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Results: 1 to 20 of 22

1.
Nat Rev Genet. 2014 Mar;15(3):163-75. doi: 10.1038/nrg3662. Epub 2014 Feb 11.

Coupling mRNA processing with transcription in time and space.

Author information

  • Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, MS8101, PO BOX 6511, Aurora, Colorado 80045, USA.

Abstract

Maturation of mRNA precursors often occurs simultaneously with their synthesis by RNA polymerase II (Pol II). The co-transcriptional nature of mRNA processing has permitted the evolution of coupling mechanisms that coordinate transcription with mRNA capping, splicing, editing and 3' end formation. Recent experiments using sophisticated new methods for analysis of nascent RNA have provided important insights into the relative amount of co-transcriptional and post-transcriptional processing, the relationship between mRNA elongation and processing, and the role of the Pol II carboxy-terminal domain (CTD) in regulating these processes.

PMID:
24514444
[PubMed - indexed for MEDLINE]
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2.
Cell Rep. 2014 Jan 30;6(2):325-35. doi: 10.1016/j.celrep.2013.12.021. Epub 2014 Jan 9.

The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.

Author information

  • 1Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
  • 2Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • 3Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
  • 4Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
  • 5Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
  • 6Genes and Development Graduate Program, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
  • 7Molecular Biology Program, University of Colorado School of Medicine, Aurora, CO 80045, USA.
  • 8Molecular Biology Program, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
  • 9Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Radiation Oncology, University Washington School of Medicine, Seattle, WA 98109, USA.
  • 10Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Genes and Development Graduate Program, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Center for Cancer Epigenetics and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: xbshi@mdanderson.org.
  • 11Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Biology Program, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: tatiana.kutateladze@ucdenver.edu.

Abstract

The histone lysine demethylase KDM5B regulates gene transcription and cell differentiation and is implicated in carcinogenesis. It contains multiple conserved chromatin-associated domains, including three PHD fingers of unknown function. Here, we show that the first and third, but not the second, PHD fingers of KDM5B possess histone binding activities. The PHD1 finger is highly specific for unmodified histone H3 (H3K4me0), whereas the PHD3 finger shows preference for the trimethylated histone mark H3K4me3. RNA-seq analysis indicates that KDM5B functions as a transcriptional repressor for genes involved in inflammatory responses, cell proliferation, adhesion, and migration. Biochemical analysis reveals that KDM5B associates with components of the nucleosome remodeling and deacetylase (NuRD) complex and may cooperate with the histone deacetylase 1 (HDAC1) in gene repression. KDM5B is downregulated in triple-negative breast cancer relative to estrogen-receptor-positive breast cancer. Overexpression of KDM5B in the MDA-MB 231 breast cancer cells suppresses cell migration and invasion, and the PHD1-H3K4me0 interaction is essential for inhibiting migration. These findings highlight tumor-suppressive functions of KDM5B in triple-negative breast cancer cells and suggest a multivalent mechanism for KDM5B-mediated transcriptional regulation.

Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

PMID:
24412361
[PubMed - in process]
PMCID:
PMC3918441
[Available on 2015/1/30]
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3.
Genet Res Int. 2012;2012:170173. doi: 10.1155/2012/170173. Epub 2012 Jan 29.

Control of Transcriptional Elongation by RNA Polymerase II: A Retrospective.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

Abstract

The origins of our current understanding of control of transcription elongation lie in pioneering experiments that mapped RNA polymerase II on viral and cellular genes. These studies first uncovered the surprising excess of polymerase molecules that we now know to be situated at the at the 5' ends of most genes in multicellular organisms. The pileup of pol II near transcription start sites reflects a ubiquitous bottle-neck that limits elongation right at the start of the transcription elongation. Subsequent seminal work identified conserved protein factors that positively and negatively control the flux of polymerase through this bottle-neck, and make a major contribution to control of gene expression.

