Name
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. |
Year | DOI | Venue |
|---|---|---|
2017 | 10.1093/bioinformatics/btx282 | BIOINFORMATICS |
Field | DocType | Volume |
Promoter,Gene,Human embryonic stem cell line,Transcription (biology),DNA binding site,Computer science,Human genome,Computational biology,Bioinformatics,Chromatin,Transcription factor | Journal | 33 |
Issue | ISSN | Citations |
17 | 1367-4803 | 0 |
PageRank | References | Authors |
0.34 | 1 | 6 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Hebing Chen | 1 | 3 | 1.06 |
| Shuai Jiang | 2 | 4 | 2.48 |
| Zhuo Zhang | 3 | 186 | 27.49 |
| Hao Li | 4 | 261 | 85.92 |
| Yiming Lu | 5 | 96 | 7.65 |
| Xiaochen Bo | 6 | 285 | 23.72 |