期刊
GENESIS
卷 51, 期 5, 页码 311-324出版社
WILEY
DOI: 10.1002/dvg.22375
关键词
transcriptional regulation; enhancer analysis; cis-regulatory regions; genomics tools; gene regulatory networks; chick embryo
资金
- European Research Council
- BBSRC
- Biotechnology and Biological Sciences Research Council [BB/K007742/1, BB/G000972/1, BB/I021647/1] Funding Source: researchfish
- Medical Research Council [1069102, G0400559, G0700095] Funding Source: researchfish
- BBSRC [BB/I021647/1, BB/G000972/1, BB/K007742/1] Funding Source: UKRI
- MRC [G0700095, G0400559] Funding Source: UKRI
The discovery of cis-regulatory elements is a challenging problem in bioinformatics, owing to distal locations and context-specific roles of these elements in controlling gene regulation. Here we review the current bioinformatics methodologies and resources available for systematic discovery of cis-acting regulatory elements and conserved transcription factor binding sites in the chick genome. In addition, we propose and make available, a novel workflow using computational tools that integrate CTCF analysis to predict putative insulator elements, enhancer prediction, and TFBS analysis. To demonstrate the usefulness of this computational workflow, we then use it to analyze the locus of the gene Sox2 whose developmental expression is known to be controlled by a complex array of cis-acting regulatory elements. The workflow accurately predicts most of the experimentally verified elements along with some that have not yet been discovered. A web version of the CTCF tool, together with instructions for using the workflow can be accessed from http://toolshed.g2.bx.psu.edu/view/mkhan1980/ctcf_analysis. For local installation of the tool, relevant Perl scripts and instructions are provided in the directory named code in the supplementary materials. genesis 51:311324. (c) 2013 Wiley Periodicals, Inc.
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