251
|
Baranello L, Wojtowicz D, Cui K, Devaiah BN, Chung HJ, Chan-Salis KY, Guha R, Wilson K, Zhang X, Zhang H, Piotrowski J, Thomas CJ, Singer DS, Pugh BF, Pommier Y, Przytycka TM, Kouzine F, Lewis BA, Zhao K, Levens D. RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription. Cell 2016; 165:357-71. [PMID: 27058666 DOI: 10.1016/j.cell.2016.02.036] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 12/01/2015] [Accepted: 02/17/2016] [Indexed: 11/24/2022]
Abstract
We report a mechanism through which the transcription machinery directly controls topoisomerase 1 (TOP1) activity to adjust DNA topology throughout the transcription cycle. By comparing TOP1 occupancy using chromatin immunoprecipitation sequencing (ChIP-seq) versus TOP1 activity using topoisomerase 1 sequencing (TOP1-seq), a method reported here to map catalytically engaged TOP1, TOP1 bound at promoters was discovered to become fully active only after pause-release. This transition coupled the phosphorylation of the carboxyl-terminal-domain (CTD) of RNA polymerase II (RNAPII) with stimulation of TOP1 above its basal rate, enhancing its processivity. TOP1 stimulation is strongly dependent on the kinase activity of BRD4, a protein that phosphorylates Ser2-CTD and regulates RNAPII pause-release. Thus the coordinated action of BRD4 and TOP1 overcame the torsional stress opposing transcription as RNAPII commenced elongation but preserved negative supercoiling that assists promoter melting at start sites. This nexus between transcription and DNA topology promises to elicit new strategies to intercept pathological gene expression.
Collapse
Affiliation(s)
| | | | - Kairong Cui
- Systems Biology Center, NHLBI/NIH, Bethesda, MD 20892, USA
| | | | - Hye-Jung Chung
- Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA
| | - Ka Yim Chan-Salis
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Kelli Wilson
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Hongliang Zhang
- Development Therapeutics Branch and Laboratory of Molecular Pharmacology, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Craig J Thomas
- Division of Preclinical Innovation, NCATS/NIH, Rockville, MD 20850, USA
| | - Dinah S Singer
- Experimental Immunology Branch, NCI/NIH, Bethesda, MD 20892, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yves Pommier
- Development Therapeutics Branch and Laboratory of Molecular Pharmacology, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Fedor Kouzine
- Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA
| | - Brian A Lewis
- Lymphoid Malignancies Branch, NCI/NIH, Bethesda, MD 20892, USA
| | - Keji Zhao
- Systems Biology Center, NHLBI/NIH, Bethesda, MD 20892, USA.
| | - David Levens
- Laboratory of Pathology, NCI/NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
252
|
The mRNA capping enzyme of Saccharomyces cerevisiae has dual specificity to interact with CTD of RNA Polymerase II. Sci Rep 2016; 6:31294. [PMID: 27503426 PMCID: PMC4977518 DOI: 10.1038/srep31294] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/15/2016] [Indexed: 11/08/2022] Open
Abstract
RNA Polymerase II (RNAPII) uniquely possesses an extended carboxy terminal domain (CTD) on its largest subunit, Rpb1, comprising a repetitive Tyr1Ser2Pro3Thr4 Ser5Pro6Ser7 motif with potential phosphorylation sites. The phosphorylation of the CTD serves as a signal for the binding of various transcription regulators for mRNA biogenesis including the mRNA capping complex. In eukaryotes, the 5 prime capping of the nascent transcript is the first detectable mRNA processing event, and is crucial for the productive transcript elongation. The binding of capping enzyme, RNA guanylyltransferases to the transcribing RNAPII is known to be primarily facilitated by the CTD, phosphorylated at Ser5 (Ser5P). Here we report that the Saccharomyces cerevesiae RNA guanylyltransferase (Ceg1) has dual specificity and interacts not only with Ser5P but also with Ser7P of the CTD. The Ser7 of CTD is essential for the unconditional growth and efficient priming of the mRNA capping complex. The Arg159 and Arg185 of Ceg1 are the key residues that interact with the Ser5P, while the Lys175 with Ser7P of CTD. These interactions appear to be in a specific pattern of Ser5PSer7PSer5P in a tri-heptad CTD (YSPTSPPS YSPTSPSP YSPTSPPS) and provide molecular insights into the Ceg1-CTD interaction for mRNA transcription.
Collapse
|
253
|
Hollander D, Naftelberg S, Lev-Maor G, Kornblihtt AR, Ast G. How Are Short Exons Flanked by Long Introns Defined and Committed to Splicing? Trends Genet 2016; 32:596-606. [PMID: 27507607 DOI: 10.1016/j.tig.2016.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/19/2022]
Abstract
The splice sites (SSs) delimiting an intron are brought together in the earliest step of spliceosome assembly yet it remains obscure how SS pairing occurs, especially when introns are thousands of nucleotides long. Splicing occurs in vivo in mammals within minutes regardless of intron length, implying that SS pairing can instantly follow transcription. Also, factors required for SS pairing, such as the U1 small nuclear ribonucleoprotein (snRNP) and U2AF65, associate with RNA polymerase II (RNAPII), while nucleosomes preferentially bind exonic sequences and associate with U2 snRNP. Based on recent publications, we assume that the 5' SS-bound U1 snRNP can remain tethered to RNAPII until complete synthesis of the downstream intron and exon. An additional U1 snRNP then binds the downstream 5' SS, whereas the RNAPII-associated U2AF65 binds the upstream 3' SS to facilitate SS pairing along with exon definition. Next, the nucleosome-associated U2 snRNP binds the branch site to advance splicing complex assembly. This may explain how RNAPII and chromatin are involved in spliceosome assembly and how introns lengthened during evolution with a relatively minimal compromise in splicing.
Collapse
Affiliation(s)
- Dror Hollander
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Shiran Naftelberg
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Alberto R Kornblihtt
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.
| |
Collapse
|
254
|
Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization. Mol Cell 2016; 63:433-44. [PMID: 27477907 DOI: 10.1016/j.molcel.2016.06.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/09/2016] [Accepted: 06/23/2016] [Indexed: 12/25/2022]
Abstract
During transcription initiation, the TFIIH-kinase Kin28/Cdk7 marks RNA polymerase II (Pol II) by phosphorylating the C-terminal domain (CTD) of its largest subunit. Here we describe a structure-guided chemical approach to covalently and specifically inactivate Kin28 kinase activity in vivo. This method of irreversible inactivation recapitulates both the lethal phenotype and the key molecular signatures that result from genetically disrupting Kin28 function in vivo. Inactivating Kin28 impacts promoter release to differing degrees and reveals a "checkpoint" during the transition to productive elongation. While promoter-proximal pausing is not observed in budding yeast, inhibition of Kin28 attenuates elongation-licensing signals, resulting in Pol II accumulation at the +2 nucleosome and reduced transition to productive elongation. Furthermore, upon inhibition, global stabilization of mRNA masks different degrees of reduction in nascent transcription. This study resolves long-standing controversies on the role of Kin28 in transcription and provides a rational approach to irreversibly inhibit other kinases in vivo.
Collapse
|
255
|
Zaborowska J, Isa NF, Murphy S. P-TEFb goes viral. Bioessays 2016; 38 Suppl 1:S75-85. [DOI: 10.1002/bies.201670912] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/23/2015] [Accepted: 09/26/2015] [Indexed: 01/31/2023]
Affiliation(s)
| | - Nur F. Isa
- Sir William Dunn School of Pathology; University of Oxford; Oxford UK
- Department of Biotechnology; Kulliyyah of Science, IIUM; Kuantan Pahang Malaysia
| | - Shona Murphy
- Sir William Dunn School of Pathology; University of Oxford; Oxford UK
| |
Collapse
|
256
|
Inada M, Nichols RJ, Parsa JY, Homer CM, Benn RA, Hoxie RS, Madhani HD, Shuman S, Schwer B, Pleiss JA. Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast. Nucleic Acids Res 2016; 44:9180-9189. [PMID: 27402158 PMCID: PMC5100562 DOI: 10.1093/nar/gkw603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/23/2016] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic gene expression requires that RNA Polymerase II (RNAP II) gain access to DNA in the context of chromatin. The C-terminal domain (CTD) of RNAP II recruits chromatin modifying enzymes to promoters, allowing for transcription initiation or repression. Specific CTD phosphorylation marks facilitate recruitment of chromatin modifiers, transcriptional regulators, and RNA processing factors during the transcription cycle. However, the readable code for recruiting such factors is still not fully defined and how CTD modifications affect related families of genes or regional gene expression is not well understood. Here, we examine the effects of manipulating the Y1S2P3T4S5P6S7 heptapeptide repeat of the CTD of RNAP II in Schizosaccharomyces pombe by substituting non-phosphorylatable alanines for Ser2 and/or Ser7 and the phosphomimetic glutamic acid for Ser7. Global gene expression analyses were conducted using splicing-sensitive microarrays and validated via RT-qPCR. The CTD mutations did not affect pre-mRNA splicing or snRNA levels. Rather, the data revealed upregulation of subtelomeric genes and alteration of the repressive histone H3 lysine 9 methylation (H3K9me) landscape. The data further indicate that H3K9me and expression status are not fully correlated, suggestive of CTD-dependent subtelomeric repression mechansims that act independently of H3K9me levels.