PMID:
22567377
[PubMed]
PMCID:
PMC3335475
Free PMC Article
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4.
Mol Cell. 2012 May 11;46(3):311-24. doi: 10.1016/j.molcel.2012.03.006. Epub 2012 Apr 5.

mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

Abstract

We report a function of human mRNA decapping factors in control of transcription by RNA polymerase II. Decapping proteins Edc3, Dcp1a, and Dcp2 and the termination factor TTF2 coimmunoprecipitate with Xrn2, the nuclear 5'-3' exonuclease "torpedo" that facilitates transcription termination at the 3' ends of genes. Dcp1a, Xrn2, and TTF2 localize near transcription start sites (TSSs) by ChIP-seq. At genes with 5' peaks of paused pol II, knockdown of decapping or termination factors Xrn2 and TTF2 shifted polymerase away from the TSS toward upstream and downstream distal positions. This redistribution of pol II is similar in magnitude to that caused by depletion of the elongation factor Spt5. We propose that coupled decapping of nascent transcripts and premature termination by the "torpedo" mechanism is a widespread mechanism that limits bidirectional pol II elongation. Regulated cotranscriptional decapping near promoter-proximal pause sites followed by premature termination could control productive pol II elongation.

Copyright © 2012 Elsevier Inc. All rights reserved.

Comment in

PMID:
22483619
[PubMed - indexed for MEDLINE]
PMCID:
PMC3806456
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5.
Nat Struct Mol Biol. 2011 Sep 25;18(10):1164-71. doi: 10.1038/nsmb.2126.

The export factor Yra1 modulates mRNA 3' end processing.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA.

Abstract

The Saccharomyces cerevisiae mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A that links export to 3' end formation. We found that an unexpected consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit Clp1 for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit; instead, Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice, particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A 3' processing factor.

PMID:
21947206
[PubMed - indexed for MEDLINE]
PMCID:
PMC3307051
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6.
Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13564-9. doi: 10.1073/pnas.1109475108. Epub 2011 Aug 1.

Pre-mRNA splicing is a determinant of histone H3K36 methylation.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, University of Colorado Health Sciences Center, Aurora, CO 80045, USA.

Abstract

A chromatin code appears to mark introns and exons with distinct patterns of nucleosome enrichment and histone methylation. We investigated whether a causal relationship exists between splicing and chromatin modification by asking whether splice-site mutations affect the methylation of histone H3K36. Deletions of the 3' splice site in intron 2 or in both introns 1 and 2 of an integrated β-globin reporter gene caused a shift in relative distribution of H3K36 trimethylation away from 5' ends and toward 3' ends. The effects of splice-site mutations correlated with enhanced retention of a U5 snRNP subunit on transcription complexes downstream of the gene. In contrast, a poly(A) site mutation did not affect H3K36 methylation. Similarly, global inhibition of splicing by spliceostatin A caused a rapid repositioning of H3K36me3 away from 5' ends in favor of 3' ends. These results suggest that the cotranscriptional splicing apparatus influences establishment of normal patterns of histone modification.

PMID:
21807997
[PubMed - indexed for MEDLINE]
PMCID:
PMC3158196
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7.
Nat Struct Mol Biol. 2010 Oct;17(10):1279-86. doi: 10.1038/nsmb.1913. Epub 2010 Sep 12.

Gene-specific RNA polymerase II phosphorylation and the CTD code.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA.

Abstract

Phosphorylation of the RNA polymerase (Pol) II C-terminal domain (CTD) repeats (1-YSPTSPS-7) is coupled to transcription and may act as a 'code' that controls mRNA synthesis and processing. To examine the code in budding yeast, we mapped genome-wide CTD Ser2, Ser5 and Ser7 phosphorylations and the CTD-associated termination factors Nrd1 and Pcf11. Phospho-CTD dynamics are not scaled to gene length and are gene-specific, with highest Ser5 and Ser7 phosphorylation at the 5' ends of well-expressed genes with nucleosome-occupied promoters. The CTD kinases Kin28 and Ctk1 markedly affect Pol II distribution in a gene-specific way. The code is therefore written differently on different genes, probably under the control of promoters. Ser7 phosphorylation is enriched on introns and at sites of Nrd1 accumulation, suggesting links to splicing and Nrd1 recruitment. Nrd1 and Pcf11 frequently colocalize, suggesting functional overlap. Unexpectedly, Pcf11 is enriched at centromeres and Pol III-transcribed genes.

