CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity

Abstract

Background The human CGGBP1 binds to GC-rich regions and interspersed repeats, maintains homeostasis of stochastic cytosine methylation and determines DNA-binding of CTCF. Interdependence between regulation of cytosine methylation and CTCF occupancy by CGGBP1 remains unknown. Results By analyzing methylated DNA-sequencing data obtained from CGGBP1-depleted cells, we report that some transcription factor-binding sites, including CTCF, resist stochastic changes in cytosine methylation. By analysing CTCF-binding sites we show that cytosine methylation changes at CTCF motifs caused by CGGBP1 depletion resist stochastic changes. These CTCF-binding sites are positioned at locations where the spread of cytosine methylation in cis depends on the levels of CGGBP1. Conclusion Our findings suggest that CTCF occupancy and functions are determined by CGGBP1-regulated cytosine methylation patterns.

Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1

“…Cell culture, heat shock, genomic DNA isolation and Nanopore sequencing Human primary fibroblasts GM02639 (Coriell cell repository) and HEK293T-CT and -KD were cultured in DMEM as described before [51,55]. For the heat stress and recovery experiments using GM02639, the increase in temperature from 37°C to 40°C was done through acclimatization of cells progressively at 38°C, 39°C and 40°C for 24h each.…”

“…An additional challenge is posed by the presence of repetitive sequences, especially the interspersed repeats, in the DNA sequence reads representing chimeric chromosomes. Our recent works on the human protein CGGBP1 have involved large scale DNA sequence data analyses [51][52][53][54][55][56]. Since loss of CGGBP1 function has been shown to accelerate chromosomal fusions in cultured fibroblasts [57], the presence of chimeric chromosomal reads in our published sequencing datasets has remained an unexplored possibility.…”

“…Since loss of CGGBP1 function has been shown to accelerate chromosomal fusions in cultured fibroblasts [57], the presence of chimeric chromosomal reads in our published sequencing datasets has remained an unexplored possibility. Interestingly, CGGBP1 is also a multifunctional protein [58] with roles in heat stress response [58,59], epigenome homeostasis [52,53,55,58,59], regulation of repetitive sequences [51,53,54] and control of endogenous DNA damage [57]. Here, we have developed a DNA sequence data analysis strategy to reliably detect chimeric chromosomal events with high confidence.…”

CGGBP1-dependent CTCF-binding sites restrict ectopic transcription

“…CTCF also prevents the spread of heterochromatin into the gene-rich euchromatin (Barkess and West 2012;Cuddapah et al 2009). A subset of CTCF-binding sites is dependent on a less well studied protein CGGBP1 (Patel et al 2020(Patel et al , 2019. Recently described CGGBP1-dependent CTCF-binding sites function as chromatin barrier elements (Patel et al 2019).…”

“…The former is conserved in vertebrates whereas the latter is present only in amniotes. One significance of the CGGBP1 regulation of CTCF binding is highlighted by our recent work that CGGBP1 levels regulate cytosine methylation at CTCF-binding motifs in a non-stochastic manner (Patel et al 2018(Patel et al , 2020.…”