Collapse
Affiliation(s)
- Maki Inada
- Biology Department, Ithaca College, Ithaca, NY 14850, USA
| | | | - Jahan-Yar Parsa
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94158, USA
| | - Christina M Homer
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94158, USA
| | - Ruby A Benn
- Biology Department, Ithaca College, Ithaca, NY 14850, USA
| | - Reyal S Hoxie
- Biology Department, Ithaca College, Ithaca, NY 14850, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94158, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Beate Schwer
- Department of Microbiology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jeffrey A Pleiss
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
257
|
Chatterjee D, Sanchez AM, Goldgur Y, Shuman S, Schwer B. Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast. RNA (NEW YORK, N.Y.) 2016; 22:1011-25. [PMID: 27165520 PMCID: PMC4911910 DOI: 10.1261/rna.056515.116] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/11/2016] [Indexed: 05/24/2023]
Abstract
Expression of fission yeast Pho1 acid phosphatase is repressed during growth in phosphate-rich medium. Repression is mediated by transcription of the prt locus upstream of pho1 to produce a long noncoding (lnc) prt RNA. Repression is also governed by RNA polymerase II CTD phosphorylation status, whereby inability to place a Ser7-PO4 mark (as in S7A) derepresses Pho1 expression, and inability to place a Thr4-PO4 mark (as in T4A) hyper-represses Pho1 in phosphate replete cells. Here we find that basal pho1 expression from the prt-pho1 locus is inversely correlated with the activity of the prt promoter, which resides in a 110-nucleotide DNA segment preceding the prt transcription start site. CTD mutations S7A and T4A had no effect on the activity of the prt promoter or the pho1 promoter, suggesting that S7A and T4A affect post-initiation events in prt lncRNA synthesis that make it less and more repressive of pho1, respectively. prt lncRNA contains clusters of DSR (determinant of selective removal) sequences recognized by the YTH-domain-containing protein Mmi1. Altering the nucleobase sequence of two DSR clusters in the prt lncRNA caused hyper-repression of pho1 in phosphate replete cells, concomitant with increased levels of the prt transcript. The isolated Mmi1 YTH domain binds to RNAs with single or tandem DSR elements, to the latter in a noncooperative fashion. We report the 1.75 Å crystal structure of the Mmi1 YTH domain and provide evidence that Mmi1 recognizes DSR RNA via a binding mode distinct from that of structurally homologous YTH proteins that recognize m(6)A-modified RNA.
Collapse
Affiliation(s)
- Debashree Chatterjee
- Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Yehuda Goldgur
- Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology and Structural Biology Programs, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| |
Collapse
|
258
|
Abstract
In this issue of Molecular Cell, Schüller et al. (2016) and Suh et al. (2016) describe genetic and mass spectrometry methodologies for mapping phosphorylation sites on the tandem repeats of the RNA polymerase II CTD. The results suggest that the CTD Code may be simpler than expected.
Collapse
Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, MD 21205, USA.
| |
Collapse
|
259
|
Milligan L, Huynh-Thu VA, Delan-Forino C, Tuck A, Petfalski E, Lombraña R, Sanguinetti G, Kudla G, Tollervey D. Strand-specific, high-resolution mapping of modified RNA polymerase II. Mol Syst Biol 2016; 12:874. [PMID: 27288397 PMCID: PMC4915518 DOI: 10.15252/msb.20166869] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Reversible modification of the RNAPII C‐terminal domain links transcription with RNA processing and surveillance activities. To better understand this, we mapped the location of RNAPII carrying the five types of CTD phosphorylation on the RNA transcript, providing strand‐specific, nucleotide‐resolution information, and we used a machine learning‐based approach to define RNAPII states. This revealed enrichment of Ser5P, and depletion of Tyr1P, Ser2P, Thr4P, and Ser7P in the transcription start site (TSS) proximal ~150 nt of most genes, with depletion of all modifications close to the poly(A) site. The TSS region also showed elevated RNAPII relative to regions further 3′, with high recruitment of RNA surveillance and termination factors, and correlated with the previously mapped 3′ ends of short, unstable ncRNA transcripts. A hidden Markov model identified distinct modification states associated with initiating, early elongating and later elongating RNAPII. The initiation state was enriched near the TSS of protein‐coding genes and persisted throughout exon 1 of intron‐containing genes. Notably, unstable ncRNAs apparently failed to transition into the elongation states seen on protein‐coding genes.
Collapse
Affiliation(s)
- Laura Milligan
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vân A Huynh-Thu
- School of Informatics, University of Edinburgh, Edinburgh, UK Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium
| | | | - Alex Tuck
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Cambridge, UK
| | - Elisabeth Petfalski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Rodrigo Lombraña
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Grzegorz Kudla
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
260
|
RNA-Free and Ribonucleoprotein-Associated Influenza Virus Polymerases Directly Bind the Serine-5-Phosphorylated Carboxyl-Terminal Domain of Host RNA Polymerase II. J Virol 2016; 90:6014-6021. [PMID: 27099314 PMCID: PMC4907247 DOI: 10.1128/jvi.00494-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/13/2016] [Indexed: 11/20/2022] Open
Abstract
Influenza viruses subvert the transcriptional machinery of their hosts to synthesize their own viral mRNA. Ongoing transcription by cellular RNA polymerase II (Pol II) is required for viral mRNA synthesis. By a process known as cap snatching, the virus steals short 5′ capped RNA fragments from host capped RNAs and uses them to prime viral transcription. An interaction between the influenza A virus RNA polymerase and the C-terminal domain (CTD) of the large subunit of Pol II has been established, but the molecular details of this interaction remain unknown. We show here that the influenza virus ribonucleoprotein (vRNP) complex binds to the CTD of transcriptionally engaged Pol II. Furthermore, we provide evidence that the viral polymerase binds directly to the serine-5-phosphorylated form of the Pol II CTD, both in the presence and in the absence of viral RNA, and show that this interaction is conserved in evolutionarily distant influenza viruses. We propose a model in which direct binding of the viral RNA polymerase in the context of vRNPs to Pol II early in infection facilitates cap snatching, while we suggest that binding of free viral polymerase to Pol II late in infection may trigger Pol II degradation. IMPORTANCE Influenza viruses cause yearly epidemics and occasional pandemics that pose a threat to human health, as well as represent a large economic burden to health care systems globally. Existing vaccines are not always effective, as they may not exactly match the circulating viruses. Furthermore, there are a limited number of antivirals available, and development of resistance to these is a concern. New measures to combat influenza are needed, but before they can be developed, it is necessary to better understand the molecular interactions between influenza viruses and their host cells. By providing further insights into the molecular details of how influenza viruses hijack the host transcriptional machinery, we aim to uncover novel targets for the development of antivirals.
Collapse
|
261
|
Hintermair C, Voß K, Forné I, Heidemann M, Flatley A, Kremmer E, Imhof A, Eick D. Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression. Sci Rep 2016; 6:27401. [PMID: 27264542 PMCID: PMC4893663 DOI: 10.1038/srep27401] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
Dynamic phosphorylation of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 heptad-repeats in the C-terminal domain (CTD) of the large subunit coordinates progression of RNA polymerase (Pol) II through the transcription cycle. Here, we describe an M phase-specific form of Pol II phosphorylated at Thr4, but not at Tyr1, Ser2, Ser5, and Ser7 residues. Thr4 phosphorylated Pol II binds to centrosomes and midbody and interacts with the Thr4-specific Polo-like kinase 1. Binding of Pol II to centrosomes does not require the CTD but may involve subunits of the non-canonical R2TP-Prefoldin-like complex, which bind to and co-localize with Pol II at centrosomes. CTD Thr4 mutants, but not Ser2 and Ser5 mutants, display severe mitosis and cytokinesis defects characterized by multipolar spindles and polyploid cells. We conclude that proper M phase progression of cells requires binding of Pol II to centrosomes to facilitate regulation of mitosis and cytokinesis in a CTD Thr4-P dependent manner.
Collapse
Affiliation(s)
- Corinna Hintermair
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Kirsten Voß
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Center of Integrated Protein Science (CIPSM), ZFP, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Martin Heidemann
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Andrew Flatley
- Institute of Molecular Immunology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
| | - Axel Imhof
- Biomedical Center Munich, Center of Integrated Protein Science (CIPSM), ZFP, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| |
Collapse
|
262
|
Gruffat H, Marchione R, Manet E. Herpesvirus Late Gene Expression: A Viral-Specific Pre-initiation Complex Is Key. Front Microbiol 2016; 7:869. [PMID: 27375590 PMCID: PMC4893493 DOI: 10.3389/fmicb.2016.00869] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/23/2016] [Indexed: 12/20/2022] Open
Abstract
During their productive cycle, herpesviruses exhibit a strictly regulated temporal cascade of gene expression that can be divided into three general stages: immediate-early (IE), early (E), and late (L). This expression program is the result of a complex interplay between viral and cellular factors at both the transcriptional and post-transcriptional levels, as well as structural differences within the promoter architecture for each of the three gene classes. Since the cellular enzyme RNA polymerase II (RNAP-II) is responsible for the transcription of herpesvirus genes, most viral promoters contain DNA motifs that are common with those of cellular genes, although promoter complexity decreases from immediate-early to late genes. Immediate-early and early promoters contain numerous cellular and viral cis-regulating sequences upstream of a TATA box, whereas late promoters differ significantly in that they lack cis-acting sequences upstream of the transcription start site (TSS). Moreover, in the case of the β- and γ-herpesviruses, a TATT box motif is frequently found in the position where the consensus TATA box of eukaryotic promoters usually localizes. The mechanisms of transcriptional regulation of the late viral gene promoters appear to be different between α-herpesviruses and the two other herpesvirus subfamilies (β and γ). In this review, we will compare the mechanisms of late gene transcriptional regulation between HSV-1, for which the viral IE transcription factors – especially ICP4 – play an essential role, and the two other subfamilies of herpesviruses, with a particular emphasis on EBV, which has recently been found to code for its own specific TATT-binding protein.
