Chromatin Accessibility Impacted by Acute CTCF Loss

Scientists at St. Jude Children’s Research Hospital report that they have found direct evidence that the transcription factor CTCF governs chromatin accessibility.

CTCF is known by biologists for being a master regulator of the genome and for heavily influencing the genome’s 3D architecture. Mutations of CTCF that lead to its absence are rare; however, mutations that affect how it binds to genes and proteins are common in cells with diseases such as cancer. While the downstream impact of CTCF on genes is well studied, less is known about the more immediate repercussions.

“There has been a gap in our knowledge of the direct effect of CTCF, which is important for understanding the process of transcription,” said Chungliang Li, senior author of the paper published recently in Genome Biology. “If you alter gene expression at the right time and place, then even a moderate change in transcription can cause a substantial change in disease development.”

The researchers used a multidisciplinary approach that makes use of an auxin-induced degron system, which degrades protein in a targeted way in a short period of time, allowing researchers to better understand its primary function. These tools were necessary to study how acute depletion of the CTCF protein would affect the cell.

“It is challenging to distinguish the true biology of CTCF, but we’ve used these tools to provide direct evidence that CTCF regulates chromatin accessibility and to provide clarity for the field,” said co-first author Beisi Xu.

The team also looked at multi-omics data, including techniques called ATAC-seq, RNA-seq, whole-genome bisulfite sequencing, Hi-C, Cut&Run, and CRISPR-Cas9 screens, as well as time-solved deep proteomic and phosphoproteomic analyses in cells carrying the auxin-induced degron.

This study highlights that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation. Because pediatric cancers have a relatively quiet genome, finding new treatments requires a better understanding of cancer biology on a fundamental level. That involves drilling down to how the processes of CTCF and transcription go awry.