Hematopoietic Transcription Factors Bind rDNA and Regulate rRNA Transcription
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA797053 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17591834.fastq.gz | Fastqsanger.gz | |||
| SRR17591835.fastq.gz | Fastqsanger.gz | |||
| SRR17591836.fastq.gz | Fastqsanger.gz | |||
| SRR17591837.fastq.gz | Fastqsanger.gz | |||
| SRR17591838.fastq.gz | Fastqsanger.gz |
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Project description:This SuperSeries is composed of the SubSeries listed below.
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Project description:Over 2000 publicly accessible human and mouse ChIP-Seq datasets for about 250 Transcription Factors and chromatin complexes from various databases (ENCODE, GEO) were mapped to custom-made human and mouse genomes containing a reference rDNA sequence of the appropriate species (Genbank U13369.1 for human, BK000964.3 for mouse). The read mapping density across the rDNA sequence was then extracted and normalized to the median in that dataset. Unbiased clustering and analysis, followed by curation, was performed to identify high-confidence patterns of rDNA occupancy for numerous hematopoietic TFs and TF families at canonical TF motif sequences. ************************ Data processing steps: FASTQs were trimmed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30 Reads were mapped to customized genomes (containing additional rDNA sequence) using Bowtie2 using the following parameter: -X 2000 Read density across the rDNA sequence was extracted using igvtools ************************
2022-01-15 | GSE191272 | GEO
Project description:hnRNP UL1 plays an important function in cell nuclei, where it is recruited to DNA damage sites and is involved in the repair of DNA double strand breaks. Furthermore, this protein is known as a transcriptional repressor of RNA polymerase II genes. In the present study, we have shown that hnRNP UL1 is also localized in the nucleoli. Revealing its function, we figured out that hnRNP UL1 stimulates rDNA gene transcription and may be involved in the transport of the proteins between the nucleolus and the nucleoplasm. Moreover, we observed that cells with hnRNP UL1 silencing are more sensitive to DNA damage, suggesting its role in rDNA repair pathways and nucleolar genome integrity. Indeed, we confirmed that hnRNP UL1 interacts with yH2A.X, RPA32, XRCC1, and Chk1 in cell nucleoli, suggesting its involvement in repairing of DNA damages.
2022-10-15 | PXD033233 | Pride
Project description:We report the effect of degradation of CEBPA (a critical myeloid lineage transcription factor) on the occupancy of core rRNA transcription machinery on rDNA in mouse GMP cells. We generated a CEBPA-Degron line by tagging endogenous alleles of the Cebpa gene with the FKBPV degron domain, and degraded CEBPA-FKBPV-FLAG fusion protein using dTAGV-1 ligand. We used anti-FLAG pulldown to demonstrate binding of CEBPA protein to rDNA at a conserved motif within the 18S transcribed region. On degradation of CEBPA, we found that RPA194 (component of Pol I) and RRN3 occupancy on rDNA were reduced, while the occupancy of upstream factors TAF1B (component of SL-1) and UBTF were unchanged. In parallel, we also found that CEBPA degradation reduced nascent rRNA transcription, cellular ribosome abundance, and cell growth. Our work indicates that the cell-type-specific transcription factor CEBPA recruits the Pol I-RRN3 complex to ribosomal DNA to promote rRNA transcription.
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Project description:Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of stress response pathways and control of lifespan. Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing or to protect chromosomal regions from spreading epigenetic control. In this study, analysis of genome-wide chromatin immunoprecipitation and expression data, suggests that several yeast transcription factors regulate subtelomeric silencing in response to various environmental stimuli through conditional association with proto-silencing regions called X elements. In this context, Oaf1p, Rox1p, Gzf1p and Phd1p control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others, including Adr1p, Yap5p and Msn4p, appear to influence boundaries of silencing, regulating telomere-proximal genes in Y' elements. The factors implicated here are known to control adjacent genes at intrachromosomal positions, suggesting their dual functionality. This study reveals a path for the coordination of subtelomeric silencing with cellular environment, and with activities of other cellular processes.
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Project description:4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected inside IGS. Our data indicate that mostly rDNA units exhibit close proximity with pericentromeric regions in different chromosomes. We also detected the contacts within a rDNA unit and between rDNA units. Examination of rDNA genome-wide contacts in HEK 293T cells using 4C approach.