PMID:
20835241
[PubMed - indexed for MEDLINE]
PMCID:
PMC3048030
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8.
Nat Struct Mol Biol. 2009 Sep;16(9):916-22. doi: 10.1038/nsmb.1652. Epub 2009 Aug 23.

Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, University of Colorado at Denver Health Sciences Center, Aurora, Colorado, USA.

Abstract

We investigated whether a continuous transcript is necessary for co-transcriptional pre-mRNA processing. Cutting an intron with the fast-cleaving hepatitis delta ribozyme, but not the slower hammerhead, inhibited splicing. Therefore, exon tethering to RNA polymerase II (Pol II) cannot rescue splicing of a transcript severed by a ribozyme that cleaves rapidly relative to the rate of splicing. Ribozyme cutting also released cap-binding complex (CBC) from the gene, suggesting that exon 1 is not tethered. Unexpectedly, cutting within exons inhibited splicing of distal introns, where exon definition is not affected, probably owing to disruption of the interactions with the CBC and the Pol II C-terminal domain that facilitate splicing. Ribozyme cutting within the mRNA also inhibited 3' processing and transcription termination. We propose that damaging the nascent transcript aborts pre-mRNA processing and that this mechanism may help to prevent association of processing factors with Pol II that is not productively engaged in transcription.

Comment in

PMID:
19701200
[PubMed - indexed for MEDLINE]
PMCID:
PMC2755206
Free PMC Article
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9.
Mol Cell Biol. 2009 Oct;29(20):5455-64. doi: 10.1128/MCB.00637-09. Epub 2009 Aug 10.

TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC, MS 8101, P.O. Box 6511, Aurora, CO 80045, USA.

Abstract

The function of human TFIIH-associated Cdk7 in RNA polymerase II (Pol II) transcription and C-terminal domain (CTD) phosphorylation was investigated in analogue-sensitive Cdk7(as/as) mutant cells where the kinase can be inhibited without disrupting TFIIH. We show that both Cdk7 and Cdk9/PTEFb contribute to phosphorylation of Pol II CTD Ser5 residues on transcribed genes. Cdk7 is also a major kinase of CTD Ser7 on Pol II at the c-fos and U snRNA genes. Furthermore, TFIIH and recombinant Cdk7-CycH-Mat1 as well as recombinant Cdk9-CycT1 phosphorylated CTD Ser7 and Ser5 residues in vitro. Inhibition of Cdk7 in vivo suppressed the amount of Pol II accumulated at 5' ends on several genes including c-myc, p21, and glyceraldehyde-3-phosphate dehydrogenase genes, indicating reduced promoter-proximal pausing or polymerase "leaking" into the gene. Consistent with a 5' pausing defect, Cdk7 inhibition reduced recruitment of the negative elongation factor NELF at start sites. A role of Cdk7 in regulating elongation is further suggested by enhanced histone H4 acetylation and diminished histone H4 trimethylation on lysine 36-two marks of elongation-within genes when the kinase was inhibited. Consistent with a new role for TFIIH at 3' ends, it was detected within genes and 3'-flanking regions, and Cdk7 inhibition delayed pausing and transcription termination.

PMID:
19667075
[PubMed - indexed for MEDLINE]
PMCID:
PMC2756882
Free PMC Article
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10.
Mol Cell. 2009 Jan 30;33(2):215-26. doi: 10.1016/j.molcel.2008.12.007. Epub 2008 Dec 24.

Cotranscriptional recruitment of the mRNA export factor Yra1 by direct interaction with the 3' end processing factor Pcf11.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.

