, Makarov EM, Kastner B, Lemm I, Urlaub H, Hartmuth K, Lührmann R. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nat Commun 2012; 3:994. [PMID: 22871813 DOI: 10.1038/ncomms1998] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 07/10/2012] [Indexed: 12/26/2022] Open
Abstract
There is little quantitative information regarding how much splicing occurs co-transcriptionally in higher eukaryotes, and it remains unclear where precisely splicing occurs in the nucleus. Here we determine the global extent of co- and post-transcriptional splicing in mammalian cells, and their respective subnuclear locations, using antibodies that specifically recognize phosphorylated SF3b155 (P-SF3b155) found only in catalytically activated/active spliceosomes. Quantification of chromatin- and nucleoplasm-associated P-SF3b155 after fractionation of HeLa cell nuclei, reveals that ~80% of pre-mRNA splicing occurs co-transcriptionally. Active spliceosomes localize in situ to regions of decompacted chromatin, at the periphery of or within nuclear speckles. Immunofluorescence microscopy with anti-P-SF3b155 antibodies, coupled with transcription inhibition and a block in splicing after SF3b155 phosphorylation, indicates that post-transcriptional splicing occurs in nuclear speckles and that release of post-transcriptionally spliced mRNA from speckles is coupled to the nuclear mRNA export pathway. Our data provide new insights into when and where splicing occurs in cells.
Collapse
Affiliation(s)
- Cyrille Girard
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Gómez Acuña LI, Fiszbein A, Alló M, Schor IE, Kornblihtt AR. Connections between chromatin signatures and splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:77-91. [PMID: 23074139 DOI: 10.1002/wrna.1142] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Splicing and alternative splicing are involved in the expression of most human genes, playing key roles in differentiation, cell cycle progression, and development. Misregulation of splicing is frequently associated to disease, which imposes a better understanding of the mechanisms underlying splicing regulation. Accumulated evidence suggests that multiple trans-acting factors and cis-regulatory elements act together to determine tissue-specific splicing patterns. Besides, as splicing is often cotranscriptional, a complex picture emerges in which splicing regulation not only depends on the balance of splicing factor binding to their pre-mRNA target sites but also on transcription-associated features such as protein recruitment to the transcribing machinery and elongation kinetics. Adding more complexity to the splicing regulation network, recent evidence shows that chromatin structure is another layer of regulation that may act through various mechanisms. These span from regulation of RNA polymerase II elongation, which ultimately determines splicing decisions, to splicing factor recruitment by specific histone marks. Chromatin may not only be involved in alternative splicing regulation but in constitutive exon recognition as well. Moreover, splicing was found to be necessary for the proper 'writing' of particular chromatin signatures, giving further mechanistic support to functional interconnections between splicing, transcription and chromatin structure. These links between chromatin configuration and splicing raise the intriguing possibility of the existence of a memory for splicing patterns to be inherited through epigenetic modifications.
Collapse
Affiliation(s)
- Luciana I Gómez Acuña
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | | | | | | | | |
Collapse
|
44
|
Misteli T, Spector DL. Protein phosphorylation and the nuclear organization of pre-mRNA splicing. Trends Cell Biol 2012; 7:135-8. [PMID: 17708924 DOI: 10.1016/s0962-8924(96)20043-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Controlled execution of transcription and pre-mRNA splicing is crucial for proper gene expression. The organization of these essential events within the cell nucleus is only beginning to be understood. Here, we describe a model for the cellular arrangement of transcription and pre-mRNA splicing based on recent biochemical and morphological data: transcription and pre-mRNA splicing are spatially and temporally coordinated, and protein phosphorylation regulates both the activity and the subnuclear localization of pre-mRNA splicing factors in nuclear subcompartments.
