bims-crepig 2025-08-03 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–08–03
33 papers selected by
Connor Rogerson, University of Cambridge

The histone core domain evolves at single-residue resolution to directly orchestrate transcription.
SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands.
Static three-dimensional structures determine fast dynamics between distal loci pairs in interphase chromosomes.
Positional distribution of transcription factor binding sites in the human genome.
Selective association of short tandem repeats with DNA-binding domains and intrinsically disordered regions of transcription factors.
DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution.
STEMIN transcription factor drives selective chromatin remodeling for gene activation within a relaxed chromatin during reprogramming in the moss Physcomitrium patens.
The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells.
Nucleosomes specify co-factor access to p53.
A transcription factor ensemble orchestrates bundle sheath expression in rice.
The molecular basis of lamin-specific chromatin interactions.
Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.
Cohesin-mediated stabilization of the CCAN complex at kinetochores in mitosis.
Nonchromatin regulatory functions of the histone variant H2A.B in SWI/SNF genomic deposition.
Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA.
Hippo signaling regulates the nuclear behavior and DNA binding times of YAP and TEAD to control transcription.
Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients.
SMARCA5 restricts chromatin accessibility to promote male meiosis and fertility in mammals.
DNA mutagenesis driven by transcription factor competition with mismatch repair.
SUMO operates from a unique long tandem repeat to keep innate immunity in check.
Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness.
eIF2A regulates cell migration in a translation-independent manner.
G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro.
Genome-wide mapping of formaldehyde-induced DNA-protein crosslinks reveals unique patterns of formation and transcription-coupled removal in mammalian cells.
RACK7 senses and fine-tunes enhancer activity.
Live imaging endogenous transcription factor dynamics reveals mechanisms of epiblast and primitive endoderm fate segregation.
USP17L promotes the 2-cell-like program through deubiquitination of H2AK119ub1 and ZSCAN4.
Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5.
Histone H4 lysine 20 methylation marks genes dynamically regulated during erythroid maturation.
A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.
HIF-independent oxygen sensing via KDM6A regulates ferroptosis.
Spinal motor neuron development and metabolism are transcriptionally regulated by nuclear factor IA.
Diffusing protein binders to intrinsically disordered proteins.

Cell Rep. 2025 Jul 29. pii: S2211-1247(25)00850-2. [Epub ahead of print]44(8): 116079

The histone core domain evolves at single-residue resolution to directly orchestrate transcription.

Zachary H Harvey, Kathryn M Stevens, Jian Yi Kok, Akihisa Osakabe, Jiaying Liu, Tobias Warnecke, Frédéric Berger.

  Nucleosomes are thought to be structural barriers to transcription, establishing a restrictive ground state that must be destabilized for gene expression. However, structural insights have revealed that transcription can proceed in the presence of nucleosomes, suggesting that this model is incomplete. Here, we reconstituted H2A.Z sequences resulting from more than a billion years of eukaryotic evolution in a single synthetic host system, interrogating their impact on transcription. We identified single-residue substitutions within the ultra-conserved core domain loop 2 (L2) of H2A.Z as sufficient to confer emergent properties and drive neofunctionalization. Such L2 neomorphs acquired a direct interaction with transcription elongation factor Spt6, rewiring gene expression by tuning polymerase processivity. We conclude that even minimal changes in histone sequences can transform their function, underscoring the evolutionary potential of the histone core domain to drive regulatory innovation and highlighting a previously unappreciated role of the histone core domain in transcriptional regulation.

Keywords:  CP: Molecular biology; H2A.Z; L2; Spt6; chromatin; evolution; transcription

DOI:  https://doi.org/10.1016/j.celrep.2025.116079
Proc Natl Acad Sci U S A. 2025 Aug 05. 122(31): e2512204122

SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands.

Jack S Hardwick, Somdutta Dhir, Angie Kirchner, Angela Simeone, Sean M Flynn, James M Edgerton, Rafael de Cesaris Araujo Tavares, Isabel Esain-Garcia, David Tannahill, Paula Golder, Jack M Monahan, Walraj S Gosal, Shankar Balasubramanian.

  In mammalian genomes, cytosine modifications form a layer of regulatory information alongside the genetic code. Decoding this information is crucial to our understanding of biology and disease. Established sequencing methods cannot simultaneously resolve cytosine's three most common forms-cytosine (C), 5-methylcytosine (mC), and 5-hydroxymethylcytosine (hmC)-across both strands of the DNA double helix. Thus, how epigenetic information is distributed in DNA remains unclear. Here, we present Strand-Coupled Tandem Cytosine Hydroxymethylation and methylation sequencing (SCoTCH-seq): an accurate and quantitative, base-resolution approach to sequence genomes, together with mC and hmC, in both strands of the same DNA fragment. We show that different forms of cytosine combine across the double helix at CpG sites to form discrete information states in the mouse epigenome. These CpG states have distinct genomic distributions-including at promoters, enhancers, and gene bodies-and have different relationships with transcription. We show that while all possible forms of hydroxymethylation occur, hmC is predominantly asymmetric and that different forms of asymmetric hmC are not equivalent. Our findings demonstrate that 5-hydroxymethylcytosine combines with different cytosine variants across the DNA double helix to form distinct states of regulatory information.

Keywords:  5-hydroxymethylcytosine; 5-methylcytosine; DNA sequencing; epigenetics

DOI:  https://doi.org/10.1073/pnas.2512204122
Sci Adv. 2025 Aug;11(31): eadx1763

Static three-dimensional structures determine fast dynamics between distal loci pairs in interphase chromosomes.

Guang Shi, Sucheol Shin, D Thirumalai.

Live-cell imaging experiments have shown that the distal dynamics between enhancers and promoters are unexpectedly rapid and incompatible with standard polymer models. The discordance between the compact static chromatin organization and dynamics is a conundrum that violates the expected structure-function relationship. We developed a theory to predict chromatin dynamics by accurately determining three-dimensional (3D) structures from static Hi-C contact maps or fixed-cell imaging data. Using the calculated 3D coordinates, the theory accurately forecasts experimentally observed two-point chromatin dynamics. It predicts rapid enhancer-promoter interactions and uncovers a scaling relationship between two-point relaxation time and genomic separation, closely matching recent measurements. The theory predicts that cohesin depletion accelerates single-locus diffusion while significantly slowing relaxation dynamics within topologically associating domains. Our results demonstrate that chromatin dynamics can be reliably inferred from static structural data, reinforcing the notion that 3D chromatin structure governs dynamic behavior. This general framework offers powerful tools for exploring chromatin dynamics across diverse biological contexts.

DOI: https://doi.org/10.1126/sciadv.adx1763
PLoS One. 2025 ;20(7): e0329226

Positional distribution of transcription factor binding sites in the human genome.

Chun-Ping Yu, Zhi Thong Soh, Maloyjo Joyraj Bhattacharjee, Wen-Hsiung Li.

