LEO1 Is Required for Efficient Entry into Quiescence, Control of H3K9 methylation and Gene Expression in Human Fibroblasts [ChIP-Seq]
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ABSTRACT:
PROVIDER: PRJNA1040795 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26840900.fastq.gz | Fastqsanger.gz | |||
| SRR26840901.fastq.gz | Fastqsanger.gz | |||
| SRR26840902.fastq.gz | Fastqsanger.gz | |||
| SRR26840903.fastq.gz | Fastqsanger.gz | |||
| SRR26840904.fastq.gz | Fastqsanger.gz |
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Project description:Abstract: (1) Background: The LEO1 (Left open reading frame 1) protein is a conserved subunit of the PAF1C complex (RNA polymerase II associated factor 1 complex). PAF1C has well-established mechanistic functions in elongation of transcription and RNA processing. We have previously shown, in fission yeast, that LEO1 is controlling histone H3K9 methylation levels by affecting the turnover of histone H3 in chromatin, and that it is essential for proper regulation of gene expression during cellular quiescence. Human fibroblasts enter a reversible quiescence state upon serum deprivation in the growth media. Here we investigate the function of LEO1 in human fibroblasts. (2) Methods: We knocked out the LEO1 gene using CRISPR/Cas9 methodology in human fibroblasts and verified that the LEO1 protein was undetectable by Western blot. We characterized the phenotype of the DLEO1 knockout cells with FACS analysis and cell growth assays. We used RNA-sequencing using spike-in controls to measure gene expression and spike-in controlled ChIP-sequencing experiments to measure the histone modification H3K9me2 genome-wide. (3) Results: Gene expression levels are altered in quiescent cells, however factors controlling chromatin and gene expression changes in quiescent human cells are largely unknown. The DLEO1 knockout fibroblasts are viable but have reduced metabolic activity compared to wild type cells. DLEO1 cells showed a slower entry into quiescence and a different morphology compared to wild type cells. Gene expression was generally reduced in quiescent wild type cells. The downregulated genes included genes involved in cell proliferation. A small number of genes were upregulated in quiescent wild type cells including several genes involved in ERK1/ERK2 and Wnt signaling. In quiescent DLEO1 cells many genes were mis-regulated compared to wild type cells. This included genes involved in Calcium ion transport and cell morphogenesis. Finally, spike-in controlled ChIP-sequencing experiments demonstrated that the histone modification H3K9me2 levels are globally increased in quiescent DLEO1 cells. (4) Conclusions: Thus, LEO1 is important for proper entry into cellular quiescence, control H3K9me2 levels and gene expression in human fibroblasts.
2023-11-29 | GSE247831 | GEO
Project description:Abstract: (1) Background: The LEO1 (Left open reading frame 1) protein is a conserved subunit of the PAF1C complex (RNA polymerase II associated factor 1 complex). PAF1C has well-established mechanistic functions in elongation of transcription and RNA processing. We have previously shown, in fission yeast, that LEO1 is controlling histone H3K9 methylation levels by affecting the turnover of histone H3 in chromatin, and that it is essential for proper regulation of gene expression during cellular quiescence. Human fibroblasts enter a reversible quiescence state upon serum deprivation in the growth media. Here we investigate the function of LEO1 in human fibroblasts. (2) Methods: We knocked out the LEO1 gene using CRISPR/Cas9 methodology in human fibroblasts and verified that the LEO1 protein was undetectable by Western blot. We characterized the phenotype of the DLEO1 knockout cells with FACS analysis and cell growth assays. We used RNA-sequencing using spike-in controls to measure gene expression and spike-in controlled ChIP-sequencing experiments to measure the histone modification H3K9me2 genome-wide. (3) Results: Gene expression levels are altered in quiescent cells, however factors controlling chromatin and gene expression changes in quiescent human cells are largely unknown. The DLEO1 knockout fibroblasts are viable but have reduced metabolic activity compared to wild type cells. DLEO1 cells showed a slower entry into quiescence and a different morphology compared to wild type cells. Gene expression was generally reduced in quiescent wild type cells. The downregulated genes included genes involved in cell proliferation. A small number of genes were upregulated in quiescent wild type cells including several genes involved in ERK1/ERK2 and Wnt signaling. In quiescent DLEO1 cells many genes were mis-regulated compared to wild type cells. This included genes involved in Calcium ion transport and cell morphogenesis. Finally, spike-in controlled ChIP-sequencing experiments demonstrated that the histone modification H3K9me2 levels are globally increased in quiescent DLEO1 cells. (4) Conclusions: Thus, LEO1 is important for proper entry into cellular quiescence, control H3K9me2 levels and gene expression in human fibroblasts.
