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Series GSE74308 Query DataSets for GSE74308
Status Public on Feb 11, 2017
Title Antisense transcription predicts a distinct chromatin environment at mammalian promoters
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Antisense transcription is common at mammalian promoters. Previous studies have largely focused on characterizing antisense transcription initiating upstream of gene transcription start sites. Here, we systematically characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human T-47D cells, investigating the genomic context of downstream antisense transcription. We find that downstream antisense transcription is widespread, with antisense transcription initiation observed within 2 kb of 28% of gene transcription start sites. Downstream antisense transcription is correlated with many regulatory features at gene promoters despite not being categorically associated with gene activation or repression. At the downstream antisense transcription start site, DNA is accessible, is enriched for protein-associated sequences motifs, and is bound by a variety of transcription factors. Downstream antisense transcription initiates between nucleosomes regularly positioned downstream of gene transcription start sites. Those nucleosomes between gene and downstream antisense transcription start sites carry histone modifications associated with active promoters, such as H3K4me3 and H3K27ac. Strikingly, this same region is bound by chromatin remodeling complexes such as HDAC and SWI/SNF. The coincidence of transcription initiation with nucleosomes displaying promoter-associated histone marks underlies an apparent connection between antisense transcription and the chromatin environment at gene promoters. The association of chromatin remodelers at sites of downstream antisense transcription initiation suggests that antisense transcription contributes to the deposition and maintenance of these chromatin features at gene promoters.
Overall design RNA-seq and Start-seq were used to characterize steady-state transcript levels and transcription initation, respectively, in T-47D cells. MNase-seq and FAIRE-seq were then performed to assess the chromatin environment at identified transcription start sites.
Contributor(s) Lavender CA, Cannady KR, Hoffman JA, Trotter KW, Gilchrist DA, Bennett BD, Burkholder AB, Burd CJ, Fargo DC, Archer TK
Citation(s) 27487356
Submission date Oct 23, 2015
Last update date May 15, 2019
Contact name Christopher Lavender
Organization name NIEHS
Street address 111 T. W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (4)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (7)
GSM1916674 Archer_T47D_StartSeq_rep1
GSM1916676 Archer_T47D_MNaseSeq
GSM1916677 Archer_T47D_FAIRESeq
BioProject PRJNA299634
SRA SRP065180

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE74308_Archer_T47D_RNASeq_FPKM_values.csv.gz 424.3 Kb (ftp)(http) CSV
GSE74308_RAW.tar 1.3 Gb (http)(custom) TAR (of BED, BW, XLSX)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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