Collapse
|
45
|
Dujardin G, Lafaille C, Petrillo E, Buggiano V, Gómez Acuña LI, Fiszbein A, Godoy Herz MA, Nieto Moreno N, Muñoz MJ, Alló M, Schor IE, Kornblihtt AR. Transcriptional elongation and alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:134-40. [PMID: 22975042 DOI: 10.1016/j.bbagrm.2012.08.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/23/2012] [Accepted: 08/29/2012] [Indexed: 12/29/2022]
Abstract
Alternative splicing has emerged as a key contributor to proteome diversity, highlighting the importance of understanding its regulation. In recent years it became apparent that splicing is predominantly cotranscriptional, allowing for crosstalk between these two nuclear processes. We discuss some of the links between transcription and splicing, with special emphasis on the role played by transcription elongation in the regulation of alternative splicing events and in particular the kinetic model of alternative splicing regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
Collapse
Affiliation(s)
- Gwendal Dujardin
- Departamento de Fisiología, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Schmid M, Jensen TH. Transcription-associated quality control of mRNP. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:158-68. [PMID: 22982197 DOI: 10.1016/j.bbagrm.2012.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/24/2012] [Accepted: 08/29/2012] [Indexed: 01/06/2023]
Abstract
Although a prime purpose of transcription is to produce RNA, a substantial amount of transcript is nevertheless turned over very early in its lifetime. During transcription RNAs are matured by nucleases from longer precursors and activities are also employed to exert quality control over the RNA synthesis process so as to discard, retain or transcriptionally silence unwanted molecules. In this review we discuss the somewhat paradoxical circumstance that the retention or turnover of RNA is often linked to its synthesis. This occurs via the association of chromatin, or the transcription elongation complex, with RNA degradation (co)factors. Although our main focus is on protein-coding genes, we also discuss mechanisms of transcription-connected turnover of non-protein-coding RNA from where important general principles are derived. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
Collapse
Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C., Denmark
| | | |
Collapse
|
47
|
Hessle V, von Euler A, González de Valdivia E, Visa N. Rrp6 is recruited to transcribed genes and accompanies the spliced mRNA to the nuclear pore. RNA (NEW YORK, N.Y.) 2012; 18:1466-1474. [PMID: 22745224 PMCID: PMC3404368 DOI: 10.1261/rna.032045.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/30/2012] [Indexed: 06/01/2023]
Abstract
Rrp6 is an exoribonuclease involved in the quality control of mRNA biogenesis. We have analyzed the association of Rrp6 with the Balbiani ring pre-mRNPs of Chironomus tentans to obtain insight into the role of Rrp6 in splicing surveillance. Rrp6 is recruited to transcribed genes and its distribution along the genes does not correlate with the positions of exons and introns. In the nucleoplasm, Rrp6 is bound to both unspliced and spliced transcripts. Rrp6 is released from the mRNPs in the vicinity of the nuclear pore before nucleo-cytoplasmic translocation. We show that Rrp6 is associated with newly synthesized transcripts during all the nuclear steps of gene expression and is associated with the transcripts independently of their splicing status. These observations suggest that the quality control of pre-mRNA splicing is not based on the selective recruitment of the exoribonuclease Rrp6 to unprocessed mRNAs.
Collapse
Affiliation(s)
- Viktoria Hessle
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Anne von Euler
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Neus Visa
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden
| |
Collapse
|
48
|
Montes M, Becerra S, Sánchez-Álvarez M, Suñé C. Functional coupling of transcription and splicing. Gene 2012; 501:104-17. [DOI: 10.1016/j.gene.2012.04.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/02/2012] [Accepted: 04/05/2012] [Indexed: 01/13/2023]
|
49
|
Hnilicová J, Staněk D. Where splicing joins chromatin. Nucleus 2012; 2:182-8. [PMID: 21818411 DOI: 10.4161/nucl.2.3.15876] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 12/14/2022] Open
Abstract
There are numerous data suggesting that two key steps in gene expression-transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and methylation and potential mechanisms of their role in splicing. It seems that whereas histone acetylation acts mainly by alterating the transcription rate, histone methylation can also influence splicing directly by recruiting various splicing components.
Collapse
Affiliation(s)
- Jarmila Hnilicová
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague
| | | |
Collapse
|
50
|
Selective forces for the origin of spliceosomes. J Mol Evol 2012; 74:226-31. [PMID: 22407435 DOI: 10.1007/s00239-012-9494-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 02/24/2012] [Indexed: 01/29/2023]
Abstract
It has been proposed that eukaryotic spliceosomes evolved from bacterial group II introns via constructive neutral changes. However, a more likely interpretation is that spliceosomes and group II introns share a common undefined RNA ancestor--a proto-spliceosome. Although, the constructive neutral evolution may have probably played some roles in the development of complexity including the evolution of modern spliceosomes, in fact, the origin, losses and the retention of spliceosomes can be explained straight-forwardly mainly by positive and negative selection: (1) proto-spliceosomes evolved in the RNA world as a mechanism to excise functional RNAs from an RNA genome and to join non-coding information (ancestral to exons) possibly designed to be degraded. (2) The complexity of proto-spliceosomes increased with the invention of protein synthesis in the RNP world and they were adopted for (a) the addition of translation signal to RNAs via trans-splicing, and for (b) the exon-shuffling such as to join together exons coding separate protein domains, to translate them as a single unit and thus to facilitate the molecular interaction of protein domains needed to be assembled to functional catalytic complexes. (3) Finally, the spliceosomes were adopted for cis-splicing of (mainly) non-coding information (contemporary introns) to yield translatable mRNAs. (4) Spliceosome-negative organisms (i.e., prokaryotes) have been selected in the DNA-protein world to save a lot of energy. (5) Spliceosome-positive organisms (i.e., eukaryotes) have been selected, because they have been completely spliceosome-dependent.
Collapse
|