1. Exploring spatially adjacent TFBS-clustered regions with Hi-C data.
- Author
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Chen H, Jiang S, Zhang Z, Li H, Lu Y, and Bo X
- Subjects
- Algorithms, Binding Sites, Cell Line, DNA metabolism, Embryonic Stem Cells metabolism, Humans, Models, Genetic, Sequence Analysis, DNA methods, Genome, Human, Genomics methods, Promoter Regions, Genetic, Software, Transcription Factors metabolism
- Abstract
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., (© The Author(s) 2017. Published by Oxford University Press.)
- Published
- 2017
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