Collapse
Affiliation(s)
- Henri Gruffat
- International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, LyonFrance; Inserm, U1111, LyonFrance.; Ecole Normale Supérieure de Lyon, LyonFrance; CNRS, UMR5308, LyonFrance; Université Lyon 1, LyonFrance
| | - Roberta Marchione
- International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, LyonFrance; Inserm, U1111, LyonFrance.; Ecole Normale Supérieure de Lyon, LyonFrance; CNRS, UMR5308, LyonFrance; Université Lyon 1, LyonFrance
| | - Evelyne Manet
- International Center for Infectiology Research, Oncogenic Herpesviruses Team, Université de Lyon, LyonFrance; Inserm, U1111, LyonFrance.; Ecole Normale Supérieure de Lyon, LyonFrance; CNRS, UMR5308, LyonFrance; Université Lyon 1, LyonFrance
| |
Collapse
|
263
|
Compe E, Egly JM. Nucleotide Excision Repair and Transcriptional Regulation: TFIIH and Beyond. Annu Rev Biochem 2016; 85:265-90. [DOI: 10.1146/annurev-biochem-060815-014857] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université de Strasbourg, 67404 Illkirch Cedex, Commune Urbaine Strasbourg, France; ,
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université de Strasbourg, 67404 Illkirch Cedex, Commune Urbaine Strasbourg, France; ,
| |
Collapse
|
264
|
Jeronimo C, Collin P, Robert F. The RNA Polymerase II CTD: The Increasing Complexity of a Low-Complexity Protein Domain. J Mol Biol 2016; 428:2607-2622. [DOI: 10.1016/j.jmb.2016.02.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 01/18/2023]
|
265
|
Sebé-Pedrós A, Ballaré C, Parra-Acero H, Chiva C, Tena JJ, Sabidó E, Gómez-Skarmeta JL, Di Croce L, Ruiz-Trillo I. The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell 2016; 165:1224-1237. [PMID: 27114036 PMCID: PMC4877666 DOI: 10.1016/j.cell.2016.03.034] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 02/03/2016] [Accepted: 03/18/2016] [Indexed: 12/16/2022]
Abstract
The unicellular ancestor of animals had a complex repertoire of genes linked to multicellular processes. This suggests that changes in the regulatory genome, rather than in gene innovation, were key to the origin of animals. Here, we carry out multiple functional genomic assays in Capsaspora owczarzaki, the unicellular relative of animals with the largest known gene repertoire for transcriptional regulation. We show that changing chromatin states, differential lincRNA expression, and dynamic cis-regulatory sites are associated with life cycle transitions in Capsaspora. Moreover, we demonstrate conservation of animal developmental transcription-factor networks and extensive network interconnection in this premetazoan organism. In contrast, however, Capsaspora lacks animal promoter types, and its regulatory sites are small, proximal, and lack signatures of animal enhancers. Overall, our results indicate that the emergence of animal multicellularity was linked to a major shift in genome cis-regulatory complexity, most notably the appearance of distal enhancer regulation.
Collapse
Affiliation(s)
- Arnau Sebé-Pedrós
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | - Cecilia Ballaré
- Center for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Helena Parra-Acero
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Cristina Chiva
- Center for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km1, 41013 Sevilla, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera Km1, 41013 Sevilla, Spain
| | - Luciano Di Croce
- Center for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, 08010 Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, 08010 Barcelona, Spain; Departament de Genètica, Universitat de Barcelona, 08028 Barcelona, Spain.
| |
Collapse
|
266
|
McNamara RP, Bacon CW, D'Orso I. Transcription elongation control by the 7SK snRNP complex: Releasing the pause. Cell Cycle 2016; 15:2115-2123. [PMID: 27152730 DOI: 10.1080/15384101.2016.1181241] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability for the eukaryotic cell to transcriptionally respond to various stimuli is critical for the overall homeostasis of the cell, and in turn, the organism. The human RNA polymerase II complex (Pol II), which is responsible for the transcription of protein-encoding genes and non-coding RNAs, is paused at promoter-proximal regions to ensure their rapid activation. In response to stimulation, Pol II pause release is facilitated by the action of positive transcription elongation factors such as the P-TEFb kinase. However, the majority of P-TEFb is held in a catalytically inactivate state, assembled into the 7SK small nuclear ribonucleoprotein (snRNP) complex, and must be dislodged to become catalytically active. In this review, we discuss mechanisms of 7SK snRNP recruitment to promoter-proximal regions and P-TEFb disassembly from the inhibitory snRNP to regulate 'on site' kinase activation and Pol II pause release.
Collapse
Affiliation(s)
- Ryan P McNamara
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Curtis W Bacon
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Iván D'Orso
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
| |
Collapse
|
267
|
Saldi T, Cortazar MA, Sheridan RM, Bentley DL. Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol 2016; 428:2623-2635. [PMID: 27107644 DOI: 10.1016/j.jmb.2016.04.017] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/27/2016] [Accepted: 04/12/2016] [Indexed: 01/07/2023]
Abstract
Pre-mRNA maturation frequently occurs at the same time and place as transcription by RNA polymerase II. The co-transcriptionality of mRNA processing has permitted the evolution of mechanisms that functionally couple transcription elongation with diverse events that occur on the nascent RNA. This review summarizes the current understanding of the relationship between transcriptional elongation through a chromatin template and co-transcriptional splicing including alternative splicing decisions that affect the expression of most human genes.
Collapse
Affiliation(s)
- Tassa Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - Michael A Cortazar
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - Ryan M Sheridan
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA.
| |
Collapse
|
268
|
Conservation and divergence of the histone code in nucleomorphs. Biol Direct 2016; 11:18. [PMID: 27048461 PMCID: PMC4822330 DOI: 10.1186/s13062-016-0119-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/22/2016] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved independently on two separate occasions in chlorarachniophytes and cryptophytes. The nucleomorphs of the two groups have evolved in a remarkably convergent manner, with numerous very similar features. Chief among them is the extreme reduction and compaction of nucleomorph genomes, with very small chromosomes and extremely short or even completely absent intergenic spaces. These characteristics pose a number of intriguing questions regarding the mechanisms of transcription and gene regulation in such a crowded genomic context, in particular in terms of the functioning of the histone code, which is common to almost all eukaryotes and plays a central role in chromatin biology. RESULTS This study examines the sequences of nucleomorph histone proteins in order to address these issues. Remarkably, all classical transcription- and repression-related components of the histone code seem to be missing from chlorarachniophyte nucleomorphs. Cryptophyte nucleomorph histones are generally more similar to the conventional eukaryotic state; however, they also display significant deviations from the typical histone code. Based on the analysis of specific components of the code, we discuss the state of chromatin and the transcriptional machinery in these nuclei. CONCLUSIONS The results presented here shed new light on the mechanisms of nucleomorph transcription and gene regulation and provide a foundation for future studies of nucleomorph chromatin and transcriptional biology.
Collapse
|
269
|
Abstract
The RNAPII-CTD functions as a binding platform for coordinating the recruitment of transcription associated factors. Altering CTD function results in gene expression defects, although mounting evidence suggests that these effects likely vary among species and loci. Here we highlight emerging evidence of species- and loci-specific functions for the RNAPII-CTD.
Collapse
Affiliation(s)
- Maria J Aristizabal
- a Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver , British Columbia , Canada
| | - Michael S Kobor
- a Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver , British Columbia , Canada
| |
Collapse
|
270
|
Irani S, Yogesha SD, Mayfield J, Zhang M, Zhang Y, Matthews WL, Nie G, Prescott NA, Zhang YJ. Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase. Sci Signal 2016; 9:ra24. [PMID: 26933063 DOI: 10.1126/scisignal.aad4805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Changes in the phosphorylation status of the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAPII) correlate with the process of eukaryotic transcription. The yeast protein regulator of transcription 1 (Rtr1) and the human homolog RNAPII-associated protein 2 (RPAP2) may function as CTD phosphatases; however, crystal structures of Kluyveromyces lactis Rtr1 lack a consensus active site. We identified a phosphoryl transfer domain in Saccharomyces cerevisiae Rtr1 by obtaining and characterizing a 2.6 Å resolution crystal structure. We identified a putative substrate-binding pocket in a deep groove between the zinc finger domain and a pair of helices that contained a trapped sulfate ion. Because sulfate mimics the chemistry of a phosphate group, this structural data suggested that this groove represents the phosphoryl transfer active site. Mutagenesis of the residues lining this groove disrupted catalytic activity of the enzyme assayed in vitro with a fluorescent chemical substrate, and expression of the mutated Rtr1 failed to rescue growth of yeast lacking Rtr1. Characterization of the phosphatase activity of RPAP2 and a mutant of the conserved putative catalytic site in the same chemical assay indicated a conserved reaction mechanism. Our data indicated that the structure of the phosphoryl transfer domain and reaction mechanism for the phosphoryl transfer activity of Rtr1 is distinct from those of other phosphatase families.
