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Series GSE85191 Query DataSets for GSE85191
Status Public on Mar 09, 2018
Title Widespread transcriptional pausing and elongation control at enhancers
Organisms Drosophila melanogaster; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Regulation by gene-distal enhancers is critical for cell-type and condition-specific patterns of gene expression. Thus, to understand the fundamental basis of gene activity in a given cell type or tissue, we must be able to identify the precise locations of enhancers, and to functionally characterize their behaviors. Herein, we demonstrate that transcription is nearly universal feature of enhancers in Drosophila and mammalian cells, and that nascent RNA-sequencing strategies are optimal for identification of both enhancers and super-enhancers. We dissect the mechanisms governing enhancer transcription and discover remarkable similarities with transcription at protein-coding genes. We show that RNA polymerase II (RNAPII) undergoes regulated pausing and release at enhancers. However, as compared to mRNA genes, RNAPII at enhancers is less stable and more prone to early termination. Further, we find that the level of histone H3 Lysine 4 (H3K4) methylation at enhancers corresponds to transcriptional activity, such that highly-active enhancers display H3K4 tri-methylation rather than H3K4 mono-methylation considered a hallmark of enhancers. Finally, our work provides insights into the unique characteristics of super-enhancers, which stimulate high-level gene expression through rapid pause release; interestingly, this property renders associated genes resistant to loss of factors that stabilize paused RNAPII.
 
Overall design 4sU experiments: 5 biological replicates were generated for Control (B-galactosidade treated) and Spt5-depletion (treated with double stranded RNA for Spt5) in S2 cells. 2 biological replicates were generated for Control and NELF-KO (4OHT treated) mouse embryonic stem cells. Start-seq: 2 biological replicates were generated for Control (B-galactosidase treated) and Spt5-depleted (treated with double stranded RNA targeting Spt5) S2 cells. 4 additional replicates of untreated samples were generated. ChIP-seq: 2 biological replicates using untreated cells were generated for all ChIP-seq datasets, with the exception of Pol II ChIP-seq for Control (B-galactosidade treated) and Spt5-dep. (Spt5 treated) S2 cells.

Please note that [1] the 'processed_data_files.tar.gz' contains the processed data files for GSM2259961-GSM2259991; [2] the other Series supplementary files are associated with GSM2866861-GSM2866870; [3] the associated files are indicated in the corresponding sample description field.
 
Contributor(s) Henriques T, Scruggs BS, Flynn RA, Inouye MO, Muse GW, Burkholder A, Fargo DC, Chang HY, Adelman K
Citation(s) 29378787
Submission date Aug 04, 2016
Last update date May 15, 2019
Contact name Karen Adelman
E-mail(s) [email protected]
Organization name Harvard Medical School
Department Biological Chemistry and Molecular Pharmacology
Street address 45 Shattuck St. LHRRB-201a
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (6)
GPL11203 Illumina Genome Analyzer IIx (Drosophila melanogaster)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
Samples (37)
GSM2259961 Adelman_Dmel_S2_4sU-RNA-seq_control_rep1
GSM2259962 Adelman_Dmel_S2_4sU-RNA-seq_control_rep2
GSM2259963 Adelman_Dmel_S2_4sU-RNA-seq_control_rep3
Relations
BioProject PRJNA336521
SRA SRP080934

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
GSE85191_Adelman_Dmel_S2_Cohesin_ChIP-seq_rep1and2.bedgraph.gz 27.8 Mb (ftp)(http) BEDGRAPH
GSE85191_Adelman_Dmel_S2_Start-seq_TSScall_rep1to4_GSM463298_5prRNA_forward.bedGraph.gz 3.2 Mb (ftp)(http) BEDGRAPH
GSE85191_Adelman_Dmel_S2_Start-seq_TSScall_rep1to4_GSM463298_5prRNA_reverse.bedGraph.gz 3.3 Mb (ftp)(http) BEDGRAPH
GSE85191_Adelman_mESC_C2cells_2i_4sU-RNA-seq_NELF-KO_rep1and2_mean_normalized_coverage_minus.bw 908.5 Mb (ftp)(http) BW
GSE85191_Adelman_mESC_C2cells_2i_4sU-RNA-seq_NELF-KO_rep1and2_mean_normalized_coverage_plus.bw 932.0 Mb (ftp)(http) BW
GSE85191_Adelman_mESC_C2cells_2i_4sU-RNA-seq_control_rep1and2_mean_normalized_coverage_minus.bw 784.4 Mb (ftp)(http) BW
GSE85191_Adelman_mESC_C2cells_2i_4sU-RNA-seq_control_rep1and2_mean_normalized_coverage_plus.bw 804.4 Mb (ftp)(http) BW
GSE85191_processed_data_files.tar.gz 3.8 Gb (ftp)(http) TAR
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