Abstract
BackgroundCTCF binding to DNA helps partition the mammalian genome into discrete structural and regulatory domains. Complete removal of CTCF from mammalian cells causes catastrophic genome dysregulation, likely due to widespread collapse of 3D chromatin looping and alterations to inter- and intra-TAD interactions within the nucleus. In contrast, Ctcf hemizygous mice with lifelong reduction of CTCF expression are viable, albeit with increased cancer incidence. Here, we exploit chronic Ctcf hemizygosity to reveal its homeostatic roles in maintaining genome function and integrity.ResultsWe find that Ctcf hemizygous cells show modest but robust changes in almost a thousand sites of genomic CTCF occupancy; these are enriched for lower affinity binding events with weaker evolutionary conservation across the mouse lineage. Furthermore, we observe dysregulation of the expression of several hundred genes, which are concentrated in cancer-related pathways, and are caused by changes in transcriptional regulation. Chromatin structure is preserved but some loop interactions are destabilized; these are often found around differentially expressed genes and their enhancers. Importantly, the transcriptional alterations identified in vitro are recapitulated in mouse tumors and also in human cancers.ConclusionsThis multi-dimensional genomic and epigenomic profiling of a Ctcf hemizygous mouse model system shows that chronic depletion of CTCF dysregulates steady-state gene expression by subtly altering transcriptional regulation, changes which can also be observed in primary tumors.
Highlights
CTCF binding to DNA helps partition the mammalian genome into discrete structural and regulatory domains
Chronic reduction of CTCF alters its chromatin binding To characterize the molecular effects of altering the concentration of CTCF protein available in the nucleus, we utilized Ctcf hemizygous mice that carry a lacZ reporter in place of the coding region of Ctcf [27] in all cells (Fig. 1a)
We derived six independent lines of embryonic fibroblasts from mice carrying a deletion of one Ctcf allele (Ctcf +/−) and six corresponding lines from Ctcf wild-type littermate controls (Fig. 1a). qPCR demonstrated that Ctcf hemizygous mouse embryonic fibroblasts (MEFs) had a 37% reduction in Ctcf mRNA compared to wild-type
Summary
CTCF binding to DNA helps partition the mammalian genome into discrete structural and regulatory domains. Complete removal of CTCF from mammalian cells causes catastrophic genome dysregulation, likely due to widespread collapse of 3D chromatin looping and alterations to inter- and intra-TAD interactions within the nucleus. The global 3D organization of the chromatin partitions the mammalian genome into discrete structural and regulatory domains [8, 10]. Chromosome architecture has multiple levels of spatial organization: megabase-scale compartments correspond to euchromatin (A) and heterochromatin (B) [11], sub-megabase regions can Numerous studies have explored the function of complete disruption of CTCF binding, both in vivo and in vitro. Acute depletion in mouse embryonic stem cells results in Aitken et al Genome Biology (2018) 19:106 almost complete removal of CTCF from the nucleus, causing genome-wide disruption of loops and TADs whereas higher-order genomic compartmentalization is unaffected [23]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
