1
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Hou H, Jin Q, Ren Y, Chen Z, Wang Q, Xu Y. Structure of the SNAPc-bound RNA polymerase III preinitiation complex. Cell Res 2023; 33:565-568. [PMID: 37165065 PMCID: PMC10313668 DOI: 10.1038/s41422-023-00819-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/23/2023] [Indexed: 05/12/2023] Open
Affiliation(s)
- Haifeng Hou
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qianwei Jin
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Zhenguo Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
- The International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.
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2
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Assembly of SNAPc, Bdp1, and TBP on the U6 snRNA Gene Promoter in Drosophila melanogaster. Mol Cell Biol 2020; 40:MCB.00641-19. [PMID: 32253345 DOI: 10.1128/mcb.00641-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/27/2020] [Indexed: 01/03/2023] Open
Abstract
U6 snRNA is transcribed by RNA polymerase III (Pol III) and has an external upstream promoter that consists of a TATA sequence recognized by the TBP subunit of the Pol III basal transcription factor IIIB and a proximal sequence element (PSE) recognized by the small nuclear RNA activating protein complex (SNAPc). Previously, we found that Drosophila melanogaster SNAPc (DmSNAPc) bound to the U6 PSE can recruit the Pol III general transcription factor Bdp1 to form a stable complex with the DNA. Here, we show that DmSNAPc-Bdp1 can recruit TBP to the U6 promoter, and we identify a region of Bdp1 that is sufficient for TBP recruitment. Moreover, we find that this same region of Bdp1 cross-links to nucleotides within the U6 PSE at positions that also cross-link to DmSNAPc. Finally, cross-linking mass spectrometry reveals likely interactions of specific DmSNAPc subunits with Bdp1 and TBP. These data, together with previous findings, have allowed us to build a more comprehensive model of the DmSNAPc-Bdp1-TBP complex on the U6 promoter that includes nearly all of DmSNAPc, a portion of Bdp1, and the conserved region of TBP.
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3
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Dergai O, Hernandez N. How to Recruit the Correct RNA Polymerase? Lessons from snRNA Genes. Trends Genet 2019; 35:457-469. [PMID: 31040056 DOI: 10.1016/j.tig.2019.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 01/03/2023]
Abstract
Nuclear eukaryotic genomes are transcribed by three related RNA polymerases (Pol), which transcribe distinct gene sets. Specific Pol recruitment is achieved through selective core promoter recognition by basal transcription factors (TFs). Transcription by an inappropriate Pol appears to be rare and to generate mostly unstable products. A collection of short noncoding RNA genes [for example, small nuclear RNA (snRNA) or 7SK RNA genes], which play essential roles in processes such as maturation of RNA molecules or control of Pol II transcription elongation, possess highly similar core promoters, and yet are transcribed for some by Pol II and for others by Pol III as a result of small promoter differences. Here we discuss the mechanisms of selective Pol recruitment to such promoters.
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Affiliation(s)
- Oleksandr Dergai
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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4
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Verma N, Hurlburt AM, Wolfe A, Kim MK, Kang YS, Kang JJ, Stumph WE. Bdp1 interacts with SNAPc bound to a U6, but not U1, snRNA gene promoter element to establish a stable protein-DNA complex. FEBS Lett 2018; 592:2489-2498. [PMID: 29932462 DOI: 10.1002/1873-3468.13169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/13/2018] [Accepted: 06/17/2018] [Indexed: 12/15/2022]
Abstract
In metazoans, U6 small nuclear RNA (snRNA) gene promoters utilize a proximal sequence element (PSE) recognized by the small nuclear RNA-activating protein complex (SNAPc). SNAPc interacts with the transcription factor TFIIIB, which consists of the subunits TBP, Brf1 (Brf2 in vertebrates), and Bdp1. Here, we show that, in Drosophila melanogaster, DmSNAPc directly recruits Bdp1 to the U6 promoter, and we identify an 87-residue region of Bdp1 involved in this interaction. Importantly, Bdp1 recruitment requires that DmSNAPc be bound to a U6 PSE rather than a U1 PSE. This is consistent with the concept that DmSNAPc adopts different conformations on U6 and U1 PSEs, which lead to the subsequent recruitment of distinct general transcription factors and RNA polymerases for U6 and U1 gene transcription.