Collapse
Affiliation(s)
- Seema Irani
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - S D Yogesha
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Joshua Mayfield
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mengmeng Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yong Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Wendy L Matthews
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Grace Nie
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nicholas A Prescott
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
271
|
Wani S, Sugita A, Ohkuma Y, Hirose Y. Human SCP4 is a chromatin-associated CTD phosphatase and exhibits the dynamic translocation during erythroid differentiation. J Biochem 2016; 160:111-20. [DOI: 10.1093/jb/mvw018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/01/2016] [Indexed: 12/24/2022] Open
|
272
|
Lu L, Fan D, Hu CW, Worth M, Ma ZX, Jiang J. Distributive O-GlcNAcylation on the Highly Repetitive C-Terminal Domain of RNA Polymerase II. Biochemistry 2016; 55:1149-58. [PMID: 26807597 DOI: 10.1021/acs.biochem.5b01280] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
O-GlcNAcylation is a nutrient-responsive glycosylation that plays a pivotal role in transcriptional regulation. Human RNA polymerase II (Pol II) is extensively modified by O-linked N-acetylglucosamine (O-GlcNAc) on its unique C-terminal domain (CTD), which consists of 52 heptad repeats. One approach to understanding the function of glycosylated Pol II is to determine the mechanism of dynamic O-GlcNAcylation on the CTD. Here, we discovered that the Pol II CTD can be extensively O-GlcNAcylated in vitro and in cells. Efficient glycosylation requires a minimum of 20 heptad repeats of the CTD and more than half of the N-terminal domain of O-GlcNAc transferase (OGT). Under conditions of saturated sugar donor, we monitored the attachment of more than 20 residues of O-GlcNAc to the full-length CTD. Surprisingly, glycosylation on the periodic CTD follows a distributive mechanism, resulting in highly heterogeneous glycoforms. Our data suggest that initial O-GlcNAcylation can take place either on the proximal or on the distal region of the CTD, and subsequent glycosylation occurs similarly over the entire CTD with nonuniform distributions. Moreover, removal of O-GlcNAc from glycosylated CTD is also distributive and is independent of O-GlcNAcylation level. Our results suggest that O-GlcNAc cycling enzymes can employ a similar mechanism to react with other protein substrates on multiple sites. Distributive O-GlcNAcylation on Pol II provides another regulatory mechanism of transcription in response to fluctuating cellular conditions.
Collapse
Affiliation(s)
- Lei Lu
- Pharmaceutical Sciences Division, School of Pharmacy, and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Dacheng Fan
- Pharmaceutical Sciences Division, School of Pharmacy, and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Chia-Wei Hu
- Pharmaceutical Sciences Division, School of Pharmacy, and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Matthew Worth
- Pharmaceutical Sciences Division, School of Pharmacy, and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Zhi-Xiong Ma
- Pharmaceutical Sciences Division, School of Pharmacy, and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Jiaoyang Jiang
- Pharmaceutical Sciences Division, School of Pharmacy, and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| |
Collapse
|
273
|
Tellier M, Ferrer-Vicens I, Murphy S. The point of no return: The poly(A)-associated elongation checkpoint. RNA Biol 2016; 13:265-71. [PMID: 26853452 DOI: 10.1080/15476286.2016.1142037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Cyclin-dependent kinases play critical roles in transcription by RNA polymerase II (pol II) and processing of the transcripts. For example, CDK9 regulates transcription of protein-coding genes, splicing, and 3' end formation of the transcripts. Accordingly, CDK9 inhibitors have a drastic effect on the production of mRNA in human cells. Recent analyses indicate that CDK9 regulates transcription at the early-elongation checkpoint of the vast majority of pol II-transcribed genes. Our recent discovery of an additional CDK9-regulated elongation checkpoint close to poly(A) sites adds a new layer to the control of transcription by this critical cellular kinase. This novel poly(A)-associated checkpoint has the potential to powerfully regulate gene expression just before a functional polyadenylated mRNA is produced: the point of no return. However, many questions remain to be answered before the role of this checkpoint becomes clear. Here we speculate on the possible biological significance of this novel mechanism of gene regulation and the players that may be involved.
Collapse
Affiliation(s)
- Michael Tellier
- a Sir William Dunn School of Pathology, University of Oxford , Oxford OX1 3RE , UK
| | - Ivan Ferrer-Vicens
- a Sir William Dunn School of Pathology, University of Oxford , Oxford OX1 3RE , UK
| | - Shona Murphy
- a Sir William Dunn School of Pathology, University of Oxford , Oxford OX1 3RE , UK
| |
Collapse
|
274
|
Suh H, Ficarro SB, Kang UB, Chun Y, Marto JA, Buratowski S. Direct Analysis of Phosphorylation Sites on the Rpb1 C-Terminal Domain of RNA Polymerase II. Mol Cell 2016; 61:297-304. [PMID: 26799764 PMCID: PMC4724063 DOI: 10.1016/j.molcel.2015.12.021] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/30/2015] [Accepted: 12/14/2015] [Indexed: 11/20/2022]
Abstract
Dynamic interactions between RNA polymerase II and various mRNA-processing and chromatin-modifying enzymes are mediated by the changing phosphorylation pattern on the C-terminal domain (CTD) of polymerase subunit Rpb1 during different stages of transcription. Phosphorylations within the repetitive heptamer sequence (YSPTSPS) of CTD have primarily been defined using antibodies, but these do not distinguish different repeats or allow comparative quantitation. Using a CTD modified for mass spectrometry (msCTD), we show that Ser5-P and Ser2-P occur throughout the length of CTD and are far more abundant than other phosphorylation sites. msCTD extracted from cells mutated in several CTD kinases or phosphatases showed the expected changes in phosphorylation. Furthermore, msCTD associated with capping enzyme was enriched for Ser5-P while that bound to the transcription termination factor Rtt103 had higher levels of Ser2-P. These results suggest a relatively sparse and simple "CTD code."
Collapse
Affiliation(s)
- Hyunsuk Suh
- Department of Biochemical Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Scott B Ficarro
- Department of Biochemical Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Un-Beom Kang
- Department of Biochemical Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Yujin Chun
- Department of Biochemical Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jarrod A Marto
- Department of Biochemical Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology and Blais Proteomics Center, Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Stephen Buratowski
- Department of Biochemical Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
275
|
Mayfield JE, Burkholder NT, Zhang YJ. Dephosphorylating eukaryotic RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:372-87. [PMID: 26779935 DOI: 10.1016/j.bbapap.2016.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 12/20/2022]
Abstract
The phosphorylation state of the C-terminal domain of RNA polymerase II is required for the temporal and spatial recruitment of various factors that mediate transcription and RNA processing throughout the transcriptional cycle. Therefore, changes in CTD phosphorylation by site-specific kinases/phosphatases are critical for the accurate transmission of information during transcription. Unlike kinases, CTD phosphatases have been traditionally neglected as they are thought to act as passive negative regulators that remove all phosphate marks at the conclusion of transcription. This over-simplified view has been disputed in recent years and new data assert the active and regulatory role phosphatases play in transcription. We now know that CTD phosphatases ensure the proper transition between different stages of transcription, balance the distribution of phosphorylation for accurate termination and re-initiation, and prevent inappropriate expression of certain genes. In this review, we focus on the specific roles of CTD phosphatases in regulating transcription. In particular, we emphasize how specificity and timing of dephosphorylation are achieved for these phosphatases and consider the various regulatory factors that affect these dynamics.
Collapse
Affiliation(s)
- Joshua E Mayfield
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nathaniel T Burkholder
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
276
|
Schüller R, Forné I, Straub T, Schreieck A, Texier Y, Shah N, Decker TM, Cramer P, Imhof A, Eick D. Heptad-Specific Phosphorylation of RNA Polymerase II CTD. Mol Cell 2016; 61:305-14. [DOI: 10.1016/j.molcel.2015.12.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/30/2015] [Accepted: 11/11/2015] [Indexed: 01/01/2023]
|
277
|
Structural and Functional Analysis of the Cdk13/Cyclin K Complex. Cell Rep 2015; 14:320-31. [PMID: 26748711 DOI: 10.1016/j.celrep.2015.12.025] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/29/2015] [Accepted: 11/30/2015] [Indexed: 12/20/2022] Open
Abstract
Cyclin-dependent kinases regulate the cell cycle and transcription in higher eukaryotes. We have determined the crystal structure of the transcription kinase Cdk13 and its Cyclin K subunit at 2.0 Å resolution. Cdk13 contains a C-terminal extension helix composed of a polybasic cluster and a DCHEL motif that interacts with the bound ATP. Cdk13/CycK phosphorylates both Ser5 and Ser2 of the RNA polymerase II C-terminal domain (CTD) with a preference for Ser7 pre-phosphorylations at a C-terminal position. The peptidyl-prolyl isomerase Pin1 does not change the phosphorylation specificities of Cdk9, Cdk12, and Cdk13 but interacts with the phosphorylated CTD through its WW domain. Using recombinant proteins, we find that flavopiridol inhibits Cdk7 more potently than it does Cdk13. Gene expression changes after knockdown of Cdk13 or Cdk12 are markedly different, with enrichment of growth signaling pathways for Cdk13-dependent genes. Together, our results provide insights into the structure, function, and activity of human Cdk13/CycK.
