Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Associates with RNA Polymerase II Pausing

AbstractRNA polymerase II (RNAPII) pausing at gene promoters is a rate-limiting step in transcription regulation. Previous studies have elucidated the coordinated actions of pausing and releasing factors that collectively modulate RNAPII pausing. In general, the involvement of chromatin remodellers in RNAPII pausing has not been well documented. Whilst LSD1 is well-known for its role in decommissioning enhancers during ESC differentiation, its role at the promoters of genes remains poorly understood despite their widespread presence at these sites. Here, we report that LSD1 is associated with RNAPII pausing at the promoter-proximal region of genes in mouse embryonic stem cells (ESCs). We demonstrate that the knockdown of LSD1 preferentially affects genes with higher RNAPII pausing than those with lower pausing and, importantly, show that the co-localization of LSD1 and MYC, a factor known to regulate pause-release, is associated with the enrichment of other RNAPII pausing factors compared to their independent counterparts. Moreover, we found that genes co-occupied by LSD1 and MYC are significantly enriched for housekeeping genes that are involved in metabolic processes and globally depleted of transcription factors compared to those bound only by LSD1. These findings reveal a pleiotropic role of LSD1 in regulating housekeeping program besides its previously known role in regulating cell identity programs. Our integrative analysis presents evidence for a previously unanticipated role of LSD1 in RNAPII pausing through its association with pause release factors in modulating cell-type specific and cell-type invariant genes.

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RNA polymerase II pausing as a context-dependent reader of the genome

Biochemistry and Cell Biology ◽

10.1139/bcb-2015-0045 ◽

2016 ◽

Vol 94 (1) ◽

pp. 82-92 ◽

Cited By ~ 16

Author(s):

Adam Scheidegger ◽

Sergei Nechaev

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Cell Types ◽

Gene Promoters ◽

Cell Type ◽

Pol Ii ◽

Cell Type Specific ◽

Pol Ii Pausing ◽

Context Dependent ◽

Specific Regulation

The RNA polymerase II (Pol II) transcribes all mRNA genes in eukaryotes and is among the most highly regulated enzymes in the cell. The classic model of mRNA gene regulation involves recruitment of the RNA polymerase to gene promoters in response to environmental signals. Higher eukaryotes have an additional ability to generate multiple cell types. This extra level of regulation enables each cell to interpret the same genome by committing to one of the many possible transcription programs and executing it in a precise and robust manner. Whereas multiple mechanisms are implicated in cell type-specific transcriptional regulation, how one genome can give rise to distinct transcriptional programs and what mechanisms activate and maintain the appropriate program in each cell remains unclear. This review focuses on the process of promoter-proximal Pol II pausing during early transcription elongation as a key step in context-dependent interpretation of the metazoan genome. We highlight aspects of promoter-proximal Pol II pausing, including its interplay with epigenetic mechanisms, that may enable cell type-specific regulation, and emphasize some of the pertinent questions that remain unanswered and open for investigation.

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ZFP281 Recruits MYC to Active Promoters in Regulating Transcriptional Initiation and Elongation

Molecular and Cellular Biology ◽

10.1128/mcb.00329-19 ◽

2019 ◽

Vol 39 (24) ◽

Cited By ~ 1

Author(s):

Zhuojuan Luo ◽

Xiaoxu Liu ◽

Hao Xie ◽

Yan Wang ◽

Chengqi Lin

Keyword(s):

Stem Cells ◽

Transcription Factor ◽

Transcriptional Regulation ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Embryonic Stem ◽

General Mechanism ◽

Transcriptional Initiation ◽

Genome Scale

ABSTRACT The roles of the MYC transcription factor in transcriptional regulation have been studied intensively. However, the general mechanism underlying the recruitment of MYC to chromatin is less clear. Here, we found that the Krüppel-like transcription factor ZFP281 plays important roles in recruiting MYC to active promoters in mouse embryonic stem cells. At the genome scale, ZFP281 is broadly associated with MYC, and the depletion of ZFP281 significantly reduces the levels of MYC and RNA polymerase II at the ZFP281- and MYC-cobound genes. Specially, we found that recruitment is required for the regulation of the Lin28a oncogene and pri-let-7 transcription. Our results therefore suggest a major role of ZFP281 in recruiting MYC to chromatin and the integration of ZFP281 and the MYC/LIN28A/Let-7 loop into a multilevel circuit.

