Biology subjects

Helsmoortel, M.

Publications and source records attributed to Helsmoortel, M..

3 recordsLinked to original sources

bioRxiv2025

Nuclear exosome targeting complexes modulate cohesin binding and enhancer-promoter interactions in 3D

Three-dimensional long-range contacts between enhancers and promoters are thought to be largely determined by loop extrusion driven by the cohesin complex and insulator factors. However, recent evidence also suggests a role for noncoding RNAs (ncRNAs), such as enhancer-associated RNAs (eRNAs) and promoter upstream transcripts (PROMPTs), in shaping enhancer-promoter connectivity. While nuclear RNA exosome, together with targeting complexes, PAXT and NEXT, control the decay of ncRNAs, it has not yet been determined whether these complexes regulate 3D contacts. Chromatin recruitment maps of ZCCHC8 (NEXT), ZFC3H1 (PAXT) and MTR4 helicase revealed that these factors that associate with sites of enhancer-promoter interactions. Depletion of NEXT, PAXT or MTR4 induced the accumulation of ncRNAs, notably enhancer-associated RNAs (eRNAs) and promoter upstream transcripts (PROMPTs). Strikingly, this further increased cohesin levels at sites accumulating ncRNAs. Chromatin conformation capture analysis revealed that MTR4 modulates the 3D long-range contacts between enhancers with their distant TSS targets. Upon loss of MTR4, contacts at anchor points increase while intraloop contacts decrease, suggesting that MTR4 facilitates loop extrusion. These data highlight a key interplay between cohesin-mediated enhancer-promoter interactions and the regulation of ncRNAs by nuclear RNA exosome that is consistent with a role for RNA in genome folding.

molecular biology↗

bioRxiv2020

Chromatin-associated MRN complex protects highly transcribing genes from genomic instability

The MRN-MDC1 complex plays a central role in the DNA damage response (DDR) and repair. Using Proteomics of Isolated Chromatin Fragments (PICh), we identified DDR factors, such as MDC1, among those that become highly associated with a genomic locus upon transcriptional activation. Purification of endogenous MDC1, in the absence of exogenous DNA damage, revealed its interaction with factors involved in gene expression and co-transcriptional RNA processing, in addition to DDR factors. ChIP-seq analysis showed that MDC1 interacting factors, MRE11 and NBS1 subunits of MRN, were co-localized throughout the genome and notably at TSSs and gene bodies of actively transcribing genes. Blockade of transcriptional elongation showed that binding of MRN was dependent on the RNAPII transcriptional complex rather than transcription per se. Depletion of MRN increased RNAPII abundance at TSSs and gene bodies of MRE11/NBS1-bound genes. Prolonged exposure of cells to either MRE11- or NBS1-depletion led to single nucleotide polymorphism formation across actively transcribing, MRE11 or NBS1 target genes. These data support a model by which association of the MRN complex with the transcriptional machinery constitutively scans active genes for transcription-induced DNA damage to preserve the integrity of the coding genome.

molecular biology↗

bioRxiv2020

NF90 Modulates Processing of a Subset of Human Pri-miRNAs

MicroRNAs are predicted to regulate the expression of more than 60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The dsRNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of pri-miRNAs. Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 22 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to acquisition of NF90 association, as determined by RNA EMSA. NF90-bound and modulated pri-miRNAs are embedded in introns of host genes and expression of several host genes is concomitantly modulated. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.

molecular biology↗