1
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Gañez-Zapater A, Mackowiak SD, Guo Y, Tarbier M, Jordán-Pla A, Friedländer MR, Visa N, Östlund Farrants AK. The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA. Mol Genet Genomics 2022; 297:463-484. [PMID: 35187582 PMCID: PMC8960663 DOI: 10.1007/s00438-022-01863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.
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Affiliation(s)
- Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Center for Genomic Regulation, 08003, Barcelona, Spain
| | - Sebastian D Mackowiak
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencies Biológicas, Valencia University, C/Dr. Moliner, 50, 46100, Burjassot, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden.
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2
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Jian Y, Shim WB, Ma Z. Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions. STRESS BIOLOGY 2021; 1:18. [PMID: 37676626 PMCID: PMC10442046 DOI: 10.1007/s44154-021-00019-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 09/08/2023]
Abstract
The SWI/SNF chromatin remodeling complex utilizes the energy of ATP hydrolysis to facilitate chromatin access and plays essential roles in DNA-based events. Studies in animals, plants and fungi have uncovered sophisticated regulatory mechanisms of this complex that govern development and various stress responses. In this review, we summarize the composition of SWI/SNF complex in eukaryotes and discuss multiple functions of the SWI/SNF complex in regulating gene transcription, mRNA splicing, and DNA damage response. Our review further highlights the importance of SWI/SNF complex in regulating plant immunity responses and fungal pathogenesis. Finally, the potentials in exploiting chromatin remodeling for management of crop disease are presented.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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3
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Yu S, Jordán-Pla A, Gañez-Zapater A, Jain S, Rolicka A, Östlund Farrants AK, Visa N. SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing. Nucleic Acids Res 2019; 46:8557-8573. [PMID: 29860334 PMCID: PMC6144808 DOI: 10.1093/nar/gky438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/08/2018] [Indexed: 12/12/2022] Open
Abstract
SWI/SNF complexes associate with genes and regulate transcription by altering the chromatin at the promoter. It has recently been shown that these complexes play a role in pre-mRNA processing by associating at alternative splice sites. Here, we show that SWI/SNF complexes are involved also in pre-mRNA 3′ end maturation by facilitating 3′ end cleavage of specific pre-mRNAs. Comparative proteomics show that SWI/SNF ATPases interact physically with subunits of the cleavage and polyadenylation complexes in fly and human cells. In Drosophila melanogaster, the SWI/SNF ATPase Brahma (dBRM) interacts with the CPSF6 subunit of cleavage factor I. We have investigated the function of dBRM in 3′ end formation in S2 cells by RNA interference, single-gene analysis and RNA sequencing. Our data show that dBRM facilitates pre-mRNA cleavage in two different ways: by promoting the association of CPSF6 to the cleavage region and by stabilizing positioned nucleosomes downstream of the cleavage site. These findings show that SWI/SNF complexes play a role also in the cleavage of specific pre-mRNAs in animal cells.
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Affiliation(s)
- Simei Yu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Shruti Jain
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
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4
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Sztacho M, Sobol M, Balaban C, Escudeiro Lopes SE, Hozák P. Nuclear phosphoinositides and phase separation: Important players in nuclear compartmentalization. Adv Biol Regul 2018; 71:111-117. [PMID: 30249540 DOI: 10.1016/j.jbior.2018.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/14/2018] [Accepted: 09/15/2018] [Indexed: 02/08/2023]
Abstract
Nuclear phosphoinositides are recognized as regulators of many nuclear processes including chromatin remodeling, splicing, transcription, DNA repair and epigenetics. These processes are spatially organized in different nuclear compartments. Phase separation is involved in the formation of various nuclear compartments and molecular condensates separated from surrounding environment. The surface of such structures spatiotemporally coordinates formation of protein complexes. PI(4,5)P2 (PIP2) integration into phase-separated structures might provide an additional step in their spatial diversification by attracting certain proteins with affinity to PIP2. Our laboratory has recently identified novel membrane-free PIP2-containing structures, so called Nuclear Lipid Islets (NLIs). We provide an evidence that these structures are evolutionary conserved in different organisms. We hypothesize that NLIs serve as a scaffolding platform which facilitates the formation of transcription factories, thus participating in the formation of nuclear architecture competent for transcription. In this review we speculate on a possible role of NLIs in the integration of various processes linked to RNAPII transcription, chromatin remodeling, actin-myosin interaction, alternative splicing and lamin structures.