Collapse
|
278
|
Generation of Recombinant Oropouche Viruses Lacking the Nonstructural Protein NSm or NSs. J Virol 2015; 90:2616-27. [PMID: 26699638 DOI: 10.1128/jvi.02849-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/15/2015] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Oropouche virus (OROV) is a midge-borne human pathogen with a geographic distribution in South America. OROV was first isolated in 1955, and since then, it has been known to cause recurring outbreaks of a dengue-like illness in the Amazonian regions of Brazil. OROV, however, remains one of the most poorly understood emerging viral zoonoses. Here we describe the successful recovery of infectious OROV entirely from cDNA copies of its genome and generation of OROV mutant viruses lacking either the NSm or the NSs coding region. Characterization of the recombinant viruses carried out in vitro demonstrated that the NSs protein of OROV is an interferon (IFN) antagonist as in other NSs-encoding bunyaviruses. Additionally, we demonstrate the importance of the nine C-terminal amino acids of OROV NSs in IFN antagonistic activity. OROV was also found to be sensitive to IFN-α when cells were pretreated; however, the virus was still capable of replicating at doses as high as 10,000 U/ml of IFN-α, in contrast to the family prototype BUNV. We found that OROV lacking the NSm protein displayed characteristics similar to those of the wild-type virus, suggesting that the NSm protein is dispensable for virus replication in the mammalian and mosquito cell lines that were tested. IMPORTANCE Oropouche virus (OROV) is a public health threat in Central and South America, where it causes periodic outbreaks of dengue-like illness. In Brazil, OROV is the second most frequent cause of arboviral febrile illness after dengue virus, and with the current rates of urban expansion, more cases of this emerging viral zoonosis could occur. To better understand the molecular biology of OROV, we have successfully rescued the virus along with mutants. We have established that the C terminus of the NSs protein is important in interferon antagonism and that the NSm protein is dispensable for virus replication in cell culture. The tools described in this paper are important in terms of understanding this important yet neglected human pathogen.
Collapse
|
279
|
Dias JD, Rito T, Torlai Triglia E, Kukalev A, Ferrai C, Chotalia M, Brookes E, Kimura H, Pombo A. Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells. eLife 2015; 4. [PMID: 26687004 PMCID: PMC4758952 DOI: 10.7554/elife.11215] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 12/18/2015] [Indexed: 12/16/2022] Open
Abstract
Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and processing of nascent RNA. Extensive phosphorylation of serine residues at the largest RNAPII subunit occurs at its structurally-disordered C-terminal domain (CTD), which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. In contrast, K7ac is associated with RNAPII elongation, Serine-2 phosphorylation and mRNA expression. We identify an unexpected balance between RNAPII K7 methylation and acetylation at gene promoters, which fine-tunes gene expression levels.
Collapse
Affiliation(s)
- João D Dias
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.,Genome Function Group, MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Graduate Program in Areas of Basic and Applied Biology, University of Porto, Porto, Portugal
| | - Tiago Rito
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Elena Torlai Triglia
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Alexander Kukalev
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Carmelo Ferrai
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.,Genome Function Group, MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom
| | - Mita Chotalia
- Genome Function Group, MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom
| | - Emily Brookes
- Genome Function Group, MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.,Genome Function Group, MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom
| |
Collapse
|
280
|
Abstract
Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential post-translational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence constraints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its components, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed.
Collapse
|
281
|
Zaborowska J, Isa NF, Murphy S. P-TEFb goes viral. ACTA ACUST UNITED AC 2015; 1:106-116. [PMID: 27398404 PMCID: PMC4863834 DOI: 10.1002/icl3.1037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/23/2015] [Accepted: 09/26/2015] [Indexed: 01/30/2023]
Abstract
Positive transcription elongation factor b (P‐TEFb), which comprises cyclin‐dependent kinase 9 (CDK9) kinase and cyclin T subunits, is an essential kinase complex in human cells. Phosphorylation of the negative elongation factors by P‐TEFb is required for productive elongation of transcription of protein‐coding genes by RNA polymerase II (pol II). In addition, P‐TEFb‐mediated phosphorylation of the carboxyl‐terminal domain (CTD) of the largest subunit of pol II mediates the recruitment of transcription and RNA processing factors during the transcription cycle. CDK9 also phosphorylates p53, a tumor suppressor that plays a central role in cellular responses to a range of stress factors. Many viral factors affect transcription by recruiting or modulating the activity of CDK9. In this review, we will focus on how the function of CDK9 is regulated by viral gene products. The central role of CDK9 in viral life cycles suggests that drugs targeting the interaction between viral products and P‐TEFb could be effective anti‐viral agents.
Collapse
Affiliation(s)
| | - Nur F Isa
- Sir William Dunn School of Pathology University of Oxford Oxford UK; Department of Biotechnology Kulliyyah of Science, IIUM Kuantan Pahang Malaysia
| | - Shona Murphy
- Sir William Dunn School of Pathology University of Oxford Oxford UK
| |
Collapse
|
282
|
Burton ZF. The Old and New Testaments of gene regulation. Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD. Transcription 2015; 5:e28674. [PMID: 25764332 PMCID: PMC4215175 DOI: 10.4161/trns.28674] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
I relate a story of genesis told from the point of view of multi-subunit RNA polymerases (RNAPs) including an Old Testament (core RNAP motifs in all cellular life) and a New Testament (the RNAP II heptad repeat carboxy terminal domain (CTD) and CTD interactome in eukarya). The Old Testament: at their active site, one class of eukaryotic interfering RNAP and ubiquitous multi-subunit RNAPs each have two-double psi β barrel (DPBB) motifs (a distinct pattern for compact 6-β sheet barrels). Between β sheets 2 and 3 of the β subunit type DPBB of all multi-subunit RNAPs is a sandwich barrel hybrid motif (SBHM) that interacts with conserved initiation and elongation factors required to utilize a DNA template. Analysis of RNAP core protein motifs, therefore, indicates that RNAP evolution can be traced from the RNA-protein world to LUCA (the last universal common ancestor) branching to LECA (the last eukaryotic common ancestor) and to the present day, spanning about 4 billion years. The New Testament: in the eukaryotic lineage, I posit that splitting RNAP functions into RNAPs I, II and III and innovations developed around the CTD heptad repeat of RNAP II and the extensive CTD interactome helps to describe how greater structural, cell cycle, epigenetic and signaling complexity co-evolved in eukaryotes relative to eubacteria and archaea.
Collapse
Affiliation(s)
- Zachary F Burton
- a Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing, MI USA
| |
Collapse
|
283
|
Mayfield JE, Fan S, Wei S, Zhang M, Li B, Ellington AD, Etzkorn FA, Zhang YJ. Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. ACS Chem Biol 2015; 10:2405-14. [PMID: 26332362 DOI: 10.1021/acschembio.5b00296] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proline isomerization greatly impacts biological signaling but is subtle and difficult to detect in proteins. We characterize this poorly understood regulatory mechanism for RNA polymerase II carboxyl terminal domain (CTD) phosphorylation state using novel, direct, and quantitative chemical tools. We determine the proline isomeric preference of three CTD phosphatases: Ssu72 as cis-proline specific, Scp1 and Fcp1 as strongly trans-preferred. Due to this inherent characteristic, these phosphatases respond differently to enzymes that catalyze the isomerization of proline, like Ess1/Pin1. We demonstrate that this selective regulation of RNA polymerase II phosphorylation state exists within human cells, consistent with in vitro assays. These results support a model in which, instead of a global enhancement of downstream enzymatic activities, proline isomerases selectively boost the activity of a subset of CTD regulatory factors specific for cis-proline. This leads to diversified phosphorylation states of CTD in vitro and in cells. We provide the chemical tools to investigate proline isomerization and its ability to selectively enhance signaling in transcription and other biological contexts.
Collapse
Affiliation(s)
- Joshua E. Mayfield
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Shuang Fan
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Shuo Wei
- 1 Cancer
Research Institute, Beth Israel Deaconess Cancer Center, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department
of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Mengmeng Zhang
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Bing Li
- Department
of Molecular Biology, UT Southwestern Medical Center, 5323 Harry Hines
Boulevard, Dallas, Texas 75390, United States
| | - Andrew D. Ellington
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Felicia A. Etzkorn
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yan Jessie Zhang
- Department
of Molecular Biosciences and Institute for Cellular and Molecular
Biology, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
284
|
Tudek A, Candelli T, Libri D. Non-coding transcription by RNA polymerase II in yeast: Hasard or nécessité? Biochimie 2015; 117:28-36. [DOI: 10.1016/j.biochi.2015.04.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/27/2015] [Indexed: 12/17/2022]
|
285
|
Schwer B, Sanchez AM, Shuman S. RNA polymerase II CTD phospho-sites Ser5 and Ser7 govern phosphate homeostasis in fission yeast. RNA (NEW YORK, N.Y.) 2015; 21:1770-80. [PMID: 26264592 PMCID: PMC4574753 DOI: 10.1261/rna.052555.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/08/2015] [Indexed: 05/08/2023]
Abstract
Phosphorylation of the tandem YSPTSPS repeats of the RNA polymerase II CTD inscribes an informational code that orchestrates eukaryal mRNA synthesis. Here we interrogate the role of the CTD in phosphate homeostasis in fission yeast. Expression of Pho1 acid phosphatase, which is repressed during growth in phosphate-rich medium and induced by phosphate starvation, is governed strongly by CTD phosphorylation status, but not by CTD repeat length. Inability to place a Ser7-PO4 mark (as in S7A) results in constitutive derepression of Pho1 expression in phosphate-replete medium. In contrast, indelible installation of a Ser7-PO4 mimetic (as in S7E) hyper-represses Pho1 in phosphate-replete cells and inhibits Pho1 induction during starvation. Pho1 phosphatase is derepressed by ablation of the CTD Ser5-PO4 mark, achieved either by mutating Ser5 in all consensus heptads to alanine, or replacing all Pro6 residues with alanine. We find that Ser5 status is a tunable determinant of Pho1 regulation, i.e., serial decrements in the number of consensus Ser5 heptads from seven to two elicits a progressive increase in Pho1 expression in phosphate-replete medium. Pho1 is also derepressed by hypomorphic mutations of the CTD kinase Cdk9. Inactivation of the CTD phosphatase Ssu72 attenuates Pho1 induction in wild-type cells and blocks Pho1 derepression in S7A cells. These experiments implicate Ser5, Pro6, and Ser7 as component letters of a CTD coding "word" that transduces a repressive transcriptional signal via serine phosphorylation.
