Bibliographic Details
| Title: |
Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome |
| Authors: |
Jia-Hsin Huang, Ryan Shun-Yuen Kwan, Zing Tsung-Yeh Tsai, Tzu-Chieh Lin, Huai-Kuang Tsai |
| Source: |
Frontiers in Genetics, Vol 9 (2018) |
| Publisher Information: |
Frontiers Media S.A., 2018. |
| Publication Year: |
2018 |
| Collection: |
LCC:Genetics |
| Subject Terms: |
transcription factor binding sites, motifs, cis-regulatory elements, TF binding specificities, open chromatins, Genetics, QH426-470 |
| More Details: |
Changes in cis-regulatory DNA sequences and transcription factor (TF) repertoires provide major sources of phenotypic diversity that shape the evolution of gene regulation in eukaryotes. The DNA-binding specificities of TFs may be diversified or produce new variants in different eukaryotic species. However, it is currently unclear how various levels of divergence in TF DNA-binding specificities or motifs became introduced into the cis-regulatory DNA regions of the genome over evolutionary time. Here, we first estimated the evolutionary divergence levels of TF binding motifs and quantified their occurrence at DNase I-hypersensitive sites. Results from our in silico motif scan and experimentally derived chromatin immunoprecipitation (TF-ChIP) show that the divergent motifs tend to be introduced in the edges of cis-regulatory regions, which is probably accompanied by the expansion of the accessible core of promoter-associated regulatory elements during evolution. We also find that the genes neighboring the expanded cis-regulatory regions with the most divergent motifs are associated with functions like development and morphogenesis. Accordingly, we propose that the accumulation of divergent motifs in the edges of cis-regulatory regions provides a functional mechanism for the evolution of divergent regulatory circuits. |
| Document Type: |
article |
| File Description: |
electronic resource |
| Language: |
English |
| ISSN: |
1664-8021 |
| Relation: |
https://www.frontiersin.org/article/10.3389/fgene.2018.00571/full; https://doaj.org/toc/1664-8021 |
| DOI: |
10.3389/fgene.2018.00571 |
| Access URL: |
https://doaj.org/article/5602c23704c84bdf9b545bbbdcf1de31 |
| Accession Number: |
edsdoj.5602c23704c84bdf9b545bbbdcf1de31 |
| Database: |
Directory of Open Access Journals |