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Affiliation(s)
- Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Can Balaban
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Sara Eliana Escudeiro Lopes
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic; Department of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., division BIOCEV, 25250, Vestec, Czech Republic; Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20, Prague, Czech Republic.
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5
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Jordán-Pla A, Yu S, Waldholm J, Källman T, Östlund Farrants AK, Visa N. SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma. BMC Genomics 2018; 19:367. [PMID: 29776334 PMCID: PMC5960078 DOI: 10.1186/s12864-018-4746-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Background Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. Results Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation. We show that 49% of the BRM target genes in S2 cells are regulated through mechanisms that do not require BRM to have an ATPase activity. We also show that the catalytic and non-catalytic mechanisms of SWI/SNF regulation operate on two subsets of genes that differ in promoter architecture and are linked to different biological processes. Conclusions This study shows that the non-catalytic role of SWI/SNF in transcription regulation is far more prevalent than previously anticipated and that the genes that are regulated by SWI/SNF through ATPase-dependent and ATPase-independent mechanisms have specialized roles in different cellular and developmental processes. Electronic supplementary material The online version of this article (10.1186/s12864-018-4746-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Simei Yu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Johan Waldholm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Thomas Källman
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
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6
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Mainland RL, Lyons TA, Ruth MM, Kramer JM. Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines. BMC Res Notes 2017; 10:647. [PMID: 29187229 PMCID: PMC5707822 DOI: 10.1186/s13104-017-2959-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/21/2017] [Indexed: 01/21/2023] Open
Abstract
Objective RNA interference is employed extensively in Drosophila research to study gene function within a specific cell-type or tissue. Thousands of transgenic Drosophila lines have been generated to express double stranded RNA for gene knockdown; however, no standardized method exists for quantifying their knockdown efficiency. Since antibodies are not available for many proteins, quantitative real-time PCR is often used. Here, we explore how primer design and RNA isolation method can influence detection of gene knockdown using qPCR. Results We tested differences in detected gene knockdown efficiency when using purified polyadenylated mRNA or total RNA as templates for cDNA synthesis. We also tested two different primer locations for each gene: one to amplify a region 5′ of the RNAi cut site, and one to amplify a region 3′ of the cut site. Consistently, the strongest gene knockdown was detected when qPCR was performed using 5′ primer sets in combination with mRNA-derived cDNA. Our results indicate that detection of undegraded mRNA cleavage fragments can result in underestimation of true knockdown efficiency for a RNAi construct. Purification of polyadenylated mRNA, combined with primers designed to amplify the non-polyadenylated 5′ mRNA cleavage fragment can avoid this problem. Electronic supplementary material The online version of this article (10.1186/s13104-017-2959-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roslyn L Mainland
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St., London, ON, N6A 5C1, Canada
| | - Taylor A Lyons
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St., London, ON, N6A 5C1, Canada
| | - Mike M Ruth
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St., London, ON, N6A 5C1, Canada
| | - Jamie M Kramer
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St., London, ON, N6A 5C1, Canada. .,Department of Biology, Faculty of Science, Western University, London, ON, Canada. .,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada.