Collapse
Affiliation(s)
- Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Ana M Sanchez
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| |
Collapse
|
286
|
Popken J, Brero A, Koehler D, Schmid VJ, Strauss A, Wuensch A, Guengoer T, Graf A, Krebs S, Blum H, Zakhartchenko V, Wolf E, Cremer T. Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos. Nucleus 2015; 5:555-89. [PMID: 25482066 PMCID: PMC4615760 DOI: 10.4161/19491034.2014.979712] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nuclear landscapes were studied during preimplantation development of bovine embryos, generated either by in vitro fertilization (IVF), or generated as cloned embryos by somatic cell nuclear transfer (SCNT) of bovine fetal fibroblasts, using 3-dimensional confocal laser scanning microscopy (3D-CLSM) and structured illumination microscopy (3D-SIM). Nuclear landscapes of IVF and SCNT embryonic nuclei were compared with each other and with fibroblast nuclei. We demonstrate that reprogramming of fibroblast nuclei in cloned embryos requires changes of their landscapes similar to nuclei of IVF embryos. On the way toward the 8-cell stage, where major genome activation occurs, a major lacuna, enriched with splicing factors, was formed in the nuclear interior and chromosome territories (CTs) were shifted toward the nuclear periphery. During further development the major lacuna disappeared and CTs were redistributed throughout the nuclear interior forming a contiguous higher order chromatin network. At all stages of development CTs of IVF and SCNT embryonic nuclei were built up from chromatin domain clusters (CDCs) pervaded by interchromatin compartment (IC) channels. Quantitative analyses revealed a highly significant enrichment of RNA polymerase II and H3K4me3, a marker for transcriptionally competent chromatin, at the periphery of CDCs. In contrast, H3K9me3, a marker for silent chromatin, was enriched in the more compacted interior of CDCs. Despite these striking similarities, we also detected major differences between nuclear landscapes of IVF and cloned embryos. Possible implications of these differences for the developmental potential of cloned animals remain to be investigated. We present a model, which integrates generally applicable structural and functional features of the nuclear landscape.
Collapse
Key Words
- 3D-CLSM, 3-dimensional confocal laser scanning microscopy
- 3D-SIM, 3-dimensional structured illumination microscopy
- B23, nucleophosmin B23
- BTA, Bos taurus
- CDC, chromatin domain cluster
- CT, chromosome territory
- EM, electron microscopy
- ENC, embryonic nuclei with conventional nuclear architecture
- ENP, embryonic nuclei with peripheral CT distribution
- H3K4me3
- H3K4me3, histone H3 with tri-methylated lysine 4
- H3K9me3
- H3K9me3, histone H3 with tri-methylated lysine 9
- H3S10p, histone H3 with phosphorylated serine 10
- IC, interchromatin compartment
- IVF, in vitro fertilization
- MCB, major chromatin body
- PR, perichromatin region
- RNA polymerase II
- RNA polymerase II-S2p, RNA polymerase II with phosphorylated serine 2 of its CTD domain
- RNA polymerase II-S5p, RNA polymerase II with phosphorylated serine 5 of its CTD domain
- SC-35, splicing factor SC-35
- SCNT, somatic cell nuclear transfer.
- bovine preimplantation development
- chromatin domain
- chromosome territory
- embryonic genome activation
- in vitro fertilization (IVF)
- interchromatin compartment
- major EGA, major embryonic genome activation
- somatic cell nuclear transfer (SCNT)
Collapse
Affiliation(s)
- Jens Popken
- a Division of Anthropology and Human Genetics ; Biocenter; LMU Munich ; Munich , Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
287
|
Mühlbacher W, Mayer A, Sun M, Remmert M, Cheung ACM, Niesser J, Soeding J, Cramer P. Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold. Proteins 2015. [PMID: 26219431 DOI: 10.1002/prot.24869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CTDK-I is a yeast kinase complex that phosphorylates the C-terminal repeat domain (CTD) of RNA polymerase II (Pol II) to promote transcription elongation. CTDK-I contains the cyclin-dependent kinase Ctk1 (homologous to human CDK9/CDK12), the cyclin Ctk2 (human cyclin K), and the yeast-specific subunit Ctk3, which is required for CTDK-I stability and activity. Here we predict that Ctk3 consists of a N-terminal CTD-interacting domain (CID) and a C-terminal three-helix bundle domain. We determine the X-ray crystal structure of the N-terminal domain of the Ctk3 homologue Lsg1 from the fission yeast Schizosaccharomyces pombe at 2.0 Å resolution. The structure reveals eight helices arranged into a right-handed superhelical fold that resembles the CID domain present in transcription termination factors Pcf11, Nrd1, and Rtt103. Ctk3 however shows different surface properties and no binding to CTD peptides. Together with the known structure of Ctk1 and Ctk2 homologues, our results lead to a molecular framework for analyzing the structure and function of the CTDK-I complex.
Collapse
Affiliation(s)
- Wolfgang Mühlbacher
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Andreas Mayer
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Mai Sun
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Michael Remmert
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Alan C M Cheung
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, Munich, 81377, Germany
| | - Jürgen Niesser
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Johannes Soeding
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, Göttingen, 37077, Germany
| |
Collapse
|
288
|
Mbogning J, Pagé V, Burston J, Schwenger E, Fisher RP, Schwer B, Shuman S, Tanny JC. Functional interaction of Rpb1 and Spt5 C-terminal domains in co-transcriptional histone modification. Nucleic Acids Res 2015; 43:9766-75. [PMID: 26275777 PMCID: PMC4787787 DOI: 10.1093/nar/gkv837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/09/2015] [Indexed: 12/11/2022] Open
Abstract
Transcription by RNA polymerase II (RNAPII) is accompanied by a conserved pattern of histone modifications that plays important roles in regulating gene expression. The establishment of this pattern requires phosphorylation of both Rpb1 (the largest RNAPII subunit) and the elongation factor Spt5 on their respective C-terminal domains (CTDs). Here we interrogated the roles of individual Rpb1 and Spt5 CTD phospho-sites in directing co-transcriptional histone modifications in the fission yeast Schizosaccharomyces pombe. Steady-state levels of methylation at histone H3 lysines 4 (H3K4me) and 36 (H3K36me) were sensitive to multiple mutations of the Rpb1 CTD repeat motif (Y1S2P3T4S5P6S7). Ablation of the Spt5 CTD phospho-site Thr1 reduced H3K4me levels but had minimal effects on H3K36me. Nonetheless, Spt5 CTD mutations potentiated the effects of Rpb1 CTD mutations on H3K36me, suggesting overlapping functions. Phosphorylation of Rpb1 Ser2 by the Cdk12 orthologue Lsk1 positively regulated H3K36me but negatively regulated H3K4me. H3K36me and histone H2B monoubiquitylation required Rpb1 Ser5 but were maintained upon inactivation of Mcs6/Cdk7, the major kinase for Rpb1 Ser5 in vivo, implicating another Ser5 kinase in these regulatory pathways. Our results elaborate the CTD ‘code’ for co-transcriptional histone modifications.
Collapse
Affiliation(s)
- Jean Mbogning
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Jillian Burston
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Emily Schwenger
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| |
Collapse
|
289
|
Chen FX, Woodfin AR, Gardini A, Rickels RA, Marshall SA, Smith ER, Shiekhattar R, Shilatifard A. PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II. Cell 2015; 162:1003-15. [PMID: 26279188 DOI: 10.1016/j.cell.2015.07.042] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 05/16/2015] [Accepted: 07/02/2015] [Indexed: 10/25/2022]
Abstract
The control of promoter-proximal pausing and the release of RNA polymerase II (Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify that Pol-II-associated factor 1 (PAF1) possesses an evolutionarily conserved function in metazoans in the regulation of promoter-proximal pausing. Reduction in PAF1 levels leads to an increased release of paused Pol II into gene bodies at thousands of genes. PAF1 depletion results in increased nascent and mature transcripts and increased levels of phosphorylation of Pol II's C-terminal domain on serine 2 (Ser2P). These changes can be explained by the recruitment of the Ser2P kinase super elongation complex (SEC) effecting increased release of paused Pol II into productive elongation, thus establishing PAF1 as a regulator of promoter-proximal pausing by Pol II.