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SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

10.1101/2021.07.09.451791 ◽

2021 ◽

Author(s):

Veronique Fischer ◽

Elisabeth Scheer ◽

Elisabeth Lata ◽

Bastien Morlet ◽

Damien Plassard ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Mammalian Cells ◽

Embryonic Stem ◽

Gene Promoters ◽

Saga Complex ◽

Self Renewal ◽

Pol Ii ◽

Histone Fold ◽

Specific Subset

Coactivator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved coactivator complex. The core module scaffolds the entire SAGA complex and adopts a histone octamer-like structure, which consists of six histone fold domain (HFD)-containing proteins forming three histone fold (HF) pairs, to which the double HFD-containing SUPT3H adds an HF pair. Spt3, the yeast ortholog of SUPT3H, interacts genetically and biochemically with the TATA binding protein (TBP) and contributes to global RNA polymerase II (Pol II) transcription. Here we demonstrate that i) SAGA purified from human U2OS or mouse embryonic stem cells (mESC) can assemble without SUPT3H; ii) SUPT3H is not essential for mESC survival, iii) SUPT3H is required for mESC growth and self-renewal, and iv) the loss of SUPT3H from mammalian cells affects the transcription of only a specific subset of genes. Accordingly, in the absence of SUPT3H no major change in TBP accumulation at gene promoters was observed. Thus, SUPT3H is not required for the assembly of SAGA, TBP recruitment, or overall Pol II transcription, but plays a role in mESC growth and self-renewal. Our data further suggest that yeast and mammalian SAGA complexes contribute to transcription regulation by distinct mechanisms.

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RNA Polymerase II-Association Factor 1 (Paf1/PD2) Maintains Self-renewal by Its Interaction with Oct3/4 in Mouse Embryonic Stem Cells

Stem Cells ◽

10.1002/stem.237 ◽

2009 ◽

pp. N/A-N/A ◽

Cited By ~ 8

Author(s):

Moorthy P. Ponnusamy ◽

Shonali Deb ◽

Parama Dey ◽

Subhankar Chakraborty ◽

Satyanarayana Rachagani ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Embryonic Stem ◽

Mouse Embryonic Stem Cells ◽

Self Renewal

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Loss of Ubp3 increases silencing, decreases unequal recombination in rDNA, and shortens the replicative life span in Saccharomyces cerevisiae

Molecular Biology of the Cell ◽

10.1091/mbc.e13-10-0591 ◽

2014 ◽

Vol 25 (12) ◽

pp. 1916-1924 ◽

Cited By ~ 3

Author(s):

David Öling ◽

Rehan Masoom ◽

Kristian Kvint

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Polymerase ◽

Life Span ◽

Rna Polymerase Ii ◽

Ribosomal Dna ◽

Genetic Evidence ◽

Wild Type ◽

Replicative Life Span ◽

Unequal Recombination

Ubp3 is a conserved ubiquitin protease that acts as an antisilencing factor in MAT and telomeric regions. Here we show that ubp3∆ mutants also display increased silencing in ribosomal DNA (rDNA). Consistent with this, RNA polymerase II occupancy is lower in cells lacking Ubp3 than in wild-type cells in all heterochromatic regions. Moreover, in a ubp3∆ mutant, unequal recombination in rDNA is highly suppressed. We present genetic evidence that this effect on rDNA recombination, but not silencing, is entirely dependent on the silencing factor Sir2. Further, ubp3∆ sir2∆ mutants age prematurely at the same rate as sir2∆ mutants. Thus our data suggest that recombination negatively influences replicative life span more so than silencing. However, in ubp3∆ mutants, recombination is not a prerequisite for aging, since cells lacking Ubp3 have a shorter life span than isogenic wild-type cells. We discuss the data in view of different models on how silencing and unequal recombination affect replicative life span and the role of Ubp3 in these processes.

