CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• The CCCTC-binding factor (CTCF) is a crucial transcriptional regulator involved in gene expression and genome 3D organization.
• CTCF mediates intra- and inter-chromosomal interactions, playing a key role in genome architecture.

Purpose of the Study:

• To update the CTCF-binding sites database (CTCFBSDB) with recent data and new functionalities.
• To integrate CTCF-binding sites with genomic topological domains derived from Hi-C experiments.

Main Methods:

• Database expansion with nearly 15 million CTCF-binding sequences from 10 species.
• Integration of CTCF-binding sites with Hi-C-defined genomic topological domains.
• Incorporation of new features such as binding site occupancy and visualization of overlapping sites.

Main Results:

• The updated CTCFBSDB now houses extensive CTCF-binding data across multiple species.
• Genomic topological domains are now linked with CTCF-binding sites, providing insights into genome organization.
• New features allow for analysis of CTCF binding site occupancy and overlap.

Conclusions:

• The enhanced CTCFBSDB provides a valuable resource for studying CTCF's role in gene regulation and 3D genome structure.
• Integration with Hi-C data offers a more comprehensive understanding of CTCF's function in genome topology.
• The updated database facilitates advanced research into CTCF-binding dynamics and interactions.