Ontology highlight
ABSTRACT:
PROVIDER: PRJNA615362 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11429773_1.fastq.gz | Fastqsanger.gz | |||
| SRR11429773_2.fastq.gz | Fastqsanger.gz | |||
| SRR11429774.fastq.gz | Fastqsanger.gz | |||
| SRR11429775_1.fastq.gz | Fastqsanger.gz | |||
| SRR11429775_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 31 |
Similar Datasets
Project description:Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a Precision nuclear Run-On and sequencing assay (PRO-seq) to map the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3' poly-adenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing . We test this ‘Complex Interaction’ model with insertional mutagenesis of the Drosophila Hsp70 core promoter. Identification of RNA polymerase active sites in Drosophila S2 cell line using PRO-seq method. Identification of transcription initiation sites in Drosophila S2 cell line using PRO-cap method. Identification of changes in RNA polymerase active sites on transgenic Hsp70 promoters upon disruption of DNA sequence elements in 3 transgenic fly lines using PRO-seq method.
2013-02-01 | E-GEOD-42117 | biostudies-arrayexpress
Project description:Quantitative analysis of the sequence determinants of transcription and translation regulation is of special relevance for systems and synthetic biology applications. Here, we developed a novel generic approach for the fast and efficient analysis of these determinants in vivo. ELM-seq (expression level monitoring by DNA methylation) uses Dam coupled to high-throughput sequencing) as a reporter that can be detected by DNA-seq. We used the genome-reduced bacterium Mycoplasma pneumoniae to show that it is a quantitative reporter. We showed that the methylase activity correlates with protein expression, does not affect cell viability, and has a large dynamic range (~10,000-fold). We applied ELM-seq to randomized libraries of promoters or 5’ untranslated regions. We found that transcription is greatly influenced by the bases around the +1 of the transcript and the Pribnow box, and we also identified several epistatic interactions (including the +1 and the “extended Pribnow”). Regarding translation initiation, we confirmed that the Shine-Dalgarno motif is not relevant, but instead, that RNA secondary structure is the main governing factor. With this in hand, we developed a predictor to help tailor gene expression in M. pneumoniae. The simple ELM-seq methodology will allow identifying and optimizing key sequence determinants for promoter strength and translation. The ELM-seq methodology allows both researchers and companies to identify and optimize in an easy and comprehensive manner, key sequence determinants for promoter strength and translation.
2017-08-29 | PXD005606 | Pride
Project description:RNA polymerase II (Pol II) pausing is a general regulatory step in transcription, yet the stability of paused Pol II varies widely between genes. Although paused Pol II stability correlates with core promoter elements, the contribution of individual sequences remains unclear, in part because no rapid assay is available for measuring the changes in Pol II pausing as a result of altered promoter sequences. Here, we overcome this hurdle by showing that ChIP-nexus captures the endogenous Pol II pausing on transfected plasmids. Using this reporter-ChIP-nexus assay in Drosophila cells, we show that the pausing stability is influenced by downstream promoter sequences, but that the strongest contribution to Pol II pausing comes from the initiator sequence, in which a single nucleotide, a G at the +2 position, is critical for stable Pol II pausing. These results establish reporter-ChIP-nexus as a valuable tool to analyze Pol II pausing.
2019-04-05 | GSE116244 | GEO
Project description:Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a Precision nuclear Run-On and sequencing assay (PRO-seq) to map the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3' poly-adenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing . We test this ‘Complex Interaction’ model with insertional mutagenesis of the Drosophila Hsp70 core promoter.
2013-02-01 | GSE42117 | GEO
Project description:Transcription initiation is an essential process for ensuring proper function of any gene, however, we still lack a unified understanding of sequence patterns and rules that explains most transcription initiation sites in human genome. By explaining transcription initiation at basepair resolution from sequence with a deep learning-inspired explainable modeling approach, here we show that simple rules can explain the vast majority of human promoters. We identified key sequence patterns that contribute to human promoter function, each activating transcription with a distinct position-specific effect curve that likely reflects its mechanism of promoting transcription initiation. Most of these position-specific effects have not been previously characterized, and we verified them using experimental perturbations of transcription factor binding sequences. We revealed the sequence basis of bidirectional transcription at promoters and the links between promoter selectivity and gene expression variation across cell types. Additionally, by analyzing 241 mammalian genomes and mouse transcription initiation site data, we showed that the sequence determinants are conserved across mammalian species. Taken together, we provide a unified model for the sequence basis of transcription initiation at basepair resolution(?) that is broadly applicable across mammalian species, which sheds new light on fundamental questions related to promoter sequence and function.