2023-11-29 | GSE247829 | GEO
Project description:LEO1 Is Required for Efficient Entry into Quiescence, Control of H3K9 methylation and Gene Expression in Human Fibroblasts
| PRJNA1040789 | ENA
Project description:LEO1 Is Required for Efficient Entry into Quiescence, Control of H3K9 methylation and Gene Expression in Human Fibroblasts [RNA-Seq]
| PRJNA1040797 | ENA
Project description: Not available
| S-EPMC10668985 | biostudies-literature
Project description:Cellular quiescence is a reversible differentiation state when cells are changing the gene expression programme to reduce metabolic functions and adapt to a new cellular environment. The epigenetic changes that accompany these alterations are not so well understood. Here we investigate the role of Leo1, a subunit of the conserved Paf1 (RNA polymerase-associated factor 1) complex, in the quiescence process using fission yeast as a model organism. Fission yeast cells enter the G0 phase of the cell cycle when exposed to nitrogen starvation and the heterochromatin regions become very dynamic. The reduction of heterochromatin in early G0 correlates with the reduced activity of target of rapamycin, TORC2, signalling. Cells lacking the Leo1 show reduced survival in G0. In these cells heterochromatin regions including subtelomeres are stabilized and many genes, including membrane transport genes, fail to be expressed. Our results suggest that Leo1 is essential for dynamic regulation of heterochromatin and gene expression during cellular quiescence.
2019-06-30 | GSE116657 | GEO
Project description:Cellular quiescence is a reversible differentiation state when cells are changing the gene expression programme to reduce metabolic functions and adapt to a new cellular environment. The epigenetic changes that accompany these alterations are not so well understood. Here we investigate the role of Leo1, a subunit of the conserved Paf1 (RNA polymerase-associated factor 1) complex, in the quiescence process using fission yeast as a model organism. Fission yeast cells enter the G0 phase of the cell cycle when exposed to nitrogen starvation and the heterochromatin regions become very dynamic. The reduction of heterochromatin in early G0 correlates with the reduced activity of target of rapamycin, TORC2, signalling. Cells lacking the Leo1 show reduced survival in G0. In these cells heterochromatin regions including subtelomeres are stabilized and many genes, including membrane transport genes, fail to be expressed. Our results suggest that Leo1 is essential for dynamic regulation of heterochromatin and gene expression during cellular quiescence.
2019-06-30 | GSE116038 | GEO
Project description:Cellular quiescence is coupled with cellular development, tissue homeostasis, and cancer progression. Both quiescence and cell cycle re-entry are controlled by active and precise regulation of gene expression. However, the roles of long noncoding RNAs (lncRNAs) during these processes remain to be elucidated. By performing a genome-wide transcriptome analyses, we identify thousands of differentially expressed lncRNAs, including ~30 of the less-characterized class of microRNA-host-gene lncRNAs (lnc-MIRHGs), during cellular quiescence and during serum-stimulation in human diploid cells. We observe that the mature MIR222HG display serum-stimulated induction due to enhanced pre-RNA splicing. Serum-stimulated binding of the pre-mRNA splicing factor SRSF1 to a micro-exon, which partially overlaps with the primary miR-222 precursor, facilitates enhanced MIR222HG splicing. In serum-stimulated cells, SRSF1 negatively regulates the Drosha/DGCR8-catalyzed cleavage of pri-miR-222, thereby increasing the cellular pool of the mature MIR222HG. Further, loss-of-function studies indicate that the mature MIR222HG facilitates the serum-stimulated cell cycle re-entry in a microRNA-independent manner. Mechanistically, MIR222HG, along with ILF3/2 complex, forms RNA:RNA duplex with DNM3OS lncRNA, thereby promoting DNM3OS stability. The current study identifies a mechanism in which the interplay between splicing versus microprocessor complex dictates the serum-induced expression of lnc-MIRHG MIR222HG for efficient cell cycle re-entry.
2020-09-07 | PXD017585 | Pride
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-11-29 | GSE247832 | GEO
Project description:Domains of heterochromatin play important roles in the maintenance and regulation of eukaryotic genomes. However, the repressive nature of heterochromatin combined with its propensity to self-propagate necessitates the existence of robust mechanisms that limit heterochromatin spreading and thereby avoid silencing of expressed genes. A number of specific sequence elements have been found to serve as barriers to heterochromatin spreading; however, the mechanisms by which spreading is curtailed are generally not well understood. Here we uncover a role for PAF complex component Leo1 in regulating heterochromatin cis-spreading. A genetic screen revealed that loss of Leo1 results in spreading of heterochromatin across a centromeric (IRC) boundary element in fission yeast. Similar heterochromatin spreading was seen upon deletion of other components of the PAF complex, but not other factors involved in transcription-coupled chromatin modification, indicating a specific role for the PAF complex in heterochromatin regulation. Loss of Leo1 is associated with reduced levels of H4K16 acetylation at the boundary, while tethering of the H4K16 acetyltransferase Mst1 to boundary chromatin suppresses heterochromatin spreading in leo1? cells, suggesting that Leo1 antagonises heterochromatin spreading by facilitating H4K16 acetylation. Interestingly, Leo1 also regulates heterochromatin spreading independently of boundaries, and loss of Leo1 causes redistribution of heterochromatin, in particular resulting in substantial expansion of telomeric heterochromatin domains. The PAF complex is known to be an important regulator of transcription-related chromatin modifications; our findings reveal a previously undescribed role for this complex in global regulation of heterochromatin spreading in cis. 8 samples: input (whole cell extract) and IP from H3K9me2 ChIP in wild-type and leo1? cells, in duplicate
2015-05-22 | E-GEOD-61688 | biostudies-arrayexpress