Abstract

We investigated recruitment of the yeast mRNA export factor Yra1 to the transcription elongation complex (TEC). Previously, the Sub2 helicase subunit of TREX was proposed to recruit Yra1. We report that Sub2 is dispensable for Yra1 recruitment, but the cleavage/polyadenylation factor, CF1A, is required. Yra1 binds directly to the Zn finger/Clp1 region of Pcf11, the pol II CTD-binding subunit of CF1A, and this interaction is conserved between their human homologs. Tethering of Pcf11 to nascent mRNA is sufficient to enhance Yra1 recruitment. Interaction with Pcf11 can therefore explain Yra1 binding to the TEC independently of Sub2. We propose that after initially binding to Pcf11, Yra1 is transferred to Sub2. Consistent with this idea, Pcf11 binds the same regions of Yra1 that also contact Sub2, indicating a mutually exclusive interaction. These results suggest a mechanism for cotranscriptional assembly of the export competent mRNP and for coordinating export with 3' end processing.

Comment in

PMID:
19110458
[PubMed - indexed for MEDLINE]
PMCID:
PMC2659397
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11.
Nat Struct Mol Biol. 2008 Jan;15(1):71-8. Epub 2007 Dec 23.

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC, MS8101, PO Box 6511, Aurora, Colorado 80045, USA.

Abstract

We investigated co-transcriptional recruitment of pre-mRNA processing factors to human genes. Capping factors associate with paused RNA polymerase II (pol II) at the 5' ends of quiescent genes. They also track throughout actively transcribed genes and accumulate with paused polymerase in the 3' flanking region. The 3' processing factors cleavage stimulation factor and cleavage polyadenylation specificity factor are maximally recruited 0.5-1.5 kilobases downstream of poly(A) sites where they coincide with capping factors, Spt5, and Ser2-hyperphosphorylated, paused pol II. 3' end processing factors also localize at transcription start sites, and this early recruitment is enhanced after polymerase arrest with the elongation factor DRB. These results suggest that promoters may help specify recruitment of 3' end processing factors. We propose a dual-pausing model wherein elongation arrests near the transcription start site and in the 3' flank to allow co-transcriptional processing by factors recruited to the pol II ternary complex.

PMID:
18157150
[PubMed - indexed for MEDLINE]
PMCID:
PMC2836588
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12.
Nat Struct Mol Biol. 2007 Mar;14(3):240-2. Epub 2007 Feb 18.

Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, University of Colorado Health Sciences Center, MS8101, P.O. Box 6511, Aurora, Colorado 80045, USA.

Abstract

Histone H3 Lys4 trimethylation (H3-K4me3) is a conserved mark of actively transcribed chromatin. Using a conditional mutant of the yeast H3-K4 methyltransferase, Set1p, we demonstrate rapid turnover of H3-K4me3 and H3-K4me2 in vivo and show this process requires Yjr119Cp, of the JARID1 family of JmjC proteins. Ectopic overexpression of mouse Jarid1B, a Yjr119Cp homolog, greatly diminished H3-K4me3 and H3-K4me2 in HeLa cells, suggesting these proteins function as K4 demethylases in vivo.

PMID:
17310255
[PubMed - indexed for MEDLINE]
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13.
Genes Dev. 2006 Apr 15;20(8):954-65. Epub 2006 Apr 5.

The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, University of Colorado Health Sciences Center at Fitzsimons, Aurora, Colorado 80045, USA.

Abstract

The torpedo model of transcription termination by RNA polymerase II proposes that a 5'-3' RNA exonuclease enters at the poly(A) cleavage site, degrades the nascent RNA, and eventually displaces polymerase from the DNA. Cotranscriptional degradation of nascent RNA has not been directly demonstrated, however. Here we report that two exonucleases, Rat1 and Xrn1, both contribute to cotranscriptional degradation of nascent RNA, but this degradation is not sufficient to cause polymerase release. Unexpectedly, Rat1 functions in both 3'-end processing and termination by enhancing recruitment of 3'-end processing factors, including Pcf11 and Rna15. In addition, the cleavage factor Pcf11 reciprocally aids in recruitment of Rat1 to the elongation complex. Our results suggest a unified allosteric/torpedo model in which Rat1 is not a dedicated termination factor, but is an integrated component of the cleavage/polyadenylation apparatus.