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7
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Abstract
Several studies propose an influence of chromatin on pre-mRNA splicing, but it is still unclear how widespread and how direct this phenomenon is. We find here that when assembled in vivo, the U2 snRNP co-purifies with a subset of chromatin-proteins, including histones and remodeling complexes like SWI/SNF. Yet, an unbiased RNAi screen revealed that the outcome of splicing is influenced by a much larger variety of chromatin factors not all associating with the spliceosome. The availability of this broad range of chromatin factors impacting splicing further unveiled their very context specific effect, resulting in either inclusion or skipping, depending on the exon under scrutiny. Finally, a direct assessment of the impact of chromatin on splicing using an in vitro co-transcriptional splicing assay with pre-mRNAs transcribed from a nucleosomal template, demonstrated that chromatin impacts nascent pre-mRNP in their competence for splicing. Altogether, our data show that numerous chromatin factors associated or not with the spliceosome can affect the outcome of splicing, possibly as a function of the local chromatin environment that by default interferes with the efficiency of splicing. Splicing is an RNA editing step allowing to produce multiple transcripts from a single gene. The gene itself is organized in chromatin, associating DNA and multiple proteins. Some proteins regulating the compaction of the chromatin also affect RNA splicing. Yet, it was unclear whether these chromatin proteins were exceptions or whether chromatin very generally affected the outcome of splicing. Here, we show that a subset of chromatin proteins is physically in interaction with the enzyme responsible for RNA splicing. In addition, several chromatin proteins not found directly associated with the splicing machinery were also able to influence RNA splicing, suggesting that chromatin compaction very globally plays a role in splicing. This finding was confirmed using the first in vitro assay combining transcription and splicing in the context of chromatin; this assay showed that assembling DNA with chromatin proteins influences the efficiency of splicing.
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8
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Fontana GA, Rigamonti A, Lenzken SC, Filosa G, Alvarez R, Calogero R, Bianchi ME, Barabino SML. Oxidative stress controls the choice of alternative last exons via a Brahma-BRCA1-CstF pathway. Nucleic Acids Res 2016; 45:902-914. [PMID: 27591253 PMCID: PMC5314785 DOI: 10.1093/nar/gkw780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 01/08/2023] Open
Abstract
Alternative splicing of terminal exons increases transcript and protein diversity. How physiological and pathological stimuli regulate the choice between alternative terminal exons is, however, largely unknown. Here, we show that Brahma (BRM), the ATPase subunit of the hSWI/SNF chromatin-remodeling complex interacts with BRCA1/BARD1, which ubiquitinates the 50 kDa subunit of the 3′ end processing factor CstF. This results in the inhibition of transcript cleavage at the proximal poly(A) site and a shift towards inclusion of the distal terminal exon. Upon oxidative stress, BRM is depleted, cleavage inhibition is released, and inclusion of the proximal last exon is favoored. Our findings elucidate a novel regulatory mechanism, distinct from the modulation of transcription elongation by BRM that controls alternative splicing of internal exons.
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Affiliation(s)
- Gabriele A Fontana
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Aurora Rigamonti
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Silvia C Lenzken
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Giuseppe Filosa
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Reinaldo Alvarez
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Raffaele Calogero
- Department of Biotechnology and Health Sciences, University of Torino, Via Nizza 52, I-10126 Torino, Italy
| | - Marco E Bianchi
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute and University, Via Olgettina 60, 20132 Milan, Italy
| | - Silvia M L Barabino
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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9
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Hodges C, Kirkland JG, Crabtree GR. The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026930. [PMID: 27413115 DOI: 10.1101/cshperspect.a026930] [Citation(s) in RCA: 276] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During the last decade, a host of epigenetic mechanisms were found to contribute to cancer and other human diseases. Several genomic studies have revealed that ∼20% of malignancies have alterations of the subunits of polymorphic BRG-/BRM-associated factor (BAF) and Polybromo-associated BAF (PBAF) complexes, making them among the most frequently mutated complexes in cancer. Recurrent mutations arise in genes encoding several BAF/PBAF subunits, including ARID1A, ARID2, PBRM1, SMARCA4, and SMARCB1 These subunits share some degree of conservation with subunits from related adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in model organisms, in which a large body of work provides insight into their roles in cancer. Here, we review the roles of BAF- and PBAF-like complexes in these organisms, and relate these findings to recent discoveries in cancer epigenomics. We review several roles of BAF and PBAF complexes in cancer, including transcriptional regulation, DNA repair, and regulation of chromatin architecture and topology. More recent results highlight the need for new techniques to study these complexes.
