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Series GSE60455 Query DataSets for GSE60455
Status Public on Nov 10, 2014
Title Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation at mammalian promoters and enhancers (PRO-seq)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design We sequenced nascent RNAs purified from run-on sequencing reactions (GRO-seq and PRO-seq) performed in two ENCODE cells lines: K562 and GM12878. We also enriched separate libraries from the same cells for the 5-meG cap associated with transcription start sites (TSSs) in order to produce a comprehensive mapping of nascent TSSs in these cells. This assay is called GRO-cap. We compared these TSSs to those identified in stable RNAs from CAGE assays to generate annotations for all TSSs based on the stability of the resulting transcript.
Contributor(s) Core L, Martins A, Lis JT, Siepel A
Citation(s) 25383968
Submission date Aug 15, 2014
Last update date May 15, 2019
Contact name Leighton James Core
Organization name Cornell University
Department Moleular Biology and Genetics
Lab John T. Lis
Street address 417 Biotechnology Building
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (1)
GSM1480327 K562 PRO-Seq
This SubSeries is part of SuperSeries:
GSE60456 Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation at mammalian promoters and enhancers
BioProject PRJNA258480
SRA SRP045616

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GSE60455_RAW.tar 343.3 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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