As transcription factors (TFs) play a major role in gene regulation, we studied their binding motifs (positional weight matrices, PWMs) and binding sites (TFBSs) in the human genome, and how TFs bind DNA motifs, including the involvement of binding co-factors. Using the chromatin immunoprecipitation sequencing data recently released by ENCODE (Encyclopedia of DNA Elements), we obtained new PWMs for 196 TFs and revised PWMs for 119 TFs. From these and the PWMs previously obtained for 235 TFs, we inferred the canonical PWMs for 500 TFs, including 243 new PWMs. Analysis revealed that most TFBSs are in introns (42.6%) and intergenic regions (31.6%), with only 11.3% in promoters. However, the TFBS density is considerably higher in promoters, showing a bell-shaped distribution of TFBSs with a peak at the transcription start site. Many TFBSs lie close to CTCF (CCCTC-binding factor) binding sites. Tethered binding is far more frequent than co-binding, with the latter often requiring co-factors.

DOI: https://doi.org/10.1371/journal.pone.0329226
Cell Syst. 2025 Jul 24. pii: S2405-4712(25)00182-6. [Epub ahead of print] 101349

Selective association of short tandem repeats with DNA-binding domains and intrinsically disordered regions of transcription factors.

Matan Vidavski, Sagie Brodsky, Wajd Manadre, Tamar Jana Lang, Vladimir Mindel, Yoav Navon, Naama Barkai.

  Short tandem repeats (STRs) are enriched in regulatory regions and can bind transcription factors (TFs), as shown for selected examples in vitro. Here, we use a library-based assay to systematically measure TF binding to STRs of 2-5 bp units within budding yeast cells. We examined STR binding by four TFs, including Msn2, and further tested six Msn2 mutants, including two that contained only the DNA-binding domain (DBD) or only the 642-aa intrinsically disordered region (IDR). We find substantial STR effects on motif-dependent and motif-independent binding, which varied between TFs. For Msn2, STR association was explained by the DBD binding at motif half-sites and the IDR favoring homopurine-homopyrimidine and AT-rich repeats. TF-preferred STRs are enriched in the human genome but remain at low frequency at yeast promoters. We discuss the implications of our results for understanding the role of STRs and their crosstalk with TF IDRs in regulating TF binding across genomes.

Keywords:  DNA; DNA binding; STR; intrinsically disordered regions; protein-DNA interactions; transcription factors

DOI:  https://doi.org/10.1016/j.cels.2025.101349
Nat Commun. 2025 Jul 28. 16(1): 6585

DynaTag for efficient mapping of transcription factors in low-input samples and at single-cell resolution.

Pascal Hunold, Giulia Pizzolato, Nadia Heramvand, Laura Kaiser, Giulia Barbiera, Olivia van Ray, Roman Thomas, Julie George, Martin Peifer, Robert Hänsel-Hertsch.

Systematic discovery of transcription factor (TF) landscapes in low-input samples and at single cell level is a major challenge in the fields of molecular biology, genetics, and epigenetics. Here, we present cleavage under Dynamic targets and Tagmentation (DynaTag), enabling robust mapping of TF-DNA interactions using a physiological salt solution during sample preparation. DynaTag uncovers occupancy alterations for 15 TFs in stem cell and cancer tissue models. We highlight changes in TF-DNA binding for NANOG, MYC, and OCT4, during stem-cell differentiation, at both bulk and single-cell resolutions. DynaTag surpasses CUT&RUN and ChIP-seq in signal-to-background ratio and resolution. Furthermore, using tumours of a small cell lung cancer model derived from a single female donor, DynaTag reveals increased chromatin occupancy of FOXA1, MYC, and the mutant p53 R248Q at enriched gene pathways (e.g. epithelial-mesenchymal transition), following chemotherapy treatment. Collectively, we believe that DynaTag represents a significant technological advancement, facilitating precise characterization of TF landscapes across diverse biological systems and complex models.

DOI: https://doi.org/10.1038/s41467-025-61797-9
Plant J. 2025 Aug;123(3): e70386

STEMIN transcription factor drives selective chromatin remodeling for gene activation within a relaxed chromatin during reprogramming in the moss Physcomitrium patens.

Ruan Morné de Villiers, Gergo Palfalvi, Akinori Kanai, Yutaka Suzuki, Mitsuyasu Hasebe, Masaki Ishikawa.

  Land plants exhibit remarkable cellular plasticity, readily reprogramming differentiated cells into stem cells in response to internal and external stimuli. While chromatin remodeling is crucial for cellular reprogramming, its interplay with gene expression during reprogramming into stem cells remains elusive. In the moss Physcomitrium patens, wounding induces reprogramming of leaf cells facing wounded cells to change into chloronema apical stem cells through the activation of the AP2/ERF transcription factor STEMIN. In this study, we employed multimodal single-nuclei RNA and ATAC sequencing to explore the interplay between gene expression and chromatin dynamics during STEMIN-mediated reprogramming. Profiling 20 883 single-nuclei from gametophores, protonemata, and cut leaves, we identified 11 distinct cell types including reprogramming leaf cells. Our analysis revealed that reprogramming leaf cells exhibit a partly relaxed chromatin landscape and STEMIN transcription factors selectively enhance accessibility at specific genomic loci essential for stem cell formation. Thus, our results indicate that wounding initiates a broad chromatin relaxation, creating a permissive environment and specific transcription factors act to refine this permissive state by specifically relaxing chromatin regions critical for reprogramming.

Keywords:  Physcomitrium patens; chromatin accessibility; gene expression; reprogramming; single‐cell analysis; stem cells; wounding

DOI:  https://doi.org/10.1111/tpj.70386
Sci Adv. 2025 Aug;11(31): eadw7108

The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells.

Zhuwei Xu, Hemant K Prajapati, Peter R Eriksson, David J Clark.

The budding yeast genome is globally accessible to DNA methyltransferases in living cells, unlike in isolated nuclei, where it is mostly inaccessible. Here, we assess the roles of the RSC, ISW1, and CHD1 adenosine 5'-triphosphate-dependent chromatin remodelers in generating nucleosome dynamics in vivo. We compare DNA methylation rates in wild-type cells and chromatin remodeler mutants by normalizing nuclear methylation rates to the nonnucleosomal mitochondrial DNA methylation rate in each strain. Depletion of both Isw1 and Chd1 increases the normalized methylation rate, suggesting that these remodelers act together to suppress nucleosome dynamics. Separate depletion of Isw1, Chd1, or Rsc8 has little effect. A decaying sine wave model used to fit nucleosome phasing data shows that nucleosome dynamics decrease with distance from the promoter in an Isw1/Chd1-dependent manner. Furthermore, the TFIIIB and TFIIIC transcription factors exhibit differential dynamics at transfer RNA genes in vivo. Our analysis provides insight into nucleosome and transcription factor dynamics in vivo.