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Affiliation(s)
- Neha Verma
- Department of Biology, Molecular Biology Institute, San Diego State University, CA, USA
| | - Ann Marie Hurlburt
- Department of Biology, Molecular Biology Institute, San Diego State University, CA, USA
| | - Angela Wolfe
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - Mun Kyoung Kim
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - Yoon Soon Kang
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - Jin Joo Kang
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - William E Stumph
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
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5
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Ohtani M. Transcriptional regulation of snRNAs and its significance for plant development. JOURNAL OF PLANT RESEARCH 2017; 130:57-66. [PMID: 27900551 DOI: 10.1007/s10265-016-0883-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/01/2016] [Indexed: 05/05/2023]
Abstract
Small nuclear RNA (snRNA) represents a distinct class of non-coding RNA molecules. As these molecules have fundamental roles in RNA metabolism, including pre-mRNA splicing and ribosomal RNA processing, it is essential that their transcription be tightly regulated in eukaryotic cells. The genome of each organism contains hundreds of snRNA genes. Although the structures of these genes are highly diverse among organisms, the trans-acting factors that regulate snRNA transcription are evolutionarily conserved. Recent studies of the Arabidopsis thaliana srd2-1 mutant, which is defective in the snRNA transcription factor, provide insight into the physiological significance of snRNA regulation in plant development. Here, I review the current understanding of the molecular mechanisms underlying snRNA transcription.
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Affiliation(s)
- Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan.
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan.
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6
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Kang JJ, Kang YS, Stumph WE. TFIIIB subunit locations on U6 gene promoter DNA mapped by site-specific protein-DNA photo-cross-linking. FEBS Lett 2016; 590:1488-97. [PMID: 27112515 DOI: 10.1002/1873-3468.12185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/05/2022]
Abstract
RNA polymerase III-transcribed U6 snRNA genes have gene-external promoters that contain TATA boxes. U6 TATA sequences are bound by TFIIIB that in Drosophila contains the three subunits TBP, Brf1, and Bdp1. The overall structure of TFIIIB is still not well understood. We have therefore studied the mode of TFIIIB binding to DNA by site-specific protein-DNA photo-cross-linking. The results indicate that a portion of Brf1 is sandwiched between Bdp1 and TBP upstream of the TATA box. Furthermore, Bdp1 traverses the DNA under the N-terminal stirrup of TBP to interact with the DNA (and very likely Brf1) downstream of the TATA sequence.
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Affiliation(s)
- Jin Joo Kang
- Department of Chemistry and Biochemistry, San Diego State University, CA, USA
| | - Yoon Soon Kang
- Department of Chemistry and Biochemistry, San Diego State University, CA, USA
| | - William E Stumph
- Department of Chemistry and Biochemistry, San Diego State University, CA, USA
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7
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Ohtani M, Takebayashi A, Hiroyama R, Xu B, Kudo T, Sakakibara H, Sugiyama M, Demura T. Cell dedifferentiation and organogenesis in vitro require more snRNA than does seedling development in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2015; 128:371-80. [PMID: 25740809 DOI: 10.1007/s10265-015-0704-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Abstract
Small nuclear RNA (snRNA) is a class of non-coding RNAs that processes pre-mRNA and rRNA. Transcription of abundant snRNA species is regulated by the snRNA activating protein complex (SNAPc), which is conserved among multicellular organisms including plants. SRD2, a putative subunit of SNAPc in Arabidopsis thaliana, is essential for development, and the point mutation srd2-1 causes severe defects in hypocotyl dedifferentiation and de novo meristem formation. Based on phenotypic analysis of srd2-1 mutant plants, we previously proposed that snRNA content is a limiting factor in dedifferentiation in plant cells. Here, we performed functional complementation analysis of srd2-1 using transgenic srd2-1 Arabidopsis plants harboring SRD2 homologs from Populus trichocarpa (poplar), Nicotiana tabacum (tobacco), Oryza sativa (rice), the moss Physcomitrella patens, and Homo sapiens (human) under the control of the Arabidopsis SRD2 promoter. Only rice SRD2 suppressed the faulty tissue culture responses of srd2-1, and restore the snRNA levels; however, interestingly, all SRD2 homologs except poplar SRD2 rescued the srd2-1 defects in seedling development. These findings demonstrated that cell dedifferentiation and organogenesis induced during tissue culture require higher snRNA levels than does seedling development.
