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Loss of transcription factor alters chromatin accessibility

Researchers have discovered that chromatin accessibility is heavily influenced by a key transcription factor that is linked to cancer. The findings of this study, published in Genome Biology, have the potential to influence future cancer treatments.

Transcription factor CTCF regulates chromatin structure

CCCTC-binding factor (CTCF) is a transcription factor that has been of great interest to researchers in recent years due to its role in regulating a critical oncogene called MYC. Known as “the master weaver of the genome”, CTCF regulates the 3D architecture of chromatin. Whilst the downstream effects of CTCF on genes are well studied, the impact of CTCF on chromatin and transcription is relatively unknown. To investigate this, a team of researchers from St Jude Children’s Research Hospital conducted several multi-omics studies on cells with decreased levels of CTCF.

“There has been a gap in our knowledge of the direct effect of CTCF, which is important for understanding the process of transcription. 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,” senior author Chunliang Li said.

Changes in chromatin accessibility

The team genetically engineered a human cell line to carry an auxin-induced degron (AID) at the CTCF loci. The AID system is a tool that induces rapid protein degradation. This allowed the researchers to engineer cells to deplete the levels of CTCF protein.

Chromatin accessibility is the degree to which nuclear macromolecules, such as transcription factors, are able to physically contact chromatinised DNA. To investigate whether genome-wide chromatin accessibility changed in response to CTCF reduction, the researchers performed ATAC-seq on their cells.

The team found that the CTCF depleted cells had a significantly different pattern of genome-wide chromatin accessibility than normal cells. The analysis also showed a strong association between CTCF binding sites and regions of changed accessibility.

Effect on DNA methylation

Scientists have previously suggested that CTCF plays a role in DNA methylation. However, controversy still surrounds this claim. To investigate the role of CTCF on DNA methylation further, the researchers used whole-genome bisulphite sequencing (WGBS) to generate DNA methylation profiles from CTCF depleted cells.

Surprisingly, the results revealed that acute CTCF depletion did not change DNA methylation patterns. The team identified a small number of differentially methylated areas, but none of these had a direct association with CTCF levels.

Effect on gene expression

Next, the team investigated the impact of acute CTCF loss on gene expression. In total, they identified 2,550 differentially expressed proteins, as well as 1,895 protein phosphorylation changes. These results indicate that CTCF loss can disrupt major components in translation and potentially derail protein translation machinery.

On the other hand, the team found that downstream genes of CTCF were scarcely altered. The genes impacted by CTCF loss were downstream of other transcription factors. This suggests that CTCF loss can trigger global changes in cells that subsequently affect various other transcription factors. 

Conclusions and future work

Overall, these results highlight that CTCF loss can significantly alter genome-wide chromatin accessibility but not DNA methylation. These findings have filled a large knowledge gap regarding how CTCF alters transcription. Researchers now have a deeper understanding of the roles of CTCF. However, scientists will have to carry out future work to further elucidate CTCF’s functions. As CTCF is known to be implicated in cancers, these results may aid the development of future cancer treatments.

Co-author Junmin Peng said:

“A better understanding of the direct effect of CTCF will help propel the field of transcription biology toward a more complete picture of how the processes are involved in diseases such as cancer.”

Photo by Braňo on Unsplash

More on these topics

Chromatin / Multi-omics / Transcriptomics