GSE120023
GSE GEOPervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [HiC-Seq]
Relations
Summary
Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA binding proteins (RBPs). Although multiple RBPs have been implicated in transcriptional control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also showed strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription.
Overall Design
Examination of RBM25-dependent chromatin structure by BL-Hi-C with 2 replicated experiments in HepG2 cells
Analysis (5 steps)
View Data Processing- Library strategy: HiC-Seq
- The ChIA-PET2 software (Li et al., 2017a) was used for quality control and identification of chromatin interactions with the following parameter setting: -A ACGCGATATCTTATC -B AGTCAGATAAGATAT -s 1 -m 1 -t 4 -k 2 -e 1 -l 15 -S 500 -M "-q 0.05" âC 1.
- PCA analysis is then applied to 40-kb resolution interaction matrix generated by HiC-Pro (Servant et al., 2015), and regions of continuous positive or negative PC1 values were used for the identification of A or B compartments (Heinz et al., 2010).
- The interaction matrix was visualized by HiCPlotter (Akdemir and Chin, 2015).
- High confident interactions were defined as those with >3 PET counts and q-value < 0.05 for downstream analysis.
Supplementary Files (1)
GEO Samples (4)
Dataset Citations (1)
SRA Experiments (4) and Runs (4)
Total: 43274 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR7868823 | 94116865 | 28235059500 | 10696.4 | Control_BLHiC_HepG2_rep1_R1.fq.gz, Control_BLHiC_HepG2_rep1_R2.fq.gz,… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR7868824 | 91604053 | 27481215900 | 10453.19 | Control_BLHiC_HepG2_rep2_R1.fq.gz, Control_BLHiC_HepG2_rep2_R2.fq.gz,… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR7868825 | 108265304 | 32479591200 | 12297.57 | RBM25.KD_BLHiC_HepG2_rep1_R1.fq.gz, RBM25.KD_BLHiC_HepG2_rep1_R2.fq.g… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR7868826 | 87459578 | 26237873400 | 9827.1 | RBM25.KD_BLHiC_HepG2_rep2_R1.fq.gz, RBM25.KD_BLHiC_HepG2_rep2_R2.fq.g… | SRA |