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Affiliation(s)
- Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan,
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8
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Takahashi H, Takigawa I, Watanabe M, Anwar D, Shibata M, Tomomori-Sato C, Sato S, Ranjan A, Seidel CW, Tsukiyama T, Mizushima W, Hayashi M, Ohkawa Y, Conaway JW, Conaway RC, Hatakeyama S. MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex. Nat Commun 2015; 6:5941. [PMID: 25575120 DOI: 10.1038/ncomms6941] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 11/24/2014] [Indexed: 01/09/2023] Open
Abstract
Regulation of transcription elongation by RNA polymerase II (Pol II) is a key regulatory step in gene transcription. Recently, the little elongation complex (LEC)-which contains the transcription elongation factor ELL/EAF-was found to be required for the transcription of Pol II-dependent small nuclear RNA (snRNA) genes. Here we show that the human Mediator subunit MED26 plays a role in the recruitment of LEC to a subset of snRNA genes through direct interaction of EAF and the N-terminal domain (NTD) of MED26. Loss of MED26 in cells decreases the occupancy of LEC at a subset of snRNA genes and results in a reduction in their transcription. Our results suggest that the MED26-NTD functions as a molecular switch in the exchange of TBP-associated factor 7 (TAF7) for LEC to facilitate the transition from initiation to elongation during transcription of a subset of snRNA genes.
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Affiliation(s)
- Hidehisa Takahashi
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Ichigaku Takigawa
- Creative Research Institution, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Masashi Watanabe
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Delnur Anwar
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Mio Shibata
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Chieri Tomomori-Sato
- Stowers Institute for Medical Research, 1000 E, 50th Street, Kansas City, Missouri 64110, USA
| | - Shigeo Sato
- Stowers Institute for Medical Research, 1000 E, 50th Street, Kansas City, Missouri 64110, USA
| | - Amol Ranjan
- Stowers Institute for Medical Research, 1000 E, 50th Street, Kansas City, Missouri 64110, USA
| | - Chris W Seidel
- Stowers Institute for Medical Research, 1000 E, 50th Street, Kansas City, Missouri 64110, USA
| | - Tadasuke Tsukiyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Wataru Mizushima
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Masayasu Hayashi
- Department of Advanced Medical Initiatives, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Joan W Conaway
- 1] Stowers Institute for Medical Research, 1000 E, 50th Street, Kansas City, Missouri 64110, USA [2] Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City KS 66160, USA
| | - Ronald C Conaway
- 1] Stowers Institute for Medical Research, 1000 E, 50th Street, Kansas City, Missouri 64110, USA [2] Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City KS 66160, USA
| | - Shigetsugu Hatakeyama
- Department of Biochemistry, Hokkaido University Graduate School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido 060-8638, Japan
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9
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Kang YS, Kurano M, Stumph WE. The Myb domain of the largest subunit of SNAPc adopts different architectural configurations on U1 and U6 snRNA gene promoter sequences. Nucleic Acids Res 2014; 42:12440-54. [PMID: 25324315 PMCID: PMC4227766 DOI: 10.1093/nar/gku905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The small nuclear RNA (snRNA) activating protein complex (SNAPc) is essential for transcription of genes that encode the snRNAs. Drosophila melanogaster SNAPc (DmSNAPc) consists of three subunits (DmSNAP190, DmSNAP50 and DmSNAP43) that form a stable complex that recognizes an snRNA gene promoter element called the PSEA. Although all three subunits are required for sequence-specific DNA binding activity, only DmSNAP190 possesses a canonical DNA binding domain consisting of 4.5 tandem Myb repeats homologous to the Myb repeats in the DNA binding domain of the Myb oncoprotein. In this study, we use site-specific protein–DNA photo-cross-linking technology followed by site-specific protein cleavage to map domains of DmSNAP190 that interact with specific phosphate positions in the U6 PSEA. The results indicate that at least two DmSNAP190 Myb repeats contact the DNA in a significantly different manner when DmSNAPc binds to a U6 PSEA versus a U1 PSEA, even though the two PSEA sequences differ at only 5 of 21 nucleotide positions. The results are consistent with a model in which the specific DNA sequences of the U1 and U6 PSEAs differentially alter the conformation of DmSNAPc, leading to the subsequent recruitment of different RNA polymerases to the U1 and U6 gene promoters.
