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 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 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

scholarly journals On emerging nuclear order

2011 ◽  
Vol 192 (5) ◽  
pp. 711-721 ◽  
Author(s):  
Indika Rajapakse ◽  
Mark Groudine
Keyword(s):  
Nuclear Organization ◽  
Chromatin State ◽  
Interphase Chromosome ◽  
Chromosome Arrangement ◽  
Technological Advances ◽  
Genome Wide ◽  
Nuclear Processes ◽  
Genomic Function

Although the nonrandom nature of interphase chromosome arrangement is widely accepted, how nuclear organization relates to genomic function remains unclear. Nuclear subcompartments may play a role by offering rich microenvironments that regulate chromatin state and ensure optimal transcriptional efficiency. Technological advances now provide genome-wide and four-dimensional analyses, permitting global characterizations of nuclear order. These approaches will help uncover how seemingly separate nuclear processes may be coupled and aid in the effort to understand the role of nuclear organization in development and disease.

scholarly journals BisMapR: a strand-specific, nuclease-based method for genome-wide R-loop detection

2021 ◽  
Author(s):  
Phillip Wulfridge ◽  
Kavitha Sarma
Keyword(s):  
Genome Stability ◽  
Antisense Transcription ◽  
Gene Promoters ◽  
Normal Cells ◽  
Disease States ◽  
Detection Strategy ◽  
Genome Wide ◽  
Loop Detection ◽  
Nucleic Acid Structures ◽  
Nuclear Processes

AbstractR-loops are three stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation as seen in some neurodevelopmental diseases and cancers and is associated with compromised genome stability. Genome-wide profiling of R-loops in normal cells and their comparison in disease states can help identify precise locations of pathogenic R-loops and advance efforts to attenuate deviant R-loops while preserving biologically important ones. Toward this, we have developed an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce high-resolution, genome-wide R-loop profiles that retain strand information. Furthermore, BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. We applied BisMapR to reveal discrete R-loop behavior at gene promoters and enhancers. We show that gene promoters exhibiting antisense transcription form R-loops in both directions. and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. Thus, BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression.

scholarly journals Distinct CoREST complexes act in a cell-type-specific manner

2019 ◽  
Author(s):  
Igor Mačinković ◽  
Ina Theofel ◽  
Tim Hundertmark ◽  
Kristina Kovač ◽  
Stephan Awe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Germ Line ◽  
Protein Complexes ◽  
Specific Gene ◽  
S2 Cells ◽  
Cell Type ◽  
Specific Gene Expression ◽  
Genome Wide ◽  
A Cell ◽  
Cell Type Specific

Abstract CoREST has been identified as a subunit of several protein complexes that generate transcriptionally repressive chromatin structures during development. However, a comprehensive analysis of the CoREST interactome has not been carried out. We use proteomic approaches to define the interactomes of two dCoREST isoforms, dCoREST-L and dCoREST-M, in Drosophila. We identify three distinct histone deacetylase complexes built around a common dCoREST/dRPD3 core: A dLSD1/dCoREST complex, the LINT complex and a dG9a/dCoREST complex. The latter two complexes can incorporate both dCoREST isoforms. By contrast, the dLSD1/dCoREST complex exclusively assembles with the dCoREST-L isoform. Genome-wide studies show that the three dCoREST complexes associate with chromatin predominantly at promoters. Transcriptome analyses in S2 cells and testes reveal that different cell lineages utilize distinct dCoREST complexes to maintain cell-type-specific gene expression programmes: In macrophage-like S2 cells, LINT represses germ line-related genes whereas other dCoREST complexes are largely dispensable. By contrast, in testes, the dLSD1/dCoREST complex prevents transcription of germ line-inappropriate genes and is essential for spermatogenesis and fertility, whereas depletion of other dCoREST complexes has no effect. Our study uncovers three distinct dCoREST complexes that function in a lineage-restricted fashion to repress specific sets of genes thereby maintaining cell-type-specific gene expression programmes.

Analysis of genome-wide contacts of forum terminus in Drosophila S2 cells

2013 ◽  
Vol 452 (1) ◽  
pp. 259-263 ◽  
Author(s):  
D. V. Sosin ◽  
O. V. Kretova ◽  
Y. V. Kravatsky ◽  
N. A. Tchurikov
Keyword(s):  
S2 Cells ◽  
Genome Wide ◽  
Drosophila S2 Cells

scholarly journals Genome‐wide analysis of RNA helicase A translation control

2008 ◽  
Vol 22 (S1) ◽  
Author(s):  
Julia Marcela Hernandez ◽  
Shuiming Qian ◽  
Alper Yilmaz ◽  
Kathleen Boris‐Lawrie
Keyword(s):  
Rna Helicase ◽  
Translation Control ◽  
Rna Helicase A ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals The role of SAGA in the transcription and export of mRNA

2019 ◽  
Vol 23 (2) ◽  
pp. 174-179
Author(s):  
E. N. Nabirochkina ◽  
M. M. Kurshakova ◽  
S. G. Georgieva ◽  
D. V. Kopytova
Keyword(s):  
Mrna Export ◽  
Rna Polymerase Iii ◽  
Polytene Chromosomes ◽  
Gene Localization ◽  
Regulation Of Transcription ◽  
Histone H2a ◽  
Messenger Ribonucleic Acid ◽  
Transcription Process ◽  
Transcription Sites ◽  
Active Transcription

SAGA/TFTC, which is a histone acetyltransferase complex, plays an important role in the regulation of transcription. We have identified that the metazoan TFTC/STAGA complexes had histone H2A and H2B deubiquitinase activity that is carried out by a DUBm (deubiquitination module). We studied the DUBm of SAGA in Drosophila melanogaster and identified Drosophila homologs of yeast DUBm components. Two subunits of DUBm (Sus1/ENY2 and Sgf11) were shown to have functions separate from DUBm function. Thus, Sus1/ENY2 was shown to be present in several different complexes. Sgf11 was found to be associated with the cap-binding complex (CBC) and recruited onto growing messenger ribonucleic acid (mRNA). Also, we have shown that Sgf11 interacted with the TREX-2/AMEX mRNA export complex and was essential for mRNA export from the nucleus. Immunostaining of the polytene chromosomes of Drosophila larvae revealed that Sgf11 is present at the sites of localization of snRNA genes. It was also found in immunostaining experiments that dPbp45, the subunit of the PBP complex, the key player in the snRNA transcription process, is associated not only with the snRNA gene localization sites, but with other sites of active transcription by PolII. We also revealed that Sgf11 was present at many active transcription sites in interbands and puffs on polytene chromosomes, Sgf11 was localized at all Brf1 (the component of the RNA polymerase III basal transcription complex) sites. We concluded that SAGA coactivated transcription of both the PolII and PolIII-dependent snRNA genes.

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