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Affiliation(s)
- Courtney Hodges
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Jacob G Kirkland
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Gerald R Crabtree
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
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10
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Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C. Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast. PLoS Genet 2015; 11:e1005074. [PMID: 25825871 PMCID: PMC4380400 DOI: 10.1371/journal.pgen.1005074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/16/2015] [Indexed: 12/19/2022] Open
Abstract
Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ΔSWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects—and is affected by—co-transcriptional splicing. It has recently become apparent that most introns are removed from pre-mRNA while the transcript is still engaged with RNA polymerase II (RNAPII). To gain insight into possible roles for chromatin in co-transcriptional splicing, we generated a genome-wide genetic interaction map in fission yeast and uncovered numerous connections between splicing and chromatin. The SWI/SNF remodeling complex is typically thought to activate gene expression by relieving barriers to polymerase elongation imposed by nucleosomes. Here we show that this remodeler is important for an early step in splicing in which Prp2, an RNA-dependent ATPase, is recruited to the assembling spliceosome to promote catalytic activation. Interestingly, introns with sub-optimal splice sites are particularly dependent on SWI/SNF, suggesting the impact of nucleosome dynamics on the kinetics of spliceosome assembly and catalysis. By monitoring nucleosome occupancy, we show significant alterations in nucleosome density in particular splicing and chromatin mutants, which generally paralleled the levels of RNAPII. Taken together, our findings challenge the notion that nucleosomes simply act as barriers to elongation; rather, we suggest that polymerase pausing at nucleosomes can activate gene expression by allowing more time for co-transcriptional splicing.
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Affiliation(s)
- Kristin L. Patrick
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Colm J. Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
| | - Jesse J. Lipp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Kelly E. Nissen
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Assen Roguev
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
- * E-mail:
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11
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Pinheiro P, Bereman MS, Burd J, Pals M, Armstrong S, Howe KJ, Thannhauser TW, MacCoss MJ, Gray SM, Cilia M. Evidence of the biochemical basis of host virulence in the greenbug aphid, Schizaphis graminum (Homoptera: Aphididae). J Proteome Res 2014; 13:2094-108. [PMID: 24588548 DOI: 10.1021/pr4012415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biotypes of aphids and many other insect pests are defined based on the phenotypic response of host plants to the insect pest without considering their intrinsic characteristics and genotypes. Plant breeders have spent considerable effort developing aphid-resistant, small-grain varieties to limit insecticide control of the greenbug, Schizaphis graminum. However, new S. graminum biotypes frequently emerge that break resistance. Mechanisms of virulence on the aphid side of the plant-insect interaction are not well understood. S. graminum biotype H is highly virulent on most small grain varieties. This characteristic makes biotype H ideal for comparative proteomics to investigate the basis of biotype virulence in aphids. In this study, we used comparative proteomics to identify protein expression differences associated with virulence. Aphid proteins involved in the tricarboxylic acid cycle, immune system, cell division, and antiapoptosis pathways were found to be up-regulated in biotype H relative to other biotypes. Proteins from the bacterial endosymbiont of aphids were also differentially expressed in biotype H. Guided by the proteome results, we tested whether biotype H had a fitness advantage compared with other S. graminum biotypes and found that biotype H had a higher reproductive fitness as compared with two other biotypes on a range of different wheat germplasms. Finally, we tested whether aphid genetics can be used to further dissect the genetic mechanisms of biotype virulence in aphids. The genetic data showed that sexual reproduction is a source of biotypic variation observed in S. graminum.