Collapse
Affiliation(s)
- Fei Xavier Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Alessandro Gardini
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
| |
Collapse
|
290
|
Srivastava R, Ahn SH. Modifications of RNA polymerase II CTD: Connections to the histone code and cellular function. Biotechnol Adv 2015; 33:856-72. [PMID: 26241863 DOI: 10.1016/j.biotechadv.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/08/2015] [Accepted: 07/28/2015] [Indexed: 12/24/2022]
Abstract
At the onset of transcription, many protein machineries interpret the cellular signals that regulate gene expression. These complex signals are mostly transmitted to the indispensable primary proteins involved in transcription, RNA polymerase II (RNAPII) and histones. RNAPII and histones are so well coordinated in this cellular function that each cellular signal is precisely allocated to specific machinery depending on the stage of transcription. The carboxy-terminal domain (CTD) of RNAPII in eukaryotes undergoes extensive posttranslational modification, called the 'CTD code', that is indispensable for coupling transcription with many cellular processes, including mRNA processing. The posttranslational modification of histones, known as the 'histone code', is also critical for gene transcription through the reversible and dynamic remodeling of chromatin structure. Notably, the histone code is closely linked with the CTD code, and their combinatorial effects enable the delicate regulation of gene transcription. This review elucidates recent findings regarding the CTD modifications of RNAPII and their coordination with the histone code, providing integrative pathways for the fine-tuned regulation of gene expression and cellular function.
Collapse
Affiliation(s)
- Rakesh Srivastava
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Seong Hoon Ahn
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea.
| |
Collapse
|
291
|
Bartkowiak B, Yan C, Greenleaf AL. Engineering an analog-sensitive CDK12 cell line using CRISPR/Cas. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1179-87. [PMID: 26189575 DOI: 10.1016/j.bbagrm.2015.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/08/2015] [Accepted: 07/14/2015] [Indexed: 11/15/2022]
Abstract
The RNA Polymerase II C-terminal domain (CTD) kinase CDK12 has been implicated as a tumor suppressor and regulator of DNA damage response genes. Although much has been learned about CDK12 and its activity, due to the lack of a specific inhibitor and the complications posed by long term RNAi depletion, much is still unknown about the particulars of CDK12 function. Therefore gaining a better understanding of CDK12's roles at the molecular level will be challenging without the development of additional tools. In order to address these issues we have used the CRISPR/Cas gene engineering system to create a mammalian cell line in which the only functional copy of CDK12 is selectively inhibitable by a cell-permeable adenine analog (analog-sensitive CDK12). Inhibition of CDK12 results in a perturbation of the phosphorylation patterns on the CTD and an arrest in cellular proliferation. This cell line should serve as a powerful tool for future studies.
Collapse
Affiliation(s)
| | - Christopher Yan
- Department of Biochemistry, Duke University Medical Center, United States
| | - Arno L Greenleaf
- Department of Biochemistry, Duke University Medical Center, United States.
| |
Collapse
|
292
|
Kimura H, Hayashi-Takanaka Y, Stasevich TJ, Sato Y. Visualizing posttranslational and epigenetic modifications of endogenous proteins in vivo. Histochem Cell Biol 2015; 144:101-9. [PMID: 26138929 PMCID: PMC4522274 DOI: 10.1007/s00418-015-1344-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2015] [Indexed: 01/29/2023]
Abstract
Protein localization and dynamics can now be visualized in living cells using the fluorescent protein fusion technique, but it is still difficult to selectively detect molecules with a specific function. As a posttranslational protein modification is often associated with a specific function, marking specifically modified protein molecules in living cells is a way to track an important fraction of protein. In the nucleus, histones are subjected to a variety of modifications such as acetylation and methylation that are associated with epigenetic gene regulation. RNA polymerase II, an enzyme that transcribes genes, is also differentially phosphorylated during the initiation and elongation of transcription. To understand the mechanism of gene regulation in vivo, we have developed methods to track histone and RNA polymerase II modifications using probes derived from modification-specific monoclonal antibodies. In Fab-based live endogenous modification labeling (FabLEM), fluorescently labeled antigen-binding fragments (Fabs) are loaded into cells. Fabs bind to target modifications in the nucleus with a binding time of a second to tens of seconds, and so the modification can be tracked without disturbing cell function. For tracking over longer periods of time or in living animals, we have also developed a genetically encoded system to express a modification-specific intracellular antibody (mintbody). Transgenic fruit fly and zebrafish that express histone H3 Lys9 acetylation-specific mintbody developed normally and remain fertile, suggesting that visualizing histone modifications in any tissue in live animals has become possible. These live cell modification tracking techniques will facilitate future studies on epigenetic regulation related to development, differentiation, and disease. Moreover, these techniques can be applied to any other protein modification, opening up new avenues in broad areas in biology and medicine.
Collapse
Affiliation(s)
- Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
| | | | | | | |
Collapse
|
293
|
Koo J, Bahk YY. In vivo putative O-GlcNAcylation of human SCP1 and evidence for possible role of its N-terminal disordered structure. BMB Rep 2015; 47:593-8. [PMID: 25081999 PMCID: PMC4261519 DOI: 10.5483/bmbrep.2014.47.10.144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase II carboxyl-terminal domain (RNAPII CTD) phosphatases are responsible for the dephosphorylation of the C-terminal domain of the small subunit of RNAPII in eukaryotes. Recently, we demonstrated the identification of several interacting partners with human small CTD phosphatase1 (hSCP1) and the substrate specificity to delineate an appearance of the dephosphorylation catalyzed by SCP1. In this study, using the established cells for inducibly expressing hSCP1 proteins, we monitored the modification of β-O-linked N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation is one of the most common post-translational modifications (PTMs). To gain insight into the PTM of hSCP1, we used the Western blot, immunoprecipitation, succinylayed wheat germ agglutininprecipitation, liquid chromatography-mass spectrometry analyses, and site-directed mutagenesis and identified the Ser41 residue of hSCP1 as the O-GlcNAc modification site. These results suggest that hSCP1 may be an O-GlcNAcylated protein in vivo, and its N-terminus may function a possible role in the PTM, providing a scaffold for binding the protein(s). [BMB Reports 2014; 47(10): 593-598]
Collapse
Affiliation(s)
- JaeHyung Koo
- Department of Brain Science, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu 711-873, Korea
| | - Young Yil Bahk
- Department of Biotechnology, Konkuk University, Chungju 380-701, Korea
| |
Collapse
|
294
|
Wani S, Hirose Y, Ohkuma Y. Human RNA polymerase II-associated protein 2 (RPAP2) interacts directly with the RNA polymerase II subunit Rpb6 and participates in pre-mRNA 3'-end formation. Drug Discov Ther 2015; 8:255-61. [PMID: 25639305 DOI: 10.5582/ddt.2014.01044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is composed of tandem repeats of the heptapeptide Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. The CTD of Pol II undergoes reversible phosphorylation during the transcription cycle, mainly at Ser2, Ser5, and Ser7. Dynamic changes in the phosphorylation patterns of the CTD are responsible for stage-specific recruitment of various factors involved in RNA processing, histone modification, and transcription elongation/termination. Human RNA polymerase II-associated protein 2 (RPAP2) was originally identified as a Pol II-associated protein and was subsequently shown to function as a novel Ser5-specific CTD phosphatase. Although a recent study suggested that RPAP2 is required for the efficient expression of small nuclear RNA genes, the role of RPAP2 in controlling the expression of protein-coding genes is unknown. Here, we demonstrate that the C-terminal region of RPAP2 interacts directly with the Pol II subunit Rpb6. Chromatin immunoprecipitation analyses of the MYC and GAPDH protein-coding genes revealed that RPAP2 occupied the coding and 3' regions. Notably, siRNA-mediated knockdown of RPAP2 caused defects in 3'-end formation of the MYC and GAPDH pre-mRNAs. These results suggest that RPAP2 controls Pol II activity through a direct interaction with Rpb6 and participates in pre-mRNA 3'-end formation.
Collapse
Affiliation(s)
- Shotaro Wani
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama
| | | | | |
Collapse
|
295
|
Schwer B, Ghosh A, Sanchez AM, Lima CD, Shuman S. Genetic and structural analysis of the essential fission yeast RNA polymerase II CTD phosphatase Fcp1. RNA (NEW YORK, N.Y.) 2015; 21:1135-1146. [PMID: 25883047 PMCID: PMC4436666 DOI: 10.1261/rna.050286.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/25/2015] [Indexed: 06/04/2023]
Abstract
Protein phosphatases regulate mRNA synthesis and processing by remodeling the carboxy-terminal domain (CTD) of RNA polymerase II (Pol2) to dynamically inscribe a Pol2 CTD code. Fission yeast Fcp1 (SpFcp1) is an essential 723-amino acid CTD phosphatase that preferentially hydrolyzes Ser2-PO4 of the YS(2)PTSPS repeat. The SpFcp1 catalytic domain (aa 140-580) is composed of a DxDxT acyl-phosphatase module (FCPH) and a BRCT module. Here we conducted a genetic analysis of SpFcp1, which shows that (i) phosphatase catalytic activity is required for vegetative growth of fission yeast; (ii) the flanking amino-terminal domain (aa 1-139) and its putative metal-binding motif C(99)H(101)Cys(109)C(112) are essential; (iii) the carboxy-terminal domain (aa 581-723) is dispensable; (iv) a structurally disordered internal segment of the FCPH domain (aa 330-393) is dispensable; (v) lethal SpFcp1 mutations R271A and R299A are rescued by shortening the Pol2 CTD repeat array; and (vi) CTD Ser2-PO4 is not the only essential target of SpFcp1 in vivo. Recent studies highlight a second CTD code involving threonine phosphorylation of a repeat motif in transcription elongation factor Spt5. We find that Fcp1 can dephosphorylate Thr1-PO4 of the fission yeast Spt5 CTD nonamer repeat T(1)PAWNSGSK. We identify Arg271 as a governor of Pol2 versus Spt5 CTD substrate preference. Our findings implicate Fcp1 as a versatile sculptor of both the Pol2 and Spt5 CTD codes. Finally, we report a new 1.45 Å crystal structure of SpFcp1 with Mg(2+) and AlF3 that mimics an associative phosphorane transition state of the enzyme-aspartyl-phosphate hydrolysis reaction.
