scholarly journals The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from gene loci

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Anand K Singh ◽  
Subhendu Roy Choudhury ◽  
Sandip De ◽  
Jie Zhang ◽  
Stephen Kissane ◽  
...  
Keyword(s):  
Polytene Chromosomes ◽  
Rna Helicase ◽  
Helicase Activity ◽  
S2 Cells ◽  
Pol Ii ◽  
Genome Wide ◽  
Transcription Sites ◽  
Nonsense Mediated Mrna Decay ◽  
Intron Recognition ◽  
Pol Iii

UPF1 is an RNA helicase that is required for nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3’UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm by a mechanism that requires its RNA helicase activity. UPF1 is associated, genome-wide, with nascent RNAs at most of the active Pol II transcription sites and at some Pol III-transcribed genes, as demonstrated microscopically on the polytene chromosomes of salivary glands and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNAs, and cells depleted of UPF1 show defects in the release of mRNAs from transcription sites and their export from the nucleus.

scholarly journals The RNA helicase UPF1 associates with mRNAs co-transcriptionally and is required for the release of mRNAs from transcription sites

2018 ◽  
Author(s):  
Anand K. Singh ◽  
Subhendu Roy Choudhury ◽  
Sandip De ◽  
Jie Zhang ◽  
Stephen Kissane ◽  
...  
Keyword(s):  
Polytene Chromosomes ◽  
Rna Helicase ◽  
S2 Cells ◽  
Genome Wide ◽  
Mrna Transcripts ◽  
Transcription Sites ◽  
Nonsense Mediated Mrna Decay ◽  
Intron Recognition ◽  
Pol Iii ◽  
Nuclear Processes

SummaryUPF1 is an RNA helicase that is required for efficient nonsense-mediated mRNA decay (NMD) in eukaryotes, and the predominant view is that UPF1 mainly operates on the 3’UTRs of mRNAs that are directed for NMD in the cytoplasm. Here we offer evidence, obtained from Drosophila, that UPF1 constantly moves between the nucleus and cytoplasm and that it has multiple functions in the nucleus. It is associated, genome-wide, with nascent RNAs at most of the active Pol II transcription sites and at some Pol III-transcribed genes, as demonstrated microscopically on the polytene chromosomes of salivary gland and by ChIP-seq analysis in S2 cells. Intron recognition seems to interfere with association and translocation of UPF1 on nascent pre-mRNA transcripts, and cells depleted of UPF1 show defects in several nuclear processes essential to correct gene expression – most strikingly, the release of mRNAs from transcription sites and mRNA export from the nucleus.

scholarly journals Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe

2021 ◽  
Author(s):  
Sandip De ◽  
Vibha Dwivedi ◽  
Jianming Wang ◽  
David M. Edwards ◽  
Wazeer Varsally ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Significant Proportion ◽  
Wild Type ◽  
Nascent Transcript ◽  
Pol Ii ◽  
Genome Wide ◽  
Nonsense Mediated Mrna Decay ◽  
Chromosomal Association ◽  
Mrna Expression Levels ◽  
Active Genes

AbstractAlthough the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive and it correlates with Pol II transcription and mRNA expression levels. While changes in Pol II occupancy were detected at only some genes in a Upf1-deficient (upf1Δ) strain, there is an increased Ser2 Pol II signal at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil and display Pol II abnormalities suggestive of Pol II hyperphosphorylation. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript Upf1 might influence Pol II phosphorylation and transcription.

scholarly journals Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yongpeng Jiang ◽  
Jie Huang ◽  
Kehuan Lun ◽  
Boyuan Li ◽  
Haonan Zheng ◽  
...  
Keyword(s):  
Pol Ii ◽  
Chromatin Interactions ◽  
Pol I ◽  
Genome Wide ◽  
Pol Iii

scholarly journals The hRPC62 subunit of human RNA polymerase III displays helicase activity

2019 ◽  
Vol 47 (19) ◽  
pp. 10313-10326 ◽  
Author(s):  
Leyla El Ayoubi ◽  
Hélène Dumay-Odelot ◽  
Aleksandar Chernev ◽  
Fanny Boissier ◽  
Lionel Minvielle-Sébastia ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Complex Formation ◽  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Dna Unwinding ◽  
Helicase Activity ◽  
5S Rna ◽  
Initiation Complex ◽  
Pol Ii ◽  
Pol Iii