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Affiliation(s)
- Yoon Soon Kang
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, San Diego, CA 92182-1030, USA
| | - Michelle Kurano
- Department of Biology, Molecular Biology Institute, San Diego State University, San Diego, CA 92182-1030, USA
| | - William E Stumph
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, San Diego, CA 92182-1030, USA
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10
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The little elongation complex functions at initiation and elongation phases of snRNA gene transcription. Mol Cell 2013; 51:493-505. [PMID: 23932780 DOI: 10.1016/j.molcel.2013.07.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/13/2013] [Accepted: 07/02/2013] [Indexed: 11/22/2022]
Abstract
The small nuclear RNA (snRNA) genes have been widely used as a model system for understanding transcriptional regulation due to the unique aspects of their promoter structure, selectivity for either RNA polymerase (Pol) II or III, and because of their unique mechanism of termination that is tightly linked with the promoter. Recently, we identified the little elongation complex (LEC) in Drosophila that is required for the expression of Pol II-transcribed snRNA genes. Here, using Drosophila and mammalian systems, we provide genetic and molecular evidence that LEC functions in at least two phases of snRNA transcription: an initiation step requiring the ICE1 subunit, and an elongation step requiring ELL.
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11
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Doherty MT, Kang YS, Lee C, Stumph WE. Architectural arrangement of the small nuclear RNA (snRNA)-activating protein complex 190 subunit (SNAP190) on U1 snRNA gene promoter DNA. J Biol Chem 2012; 287:39369-79. [PMID: 23038247 PMCID: PMC3501025 DOI: 10.1074/jbc.m112.407775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/01/2012] [Indexed: 11/06/2022] Open
Abstract
Myb repeats ∼52 amino acid residues in length were first characterized in the oncogenic Myb transcription factor, which contains three tandem Myb repeats in its DNA-binding domain. Proteins of this family normally contain either one, two, or three tandem Myb repeats that are involved in protein-DNA interactions. The small nuclear RNA (snRNA)-activating protein complex (SNAPc) is a heterotrimeric transcription factor that is required for expression of small nuclear RNA genes. This complex binds to an essential promoter element, the proximal sequence element, centered ∼50 base pairs upstream of the transcription start site of snRNA genes. SNAP190, the largest subunit of SNAPc, uncharacteristically contains 4.5 tandem Myb repeats. Little is known about the arrangement of the Myb repeats in the SNAPc-DNA complex, and it has not been clear whether all 4.5 Myb repeats contact the DNA. By using a site-specific protein-DNA photo-cross-linking assay, we have now mapped specific nucleotides where each of the Myb repeats of Drosophila melanogaster SNAP190 interacts with a U1 snRNA gene proximal sequence element. The results reveal the topological arrangement of the 4.5 SNAP190 Myb repeats relative to the DNA and to each other when SNAP190 is bound to a U1 promoter as a subunit of SNAPc.
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Affiliation(s)
| | - Yoon Soon Kang
- Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
| | - Cheryn Lee
- Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
| | - William E. Stumph
- Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030
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12
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James Faresse N, Canella D, Praz V, Michaud J, Romascano D, Hernandez N. Genomic study of RNA polymerase II and III SNAPc-bound promoters reveals a gene transcribed by both enzymes and a broad use of common activators. PLoS Genet 2012; 8:e1003028. [PMID: 23166507 PMCID: PMC3499247 DOI: 10.1371/journal.pgen.1003028] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 08/24/2012] [Indexed: 12/23/2022] Open
Abstract
SNAPc is one of a few basal transcription factors used by both RNA polymerase (pol) II and pol III. To define the set of active SNAPc-dependent promoters in human cells, we have localized genome-wide four SNAPc subunits, GTF2B (TFIIB), BRF2, pol II, and pol III. Among some seventy loci occupied by SNAPc and other factors, including pol II snRNA genes, pol III genes with type 3 promoters, and a few un-annotated loci, most are primarily occupied by either pol II and GTF2B, or pol III and BRF2. A notable exception is the RPPH1 gene, which is occupied by significant amounts of both polymerases. We show that the large majority of SNAPc-dependent promoters recruit POU2F1 and/or ZNF143 on their enhancer region, and a subset also recruits GABP, a factor newly implicated in SNAPc-dependent transcription. These activators associate with pol II and III promoters in G1 slightly before the polymerase, and ZNF143 is required for efficient transcription initiation complex assembly. The results characterize a set of genes with unique properties and establish that polymerase specificity is not absolute in vivo. SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and others RNA polymerase III. We have examined all SNAPc-bound promoters present in the human genome. We find a surprisingly small number of them, some 70 promoters. Among these, the large majority is bound by either RNA polymerase II or RNA polymerase III, as expected, but one gene hitherto considered an RNA polymerase III gene is also occupied by significant levels of RNA polymerase II. Both RNA polymerase II and RNA polymerase III SNAPc-dependent promoters use a largely overlapping set of a few transcription activators, including GABP, a novel factor implicated in snRNA gene transcription.