2014-10-04 | E-GEOD-49193 | biostudies-arrayexpress
Project description:ACAA2 and OGDH bind to H2A.Z-occupied transcription start sites
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Project description:Transcription factors (TFs) regulate transcription by binding to the specific sequences at the promoter region. However, the mechanisms and functions of TFs binding within the coding sequences (CDS) remain largely elusive in prokaryotes. To this end, we collected 409 data sets for bacterial TFs, including 104 chromatin immunoprecipitation sequencing (ChIP-seq) assays and 305 data sets from the systematic evolution of ligands by exponential enrichment (SELEX) in seven model bacteria. Interestingly, these TFs displayed the same binding capabilities for both coding and intergenic regions. Subsequent biochemical and genetic experiments demonstrated that several TFs bound to the coding regions and regulated the transcription of the binding or adjacent genes. Strand-specific RNA sequencing revealed that these CDS-binding TFs regulated the activity of the cryptic promoters, resulting in the altered transcription of the corresponding antisense RNA. TF RhpR hindered the transcriptional elongation of a subgenic transcript within a CDS. A ChIP-seq and Ribo-seq coanalysis revealed that RhpR influenced the translational efficiency of binding genes. Taken together, the present study reveals three regulatory mechanisms of CDS-bound TFs within individual genes, operons, and antisense RNAs, which demonstrate the variability of the regulatory mechanisms of TFs and expand upon the complexity of bacterial transcriptomes. IMPORTANCE Although bacterial TFs regulate transcription by binding to specific sequences at the promoter region, little is known about the mechanisms and functions of TFs binding within the CDS. In this study, we show that bacterial TFs have same binding pattern in both CDS and promoter regions, and we reveal three regulatory mechanisms of CDS-bound TF that together demonstrate the complexity of the regulatory mechanisms of bacterial TFs and the wide spread of internal cryptic promoters in CDS.
| S-EPMC9600179 | biostudies-literature
Project description:The objective of this study was to determine the effect of a small-molecule Pol I inhibitor, BMH-21, on rRNA synthesis in vivo. NET-seq was performed to determine the Pol I occupancy after BMH-21 treatment, as compared to vehicle-treatment (phosphate buffer control). Our findings suggest that BMH-21 treatment reduces Pol I occupancy on the rDNA template. Additionally, BMH-21 induces repositioning of Pol I in AT-rich rDNA regions that are directly upstream from GC-rich regions. This study suggests that BMH-21 is a powerful inhibitor of transcription by Pol I, and gives a potential mechanism of action for this inhibitor in vivo.
2021-05-26 | GSE175553 | GEO
Project description:To sustain growth, budding yeast actively transcribes its ribosomal gene array (rDNA) in the nucoleolus to produce ribosomes and proteins. However, intense transcription during rDNA replication may provoke collisions between RNA polymerase I (Pol I) and the replisome, may cause replication fork instability, double-strand breaks, local recombinations and rDNA instability. The latter is manifested by rDNA array expansion or reduction and the formation of extrachromosomal rDNA circles, anomalies that accelerate aging in yeast. Transcription also interferes with the resolution, condensation and segregation of the sister chromatid rDNA arrays. As a consequence, rDNA segregation lags behind the rest of the yeast genome and occurs in late anaphase when rDNA transcription is temporarily shut off. How yeast promotes the stability and transmission of its rDNA array while satisfying a constant need for ribosomes remains unclear. Here we show that the downregulation of Pol I by the conserved cell cycle kinase Rio1 spatiotemporally coordinates rDNA transcription, replication and segregation. More specifically, Rio1 activity promotes copy-number stability of the replicating rDNA array by curtailing Pol I activity and by localising the histone deacetylase Sir2, which establishes a heterochromatic state that silences rDNA transcription. At anaphase entry, Rio1 and the Cdc14 phosphatase target Pol I subunit Rpa43 to dissociate Pol I from the 35S rDNA promoter. The rDNA locus then condensates and segregates, thereby concluding the genome transmission process. Rio1 is involved in ribosome maturation in the cytoplasm of budding yeast and human cells. Additional engagements in the cytoplasm or roles in the nucleus are unknown. Our study describes its first nuclear engagement as a Pol I silencing kinase. This activity may prove highly relevant as dysregulated RNA polymerase I activity has been associated with cancer initiation and proliferation.
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