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Series GSE169407 Query DataSets for GSE169407
Status Public on Jul 14, 2022
Title The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [ChIP_seq_flyheads]
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin insulators are involved in transcription regulation and long-range chromatin contacts. In Drosophila the Boundary Element-Associated Factor Of 32kD (BEAF-32) binds to promoters of housekeeping genes and the boundaries of Topological Associated Domains (TAD) and is involved in the regulation of long-range targets by mechanisms that remain incompletely understood. Here we show that Relative-Of-WOC (ROW), which is part of the Heterochromatin Protein 1c (HP1c) complex, is essential for the long-range transcription regulation mediated by BEAF-32. We found that ROW physically interacts with the insulator complex proteins BEAF-32 and Chromator, as well as with HP1c, HP1b, and Without Children (WOC). Moreover, we found that ROW binds AT-rich sequences flanked by BEAF-32 motifs, which are located at promoters of housekeeping genes and in TAD boundaries. In agreement with these results, the genome distribution of ROW strongly correlated with BEAF-32 and WOC, but at a lower level with HP1c and HP1b. Knockdown of row resulted in downregulation of genes that are long-range targets of BEAF-32, are indirectly bound by BEAF-32 and ROW, and enriched with factors associated with RNA polymerase II pausing. These results suggest that ROW and BEAF-32 are involved in the recruitment of protein complexes required for transcription activation and long-range contacts between promoters of housekeeping and inducible genes.
 
Overall design Binding profile of ROW (triplicate), HP1c (triplicate), HP1b (duplicate), WOC (triplicate), H3K4me3 (triplicate) and igG (duplicate) in Drosophila fly heads.
 
Contributor(s) Herman N, Kadener S, Shifman S
Citation(s) 36245419
Submission date Mar 23, 2021
Last update date Oct 24, 2022
Contact name Neta Herman
E-mail(s) [email protected], [email protected]
Organization name Hebrew University Of Jerusalem, Migal
Department Gentics, Nutrition
Lab Shagiv Shifman; Opatovsky Itai
Street address Kiryat Shemona
City Jerusalem, Kiryat Shemona
ZIP/Postal code 1101202
Country Israel
 
Platforms (1)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (16)
GSM5202035 hp1b_rep1
GSM5202036 hp1b_rep2
GSM5202037 hp1c_rep1
This SubSeries is part of SuperSeries:
GSE169415 The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes
Relations
BioProject PRJNA716543
SRA SRP311793

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
GSE169407_RAW.tar 281.7 Mb (http)(custom) TAR (of BW)
GSE169407_h3k4me3.narrowPeak.gz 128.6 Kb (ftp)(http) NARROWPEAK
GSE169407_hp1b_peaks.bed.gz 21.0 Kb (ftp)(http) BED
GSE169407_hp1c_peaks.bed.gz 35.1 Kb (ftp)(http) BED
GSE169407_row_peaks.bed.gz 43.5 Kb (ftp)(http) BED
GSE169407_woc_peaks.bed.gz 40.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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