Targeted intragenic demethylation initiates chromatin rewiring for gene activation

Yanjing V. Liu; Mahmoud Adel Bassal; Migara Kavishka Jayasinghe; Quy Xiao Xuan Lin; Chan-Shuo Wu; Jing Ping Tang; Junsu Kwon; Qiling Zhou; Hong Kee Tan; Alexander K. Ebralidze; Minh T. N. Le; Li Chai; Touati Benoukraf; Annalisa Di Ruscio; Daniel Geoffrey Tenen

doi:10.1101/2020.07.16.205922

GeneticsbioRxivJul 16, 2020

Preprint

Targeted intragenic demethylation initiates chromatin rewiring for gene activation

Yanjing V. Liu iD, Mahmoud Adel Bassal iD, Migara Kavishka Jayasinghe iD, Quy Xiao Xuan Lin iD, Chan-Shuo Wu iD, Jing Ping Tang iD, Junsu Kwon iD, Qiling Zhou iD, Hong Kee Tan iD, Alexander K. Ebralidze, Minh T. N. Le iD, Li Chai iD, Touati Benoukraf iD, Annalisa Di Ruscio iD, Daniel Geoffrey Tenen iD

Abstract

Aberrant DNA methylation in the region surrounding the transcription start site is a hallmark of gene silencing in cancer. Currently approved demethylating agents lack specificity and exhibit high toxicity. Herein we show, using the p16 gene as an example, that targeted demethylation of the promoter-exon 1-intron 1 (PrExI) region initiates an epigenetic wave of local chromatin remodeling and distal long-range interactions, culminating in gene-locus specific activation. Through development of CRISPR-DiR (DNMT1-interacting RNA), in which ad hoc edited guides block methyltransferase activity in a locus-specific fashion, we demonstrate that demethylation is coupled to epigenetic and topological changes. These results suggest the existence of a specialized "demethylation firing center (DFC)" which can be switched on by an adaptable and selective RNA-mediated approach for locus-specific transcriptional activation. One Sentence SummaryLocus demethylation via CRISPR-DiR reshapes chromatin structure and specifically reactivates its cognate gene.

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