Biology subjects

Demmerle, J.

Publications and source records attributed to Demmerle, J..

5 recordsLinked to original sources

bioRxiv2025

Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping

Cells continually face environmental stressors that challenge homeostasis, yet how three-dimensional (3D) chromatin structure contributes to these stress responses remains unclear under hyperosmotic conditions. To investigate this, we map 3D chromatin structure, its molecular drivers, and transcriptional outcomes during sorbitol-induced hyperosmotic stress. Within 1 hour of sorbitol treatment, pre-existing loops and domains collapse, while several hundred de novo sorbitol-induced loops emerge. These loops are punctate, longer-range, and transient. 3D chromatin structure largely returns to baseline conditions by 24 hours. Loop reorganization is consistent across cell types and hyperosmotic stimuli. Sorbitol-induced loops require cohesin but not CTCF, and anchors are enriched at active promoters harboring GC-rich transcription factor motifs. Genes at these anchors show delayed activation following loop formation, consistent with loops acting upstream of transcription. Together, hyperosmotic stress triggers rapid, reversible, CTCF-independent chromatin reorganization that correlates with transcriptional adaptation.

genomics↗

bioRxiv2025

TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin

TEA domain transcription factor 1 (TEAD1), a Hippo pathway transcription factor important in cellular homeostasis and development, is increasingly implicated in cancer biology. Here, we reveal a novel role for TEAD1 in organizing nuclear condensates, independent of active transcription. Using high-resolution imaging, ChIP-seq, RNA-seq and proximity-based proteomics, we demonstrate that in patient-derived renal cell carcinoma cells, TEAD1 forms micron-sized condensates by binding to the heterochromatic pericentromeric regions using its DNA-binding domain. TEAD-specific MCAT motifs selectively enrich and cluster in the pericentromeric region, specifically seeding TEAD1 condensates. TEAD1 condensates do not activate transcription but instead serve as depots for excess TEAD1, and disrupting TEAD1 condensates leads to increases in YAP/TEAD target gene expression. This organization of TEAD1 contrasts with that observed in other genomic regions of both RCC and normal kidney cells, in which TEAD1 associates with markers of active transcription. Our findings provide a mechanistic framework for TEAD1s dual regulatory roles, offering new insights into its contribution to transcriptional dysregulation and tumor progression.

cell biology↗

bioRxiv2025

Paraspeckle Protein NONO Regulates Active Chromatin by Allosterically Stimulating NSD1

NSD1 is a key lysine methyltransferase for di-methylation of lysine 36 of histone H3 (H3K36me2) essential for the establishment of active chromatin domains. While the loss of NSD1 catalytic activity halts embryonic development and a gain of that drives oncogenesis in leukemia and glioma, the regulatory mechanisms that control NSD1 activity in these processes remain poorly understood. Here, we uncover that NSD1 requires allosteric activation through the aromatic pocket of its PWWP2 domain. Surprisingly, we identify that NSD1-PWWP2 binds to a non-canonical target, nuclear paraspeckle protein NONO, and this protein-protein interaction allosterically stimulates the catalytic activity of NSD1. Mouse embryonic stem cells (mESC) engineered with mutations in the aromatic pocket of NSD1-PWWP2 cannot differentiate into neural progenitor cells (NPC), and genetic depletion of NONO partially phenocopied this defect at cellular and transcriptional levels, potentially explaining the neurodevelopmental disorder phenotypes in NSD1- or NONO-deficient patients. Our work revealed a novel mechanism driving active chromatin domain formation and has critical implications in the interplay between nuclear paraspeckles and active chromatin, and a vulnerability of NSD1 for therapeutic interventions. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/634125v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@162db10org.highwire.dtl.DTLVardef@11c18f9org.highwire.dtl.DTLVardef@1aba4d4org.highwire.dtl.DTLVardef@1d2687d_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIThe catalytic activity of NSD1 requires the aromatic pocket of its PWWP2 domain C_LIO_LIThe aromatic pocket of NSD1-PWWP2 binds to a non-canonical target, paraspeckle protein NONO, which allosterically stimulates NSD1 C_LIO_LIDisruption of the assemblies of paraspeckles dampens global H3K36me2 levels C_LIO_LINONO deficiency partially phenocopies the defects of neural differentiation in NSD1-knockout embryonic stem cells C_LI

biochemistry↗

bioRxiv2022

YAP condensates are highly organized hubs for YAP/TEAD transcription

YAP/TEAD signaling is essential for organismal development, cell proliferation, and cancer progression. As a transcriptional coactivator, how YAP activates its downstream target genes is incompletely understood. YAP forms biomolecular condensates in response to hyperosmotic stress, concentrating transcription-related factors to activate downstream target genes. However, whether YAP forms condensates under other signals, how YAP condensates organize and function, and how YAP condensates activate transcription in general are unknown. Here, we report that endogenous YAP forms sub-micron scale condensates in response to Hippo pathway regulation and actin cytoskeletal tension. The transcription factor TEAD1 actively stabilizes YAP condensates, which also recruit BRD4, a coactivator that is enriched at active enhancers. Using single molecule tracking, we found that YAP condensates slowed YAP diffusion within condensate boundaries, a possible mechanism for promoting YAP target search. These results reveal that YAP condensate formation is a highly regulated process that is critical for YAP/TEAD target gene expression.

cell biology↗

bioRxiv2021

Homeobox transcription factor MNX1 is crucial for restraining the expression of pan-neuronal genes in motor neurons

Motor neurons (MNs) control muscle movement and are essential for breathing, walking and fine motor skills. Motor Neuron and Pancreas Homeobox 1 (MNX1) has long been recognized as a key marker of the MN lineage. Deficiency of the Mnx1 gene in mice results in early postnatal lethality - likely by causing abnormal MN development and respiratory malfunction. However, the genome-wide targets and exact regulatory function of Mnx1 in MNs remains unresolved. Using an in vitro model for efficient MN induction from mouse embryonic stem cells, we identified about six thousand MNX1-bound loci, of which half are conserved enhancers co-bound by the core MN-inducing factors ISL1 and LHX3, while the other half are promoters for housekeeping-like genes. Despite its widespread binding, disruption of Mnx1 affects the activity of only a few dozen MNX1-bound loci, and causes mis-regulation of about one hundred genes, the majority of which are up-regulated pan-neuronal genes with relatively higher expression in the brain compared to MNs. Integration of genome-wide binding, transcriptomic and epigenomic data in the wild-type and Mnx1-disrupted MNs predicts that Pbx3 and Pou6f2 are two putative direct targets of MNX1, and both are homeobox transcription factors highly expressed in the central nervous system. Our results suggest that MNX1 is crucial for restraining the expression of many pan-neuronal genes in MNs, likely in an indirect fashion. Further, the rarity of direct targets in contrast to the widespread binding of MNX1 reflects a distinctive mode of transcriptional regulation by homeobox transcriptional factors.

molecular biology↗