3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes

Abstract

Studying the dynamics of three-dimensional (3D) chromatin structure is essential to understand biological processes in the cell nucleus. Recent publications based on integrative analysis of multi-omics studies have provided comprehensive and multilevel insights into 3D genome organization emphasizing its role during transcriptional regulation. While enhancers are regulatory elements that play a central role in the spatiotemporal control of gene expression, chromatin looping has been broadly accepted as a means for enhancer-promoter interactions allowing them to stablish cell-type-specific gene expression signatures. On the other hand, G-quadruplexes (G4s) are non-canonical DNA secondary structures that are both, enriched at promoters and related to increased gene expression. However, the role of G4s in promoter-distal regulatory elements, such as super-enhancers (SE), as well as in 3D genome organization and chromatin looping mediating long-range enhancer-promoter interactions has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we found that nuclearmiR-9is required for chromatin features related to increased transcriptional activity, such as broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4) and G4s. Moreover, we show that nuclearmiR-9is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical regulator of proliferation programs in cancer and fibrosis.

Implications in Cancer of Nuclear Micro RNAs, Long Non-Coding RNAs, and Circular RNAs Bound by PRC2 and FUS

“…Remarkably, the hexanucleotide 3′-terminal motif of miR-29b acts as a transferable nuclear localization element that directs nuclear enrichment of other miRNAs or small interfering RNAs to which it is attached. Moreover, we found by sequence alignment analysis that a partially conserved and extended version of this nuclear shuttling motif is present in mouse and human miRNAs that have been functionally characterized in the cell nucleus [ 46 ]. The presence of a nuclear shuttling motif in various miRNAs, which in turn is conserved across species, suggests the existence of a common mechanism regulating the enrichment of these miRNAs in the cell nucleus, thereby indicating that even miRNAs with common seed sequences can have diverse functions and regulatory capacities due to distinct subcellular localizations, underscoring the complexity of miRNA-mediated regulation.…”

“…Highlighting the role of miR-9 in the cell nucleus, we recently published a sequencing experiment after chromatin isolation by miRNA purification (ChIRP-seq) in mouse lung fibroblasts showing that miR-9 is enriched at promoters and super-enhancers of genes that are responsive to tissue growth factor beta 1 (TGFB1) signaling [ 46 ]. Further, we found that nuclear miR-9 is required for chromatin features related to increased transcriptional activity, including broad domains of the euchromatin histone mark histone 3 tri-methylated lysine 4 (H3K4me3) and the non-canonical DNA secondary structures G-quadruplex (G4).…”