DOI: https://doi.org/10.1126/sciadv.adw7108
Mol Cell. 2025 Jul 23. pii: S1097-2765(25)00577-5. [Epub ahead of print]

Nucleosomes specify co-factor access to p53.

Deyasini Chakraborty, Colby R Sandate, Luke Isbel, Georg Kempf, Joscha Weiss, Simone Cavadini, Lukas Kater, Jan Seebacher, Zuzanna Kozicka, Lisa Stoos, Ralph S Grand, Dirk Schübeler, Alicia K Michael, Nicolas H Thomä.

  Pioneer transcription factors (TFs) engage chromatinized DNA motifs. However, it is unclear how the resultant TF-nucleosome complexes are decoded by co-factors. In humans, the TF p53 regulates cell-cycle progression, apoptosis, and the DNA damage response, with a large fraction of p53-bound sites residing in nucleosome-harboring inaccessible chromatin. We examined the interaction of chromatin-bound p53 with co-factors belonging to the ubiquitin proteasome system (UPS). At two distinct motif locations on the nucleosome (super-helical location [SHL]-5.7 and SHL+5.9), the E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. A corresponding cryo-electron microscopy (cryo-EM) structure shows USP7 engaged with p53 and nucleosomes. Our work illustrates how chromatin imposes a co-factor-selective barrier for p53 interactors, whereby flexibly tethered interaction domains of co-factors and TFs govern compatibility between co-factors, TFs, and chromatin.

Keywords:  genome regulation; transcription; transcription co-factors

DOI:  https://doi.org/10.1016/j.molcel.2025.06.027
Nat Commun. 2025 Jul 31. 16(1): 7040

A transcription factor ensemble orchestrates bundle sheath expression in rice.

Lei Hua, Na Wang, Susan Stanley, Ruth M Donald, Satish Kumar Eeda, Kumari Billakurthi, Ana Rita Borba, Julian M Hibberd.

C4 photosynthesis has evolved in over sixty plant lineages and improves photosynthetic efficiency by ~50%. One unifying character of C4 plants is photosynthetic activation of a compartment such as the bundle sheath, but gene regulatory networks controlling this cell type are poorly understood. In Arabidopsis, a bipartite MYC-MYB transcription factor module restricts gene expression to these cells, but in grasses the regulatory logic allowing bundle sheath gene expression has not been defined. Using the global staple and C3 crop rice, we find that the SULFITE REDUCTASE promoter is sufficient for strong bundle sheath expression. This promoter encodes an intricate cis-regulatory logic with multiple activators and repressors acting combinatorially. Within this landscape we identify a distal cis-regulatory module (CRM) activated by an ensemble of transcription factors from the WRKY, G2-like, MYB-related, DOF, IDD and bZIP families. This module is necessary and sufficient to pattern gene expression to the rice bundle sheath. Oligomerisation of the CRM and fusion to core promoters containing Y-patches allow activity to be increased 220-fold. This CRM generates bundle sheath-specific expression in Arabidopsis indicating deep conservation in function between monocotyledons and dicotyledons. In summary, we identify an ancient, short, and tuneable CRM patterning expression to the bundle sheath that we anticipate will be useful for engineering this cell type in various crop species.

DOI: https://doi.org/10.1038/s41467-025-62087-0
Nat Struct Mol Biol. 2025 Aug 01.

The molecular basis of lamin-specific chromatin interactions.

Baihui Wang, Rafael Kronenberg-Tenga, Valentina Rosti, Emanuele Di Patrizio Soldateschi, Qiang Luo, Ugo Maria Iannacchero, Louise Pinet, Matthias Eibauer, Rajaa Boujemaa-Paterski, Benjamin Schuler, Chiara Lanzuolo, Ohad Medalia.

In the cell nucleus, chromatin is anchored to the nuclear lamina, a network of lamin filaments and binding proteins that underly the inner nuclear membrane. The nuclear lamina is involved in chromatin organization through the interaction of lamina-associated domains within the densely packed heterochromatin regions. Using cryo-focused ion beam milling in conjunction with cryo-electron tomography, we analyzed the distribution of nucleosomes at the lamin-chromatin interface at the nanometer scale. Depletion of lamins A and C reduced nucleosome concentration at the nuclear periphery, while B-type lamin depletion contributed to nucleosome density in proximity to the lamina but not further away. We then investigated whether specific lamins can mediate direct interactions with chromatin. Using cryo-electron microscopy, we identified a specific binding motif of the lamin A tail domain that interacts with nucleosomes, distinguishing it from the other lamin isoforms. Furthermore, we examined chromatin structure dynamics using a genome-wide analysis that revealed lamin-dependent macroscopic-scale alterations in gene expression and chromatin remodeling. Our findings provide detailed insights into the dynamic and structural interplay between lamin isoforms and chromatin, molecular interactions that shape chromatin architecture and epigenetic regulation.

DOI: https://doi.org/10.1038/s41594-025-01622-5
Bioinformatics. 2025 Aug 01. pii: btaf435. [Epub ahead of print]

Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.

Daniel J Mullen, Zexun Wu, Ethan Nelson-Moore, Huan Cao, Lauren Han, Ite A Offringa, Suhn K Rhie.

SUMMARY: There is a lack of publicly available bioinformatic tools that can be widely used by researchers to identify transcription factors (TFs) that regulate cell type-specific regulatory elements (REs). To address this, we developed the Tracing regulatory Element Networks using Epigenetic Traits (TENET) R/Bioconductor package. By collecting hundreds of histone mark and open chromatin datasets from a variety of cell lines, primary cells, and tissues, and comparing these features along with matched DNA methylation and gene expression data, TENET identifies TFs and REs linked to a specific cell type. Moreover, we developed methods to interrogate findings using motifs, clinical information, and other genomic and chromatin conformation capture datasets, and applied them to pan-cancer data, highlighting TFs and REs associated with ten different cancer types. TENET enables researchers to better characterize the three-dimensional epigenomes of cell types of interest for future clinical applications.
AVAILABILITY AND IMPLEMENTATION: TENET is available at http://bioconductor.org/packages/TENET. Curated functional genomic datasets utilized by TENET are available at http://bioconductor.org/packages/TENET.AnnotationHub. Example datasets are available at http://bioconductor.org/packages/TENET.ExperimentHub.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btaf435
Curr Biol. 2025 Jul 22. pii: S0960-9822(25)00877-2. [Epub ahead of print]

Cohesin-mediated stabilization of the CCAN complex at kinetochores in mitosis.

Julian Haase, Koly Aktar, Mary Kate Bonner, Leonard Colin, Hindol Gupta, Briana E Marinoni, David O Morgan, Alexander E Kelly.