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Affiliation(s)
- Patricia Pinheiro
- Department of Entomology, Cornell University , 2130 Comstock Hall, Ithaca, New York 14853 United States
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12
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Yu S, Waldholm J, Böhm S, Visa N. Brahma regulates a specific trans-splicing event at the mod(mdg4) locus of Drosophila melanogaster. RNA Biol 2014; 11:134-45. [PMID: 24526065 DOI: 10.4161/rna.27866] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The mod(mdg4) locus of Drosophila melanogaster contains several transcription units encoded on both DNA strands. The mod(mdg4) pre-mRNAs are alternatively spliced, and a very significant fraction of the mature mod(mdg4) mRNAs are formed by trans-splicing. We have studied the transcripts derived from one of the anti-sense regions within the mod(mdg4) locus in order to shed light on the expression of this complex locus. We have characterized the expression of anti-sense mod(mdg4) transcripts in S2 cells, mapped their transcription start sites and cleavage sites, identified and quantified alternatively spliced transcripts, and obtained insight into the regulation of the mod(mdg4) trans-splicing. In a previous study, we had shown that the alternative splicing of some mod(mdg4) transcripts was regulated by Brahma (BRM), the ATPase subunit of the SWI/SNF chromatin-remodeling complex. Here we show, using RNA interference and overexpression of recombinant BRM proteins, that the levels of BRM affect specifically the abundance of a trans-spliced mod(mdg4) mRNA isoform in both S2 cells and larvae. This specific effect on trans-splicing is accompanied by a local increase in the density of RNA polymerase II and by a change in the phosphorylation state of the C-terminal domain of the large subunit of RNA polymerase II. Interestingly, the regulation of the mod(mdg4) splicing by BRM is independent of the ATPase activity of BRM, which suggests that the mechanism by which BRM modulates trans-splicing is independent of its chromatin-remodeling activity.
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Affiliation(s)
- Simei Yu
- Department of Molecular Biosciences; The Wenner-Gren Institute; Stockholm University; Stockholm, Sweden
| | - Johan Waldholm
- Department of Molecular Biosciences; The Wenner-Gren Institute; Stockholm University; Stockholm, Sweden
| | - Stefanie Böhm
- Department of Molecular Biosciences; The Wenner-Gren Institute; Stockholm University; Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences; The Wenner-Gren Institute; Stockholm University; Stockholm, Sweden
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13
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Jin Y, Xu J, Yin MX, Lu Y, Hu L, Li P, Zhang P, Yuan Z, Ho MS, Ji H, Zhao Y, Zhang L. Brahma is essential for Drosophila intestinal stem cell proliferation and regulated by Hippo signaling. eLife 2013; 2:e00999. [PMID: 24137538 PMCID: PMC3796317 DOI: 10.7554/elife.00999] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/08/2013] [Indexed: 11/13/2022] Open
Abstract
Chromatin remodeling processes are among the most important regulatory mechanisms in controlling cell proliferation and regeneration. Drosophila intestinal stem cells (ISCs) exhibit self-renewal potentials, maintain tissue homeostasis, and serve as an excellent model for studying cell growth and regeneration. In this study, we show that Brahma (Brm) chromatin-remodeling complex is required for ISC proliferation and damage-induced midgut regeneration in a lineage-specific manner. ISCs and enteroblasts exhibit high levels of Brm proteins; and without Brm, ISC proliferation and differentiation are impaired. Importantly, the Brm complex participates in ISC proliferation induced by the Scalloped-Yorkie transcriptional complex and that the Hippo (Hpo) signaling pathway directly restricted ISC proliferation by regulating Brm protein levels by inducing caspase-dependent cleavage of Brm. The cleavage resistant form of Brm protein promoted ISC proliferation. Our findings highlighted the importance of Hpo signaling in regulating epigenetic components such as Brm to control downstream transcription and hence ISC proliferation. DOI:http://dx.doi.org/10.7554/eLife.00999.001.
