Virus Dataset Detail

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Dataset Information
Accession GSE100266
Status 2017/8/21
Title The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin Remodeling Complexes
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing;Expression profiling by high throughput sequencing
Summary BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a novel corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells and was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent HIV-1 promoter, which was dependent on the activity of BAF, a SWI/SNF chromatin-remodeling complex with known repressive functions in HIV-1 transcription. BRD4S directly bound BRG1, a catalytic subunit of BAF, via its bromo- and ET domains and was necessary for BRG1 recruitment to latent HIV-1 chromatin. Using ChIP-seq combined with ATAC-seq data, we found that the latent HIV-1 promoter phenotypically resembles endogenous LTR sequences, pointing to a select role of BRD4S:BRG1 complexes in genomic silencing of invasive retroelements.
Samples
GSM ID Sample info Characteristics Description
GSM2676822 2_JQ1_ATAC treatment:JQ1 transposed genomic DNA
GSM2676823 1_scramble_RNA genotype:control RNA-seq_DEGs
GSM2676824 1_long_BRD4_KD_RNA genotype:long_BRD4_KD RNA-seq_DEGs
GSM2676825 1_short_BRD4_KD_RNA genotype:short_BRD4_KD RNA-seq_DEGs
GSM2676826 1_both_BRD4_KD_RNA genotype:both_BRD4_KD RNA-seq_DEGs
GSM2676827 2_scramble_RNA genotype:control RNA-seq_DEGs
GSM2676828 2_long_BRD4_KD_RNA genotype:long_BRD4_KD RNA-seq_DEGs
GSM2676829 2_short_BRD4_KD_RNA genotype:short_BRD4_KD RNA-seq_DEGs
GSM2676830 2_both_BRD4_KD_RNA genotype:both_BRD4_KD RNA-seq_DEGs
GSM2676799 1_DMSO_BRD4 treatment:DMSO; chip antibody:Abcam ab128874 -
GSM2676800 1_DMSO_BRG1 treatment:DMSO; chip antibody:Abcam ab110641 -
GSM2676801 1_DMSO_polII treatment:DMSO; chip antibody:Santa Cruz N-20, sc-899 -
GSM2676802 1_JQ1_BRD4 treatment:JQ1; chip antibody:Abcam ab128874 -
GSM2676803 1_JQ1_BRG1 treatment:JQ1; chip antibody:Abcam ab110641 -
GSM2676804 1_JQ1_polII treatment:JQ1; chip antibody:Santa Cruz N-20, sc-899 -
GSM2676805 2_DMSO_BRD4 treatment:DMSO; chip antibody:Abcam ab128874 -
GSM2676806 2_DMSO_BRG1 treatment:DMSO; chip antibody:Abcam ab110641 -
GSM2676807 2_DMSO_polII treatment:DMSO; chip antibody:Santa Cruz N-20, sc-899 -
GSM2676808 2_JQ1_BRD4 treatment:JQ1; chip antibody:Abcam ab128874 -
GSM2676809 2_JQ1_BRG1 treatment:JQ1; chip antibody:Abcam ab110641 -
GSM2676810 2_JQ1_polII treatment:JQ1; chip antibody:Santa Cruz N-20, sc-899 -
GSM2676811 3_DMSO_BRD4 treatment:DMSO; chip antibody:Abcam ab128874 -
GSM2676812 3_JQ1_BRD4 treatment:JQ1; chip antibody:Abcam ab128874 -
GSM2676813 1_DMSO_input treatment:DMSO; chip antibody:none -
GSM2676814 1_JQ1_input treatment:JQ1; chip antibody:none -
GSM2676815 2_DMSO_input treatment:DMSO; chip antibody:none -
GSM2676816 2_JQ1_input treatment:JQ1; chip antibody:none -
GSM2676817 3_DMSO_input treatment:DMSO; chip antibody:none -
GSM2676818 3_JQ1_input treatment:JQ1; chip antibody:none -
GSM2676819 1_DMSO_ATAC treatment:DMSO transposed genomic DNA
GSM2676820 1_JQ1_ATAC treatment:JQ1 transposed genomic DNA
GSM2676821 2_DMSO_ATAC treatment:DMSO transposed genomic DNA
Platform GPL16791  : Illumina HiSeq 2500 (Homo sapiens)
Literature 28844864  
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* p<0.05 ** p<0.01