  The constitutive centromere-associated network (CCAN) of the inner kinetochore links CENP-A-containing nucleosomes of the centromere to the outer kinetochore, ensuring accurate chromosome segregation during mitosis. CCAN binding at the centromere is stabilized upon mitotic entry, but the underlying mechanisms remain unclear. Here, we demonstrate that cohesin is essential for CCAN stability. The chromosomal passenger complex (CPC), independently of its kinase subunit Aurora B, regulates cohesin-mediated CCAN stability via heterochromatin protein-1 (HP1), Haspin kinase, and phosphorylation of the cohesin-release factor WAPL, which weakens WAPL's affinity for PDS5B. While cohesin depletion disrupts CCAN stability, neither separase-mediated cohesin cleavage nor depletion of the cohesion-essential Esco2 acetyltransferase affects CCAN stability, indicating that cohesin stabilizes the CCAN independently of sister chromatid cohesion. Furthermore, we show that WAPL phosphorylation maintains a centromere-proximal pool of cohesin and promotes the formation of the primary constriction. These findings establish a non-cohesive function of cohesin in stabilizing the CCAN during mitosis and suggest that cohesin-mediated organization of centromeric chromatin strengthens kinetochore engagement to ensure faithful chromosome segregation.

Keywords:  Aurora B; CCAN; CENP-C; CPC; HP1; WAPL; centromere; cohesin; kinetochore; non-cohesive

DOI:  https://doi.org/10.1016/j.cub.2025.07.011
Sci Adv. 2025 Jul 25. 11(30): eadx1568

Nonchromatin regulatory functions of the histone variant H2A.B in SWI/SNF genomic deposition.

Xuanzhao Jiang, Jiayu Wen, Mary L Nelson, Yasmin Dijkwel, Bradley Cairns, Uta-Maria Bauer, Gene Hart-Smith, Tatiana A Soboleva, David J Tremethick.

The replacement of canonical histones with their variant forms enables the dynamic and context-dependent regulation of the mammalian genome. Histone variants also play key roles in various pathological processes including malignancies. Among these, the aberrant expression of the testis-specific histone variant H2A.B contributes to the pathogenesis of Hodgkin lymphoma. The multifunctionality of histone variants is regulated by their posttranslational modifications (PTMs). However, the PTMs of H2A.B and their functional implications are unknown. Here, we demonstrate that the Amino terminus of H2A.B serves as a central hub for a diverse range of gene regulatory protein-protein interactions, orchestrated by phosphorylation and arginine methylation. This includes a mechanism whereby non-chromatin-bound H2A.B associates with SWI/SNF, which limits its access to the genome. Last, we identify phosphorylated H2A.B as a previously uncharacterized marker of active RNA polymerase II transcription start sites. These findings elucidate a central role for H2A.B in genome regulation and highlight the importance of its PTMs in modulating its multifunctional roles.

DOI: https://doi.org/10.1126/sciadv.adx1568
Mol Cell. 2025 Jul 17. pii: S1097-2765(25)00579-9. [Epub ahead of print]

Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA.

Pradeep Kumar Reddy Cingaram, Felipe Beckedorff, Jingyin Yue, Fan Liu, Helena Gomes Dos Santos, Harikumar Arigela, Ramin Shiekhattar.

  Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping transcriptomes with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq), enabling efficient transcriptome mapping within a single day (∼12 h), increasing ligation efficiency, abolishing adapter dimers, and reducing sample loss and RNA degradation. Rapid PRO-seq allows for transcriptome mapping using 5,000 cells and is applicable to mouse hematopoietic progenitor cells (mHPCs) as well as mouse neurons. Using acute depletion of INTS11 in neuronal cells, we pinpoint a critical role for INTS11 as a regulator of genes in neurodevelopmental disorders. Taken together, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.

Keywords:  INTS11; Integrator complex; RNA polymerase II; enhancer RNA; hematopoietic progenitor cells; nascent transcription; neurodevelopmental genes; rapid PRO-seq; transcriptional elongation; transcriptional pausing

DOI:  https://doi.org/10.1016/j.molcel.2025.06.029
Sci Adv. 2025 Jul 25. 11(30): eadw4974

Hippo signaling regulates the nuclear behavior and DNA binding times of YAP and TEAD to control transcription.

Benjamin Kroeger, Samuel A Manning, Varshini Mohan, Jieqiong Lou, Guizhi Sun, Sara Lamont, Alex J McCann, Mathias Francois, Jose M Polo, Elizabeth Hinde, Kieran F Harvey.

Over the past two decades, genetic and proteomic screens have identified the Hippo pathway as a complex signaling network that controls tissue growth and human cancer. Despite these advances, our understanding of how Hippo signaling regulates transcription is less clear. To address this, we used live microscopy to study the nuclear behavior of the major Hippo pathway transcription effectors, YAP and TEADs. We reveal that TEADs are a major determinant of YAP DNA binding and nuclear mobility, while YAP minorly influences TEADs. YAP and TEAD1 associate with DNA for longer periods in cells with intrinsically low Hippo pathway activity and upon acute Hippo pathway perturbation. TEAD1 binds the genome on a broad range of timescales, and this is extended substantially in nuclear condensates. Last, a cancer-associated YAP fusion protein exhibits substantially different biophysical behavior than either YAP or TEAD1. Thus, we reveal that Hippo signaling regulates transcription, in part, by influencing the DNA binding times of YAP and TEADs.

DOI: https://doi.org/10.1126/sciadv.adw4974
Blood. 2025 Jul 29. pii: blood.2024028019. [Epub ahead of print]

Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients.

Alastair Smith, Nicholas David Robert Denny, Catherine Chahrour, Kim Sharp, Marta Arachi, Ana Maria Dopico-Fernandez, Natalina Elliott, Joe Harman, Thomas Jackson, Huimin Geng, Owen Smith, Jonathan Bond, Irene Roberts, Ronald W W Stam, Nicholas Crump, James Davies, Anindita Roy, Thomas A Milne.

Genetic alterations alone cannot account for the diverse phenotypes of cancer cells. Even cancers with the same driver mutation show significant transcriptional heterogeneity and varied responses to therapy. However, the mechanisms underpinning this heterogeneity remain under-explored. Here, we find that novel enhancer usage is a common feature in acute lymphoblastic leukemia (ALL). In particular, KMT2A::AFF1 ALL, an aggressive leukemia with a poor prognosis and a low mutational burden, exhibits substantial transcriptional heterogeneity between individuals. Using single cell multiome analysis and extensive chromatin profiling, we reveal that much transcriptional heterogeneity in KMT2A::AFF1 ALL is driven by novel enhancer usage. By generating high resolution Micro Capture-C data in primary patient samples, we identify patient-specific enhancer activity at key oncogenes such as MEIS1 and RUNX2, driving high levels of expression of both oncogenes in a patient-specific manner. Overall, our data show that enhancer heterogeneity is highly prevalent in KMT2A::AFF1 ALL and may be a mechanism that drives transcriptional heterogeneity in cancer more generally.