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Affiliation(s)
- Yunyun Jin
- State Key Laboratory of Cell Biology , Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , China
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14
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Abstract
Precursor mRNA splicing is one of the most highly regulated processes in metazoan species. In addition to generating vast repertoires of RNAs and proteins, splicing has a profound impact on other gene regulatory layers, including mRNA transcription, turnover, transport, and translation. Conversely, factors regulating chromatin and transcription complexes impact the splicing process. This extensive crosstalk between gene regulatory layers takes advantage of dynamic spatial, physical, and temporal organizational properties of the cell nucleus, and further emphasizes the importance of developing a multidimensional understanding of splicing control.
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15
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Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz MJ. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 2013; 14:153-65. [PMID: 23385723 DOI: 10.1038/nrm3525] [Citation(s) in RCA: 575] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alternative splicing was discovered simultaneously with splicing over three decades ago. Since then, an enormous body of evidence has demonstrated the prevalence of alternative splicing in multicellular eukaryotes, its key roles in determining tissue- and species-specific differentiation patterns, the multiple post- and co-transcriptional regulatory mechanisms that control it, and its causal role in hereditary disease and cancer. The emerging evidence places alternative splicing in a central position in the flow of eukaryotic genetic information, between transcription and translation, in that it can respond not only to various signalling pathways that target the splicing machinery but also to transcription factors and chromatin structure.
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Affiliation(s)
- Alberto R Kornblihtt
- Departamento de Fisiología, Biología Molecular y Celular e Instituto de Fisiología, Biología Molecular y Neurociencias, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina.
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16
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Kondrashov A, Meijer HA, Barthet-Barateig A, Parker HN, Khurshid A, Tessier S, Sicard M, Knox AJ, Pang L, de Moor CH. Inhibition of polyadenylation reduces inflammatory gene induction. RNA (NEW YORK, N.Y.) 2012; 18:2236-2250. [PMID: 23118416 PMCID: PMC3504674 DOI: 10.1261/rna.032391.112] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 09/14/2012] [Indexed: 05/31/2023]
Abstract
Cordycepin (3' deoxyadenosine) has long been used in the study of in vitro assembled polyadenylation complexes, because it terminates the poly(A) tail and arrests the cleavage complex. It is derived from caterpillar fungi, which are highly prized in Chinese traditional medicine. Here we show that cordycepin specifically inhibits the induction of inflammatory mRNAs by cytokines in human airway smooth muscle cells without affecting the expression of control mRNAs. Cordycepin treatment results in shorter poly(A) tails, and a reduction in the efficiency of mRNA cleavage and transcription termination is observed, indicating that the effects of cordycepin on 3' processing in cells are similar to those described in in vitro reactions. For the CCL2 and CXCL1 mRNAs, the effects of cordycepin are post-transcriptional, with the mRNA disappearing during or immediately after nuclear export. In contrast, although the recruitment of RNA polymerase II to the IL8 promoter is also unaffected, the levels of nascent transcript are reduced, indicating a defect in transcription elongation. We show that a reporter construct with 3' sequences from a histone gene is unaffected by cordycepin, while CXCL1 sequences confer cordycepin sensitivity to the reporter, demonstrating that polyadenylation is indeed required for the effect of cordycepin on gene expression. In addition, treatment with another polyadenyation inhibitor and knockdown of poly(A) polymerase α also specifically reduced the induction of inflammatory mRNAs. These data demonstrate that there are differences in the 3' processing of inflammatory and housekeeping genes and identify polyadenylation as a novel target for anti-inflammatory drugs.
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Affiliation(s)
- Alexander Kondrashov
- School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Hedda A. Meijer
- School of Clinical Sciences, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | | | - Hannah N. Parker
- School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Asma Khurshid
- School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Sarah Tessier
- School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Marie Sicard
- School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Alan J. Knox
- School of Clinical Sciences, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Linhua Pang
- School of Clinical Sciences, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Cornelia H. de Moor
- School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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17
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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]
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