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Affiliation(s)
- Nicole James Faresse
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Donatella Canella
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joëlle Michaud
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - David Romascano
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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13
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Requirement for SNAPC1 in transcriptional responsiveness to diverse extracellular signals. Mol Cell Biol 2012; 32:4642-50. [PMID: 22966203 DOI: 10.1128/mcb.00906-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Initiation of transcription of RNA polymerase II (RNAPII)-dependent genes requires the participation of a host of basal transcription factors. Among genes requiring RNAPII for transcription, small nuclear RNAs (snRNAs) display a further requirement for a factor known as snRNA-activating protein complex (SNAPc). The scope of the biological function of SNAPc and its requirement for transcription of protein-coding genes has not been elucidated. To determine the genome-wide occupancy of SNAPc, we performed chromatin immunoprecipitation followed by high-throughput sequencing using antibodies against SNAPC4 and SNAPC1 subunits. Interestingly, while SNAPC4 occupancy was limited to snRNA genes, SNAPC1 chromatin residence extended beyond snRNA genes to include a large number of transcriptionally active protein-coding genes. Notably, SNAPC1 occupancy on highly active genes mirrored that of elongating RNAPII extending through the bodies and 3' ends of protein-coding genes. Inhibition of transcriptional elongation resulted in the loss of SNAPC1 from the 3' ends of genes, reflecting a functional association between SNAPC1 and elongating RNAPII. Importantly, while depletion of SNAPC1 had a small effect on basal transcription, it diminished the transcriptional responsiveness of a large number of genes to two distinct extracellular stimuli, epidermal growth factor (EGF) and retinoic acid (RA). These results highlight a role for SNAPC1 as a general transcriptional coactivator that functions through elongating RNAPII.
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14
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Xiao T, Wang Y, Luo H, Liu L, Wei G, Chen X, Sun Y, Chen X, Skogerbø G, Chen R. A differential sequencing-based analysis of the C. elegans noncoding transcriptome. RNA (NEW YORK, N.Y.) 2012; 18:626-639. [PMID: 22345127 PMCID: PMC3312551 DOI: 10.1261/rna.030965.111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 12/22/2011] [Indexed: 05/31/2023]
Abstract
Noncoding RNAs are increasingly being recognized as important players in eukaryote biology. However, despite major efforts in mapping the Caenorhabditis elegans transcriptome over the last couple of years, nonpolyadenylated and intermediate-size noncoding RNAs (is-ncRNAs) are still incompletely explored. We have combined an enzymatic approach with full-length RNA-Seq of is-ncRNAs in C. elegans. A total of 473 novel is-ncRNAs has been identified, of which a substantial fraction was associated with transcription factor binding sites and developmentally regulated expression patterns. Analysis of sequence and secondary structure permitted classification of more than 200 is-ncRNAs into several known RNA classes, while another 33 is-ncRNAs were identified as belonging to two previously uncharacterized groups of is-ncRNAs. Three of the unclassified is-ncRNAs contain the 5' Alu domain common to SRP RNAs and specifically bound with the SRP9/14 heterodimer in vitro. One of these (inc394) showed 65% sequence identity with the human, neuron-specific BC200 RNA. Structure-based clustering analysis and in vitro binding experiments supported the notion that the nematode stem-bulge RNAs (sbRNAs) are homologs (or functional analogs) of the Y RNAs. Moreover, analysis of the differential libraries showed that some mature snoRNAs undergo secondary 5' cap modification after processing of the primary transcript, thus suggesting the existence of a wider range of functional RNAs arising from processed and modified fragments of primary transcripts.
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Affiliation(s)
- Tengfei Xiao
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of the Chinese Academy of Science, Beijing 100080, China
| | - Yunfei Wang
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huaxia Luo
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of the Chinese Academy of Science, Beijing 100080, China
| | - Lihui Liu
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of the Chinese Academy of Science, Beijing 100080, China
| | - Guifeng Wei
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of the Chinese Academy of Science, Beijing 100080, China
| | - Xiaowei Chen
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of the Chinese Academy of Science, Beijing 100080, China
| | - Yu Sun
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of the Chinese Academy of Science, Beijing 100080, China
| | - Xiaomin Chen
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Geir Skogerbø
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Runsheng Chen
- Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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15
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Hung KH, Stumph WE. Localization of residues in a novel DNA-binding domain of DmSNAP43 required for DmSNAPc DNA-binding activity. FEBS Lett 2012; 586:841-6. [PMID: 22449969 DOI: 10.1016/j.febslet.2012.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/05/2012] [Accepted: 02/09/2012] [Indexed: 11/28/2022]
Abstract
Transcription of snRNA genes depends upon the recognition of the proximal sequence element (PSE) by the snRNA activating protein complex SNAPc. In Drosophila melanogaster, all subunits of DmSNAPc (DmSNAP43, DmSNAP50, and DmSNAP190) are required for PSE-binding activity. Previous work demonstrated that a non-canonical DmSNAP43 domain bounded by residues 193-272 was essential for DmSNAPc to bind to the PSE. In this study, the contribution of amino acid residues within this domain to DNA binding by DmSNAPc was investigated by alanine-scanning mutagenesis. The results have identified two clusters of residues within this domain required for the sequence-specific DNA-binding activity of DmSNAPc.