DOI: https://doi.org/10.1182/blood.2024028019
Proc Natl Acad Sci U S A. 2025 Aug 05. 122(31): e2422356122

SMARCA5 restricts chromatin accessibility to promote male meiosis and fertility in mammals.

Shubhangini Kataruka, Aushaq B Malla, Shannon R Rainsford, Benjamin William Walters, Rachel A Heuer, Kira L Marshall, Bluma J Lesch.

  Establishment of correct chromatin configuration in male meiosis is essential for sperm formation and male fertility. However, how chromatin remodeling contributes to meiotic progression in male germ cells is not well understood. Here, we find that the ISWI family ATP-dependent chromatin remodeling factor SMARCA5 (SNF2H) plays a critical role in regulating meiotic prophase progression during spermatogenesis in mice. Male mice with germ cell-specific depletion of SMARCA5 are infertile and unable to form sperm. Conditional knockout of Smarca5 results in meiotic progression failure, with abnormal spermatocytes appearing at the pachytene stage of meiosis I and subsequent accumulation of defects in chromosome synapsis, DNA repair, and transposon control, along with elevated rates of apoptosis. SMARCA5 interacts with known cofactors BAZ1A/ACF and BAZ2A/TIP5, as well as numerous DNA repair and recombination factors, in the testis. Single cell RNA sequencing confirmed failure to achieve a normal transcriptional state in premeiotic spermatogonia and during meiotic prophase, with reduced levels of meiotic gene transcripts and increasingly aberrant transcriptional states at later stages of spermatogenic development. Transcriptional misregulation in meiotic prophase was preceded by a widespread increase in chromatin accessibility in spermatogonia at promoters and repeat elements. Our findings suggest that SMARCA5 restricts chromatin accessibility in male germ cells to guide appropriate chromatin remodeling during meiotic recombination, contrasting with its role promoting chromatin accessibility during female meiosis.

Keywords:  chromatin; fertility; gene regulation; germ cells; spermatogenesis

DOI:  https://doi.org/10.1073/pnas.2422356122
Cell. 2025 Jul 23. pii: S0092-8674(25)00792-5. [Epub ahead of print]

DNA mutagenesis driven by transcription factor competition with mismatch repair.

Wei Zhu, Yuning Zhang, Harshit Sahay, Hana Wasserman, Ariel Afek, Jonathan Williams, Samantha Shaltz, Caitlin Johnson, Kyle Pinheiro, David M MacAlpine, Keith R Weninger, Dorothy A Erie, Sue Jinks-Robertson, Raluca Gordân.

  Despite the remarkable fidelity of eukaryotic DNA replication, nucleotide misincorporation errors occur in every replication cycle, generating mutations that drive genetic diseases and genome evolution. Here, we show that transcription factor (TF) proteins, key players in gene regulation, can increase mutagenesis from replication errors by directly competing with the recognition of DNA mismatches by MutSα, the primary initiator of eukaryotic mismatch repair (MMR). We demonstrate this TF-induced mutagenesis mechanism using a yeast genetic assay that quantifies the accumulation of mutations in TF binding sites. Analyses of human cancer mutations recapitulate the trends observed in yeast, with mutations arising from MYC-bound mismatches being enriched in MMR-proficient cells. These findings implicate TF-MMR competition as a critical determinant of somatic hypermutation at TF binding sites in cancer. Furthermore, our results provide a molecular mechanism for the higher-than-expected rate of rare genetic variants at TF binding sites, with important implications for regulatory DNA evolution.

Keywords:  DNA mismatch repair; DNA mutagenesis; DNA replication errors; MutSα; competition with mismatch repair; hypermutation; mutation patterns; mutations in transcription factor binding sites; transcription factors

DOI:  https://doi.org/10.1016/j.cell.2025.07.003
Nucleic Acids Res. 2025 Jul 19. pii: gkaf750. [Epub ahead of print]53(14):

SUMO operates from a unique long tandem repeat to keep innate immunity in check.

Amandine Goffeney, Ivo A Hendriks, Victoria Morel, Yann Loe-Mie, François Charon, Michael L Nielsen, Jack-Christophe Cossec, Daan Noordermeer, Jacob-Sebastian Seeler, Anne Dejean.

The SUMO pathway mainly functions to repress innate immunity in myeloid cells. Inactivating sumoylation triggers a strong, noncanonical, type I interferon (IFN1) response, amplified and coupled with inflammation upon stimulation. These findings transposed to pre-clinical models with the demonstration that sumoylation inhibitors activate antitumor immunity in an IFN1-dependent manner. Yet, how sumoylation represses immune signaling remains largely unknown. Here, we identified MORC3, a negative regulator of IFNB1, as the top SUMO2/3 substrate in myeloid cells. We show that, in monocytes, SUMO functions to repress basal IFNB1 in cis through a single long tandem repeat regulated by MORC3 [MORC3-regulated element (MRE)] that concentrates multiple motifs for the myeloid-enriched PU.1 factor. Inhibiting sumoylation induces a 3D genome reorganization nucleated from the MRE, which acquires both insulator and PU.1-activated enhancer activities, together with loss of H3.3 and H3K9me3 repressive marks and recruitment of PU.1. Paradoxically, MORC3, that interacts with PU.1, is massively recruited, yet unable to repress the MRE. Finally, we show that both sumoylation and MORC3 ATPase cycle are critical for MORC3 repressive activity. Our study thus uncovers an unconventional mechanism in which sumoylation, in concert with MORC3, orchestrates a metastable H3.3/H3K9me3 heterochromatin state on a multi-PU.1 binding platform to prevent an uncontrolled myeloid-specific immune response.

DOI: https://doi.org/10.1093/nar/gkaf750
Genes Dev. 2025 Jul 28.

Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness.

Aishwarya S Pawar, Patrick Somers, Aleena Alex, Jason Grana, Victoria K Feist, Subin S George, Sapana S Jalnapurkar, Charles Antony, Roman Verner, Sanese K White-Brown, Mohit Khera, María Saraí Mendoza-Figueroa, Kathy Fange Liu, Jennifer J D Morrissette, Sandeep Gurbuxani, Vikram R Paralkar.

  Myeloid leukemias are heterogeneous cancers with diverse mutations, sometimes in genes with unclear roles and unknown functional partners. PHF6 and PHIP are two poorly understood chromatin-binding proteins recurrently mutated in acute myeloid leukemia (AML). PHF6 mutations are associated with poorer outcomes, whereas PHIP was recently identified as the most common selective mutation in Black patients with AML. Here, we show that Phf6 knockout converts Flt3-ITD-driven mouse chronic myelomonocytic leukemia (CMML) into AML with reduced survival. Using cell line models, we show that PHF6 is a transcriptional repressor that suppresses a limited stemness gene network and that PHF6 missense mutations, classified by current clinical algorithms as variants of unknown significance, produce unstable or nonfunctional protein. We present multiple lines of evidence converging on a critical mechanistic connection between PHF6 and PHIP. We show that PHIP loss phenocopies PHF6 loss and that PHF6 requires PHIP to occupy chromatin and exert its downstream transcriptional program. Our work unifies PHF6 and PHIP, two disparate leukemia mutated proteins, into a common functional complex that suppresses AML stemness.