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Rethinking the role of TFIIF in transcript initiation by RNA polymerase II

Transcription ◽

10.4161/trns.20725 ◽

2012 ◽

Vol 3 (4) ◽

pp. 156-159 ◽

Cited By ~ 16

Author(s):

Donal S. Luse

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Transcript Initiation

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The chromatin remodeler Ino80 mediates RNAPII pausing site determination

Genome Biology ◽

10.1186/s13059-021-02500-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Youngseo Cheon ◽

Sungwook Han ◽

Taemook Kim ◽

Daehee Hwang ◽

Daeyoup Lee

Keyword(s):

Rna Polymerase Ii ◽

Transcriptional Start Site ◽

Regulation Of Gene Expression ◽

Embryonic Stem ◽

Start Site ◽

Chromatin Remodeler ◽

Close Relationship ◽

Early Transcription ◽

Different Characteristics

Abstract Background Promoter-proximal pausing of RNA polymerase II (RNAPII) is a critical step for the precise regulation of gene expression. Despite the apparent close relationship between promoter-proximal pausing and nucleosome, the role of chromatin remodeler governing this step has mainly remained elusive. Results Here, we report highly confined RNAPII enrichments downstream of the transcriptional start site in Saccharomyces cerevisiae using PRO-seq experiments. This non-uniform distribution of RNAPII exhibits both similar and different characteristics with promoter-proximal pausing in Schizosaccharomyces pombe and metazoans. Interestingly, we find that Ino80p knockdown causes a significant upstream transition of promoter-proximal RNAPII for a subset of genes, relocating RNAPII from the main pausing site to the alternative pausing site. The proper positioning of RNAPII is largely dependent on nucleosome context. We reveal that the alternative pausing site is closely associated with the + 1 nucleosome, and nucleosome architecture around the main pausing site of these genes is highly phased. In addition, Ino80p knockdown results in an increase in fuzziness and a decrease in stability of the + 1 nucleosome. Furthermore, the loss of INO80 also leads to the shift of promoter-proximal RNAPII toward the alternative pausing site in mouse embryonic stem cells. Conclusions Based on our collective results, we hypothesize that the highly conserved chromatin remodeler Ino80p is essential in establishing intact RNAPII pausing during early transcription elongation in various organisms, from budding yeast to mouse.

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Rpb7 Can Interact with RNA Polymerase II and Support Transcription during Some Stresses Independently of Rpb4

Molecular and Cellular Biology ◽

10.1128/mcb.19.4.2672 ◽

1999 ◽

Vol 19 (4) ◽

pp. 2672-2680 ◽

Cited By ~ 48

Author(s):

Ayelet Sheffer ◽

Mazal Varon ◽

Mordechai Choder

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Stress Conditions ◽

Cold Sensitivity ◽

Starvation Period ◽

Wild Type ◽

Pol Ii ◽

Growth Phenotype ◽

Mild Temperature

ABSTRACT Rpb4 and Rpb7 are two yeast RNA polymerase II (Pol II) subunits whose mechanistic roles have recently started to be deciphered. Although previous data suggest that Rpb7 can stably interact with Pol II only as a heterodimer with Rpb4, RPB7 is essential for viability, whereas RPB4 is essential only during some stress conditions. To resolve this discrepancy and to gain a better understanding of the mode of action of Rpb4, we took advantage of the inability of cells lacking RPB4 (rpb4Δ, containing Pol IIΔ4) to grow above 30°C and screened for genes whose overexpression could suppress this defect. We thus discovered that overexpression of RPB7 could suppress the inability ofrpb4Δ cells to grow at 34°C (a relatively mild temperature stress) but not at higher temperatures. Overexpression ofRPB7 could also partially suppress the cold sensitivity ofrpb4Δ strains and fully suppress their inability to survive a long starvation period (stationary phase). Notably, however, overexpression of RPB4 could not override the requirement for RPB7. Consistent with the growth phenotype, overexpression of RPB7 could suppress the transcriptional defect characteristic of rpb4Δ cells during the mild, but not during a more severe, heat shock. We also demonstrated, through two reciprocal coimmunoprecipitation experiments, a stable interaction of the overproduced Rpb7 with Pol IIΔ4. Nevertheless, fewer Rpb7 molecules interacted with Pol IIΔ4 than with wild-type Pol II. Thus, a major role of Rpb4 is to augment the interaction of Rpb7 with Pol II. We suggest that Pol IIΔ4 contains a small amount of Rpb7 that is sufficient to support transcription only under nonstress conditions. When RPB7 is overexpressed, more Rpb7 assembles with Pol IIΔ4, enough to permit appropriate transcription also under some stress conditions.

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