Comment in

PMID:
16598041
[PubMed - indexed for MEDLINE]
PMCID:
PMC1472303
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14.
Mol Cell. 2005 Dec 9;20(5):747-58.

Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, 80045, USA.

Abstract

We report a functional connection between splicing and transcript release from the DNA. A Pol II CTD mutant inhibited not only splicing but also RNA release from the site of transcription. A ribozyme situated downstream of the gene restored accurate splicing inhibited by the CTD mutant or a mutant poly(A) site, suggesting that cleavage liberates RNA from a niche that is inaccessible to splicing factors. Although ribozyme cleavage enhanced splicing, 3' end processing was impaired, indicating that an intact RNA chain linking the poly(A) site to Pol II is required for optimal processing. Surprisingly, poly(A)(-) beta-globin mRNA with a ribozyme-generated 3' end was exported to the cytoplasm. Ribozyme cleavage can therefore substitute for normal 3' end processing in stimulating splicing and mRNA export. We propose that mRNA biogenesis is coordinated by preventing splicing near the 3' end until the transcript is released by poly(A) site cleavage.

PMID:
16337598
[PubMed - indexed for MEDLINE]
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15.
EMBO J. 2005 Jul 6;24(13):2379-90. Epub 2005 Jun 9.

Altered nucleosome occupancy and histone H3K4 methylation in response to 'transcriptional stress'.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, CO 80045, USA.

Abstract

We report that under 'transcriptional stress' in budding yeast, when most pol II activity is acutely inhibited, rapid deposition of nucleosomes occurs within genes, particularly at 3' positions. Whereas histone H3K4 trimethylation normally marks 5' ends of highly transcribed genes, under 'transcriptional stress' induced by 6-azauracil (6-AU) and inactivation of pol II, TFIIE or CTD kinases Kin28 and Ctk1, this mark shifted to the 3' end of the TEF1 gene. H3K4Me3 at 3' positions was dynamic and could be rapidly removed when transcription recovered. Set1 and Chd1 are required for H3K4 trimethylation at 3' positions when transcription is inhibited by 6-AU. Furthermore, Deltachd1 suppressed the growth defect of Deltaset1. We suggest that a 'transcriptional stress' signal sensed through Set1, Chd1, and possibly other factors, causes H3K4 hypermethylation of newly deposited nucleosomes at downstream positions within a gene. This response identifies a new role for H3K4 trimethylation at the 3' end of the gene, as a chromatin mark associated with impaired pol II transcription.

PMID:
15944735
[PubMed - indexed for MEDLINE]
PMCID:
PMC1173152
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16.
Curr Opin Cell Biol. 2005 Jun;17(3):251-6.

Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors.

Author information

  • Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, Colorado 80045, USA. David.Bentley@UCHSC.edu

Abstract

The universal pre-mRNA processing events of 5' end capping, splicing, and 3' end formation by cleavage/polyadenylation occur co-transcriptionally. As a result, the substrate for mRNA processing factors is a nascent RNA chain that is being extruded from the RNA polymerase II exit channel at 10-30 bases per second. How do processing factors find their substrate RNAs and complete most mRNA maturation before transcription is finished? Recent studies suggest that this task is facilitated by a combination of protein-RNA and protein-protein interactions within a 'mRNA factory' that comprises the elongating RNA polymerase and associated processing factors. This 'factory' undergoes dynamic changes in composition as it traverses a gene and provides the setting for regulatory interactions that couple processing to transcriptional elongation and termination.

PMID:
15901493
[PubMed - indexed for MEDLINE]
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17.
Mol Cell Biol. 2004 Oct;24(20):8963-9.

RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3'-end formation.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado Health Science Center at Fitzsimons, P.O. Box 6511, Aurora, CO 80045, USA.