Keywords:  chromatin; leukemia; myeloid; stemness

DOI:  https://doi.org/10.1101/gad.352602.125
Sci Adv. 2025 Aug;11(31): eadu5668

eIF2A regulates cell migration in a translation-independent manner.

Jennifer Jungfleisch, Neus Mestre-Farràs, Raúl Gómez-Riera, Oriane Pourcelot, Edouard Bertrand, Nadia Halidi, Fátima Gebauer.

The RNA-binding protein eukaryotic translation initiation factor 2A (eIF2A) is an alternative translation initiation factor shown to drive tumor formation by facilitating translation from near-cognate initiation codons. Here, we uncover a function for eIF2A in regulating cell migration in a manner independent of overt control of translation. Using a melanoma cell model consisting of nontumoral melanocytic Mel-ST cells and their metastatic counterpart obtained by H-Ras transformation, we unexpectedly find minimal effects of eIF2A depletion on translation. Interactome studies identified centrosomal proteins as major binding partners of eIF2A. We found that eIF2A colocalizes with the centrosome, enhances centrosome composition, and promotes centrosome orientation during cell migration. Migration requires the C-terminal disordered region of eIF2A, involved in mRNA binding. Interaction with mRNA, however, does not require ongoing translation. These findings reveal a role for eIF2A in centrosome dynamics beyond its traditional function in translation.

DOI: https://doi.org/10.1126/sciadv.adu5668
Nucleic Acids Res. 2025 Jul 19. pii: gkaf726. [Epub ahead of print]53(14):

G-quadruplexes as potential traps for superenhancer marker BRD4: ligand-sensitive binding and co-separation in vitro.

Iuliia I Pavlova, Olga M Ivanova, Mikhail S Iudin, Anastasiya V Surdina, Nikolay A Barinov, Margarita E Bogomiakova, Sergey D Oreshkov, Zakhar O Shenkarev, Vjacheslav V Severov, Dmitriy V Klinov, Victoria O Shender, Alexandra N Bogomazova, Maria A Lagarkova, Anna M Varizhuk, Vladimir B Tsvetkov.

G-quadruplexes (G4s) are prevalent at promoters and superenhancers (SEs), exclude nucleosomes, and recruit transcription factors. This study sought to determine whether the nucleosome exclusion affects the recruitment of the SE marker BRD4, which typically binds to acetylated histones and facilitates SE-promoter contacts via the phase separation-dependent mechanism. Analyses of the available whole-genome data revealed that SEs with the highest G4 density were depleted of nucleosomes but not of BRD4. This led us to test the possibility of histone-independent BRD4 maintenance at G4-rich SEs. A typical SE G4 destabilized a nearby nucleosome in vitro and, unlike B-DNA, bound weakly to BRD4 bromodomains. Similar to an acetylated nucleosome, the G4 promoted phase separation in BRD4 solutions. This effect was not altered by the histone competitor JQ1. However, it was attenuated by two known G4 ligands, suggesting that they could disrupt SE-promoter communication in cells. Consistently, these ligands downregulated several genes regulated by G4-rich SE-contacting promoters more efficiently than they did SE-independent genes. Our findings underscore the significance of G4-rich SEs as transcriptional regulators and provide new insights into their organization.

DOI: https://doi.org/10.1093/nar/gkaf726
Nucleic Acids Res. 2025 Jul 19. pii: gkaf720. [Epub ahead of print]53(14):

Genome-wide mapping of formaldehyde-induced DNA-protein crosslinks reveals unique patterns of formation and transcription-coupled removal in mammalian cells.

Duha Alshareef, Charlie T Nguyen, Kayla N Tucker, Micah D Gearhart, Natalia Y Tretyakova, Colin Campbell.

DNA-protein crosslinks (DPCs) form following exposure to various alkylating agents, including environmental carcinogens, cancer chemotherapeutics, and reactive aldehydes. If not repaired, DPCs can interfere with key biological processes such as transcription and replication and activate programmed cell death. A growing body of evidence implicates nucleotide excision repair (NER), homologous recombination, and other mechanisms in the removal of DPCs. However, the effects of genomic context on DPC formation and removal have not been comprehensively addressed. Using a combination of next-generation sequencing and DPC enrichment via protein precipitation, we show that DPCs induced following exposure to formaldehyde are non-randomly distributed across the human genome, based on chromatin state. The data further show that the efficiency of DPC removal correlates with transcription at loci transcribed by RNA polymerase II. Data presented herein indicate that efficient removal of chromosomal DPCs requires both the Cockayne syndrome group B gene as well as "downstream" TC-NER factor xeroderma pigmentosum group A gene. In contrast, loci transcribed by RNA polymerase I showed no evidence of transcription-coupled DPC removal. Taken together, our results indicate that complex interactions between chromatin organization, transcriptional activity, and numerous DNA repair pathways dictate genomic patterns of DPC formation and removal.

DOI: https://doi.org/10.1093/nar/gkaf720
iScience. 2025 Aug 15. 28(8): 113083

RACK7 senses and fine-tunes enhancer activity.

Li Dong, Daixuan Zhang, Ying Cai, Min Zeng, Mandi Mu, Peng Zhao, Jin Wang, Siyi Cheng, Qingqing Cai, Jian Zhang, Yajun Hu, Lei Zhang, Li Tan, Feizhen Wu, Yujiang Geno Shi, Wenqi Xu, Hongjie Shen.

  Enhancers regulate dynamic gene expression in a spatiotemporal specific manner. A number of positive as well as negative regulators of enhancers have been reported so far. However, whether and how these regulators sense enhancer activity dynamics remains unclear. In this study, we show that a specific enhancer regulator, RACK7, swiftly re-distributes from repressed enhancers to activated enhancers in response to a plethora of acute stimulations. We further show that this process depends on transcription and RACK7 positively regulates enhancer activation by promoting the recruitment of RNA polymerase II. Taken together, our findings suggest that RACK7 senses enhancer activity changes and facilitates their activation during acute stimulations.

Keywords:  Biochemistry; Molecular mechanism of gene regulation; Transcriptomics

DOI:  https://doi.org/10.1016/j.isci.2025.113083
Curr Biol. 2025 Jul 26. pii: S0960-9822(25)00897-8. [Epub ahead of print]

Live imaging endogenous transcription factor dynamics reveals mechanisms of epiblast and primitive endoderm fate segregation.