Abstract In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3′-5′ DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα.

scholarly journals RecQL5 Promotes Genome Stabilization through Two Parallel Mechanisms—Interacting with RNA Polymerase II and Acting as a Helicase

2010 ◽  
Vol 30 (10) ◽  
pp. 2460-2472 ◽  
Author(s):  
M. Nurul Islam ◽  
David Fox ◽  
Rong Guo ◽  
Takemi Enomoto ◽  
Weidong Wang
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Genome Stability ◽  
Transcriptional Regulators ◽  
Helicase Activity ◽  
Parallel Mechanisms ◽  
Recq Helicase ◽  
Pol Ii ◽  
Kix Domain ◽  
Genome Stabilization

ABSTRACT The RecQL5 helicase is essential for maintaining genome stability and reducing cancer risk. To elucidate its mechanism of action, we purified a RecQL5-associated complex and identified its major component as RNA polymerase II (Pol II). Bioinformatics and structural modeling-guided mutagenesis revealed two conserved regions in RecQL5 as KIX and SRI domains, already known in transcriptional regulators for Pol II. The RecQL5-KIX domain binds both initiation (Pol IIa) and elongation (Pol IIo) forms of the polymerase, whereas the RecQL5-SRI domain interacts only with the elongation form. Fully functional RecQL5 requires both helicase activity and associations with the initiation polymerase, because mutants lacking either activity are partially defective in the suppression of sister chromatid exchange and resistance to camptothecin-induced DNA damage, and mutants lacking both activities are completely defective. We propose that RecQL5 promotes genome stabilization through two parallel mechanisms: by participation in homologous recombination-dependent DNA repair as a RecQ helicase and by regulating the initiation of Pol II to reduce transcription-associated replication impairment and recombination.

scholarly journals Dephosphorylation and Genome-Wide Association of Maf1 with Pol III-Transcribed Genes during Repression

2006 ◽  
Vol 22 (5) ◽  
pp. 633-644 ◽  
Author(s):  
Douglas N. Roberts ◽  
Boris Wilson ◽  
Jason T. Huff ◽  
Allen J. Stewart ◽  
Bradley R. Cairns
Keyword(s):  
Genome Wide Association ◽  
Genome Wide ◽  
Pol Iii

Genome-wide regulations of the pre-initiation complex formation and elongating RNA polymerase II by an E3 ubiquitin ligase, San1.

2021 ◽  
Author(s):  
Priyanka Barman ◽  
Rwik Sen ◽  
Amala Kaja ◽  
Jannatul Ferdoush ◽  
Shalini Guha ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Ubiquitin Ligase ◽  
Nuclear Protein ◽  
Protein Quality ◽  
Initiation Complex ◽  
Pol Ii ◽  
Intrinsically Disordered ◽  
Genome Wide

San1 ubiquitin ligase is involved in nuclear protein quality control via its interaction with intrinsically disordered proteins for ubiquitylation and proteasomal degradation. Since several transcription/chromatin regulatory factors contain intrinsically disordered domains and can be inhibitory to transcription when in excess, San1 might be involved in transcription regulation. To address this, we analyzed the role of San1 in genome-wide association of TBP [that nucleates pre-initiation complex (PIC) formation for transcription initiation] and RNA polymerase II (Pol II). Our results reveal the roles of San1 in regulating TBP recruitment to the promoters and Pol II association with the coding sequences, and hence PIC formation and coordination of elongating Pol II, respectively. Consistently, transcription is altered in the absence of San1. Such transcriptional alteration is associated with impaired ubiquitylation and proteasomal degradation of Spt16 and gene association of Paf1, but not the incorporation of centromeric histone, Cse4, into the active genes in Δsan1 . Collectively, our results demonstrate distinct functions of a nuclear protein quality control factor in regulating the genome-wide PIC formation and elongating Pol II (and hence transcription), thus unraveling new gene regulatory mechanisms.

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