Ontology highlight
ABSTRACT:
PROVIDER: PRJNA258294 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1552480.fastq.gz | Fastqsanger.gz | |||
| SRR1552481.fastq.gz | Fastqsanger.gz | |||
| SRR1554311.fastq.gz | Fastqsanger.gz | |||
| SRR1552482.fastq.gz | Fastqsanger.gz | |||
| SRR1554312.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation at mammalian promoters and enhancers (GRO-cap)
| PRJNA258295 | ENA
Project description:Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation at mammalian promoters and enhancers (GRO-seq)
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Project description:Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation at mammalian promoters and enhancers (PRO-seq)
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Project description:Despite the conventional distinction between promoters and enhancers, they share many features in mammals, including divergent transcription and similar modes of transcription factor (TF) binding. Here, we examine the architecture of transcription initiation genome-wide through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines using a nuclear run-on protocol called GRO-cap. This method captures TSSs for both stable and unstable transcripts, thus allowing us to conduct detailed comparisons between thousands of promoters and enhancers in human cells. These analyses reveal a common architecture of initiation at both promoters and enhancers, including tightly spaced (110 bp) divergent initiation that features similar frequencies of core-promoter sequence elements, highly-positioned flanking nucleosomes, and two modes of TF binding. Transcript elongation stability, a feature determined after transcription initiation, provides a more fundamental distinction between promoters and enhancers than the relative abundance of histone modifications and the presence of TFs or coactivators. These results support a unified model of transcription initiation at both promoters and enhancers.
2014-11-10 | GSE60455 | GEO
Project description:Despite the conventional distinction between promoters and enhancers, they share many features in mammals, including divergent transcription and similar modes of transcription factor (TF) binding. Here, we examine the architecture of transcription initiation genome-wide through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines using a nuclear run-on protocol called GRO-cap. This method captures TSSs for both stable and unstable transcripts, thus allowing us to conduct detailed comparisons between thousands of promoters and enhancers in human cells. These analyses reveal a common architecture of initiation at both promoters and enhancers, including tightly spaced (110 bp) divergent initiation that features similar frequencies of core-promoter sequence elements, highly-positioned flanking nucleosomes, and two modes of TF binding. Transcript elongation stability, a feature determined after transcription initiation, provides a more fundamental distinction between promoters and enhancers than the relative abundance of histone modifications and the presence of TFs or coactivators. These results support a unified model of transcription initiation at both promoters and enhancers.
2014-11-10 | GSE60454 | GEO
Project description:Despite the conventional distinction between promoters and enhancers, they share many features in mammals, including divergent transcription and similar modes of transcription factor (TF) binding. Here, we examine the architecture of transcription initiation genome-wide through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines using a nuclear run-on protocol called GRO-cap. This method captures TSSs for both stable and unstable transcripts, thus allowing us to conduct detailed comparisons between thousands of promoters and enhancers in human cells. These analyses reveal a common architecture of initiation at both promoters and enhancers, including tightly spaced (110 bp) divergent initiation that features similar frequencies of core-promoter sequence elements, highly-positioned flanking nucleosomes, and two modes of TF binding. Transcript elongation stability, a feature determined after transcription initiation, provides a more fundamental distinction between promoters and enhancers than the relative abundance of histone modifications and the presence of TFs or coactivators. These results support a unified model of transcription initiation at both promoters and enhancers.
2014-11-10 | GSE60453 | GEO
Project description:Dogs exhibit high genetic diversity due to extensive breeding, and provide a versatile model for genetics, evolution, and complex traits. While RNA synthesis and transcriptional architecture of promoters and enhancers have been extensively analyzed in human, mouse, and fly, little is known about the mechanisms that coordinate gene and enhancer transcription in dog. Here, we combine precision run-on sequencing (PRO-seq) and strand-specific mRNA-seq (mRNA-seq) to measure nascent transcription, mRNA expression and mRNA stability in golden retriever macrophage (DH82) cells. Tracking transcription at nucleotide-resolution uncovers the precise transcription start nucleotides (TSN) genome-wide, identifies the exact locations of promoters and transcribed enhancers, and quantifies transcription machineries at initiation, promoter proximal pause, gene bodies, and termination windows. Moreover, we trigger an instant transcriptional reprogramming using heat shock, and track at nucleotide-resolution, how dog cells coordinate RNA synthesis and mRNA expression across the genome. Taken together, this study describes the transcriptional landscape at nucleotide-resolution, measures RNA synthesis, mRNA expression and mRNA-stability, and identifies mechanisms of gene and enhancer reprogramming in Canis lupus familiaris.
2025-11-06 | GSE274105 | GEO
Project description:Dogs exhibit high genetic diversity due to extensive breeding, and provide a versatile model for genetics, evolution, and complex traits. While RNA synthesis and transcriptional architecture of promoters and enhancers have been extensively analyzed in human, mouse, and fly, little is known about the mechanisms that coordinate gene and enhancer transcription in dog. Here, we combine precision run-on sequencing (PRO-seq) and strand-specific mRNA-seq (mRNA-seq) to measure nascent transcription, mRNA expression and mRNA stability in golden retriever macrophage (DH82) cells. Tracking transcription at nucleotide-resolution uncovers the precise transcription start nucleotides (TSN) genome-wide, identifies the exact locations of promoters and transcribed enhancers, and quantifies transcription machineries at initiation, promoter proximal pause, gene bodies, and termination windows. Moreover, we trigger an instant transcriptional reprogramming using heat shock, and track at nucleotide-resolution, how dog cells coordinate RNA synthesis and mRNA expression across the genome. Taken together, this study describes the transcriptional landscape at nucleotide-resolution, measures RNA synthesis, mRNA expression and mRNA-stability, and identifies mechanisms of gene and enhancer reprogramming in Canis lupus familiaris.
2025-11-06 | GSE274106 | 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.
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Project description:Using a transcriptome-wide profiling approach to map translation initiation start sites in human beta-cells under standard and inflammatory conditions, we identifies non-canonical start sites and translation initiation within lncRNA.
2021-02-23 | GSE167223 | GEO