Rebecca P Kim-Yip, David Denberg, Denis F Faerberg, Hayden Nunley, Isabella Leite, Madeleine Chalifoux, Bradley Joyce, Jared Toettcher, Bin Gu, Eszter Posfai.

  The segregation of the epiblast (EPI) and primitive endoderm (PE) cell types in the preimplantation mouse embryo is not only a crucial decision that sets aside the precursors of the embryo proper from extraembryonic cells, respectively, but also has served as a central model to study a key concept in mammalian development: how much of developmental patterning is predetermined vs. stochastically emergent. Here, we address this question by quantitative live imaging of multiple endogenously tagged transcription factors key to this fate decision and trace their dynamics at a single-cell resolution through the formation of EPI and PE cell fates. Strikingly, we reveal an initial symmetry breaking event, the formation of a primary EPI cell lineage, and show that this is linked to the dynamics of the prior inner cell mass/trophectoderm fate decision through the expression of SOX2. This primary EPI lineage, through fibroblast growth factor (FGF) signaling, induces an increase in the transcription factor GATA6 in other inner cell mass cells, setting them on the course toward PE differentiation. Interestingly, this trajectory can switch during a defined developmental window, leading to the emergence of secondary EPI cells. Finally, we show that early expression levels of NANOG, which are seemingly stochastic, can bias whether a cell's trajectory switches to secondary EPI or continues as PE. Our data give unique insight into how fate patterning is initiated and propagated during unperturbed embryonic development through the interplay of lineage-history-biased and stochastic cell-intrinsic molecular features, unifying previous models of EPI/PE segregation.

Keywords:  GATA6; ICM; NANOG; SOX2; blastocyst; epiblast; live imaging; mouse; preimplantation embryo; primitive endoderm

DOI:  https://doi.org/10.1016/j.cub.2025.07.031
Nat Commun. 2025 Aug 01. 16(1): 7071

USP17L promotes the 2-cell-like program through deubiquitination of H2AK119ub1 and ZSCAN4.

Panpan Shi, Xukun Lu, Kairang Jin, Linlin Liu, Guoxing Yin, Wenying Wang, Jiao Yang, Lijuan Wang, Lijun Dong, Wei Xie, Lin Liu.

In mouse, minor zygotic genome activation (ZGA) precedes and is essential for major ZGA in two-cell (2C) embryos. A subset of ZGA genes (known as "2C" genes) are also activated in a rare population of embryonic stem cells (ESCs) (2C-like cells). However, the functions of the 2C genes are not fully understood. Here, we find that one family of the 2C genes, Usp17l, plays critical roles in transcriptional and post-translational regulation of the 2C-like state in mESCs. Specifically, USP17LE, a member of the USP17L family, deubiquitinates H2AK119ub1 and promotes the expression of Dux and the downstream 2C genes and retrotransposons. Moreover, USP17LE deubiquitinates and stabilizes ZSCAN4. In mouse pre-implantation embryos, Dux is marked by strong H2AK119ub1 except for the 1-cell and early 2-cell stages. Usp17le overexpression reduces H2AK119ub1 and promotes Dux and 2C gene activation. Thus, our findings identify USP17L as a potential regulator of the 2C program.

DOI: https://doi.org/10.1038/s41467-025-62303-x
Nucleic Acids Res. 2025 Jul 19. pii: gkaf734. [Epub ahead of print]53(14):

Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5.

Wanqiang Xue, Yaoyao Han, Ying Tian, Junzheng Wang, Zhiyuan Xie, Xin Zheng, Xue Yue, Siqi Dong, Huimin Li, Zhen Luo, Siqiu Zhang, Ying Yang, Zhe Zou, Wei Li, Nana Ma, Fangjie Zhu, Chunlai Chen, Yimeng Yin, Yixiao Zhang, Ke Xu.

Among the regulatory factor X (RFX) transcription factor family, RFX5 is uniquely reported to bind nucleosomes and induce nucleosome remodeling in vivo. Dysfunctions in RFX5 have been implicated in various diseases. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the RFX5-nucleosome complex, revealing that the extended DNA binding domain (eDBD) of RFX5 binds to the nucleosome at superhelical location +2. RFX5 eDBD engages not only with nucleosomal DNA but also with histones through extensive interactions. Compared to the structure of a free nucleosome, RFX5 eDBD induces localized distortion of the bound DNA gyre and detachment of the adjacent DNA gyre in the RFX5-nucleosome complex. This structural alteration could potentially increase DNA accessibility and enhance transcriptional activity in vivo. Overall, our study provides novel insights into the mechanisms by which RFX5 eDBD interacts with and destabilizes nucleosomes.

DOI: https://doi.org/10.1093/nar/gkaf734
Epigenetics Chromatin. 2025 Jul 26. 18(1): 48

Histone H4 lysine 20 methylation marks genes dynamically regulated during erythroid maturation.

Kristin Murphy, Michael Getman, Xiurui Lv, Zachary Murphy, Deanna Abid, Nabil Rahman, Michael Bulger, Laurie Steiner.

   BACKGROUND: Methylation of H4K20 has been implicated in the regulation of gene expression but also plays essential roles in numerous cellular functions, making studies of its effects on transcription challenging. To gain insights into the role of H4K20 methylation in regulating gene expression, we studied H4K20me1 and H4K20me3 in the context of the well-characterized erythroid differentiation of human hematopoietic stem and progenitor cells.
RESULTS: H4K20me1 enrichment over the gene body was strongly correlated with expression changes. During erythroid differentiation, there was a dramatic decline in the level of RNA Polymerase II (Pol II); H4K20me1 was lost where Pol II was lost, and gained at genes where Pol II occupancy was maintained and transcripts were upregulated. We did identify a small subset of highly expressed genes, including beta-globin, that had a dramatic loss of H4K20me1 during erythroid differentiation, despite a substantial gain of Pol II. The histone demethylase PHF8 was present at these genes, as well as at the transcription start site of many active genes. In contrast to H4K20me1 over gene bodies correlating with transcription, enrichment at the transcription start site occurred at genes with low levels of Pol II occupancy and RNA expression throughout erythroid differentiation. The majority of H4K20me3 was present over intergenic regions, consistent with its well-established role as a repressor of repetitive elements. Intriguingly, H4K20me3 was also present at the transcription start site of genes with H4K20me1 over the gene body. At these genes, H4K20me3 levels were highly correlated with chromatin accessibility at the transcription start site, and an elevated Pol II pausing index. There was a dramatic loss of H4K20me3 occupancy in genic, but not intergenic, regions during erythroid differentiation.
CONCLUSIONS: There are dynamic changes in H4K20 methylation during cellular differentiation that correlate strongly with Pol II occupancy and activity. These changes occurred in genic regions, with H4K20me3 at the transcription start site correlated with Pol II pausing, and H4K20me1 gene body levels tightly linked with transcriptional changes. Together, these data provide important insights into the role of H4K20 methylation in the regulation of gene expression during cellular differentiation.

