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Exploring spatially adjacent TFBS-clustered regions with Hi-C data

Chen, Hebing, Jiang, Shuai, Zhang, Zhuo, Li, Hao, Lu, Yiming, Bo, Xiaochen
Bioinformatics 2017 v.33 no.17 pp. 2611-2614
algorithms, binding sites, bioinformatics, chromatin, embryonic stem cells, genes, human cell lines, humans, models, regulatory sequences, transcription (genetics), transcription factors
Motivation: Transcription factor binding sites (TFBSs) are clustered in the human genome, forming the TFBS-clustered regions that regulate gene transcription, which requires dynamic chromatin configurations between promoters and distal regulatory elements. Here, we propose a regulatory model called spatially adjacent TFBS-clustered regions (SATs), in which TFBS-clustered regions are connected by spatial proximity as identified by high-resolution Hi-C data. Results: TFBS-clustered regions forming SATs appeared less frequently in gene promoters than did isolated TFBS-clustered regions, whereas SATs as a whole appeared more frequently. These observations indicate that multiple distal TFBS-clustered regions combined to form SATs to regulate genes. Further examination confirmed that a substantial portion of genes regulated by SATs were located between the paired TFBS-clustered regions instead of the downstream. We reconstructed the chromosomal conformation of the H1 human embryonic stem cell line using the ShRec3D algorithm and proposed the SAT regulatory model. Contact:ylu.phd@gmail.com or boxc@bmi.ac.cn Supplementary information:Supplementary data are available at Bioinformatics online.