Collapse
Affiliation(s)
- Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Agnidipta Ghosh
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Ana M Sanchez
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA Howard Hughes Medical Institute, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| |
Collapse
|
296
|
Ke X, McKnight RA, Gracey Maniar LE, Sun Y, Callaway CW, Majnik A, Lane RH, Cohen SS. IUGR increases chromatin-remodeling factor Brg1 expression and binding to GR exon 1.7 promoter in newborn male rat hippocampus. Am J Physiol Regul Integr Comp Physiol 2015; 309:R119-27. [PMID: 25972460 DOI: 10.1152/ajpregu.00495.2014] [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: 12/02/2014] [Accepted: 05/11/2015] [Indexed: 12/15/2022]
Abstract
Intrauterine growth restriction (IUGR) increases the risk for neurodevelopment delay and neuroendocrine reprogramming in both humans and rats. Neuroendocrine reprogramming involves the glucocorticoid receptor (GR) gene that is epigenetically regulated in the hippocampus. Using a well-characterized rodent model, we have previously shown that IUGR increases GR exon 1.7 mRNA variant and total GR expressions in male rat pup hippocampus. Epigenetic regulation of GR transcription may involve chromatin remodeling of the GR gene. A key chromatin remodeler is Brahma-related gene-1(Brg1), a member of the ATP-dependent SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling complex. Brg1 regulates gene expression by affecting nucleosome repositioning and recruiting transcriptional components to target promoters. We hypothesized that IUGR would increase hippocampal Brg1 expression and binding to GR exon 1.7 promoter, as well as alter nucleosome positioning over GR promoters in newborn male pups. Further, we hypothesized that IUGR would lead to accumulation of specificity protein 1 (Sp1) and RNA pol II at GR exon 1.7 promoter. Indeed, we found that IUGR increased Brg1 expression and binding to GR exon 1.7 promoter. We also found that increased Brg1 binding to GR exon 1.7 promoter was associated with accumulation of Sp1 and RNA pol II carboxy terminal domain pSer-5 (a marker of active transcription). Furthermore, the transcription start site of GR exon 1.7 was located within a nucleosome-depleted region. We speculate that changes in hippocampal Brg1 expression mediate GR expression and subsequently trigger neuroendocrine reprogramming in male IUGR rats.
Collapse
Affiliation(s)
- Xingrao Ke
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin; Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Robert A McKnight
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Ying Sun
- Bioinformatics-Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Christopher W Callaway
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Amber Majnik
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert H Lane
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Susan S Cohen
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin;
| |
Collapse
|
297
|
Laitem C, Zaborowska J, Isa NF, Kufs J, Dienstbier M, Murphy S. CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II-transcribed genes. Nat Struct Mol Biol 2015; 22:396-403. [PMID: 25849141 PMCID: PMC4424039 DOI: 10.1038/nsmb.3000] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 03/06/2015] [Indexed: 12/23/2022]
Abstract
Transcription through early-elongation checkpoints requires phosphorylation of negative transcription elongation factors (NTEFs) by the cyclin-dependent kinase (CDK) 9. Using CDK9 inhibitors and global run-on sequencing (GRO-seq), we have mapped CDK9 inhibitor-sensitive checkpoints genome wide in human cells. Our data indicate that early-elongation checkpoints are a general feature of RNA polymerase (pol) II-transcribed human genes and occur independently of polymerase stalling. Pol II that has negotiated the early-elongation checkpoint can elongate in the presence of inhibitors but, remarkably, terminates transcription prematurely close to the terminal polyadenylation (poly(A)) site. Our analysis has revealed an unexpected poly(A)-associated elongation checkpoint, which has major implications for the regulation of gene expression. Interestingly, the pattern of modification of the C-terminal domain of pol II terminated at this new checkpoint largely mirrors the pattern normally found downstream of the poly(A) site, thus suggesting common mechanisms of termination.
Collapse
Affiliation(s)
- Clélia Laitem
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Nur F Isa
- 1] Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. [2] Department of Biotechnology, International Islamic University Malaysia, Pahang, Malaysia
| | - Johann Kufs
- Faculty of Science, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Martin Dienstbier
- Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| |
Collapse
|
298
|
Estarás C, Benner C, Jones KA. SMADs and YAP compete to control elongation of β-catenin:LEF-1-recruited RNAPII during hESC differentiation. Mol Cell 2015; 58:780-93. [PMID: 25936800 DOI: 10.1016/j.molcel.2015.04.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/23/2015] [Accepted: 03/27/2015] [Indexed: 01/13/2023]
Abstract
The Wnt3a/β-catenin and Activin/SMAD2,3 signaling pathways synergize to induce endodermal differentiation of human embryonic stem cells; however, the underlying mechanism is not well understood. Using ChIP-seq and GRO-seq analyses, we show here that Wnt3a-induced β-catenin:LEF-1 enhancers recruit cohesin to direct enhancer-promoter looping and activate mesendodermal (ME) lineage genes. Moreover, we find that LEF-1 and other hESC enhancers recruit RNAPII complexes (eRNAPII) that are highly phosphorylated at Ser5, but not Ser7. Wnt3a signaling further increases Ser5P-RNAPII at LEF-1 sites and ME gene promoters, indicating that elongation remains limiting. However, subsequent Activin/SMAD2,3 signaling selectively increases transcription elongation, P-TEFb occupancy, and Ser7P-RNAPII levels at these genes. Finally, we show that the Hippo regulator, YAP, functions with TEAD to regulate binding of the NELF negative elongation factor and block SMAD2,3 induction of ME genes. Thus, the Wnt3a/β-catenin and Activin/SMAD2,3 pathways act in concert to counteract YAP repression and upregulate ME genes during early hESC differentiation.
Collapse
Affiliation(s)
- Conchi Estarás
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chris Benner
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Katherine A Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
299
|
Baillat D, Wagner EJ. Integrator: surprisingly diverse functions in gene expression. Trends Biochem Sci 2015; 40:257-64. [PMID: 25882383 DOI: 10.1016/j.tibs.2015.03.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 01/06/2023]
Abstract
The discovery of the metazoan-specific Integrator (INT) complex represented a breakthrough in our understanding of noncoding U-rich small nuclear RNA (UsnRNA) maturation and has triggered a reevaluation of their biosynthesis mechanism. In the decade since, significant progress has been made in understanding the details of its recruitment, specificity, and assembly. While some discrepancies remain on how it interacts with the C-terminal domain (CTD) of the RNA polymerase II (RNAPII) and the details of its recruitment to UsnRNA genes, preliminary models have emerged. Recent provocative studies now implicate INT in the regulation of protein-coding gene transcription initiation and RNAPII pause-release, thereby broadening the scope of INT functions in gene expression regulation. We discuss the implications of these findings while putting them into the context of what is understood about INT function at UsnRNA genes.
Collapse
Affiliation(s)
- David Baillat
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, Houston, TX 77030, USA.
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
| |
Collapse
|
300
|
Ekumi KM, Paculova H, Lenasi T, Pospichalova V, Bösken CA, Rybarikova J, Bryja V, Geyer M, Blazek D, Barboric M. Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex. Nucleic Acids Res 2015; 43:2575-89. [PMID: 25712099 PMCID: PMC4357706 DOI: 10.1093/nar/gkv101] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 01/05/2015] [Accepted: 01/30/2015] [Indexed: 12/11/2022] Open
Abstract
The Cdk12/CycK complex promotes expression of a subset of RNA polymerase II genes, including those of the DNA damage response. CDK12 is among only nine genes with recurrent somatic mutations in high-grade serous ovarian carcinoma. However, the influence of these mutations on the Cdk12/CycK complex and their link to cancerogenesis remain ill-defined. Here, we show that most mutations prevent formation of the Cdk12/CycK complex, rendering the kinase inactive. By examining the mutations within the Cdk12/CycK structure, we find that they likely provoke structural rearrangements detrimental to Cdk12 activation. Our mRNA expression analysis of the patient samples containing the CDK12 mutations reveals coordinated downregulation of genes critical to the homologous recombination DNA repair pathway. Moreover, we establish that the Cdk12/CycK complex occupies these genes and promotes phosphorylation of RNA polymerase II at Ser2. Accordingly, we demonstrate that the mutant Cdk12 proteins fail to stimulate the faithful DNA double strand break repair via homologous recombination. Together, we provide the molecular basis of how mutated CDK12 ceases to function in ovarian carcinoma. We propose that CDK12 is a tumor suppressor of which the loss-of-function mutations may elicit defects in multiple DNA repair pathways, leading to genomic instability underlying the genesis of the cancer.
Collapse
Affiliation(s)
- Kingsley M Ekumi
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Hana Paculova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Tina Lenasi
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Vendula Pospichalova
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
| | - Christian A Bösken
- Center of Advanced European Studies and Research, Group Physical Biochemistry, 53175 Bonn, Germany
| | - Jana Rybarikova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Vitezslav Bryja
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Matthias Geyer
- Center of Advanced European Studies and Research, Group Physical Biochemistry, 53175 Bonn, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Matjaz Barboric
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| |
Collapse
|