Co-optation of Tandem DNA Repeats for the Maintenance of Mesenchymal Identity

Abstract

Tandem repeats (TRs) are generated by DNA replication errors and retain a high level of instability, which in principle would make them unsuitable for integration into gene regulatory networks. However, the appearance of DNA sequence motifs recognized by transcription factors may turn TRs into functional cis-regulatory elements, thus favoring their stabilization in genomes. Here, we show that, in human cells, the transcriptional repressor ZEB1, which promotes the maintenance of mesenchymal features largely by suppressing epithelial genes and microRNAs, occupies TRs harboring dozens of copies of its DNA-binding motif within genomic loci relevant for maintenance of epithelial identity. The deletion of one such TR caused quasi-mesenchymal cancer cells to reacquire epithelial features, partially recapitulating the effects of ZEB1 gene deletion. These data demonstrate that the high density of identical motifs in TRs can make them suitable platforms for recruitment of transcriptional repressors, thus promoting their exaptation into pre-existing cis-regulatory networks.

FOXA 2 controls the cis ‐regulatory networks of pancreatic cancer cells in a differentiation grade‐specific manner

“…In the context of an effort to determine how the transcriptional networks operating in exocrine pancreas are rewired in PDACs (Diaferia et al, 2016;Balestrieri et al, 2018), we report here that while FOXA1 and FOXA2 are co-expressed in well-differentiated PDAC cells, they are dissociated in the less differentiated cellular component, in which only FOXA2 is expressed, albeit nonuniformly. This dissociation is reminiscent of normal embryonic development, in which FOXA2 is expressed before FOXA1 (Sasaki & Hogan, 1993), thus explaining the inability of the latter to ◀ Figure 6.…”

“…ChIP-seq was carried out using previously described protocols (Curina et al, 2017;Balestrieri et al, 2018) on an Illumina HiSeq 2000 platform. 10 6 (H3K27ac) or 50-150 × 10 6 (TFs) were either fixed with formaldehyde as described before (for H3K27ac, FOXA2, HOXB8, and JUNB ChIP-seq) or fixed with a double cross-linking protocol (for FOS ChIP-seq).…”

“…DNA was either purified with QIAquick columns (Qiagen) or solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter) and then quantified with QuantiFluor (Promega). DNA libraries were prepared for HiSeq 2000 or NextSeq 500 sequencing as described (Balestrieri et al, 2018).…”

“…We have recently undertaken a systematic effort aiming at dissecting the transcriptional regulatory networks underlying alterations of differentiation in human PDAC (Diaferia et al, 2016;Balestrieri et al, 2018). Together with TFs expressed irrespective of cytological differentiation, we identified and initially characterized a panel of TFs selectively expressed or active in either low-grade (epithelial and well-differentiated) or high-grade (quasi-mesenchymal and poorly differentiated) PDAC cells (Diaferia et al, 2016).…”

A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence

“…In this study, we found that two enhancers in the mouse genome exhibit an exceptional density of PU.1 motifs, which are triggers for outlier levels of TRIM33 recruitment to cause repression of neighboring genes Bim and Atp1b3 (Wang et al, 2015a). In a recent study, it was found that DNA replication errors can produce tandem repeats to produce homotypic TF binding sites, which can promote the evolution of novel cis -regulatory elements (Balestrieri et al, 2018). Based on these findings, we propose that homotypic motif clustering as a general mechanism by which transcription factors and cofactors become endowed with high-precision regulatory functions during evolution.…”