Abstract

We investigated the role of RNA polymerase II (pol II) carboxy-terminal domain (CTD) phosphorylation in pre-mRNA processing coupled and uncoupled from transcription in Xenopus oocytes. Inhibition of CTD phosphorylation by the kinase inhibitors 5,6-dichloro-1beta-D-ribofuranosyl-benzimidazole and H8 blocked transcription-coupled splicing and poly(A) site cleavage. These experiments suggest that pol II CTD phosphorylation is required for efficient pre-mRNA splicing and 3'-end formation in vivo. In contrast, processing of injected pre-mRNA was unaffected by either kinase inhibitors or alpha-amanitin-induced depletion of pol II. pol II therefore does not appear to participate directly in posttranscriptional processing, at least in frog oocytes. Together these experiments show that the influence of the phosphorylated CTD on pre-mRNA splicing and 3'-end processing is mediated by transcriptional coupling.

PMID:
15456870
[PubMed - indexed for MEDLINE]
PMCID:
PMC517882
Free PMC Article
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18.
Exp Cell Res. 2004 May 15;296(1):91-7.

The link between mRNA processing and transcription: communication works both ways.

Author information

  • 1Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver, CO 80262, USA.

Abstract

Many pre-mRNA processing events including 5' end capping, splicing out introns, and 3' end maturation by cleavage or polyadenylation occur while the nascent RNA chain is being synthesized by RNA polymerase II. As a consequence of this arrangement, the physiological substrate for most processing factors is not a solitary pre-RNA but instead a ternary complex comprising a growing RNA chain spewing from the exit channel of an RNA polymerase II molecule as it speeds along a chromatin template at 1000-2000 bases/min. mRNA processing factors make protein-protein contacts with elongating pol II in a complex we have dubbed the "mRNA factory," which carries out synthesis, processing, and packaging of the transcript. Recent studies have shown that the "mRNA factory" is a dynamic complex whose composition changes as it traverses the length of a gene. This complex is also the setting for a growing number of regulatory interactions, which influence the function of both the processing and transcription machineries.

PMID:
15120999
[PubMed - indexed for MEDLINE]
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19.
Mol Cell. 2002 May;9(5):1101-11.

Functional interaction of yeast pre-mRNA 3' end processing factors with RNA polymerase II.

Author information

  • 1Department Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Denver 80262, USA.

Abstract

The RNA polymerase II CTD is essential for 3' end cleavage of metazoan pre-mRNAs and binds 3' end processing factors in vitro. We show genetic and biochemical interactions between the CTD and the Pcf11 subunit of the yeast cleavage/polyadenylation factor, CFIA. In vitro binding to Pcf11 required phosphorylation of the CTD on Ser2 in the YSPTSPS heptad repeats. Deletion of the yeast CTD reduced the efficiency of cleavage at poly(A) sites, and the length of poly(A) tails suggesting that it helps couple 3' end formation with transcription. Consistent with this model, the 3' end processing factors CFIA, CFIB, and PFI were recruited to genes progressively, starting at the 5' end, in a process that required ongoing transcription.

PMID:
12049745
[PubMed - indexed for MEDLINE]
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20.
Cancer Res. 2002 Mar 1;62(5):1420-4.

Subcellular localization of NAD(P)H:quinone oxidoreductase 1 in human cancer cells.

Author information

  • 1Department of Pharmaceutical Sciences, University of Colorado Health Sciences Center, Denver, Colorado 80017, USA.

Abstract

NAD(P)H:quinone oxidoreductase 1 (NQO1) is implicated in both chemoprevention and bioactivation of DNA-damaging antitumor agents. NQO1 is mainly cytosolic, but distribution in other cellular compartments, particularly in tumor cells, is poorly defined. Nuclear NQO1 in HT29 human colon carcinoma and H661 human non-small cell lung cancer cells was observed using both confocal microscopy and immunoelectron microscopy. NQO1 was not detected in mitochondria, golgi, or endoplasmic reticulum. In addition, purified intact nuclei from HT29 cells contained immunoreactive NQO1, which was catalytically active as determined by conventional activity assay. In summary, we have confirmed the presence of nuclear NQO1, which has implications for chemoprotection and bioactivation of DNA-damaging antitumor agents.

PMID:
11888914
[PubMed - indexed for MEDLINE]
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