Virendra K. Chaudhri, Krista Dienger-Stambaugh, Zhiguo Wu, Mahesh Shrestha, Harinder Singh
Mammalian genomic states are distinguished by their chromatin and transcription profiles. Most genomic analyses rely on chromatin profiling to infer cis-regulomes controlling distinctive cellular states. By coupling FAIRE-seq with STARR-seq and integrating Hi-C we assemble a functional cis-regulome for activated murine B-cells. Within 55,130 accessible chromatin regions we delineate 9,989 active enhancers communicating with 7,530 promoters. The cis-regulome is dominated by long range enhancer-promoter interactions (>100kb) and complex combinatorics, implying rapid evolvability. Genes with multiple enhancers display higher rates of transcription and multi-genic enhancers manifest graded levels of H3K4me1 and H3K27ac in poised and activated states, respectively. Motif analysis of pathway-specific enhancers reveals diverse transcription factor (TF) codes controlling discrete processes. The cis-regulome strikingly enriches for combinatorial DNA binding regions of lineage determining TFs. Their genomic binding patterns reveal that onset of chromatin accessibility is associated with binding of simpler combinations whereas enhancer function requires greater complexity.
Virendra K. Chaudhri, Krista Dienger-Stambaugh, Zhiguo Wu, Mahesh Shrestha, Harinder Singh. Organizational properties of a functional mammalian cis-regulome. 2019-02-15. https://doi.org/10.1101/550897
FAIRE-derived genomic fragments from LPS-activated murine splenic B cells were cloned into a self-transcribing active regulatory region (STARR-seq) plasmid and electroporated into activated B cells. Libraries transfected at 48 hours (24-hour readout) or 60 hours (12-hour readout) after LPS activation were harvested at 72 hours; combined peak calls identify functional accessible enhancers.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 11 files (ZIP)41590_2019_565_MOESM2_ESM.xlsxGSE121753_CD43Neg_BCells_RNAseq.txt.gzGSE121753_FAIREseq_aB_peaks.bed.gzGSE121753_family.soft.gzGSE121753_H3K27ac_aB_peaks.bed.gzGSE121753_H3K27ac_aB_SuperEnhancers.bed.gzGSE121753_H3K4me3_aB_peaks.bed.gzGSE121753_HiC_Filtered_Enhancer_Promoter_Interactions.txt.gzGSE121753_series.geo.txtGSE121753_STARRseq_aB_peaks.bed.gzGSE121753_STARRseq_aB_peaks_overlap_FAIREseqPeaks.bed.gz