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Affiliation(s)
- Ko-Hsuan Hung
- Department of Biology, San Diego State University, San Diego, CA 92182-1030, United States
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16
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Mutation of zebrafish Snapc4 is associated with loss of the intrahepatic biliary network. Dev Biol 2011; 363:128-37. [PMID: 22222761 DOI: 10.1016/j.ydbio.2011.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 12/13/2011] [Accepted: 12/16/2011] [Indexed: 10/14/2022]
Abstract
Biliary epithelial cells line the intrahepatic biliary network, a complex three-dimensional network of conduits. The loss of differentiated biliary epithelial cells is the primary cause of many congenital liver diseases. We identified a zebrafish snapc4 (small nuclear RNA-activating complex polypeptide 4) mutant in which biliary epithelial cells initially differentiate but subsequently disappear. In these snapc4 mutant larvae, biliary epithelial cells undergo apoptosis, leading to degeneration of the intrahepatic biliary network. Consequently, in snapc4 mutant larvae, biliary transport of ingested fluorescent lipids to the gallbladder is blocked. Snapc4 is the largest subunit of a protein complex that regulates small nuclear RNA (snRNA) transcription. The snapc4(s445) mutation causes a truncation of the C-terminus, thereby deleting the domain responsible for a specific interaction with Snapc2, a vertebrate specific subunit of the SNAP complex. This mutation leads to a hypomorphic phenotype, as only a subset of snRNA transcripts are quantitatively altered in snapc4(s445) mutant larvae. snapc2 knockdown also disrupts the intrahepatic biliary network in a similar fashion as in snapc4(s445) mutant larvae. These data indicate that the physical interaction between Snapc2 and Snapc4 is important for the expression of a subset of snRNAs and biliary epithelial cell survival in zebrafish.
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17
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Hung KH, Stumph WE. Regulation of snRNA gene expression by the Drosophila melanogaster small nuclear RNA activating protein complex (DmSNAPc). Crit Rev Biochem Mol Biol 2010; 46:11-26. [PMID: 20925482 DOI: 10.3109/10409238.2010.518136] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The small nuclear RNAs (snRNAs) are an essential class of non-coding RNAs first identified over 30 years ago. Many of the well-characterized snRNAs are involved in RNA processing events. However, it is now evident that other small RNAs, synthesized using similar mechanisms, play important roles at many stages of gene expression. The accurate and efficient control of the expression of snRNA (and related) genes is thus critical for cell survival. All snRNA genes share a very similar promoter structure, and their transcription is dependent upon the same multi-subunit transcription factor, termed the snRNA activating protein complex (SNAPc). Despite those similarities, some snRNA genes are transcribed by RNA polymerase II (Pol II), but others are transcribed by RNA polymerase III (Pol III). Thus snRNA genes provide a unique opportunity to understand how RNA polymerase specificity is determined and how distinct transcription machineries can interact with a common factor. This review will describe efforts taken toward solving those questions by using the fruit fly as a model organism. Drosophila melanogaster SNAPc (DmSNAPc) binds to a proximal sequence element (PSEA) present in both Pol II and Pol III snRNA promoters. Just a few differences in nucleotide sequence in the Pol II and Pol III PSEAs play a major role in determining RNA polymerase specificity. Furthermore, these same nucleotide differences result in alternative conformations of DmSNAPc on Pol II and Pol III snRNA gene promoters. It seems likely that these DNA-induced alternative DmSNAPc conformations are responsible for the differential recruitment of the distinct transcriptional machineries.
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Affiliation(s)
- Ko-Hsuan Hung
- Department of Biology and Molecular Biology Institute, San Diego State University, San Diego, CA 92182-1030, USA
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