Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability

Abstract

Topoisomerase 1, an enzyme that relieves superhelical tension, is implicated in transcription-associated mutagenesis and genome instability-associated with neurodegenerative diseases as well as activation-induced cytidine deaminase. From proteomic analysis of TOP1-associated proteins, we identify SMARCA4, an ATP-dependent chromatin remodeller; FACT, a histone chaperone; and H3K4me3, a transcriptionally active chromatin marker. Here we show that SMARCA4 knockdown in a B-cell line decreases TOP1 recruitment to chromatin, and leads to increases in Igh/c-Myc chromosomal translocations, variable and switch region mutations and negative superhelicity, all of which are also observed in response to TOP1 knockdown. In contrast, FACT knockdown inhibits association of TOP1 with H3K4me3, and severely reduces DNA cleavage and Igh/c-Myc translocations, without significant effect on TOP1 recruitment to chromatin. We thus propose that SMARCA4 is involved in the TOP1 recruitment to general chromatin, whereas FACT is required for TOP1 binding to H3K4me3 at non-B DNA containing chromatin for the site-specific cleavage.

Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51

“…The topoisomerases TOP1 and TOP2 cooperate to optimize transcription through induction of single-strand breaks and double-strand breaks, respectively (Pommier et al, 2016;Teves and Henikoff, 2014;King et al, 2013;Husain et al, 2016). Several reports have shown that TOP2 isoforms are associated with DSBs and transcriptional activity (Ju et al, 2006;Madabhushi et al, 2015;Bunch et al, 2015;Canela et al, 2019).…”

The Top1 paradox: Friend and foe of the eukaryotic genome

“…Importantly, the DNA relaxation activity of Top1 in human cell lines is stimulated by interaction with the phosphorylated C-terminal domain of RNAPII and that this association facilitates promoter escape as well as elongation past natural pause sites. In addition to a direct interaction with RNAPII, human Top1 is recruited to transcriptionally active chromatin via interaction with chromatin remodeling factors [13]. …”

“…The significance of Top1 in suppressing the accumulation of R-loop and/or G4-DNA structures at the switch regions is expected to be relevant to the effectiveness of acquired immunity as well as the development of B cell-derived malignancies. Indeed, the IgH-cMYC translocation frequency, along with CSR efficiency, was recently shown to be significantly elevated by knock-down of Top1 or SMARCA4, a chromatin remodeler responsible for recruiting Top1 to IgH switch regions in an AID-expressing B-cell line [13]. Making an indisputable connection between Top1 regulation in cancer development and its role as a regulator of genome instability at G4 sequences will require further research.…”

Inflammatory factor receptor Toll‐like receptor 4 controls telomeres through heterochromatin protein 1 isoforms in liver cancer stem cell

“…Moreover, Exo1 extensively resects both telomere ends, generating transient long 3′ overhangs in S phase/G2 phase checkpoint. CST/AAF, a DNA polα primase accessory factor, binds POT1b and shortens the extended overhangs produced by Exo1, likely through fill‐in synthesis 20, 21. Furthermore, genetic variants in telomere maintenance genes are associated with genomic instability, cancer risk and cancer metastasis 22, 23, 24…”

“…CST/AAF, a DNA pola primase accessory factor, binds POT1b and shortens the extended overhangs produced by Exo1, likely through fill-in synthesis. 20,21 Furthermore, genetic variants in telomere maintenance genes are associated with genomic instability, cancer risk and cancer metastasis. [22][23][24] In this study, we attempted to elucidate TLR4 functions during the malignant growth of liver cancer stem cells.…”