The Skok Lab uses fluorescent in situ hybridization (FISH), live imaging, genome wide chromosome conformation capture (3C) and analytical aspects of chromosome folding with the tools of genetics to understand how higher-order mechanisms help preserve genome integrity and regulate gene expression.

Dr Skok’s pioneering work revealed how reversible chromatin interactions contribute to the regulation of antigen receptor gene recombination during lymphocyte development. During the last few years, the lab has focused on understanding how chromatin organization impacts gene regulation through the sharing of regulatory elements, including those that emanate from transposons.

The Skoklab has also extended their research to the question of how alterations in nuclear organization contribute to oncogenic transcriptional programs. One aspect of this is trying to understand how alterations in the balance of histone modifications impact changes in chromatin architecture in a manner that activates oncogenes. Another aspect is in investigating the impact of architectural proteins on gene regulation and cancer outcome.

ABSTRACT

Title: Defining the relative and combined contributions of CTCF and CTCFL to genomic regulation and impact on cancer

Summary: Expression of CTCFL, the paralog of CTCF, is normally limited to the developing testis. However, it is also aberrantly activated in many cancers. While it is known that CTCFL can bind competitively to a subset of CTCF binding sites as well as unique CTCFL sites, it is not understood to what extent CTCFL deregulates transcription on its own or by opposing CTCF.

Using an inducible complementation system, we analyzed the impact of expressing CTCFL in the presence or absence of endogenous CTCF. We show that CTCF’s and CTCFL’s unique and overlapping binding sites differ in their DNA motifs, genomic distribution with respect to promoters and intronic or intergenic regions, as well as local chromatin folding.

CTCFL does not share CTCF‘s role in chromosome organization, which we link to its inability to interact with cohesin. Nevertheless, CTCFL expression can disrupt CTCF-mediated looping. Using chimeric proteins, we demonstrate that, while the N/C domains of CTCF mediate the interaction with cohesin, proper insulation of chromosome domains can only be mediated by full-length CTCF.

Nonetheless, the N/C domains of both CTCF and CTCFL contribute to the specificity in how each paralog targets DNA and regulates gene transcription. This study clarifies the relative and combined contribution of CTCF and CTCFL to chromosome organization and transcription, with direct implications for understanding how their co-expression deregulates transcription in cancer.