Keywords:  Differentiation; Erythropoiesis; H4K20me1; H4K20me3; Histone methylation

DOI:  https://doi.org/10.1186/s13072-025-00609-2
Nat Biotechnol. 2025 Jul 25.

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.

Alexander Sasse, Debashish Ray, Kaitlin U Laverty, Cyrus L Tam, Mihai Albu, Hong Zheng, Yevgen Levdansky, Olga Lyudovyk, Taykhoom Dalal, Kate Nie, Cedrik Magis, Cedric Notredame, Eugene Valkov, Matthew T Weirauch, Timothy R Hughes, Quaid Morris.

RNA-binding proteins (RBPs) are key regulators of gene expression; however, their RNA-binding specificities, that is, motifs, have not been comprehensively determined. Here we introduce Eukaryotic Protein-RNA Interactions (EuPRI), a freely available resource of RNA motifs for 34,746 RBPs from 690 eukaryotes. EuPRI includes in vitro binding data for 504 RBPs, including newly collected RNAcompete data for 174 RBPs, along with thousands of predicted motifs. We predict these motifs with an algorithm, Joint Protein-Ligand Embedding, which can detect distant homology relationships and map specificity-determining peptides. EuPRI quadruples the number of available RBP motifs, expanding the motif repertoire across all major eukaryotic clades and assigning motifs to the majority of human RBPs. We demonstrate the utility of EuPRI for inferring post-transcriptional function and evolutionary relationships by identifying rapid, recent evolution of post-transcriptional regulatory networks in worms and plants, in contrast to the vertebrate RNA motif set, which has remained relatively stable after a large expansion between the metazoan and vertebrate ancestors.

DOI: https://doi.org/10.1038/s41587-025-02733-6
Mol Cell. 2025 Jul 15. pii: S1097-2765(25)00580-5. [Epub ahead of print]

HIF-independent oxygen sensing via KDM6A regulates ferroptosis.

Alexander M Minikes, Pei Liu, Hua Wang, Jiachen Hu, Hanan Alwaseem, Yueming Li, Xuejun Jiang.

  Ferroptosis, a metabolic cell death process driven by iron-dependent phospholipid peroxidation, is implicated in various pathologies, including cancer. While metabolic factors such as glucose, lipids, and multiple amino acids have all been demonstrated to modulate ferroptosis, the role of oxygen, another fundamental metabolic component, in ferroptosis is not fully understood. Here, we show that cells acclimated to a low oxygen environment develop marked resistance to ferroptosis, and this resistance is independent of canonical oxygen-sensing pathway mediated by prolyl hydroxylases (PHDs) and HIF transcription factors. Instead, hypoxia suppresses ferroptosis by inhibiting KDM6A, a tumor suppressor and oxygen-dependent histone demethylase, leading to reduced expression of its transcriptional targets, including lipid metabolic enzymes ACSL4 and ETNK1, thus rewiring cellular phospholipid profile to a ferroptosis-resistant state. Relevant to cancer, pharmacological inhibition of the oncogenic histone methyltransferase EZH2, which opposes KDM6A activity, restored ferroptosis sensitivity of xenograft bladder tumor tissues harboring KDM6A mutation.

Keywords:  ACSL4; ETNK1; KDM6A; KMT2D; bladder cancer; cancer therapy; ferroptosis; hypoxia; lipid metabolism; oxygen sensing

DOI:  https://doi.org/10.1016/j.molcel.2025.07.001
Sci Adv. 2025 Aug;11(31): eadu3346

Spinal motor neuron development and metabolism are transcriptionally regulated by nuclear factor IA.

Julia Gauberg, Sarah Jenkins, Kevin B Moreno, Karthik Jayaraman, Sara Abumeri, Alisa Salazar, Hiruy S Meharena, Stacey M Glasgow.

Neural circuits governing all motor behaviors in vertebrates rely on the proper development of motor neurons and their precise targeting of limb muscles. Transcription factors are essential for motor neuron development, regulating their specification, migration, and axonal targeting. While transcriptional regulation of the early stages of motor neuron specification is well established, much less is known about the role of transcription factors in the later stages of maturation and muscle targeting. Defining the molecular mechanisms of these later stages is critical for elucidating how motor circuits are constructed. Here, we demonstrate that the transcription factor nuclear factor IA (NFIA) is required for motor neuron positioning, axonal branching, and neuromuscular junction formation. Moreover, we find that NFIA is required for proper mitochondrial function and adenosine triphosphate production, providing an important link between transcription factors and metabolism during motor neuron development. Together, these findings underscore the critical role of NFIA in instructing the assembly of spinal circuits for movement.

DOI: https://doi.org/10.1126/sciadv.adu3346
Nature. 2025 Jul 30.

Diffusing protein binders to intrinsically disordered proteins.

Caixuan Liu, Kejia Wu, Hojun Choi, Hannah L Han, Xueli Zhang, Joseph L Watson, Green Ahn, Jason Z Zhang, Sara Shijo, Lydia L Good, Charlotte M Fischer, Asim K Bera, Alex Kang, Evans Brackenbrough, Brian Coventry, Derrick R Hick, Seema Qamar, Xinting Li, Justin Decarreau, Stacey R Gerben, Wei Yang, Inna Goreshnik, Dionne Vafeados, Xinru Wang, Mila Lamb, Analisa Murray, Sebastian Kenny, Magnus S Bauer, Andrew N Hoofnagle, Ping Zhu, Tuomas P J Knowles, David Baker.

Proteins that bind to intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) with high affinity and specificity could be useful for therapeutic and diagnostic applications1-4. However, a general methodology for targeting IDPs or IDRs has yet to be developed. Here we show that starting only from the target sequence of the input, and freely sampling both target and binding protein conformations, RFdiffusion5 can generate binders to IDPs and IDRs in a wide range of conformations. We used this approach to generate binders to the IDPs amylin, C-peptide, VP48 and BRCA1_ARATH in diverse conformations with a dissociation constant (Kd) ranging from 3 to 100 nM. For the IDRs G3BP1, common cytokine receptor γ-chain (IL-2RG) and prion protein, we diffused binders to β-strand conformations of the targets, obtaining Kd between 10 and 100 nM. Fluorescence imaging experiments show that the binders bind to their respective targets in cells. The G3BP1 binder disrupts stress granule formation in cells, and the amylin binder inhibits amyloid fibril formation and dissociates existing fibres, enables targeting of both monomeric and fibrillar amylin to lysosomes, and increases the sensitivity of mass spectrometry-based amylin detection. Our approach should be useful for creating binders to flexible IDPs or IDRs spanning a wide range of intrinsic conformational preferences.

DOI: https://doi.org/10.1038/s41586-025-09248-9