2024-07-10 | GSE248771 | GEO
Project description:How DNA sequence affects the dynamics and position of RNA Polymerase II during transcription remains poorly understood. Here we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, which was composed of both existing and novel DNA sequence motifs, allowing us to redefine molecular models of both core transcriptional processes. Our results implicate the strength of base pairing between A-T or G-C dinucleotides as key determinants to the position of Pol II initiation and pause. We reveal substantial and heritable differences in the position of transcription termination, which frequently do not affect the composition of the mature mRNA. Finally, we identified frequent, organ-specific changes in transcription that affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.
2021-05-31 | GSE174171 | GEO
Project description:Transcription by RNA polymerase II (RNA Pol II) depends on transcription factors and chromatin factors. Here we use rapid factor depletion and multiomics analysis to investigate how a histone chaperone, FAcilitates Chromatin Transcription (FACT), influence nascent transcription by RNA PolII in human cells. Depletion of a FACT subunit, SSRP1, led to rapid changes in chromatin structure and concomitantly strongly compromised RNA synthesis. FACT depletion led to a multilayered transcriptional defect, including loss of promoter proximal pausing, deregulated release into elongation and drop-off of RNA Pol II in promoter-distant gene regions. We combined these analyses with biochemical dissection of transcription of a chromatinized template to show that FACT supports both elongation and pausing of RNA Pol II. Our study also provides new evidence how the position of promoter proximal pausing is defined by the +1 nucleosome in human cells.
2024-05-30 | GSE242376 | GEO
Project description:Transcription by RNA polymerase II (RNA Pol II) depends on transcription factors and chromatin factors. Here we use rapid factor depletion and multiomics analysis to investigate how a histone chaperone, FAcilitates Chromatin Transcription (FACT), influence nascent transcription by RNA PolII in human cells. Depletion of a FACT subunit, SSRP1, led to rapid changes in chromatin structure and concomitantly strongly compromised RNA synthesis. FACT depletion led to a multilayered transcriptional defect, including loss of promoter proximal pausing, deregulated release into elongation and drop-off of RNA Pol II in promoter-distant gene regions. We combined these analyses with biochemical dissection of transcription of a chromatinized template to show that FACT supports both elongation and pausing of RNA Pol II. Our study also provides new evidence how the position of promoter proximal pausing is defined by the +1 nucleosome in human cells.
2024-05-30 | GSE242379 | GEO
Project description:Transcription by RNA polymerase II (RNA Pol II) depends on transcription factors and chromatin factors. Here we use rapid factor depletion and multiomics analysis to investigate how a histone chaperone, FAcilitates Chromatin Transcription (FACT), influence nascent transcription by RNA PolII in human cells. Depletion of a FACT subunit, SSRP1, led to rapid changes in chromatin structure and concomitantly strongly compromised RNA synthesis. FACT depletion led to a multilayered transcriptional defect, including loss of promoter proximal pausing, deregulated release into elongation and drop-off of RNA Pol II in promoter-distant gene regions. We combined these analyses with biochemical dissection of transcription of a chromatinized template to show that FACT supports both elongation and pausing of RNA Pol II. Our study also provides new evidence how the position of promoter proximal pausing is defined by the +1 nucleosome in human cells.
2024-05-30 | GSE242378 | GEO
Project description:Transcription by RNA polymerase II (RNA Pol II) depends on transcription factors and chromatin factors. Here we use rapid factor depletion and multiomics analysis to investigate how a histone chaperone, FAcilitates Chromatin Transcription (FACT), influence nascent transcription by RNA PolII in human cells. Depletion of a FACT subunit, SSRP1, led to rapid changes in chromatin structure and concomitantly strongly compromised RNA synthesis. FACT depletion led to a multilayered transcriptional defect, including loss of promoter proximal pausing, deregulated release into elongation and drop-off of RNA Pol II in promoter-distant gene regions. We combined these analyses with biochemical dissection of transcription of a chromatinized template to show that FACT supports both elongation and pausing of RNA Pol II. Our study also provides new evidence how the position of promoter proximal pausing is defined by the +1 nucleosome in human cells.
2024-05-30 | GSE242374 | GEO