bims-crepig 2025-02-23 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–02–23
thirty papers selected by
Connor Rogerson, University of Cambridge

CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer.
Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin.
Allovalent scavenging of activation domains in the transcription factor ANAC013 gears transcriptional regulation.
Topological identification and interpretation for single-cell epigenetic regulation elucidation in multi-tasks using scAGDE.
A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes.
Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability.
Synergistic and antagonistic activities of IRF8 and FOS enhancer pairs during an immune-cell fate switch.
PSPC1 exerts an oncogenic role in AML by regulating a leukemic transcription program in cooperation with PU.1.
Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis.
Native stem cell transcriptional circuits define cardinal features of high-risk leukemia.
Biomolecular condensation of human IDRs initiates endogenous transcription via intrachromosomal looping or high-density promoter localization.
SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state.
Sustained NF-κB activation allows mutant alveolar stem cells to co-opt a regeneration program for tumor initiation.
A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators.
Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.
CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association.
The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.
The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency.
Colorectal cancer hot spot mutations attenuate the ASXL-MLL4 interaction.
An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters.
Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens.
Haspin kinase binds to a nucleosomal DNA supergroove.
ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.
Direct ionic stress sensing and mitigation by the transcription factor NFAT5.
Explainable artificial intelligence of DNA methylation-based brain tumor diagnostics.
Dynamic properties of transcriptional condensates modulate CRISPRa-mediated gene activation.
The histone demethylase dLsd1 regulates organ size by silencing transposable elements.
The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers.
Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition.
Multiomic single-cell profiling identifies critical regulators of postnatal brain.

Cell Rep. 2025 Feb 14. pii: S2211-1247(25)00083-X. [Epub ahead of print]44(2): 115312

CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer.

Rachel R Xiang, Shin-Ai Lee, Caroline F Tyndall, Anusha R Bhatia, JuanJuan Yin, Cassandra Singler, Benjamin J Hauk, Matthew P Kipp, David Y Takeda.

  Amplification of the androgen receptor (AR) locus is the most frequent alteration in metastatic castration-resistant prostate cancer (CRPC). Recently, it was discovered that an enhancer of the AR is co-amplified with the AR gene body and contributes to increased AR transcription and resistance to androgen deprivation therapy. However, the mechanism of enhancer activation in advanced disease is unknown. Here, we used CRISPR-Cas9 screening to identify transcription factors that bind to the AR enhancer and modulate enhancer-mediated AR transcription. We demonstrate that HOXB13, GATA2, and TFAP2C bind the AR enhancer in patient-derived xenografts and directly impact features associated with an active chromatin state. Interestingly, the AR enhancer belongs to a set of regulatory elements that require HOXB13 to maintain FOXA1 binding, further delineating the role of HOXB13 in CRPC. This work provides a framework to functionally identify trans-acting factors required for the activation of disease-related noncoding regulatory elements.

Keywords:  CP: Cancer; CP: Molecular biology; CRISPR; CRPC; androgen receptor; enhancer; epigenetics; functional genomics; prostate cancer

DOI:  https://doi.org/10.1016/j.celrep.2025.115312
Nat Struct Mol Biol. 2025 Feb 21.

Structural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin.

Tomoya Kujirai, Kenta Echigoya, Yusuke Kishi, Mai Saeki, Tomoko Ito, Junko Kato, Lumi Negishi, Hiroshi Kimura, Hiroshi Masumoto, Yoshimasa Takizawa, Yukiko Gotoh, Hitoshi Kurumizaka.

Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In embryonic neural progenitor cells, DEK colocalizes with H3 K27 trimethylation (H3K27me3), the facultative heterochromatin mark. DEK stimulates the methyltransferase activity of Polycomb repressive complex 2 (PRC2), which is responsible for H3K27me3 deposition in vitro. Cryo-electron microscopy structures of the DEK-nucleosome complexes reveal that DEK binds the nucleosome by its tripartite DNA-binding mode on the dyad and linker DNAs and interacts with the nucleosomal acidic patch by its newly identified histone-binding region. The DEK-nucleosome interaction mediates linker DNA reorientation and induces chromatin compaction, which may facilitate PRC2 activation. These findings provide mechanistic insights into chromatin structure-mediated gene regulation by DEK.

DOI: https://doi.org/10.1038/s41594-025-01493-w
Nucleic Acids Res. 2025 Feb 08. pii: gkaf065. [Epub ahead of print]53(4):

Allovalent scavenging of activation domains in the transcription factor ANAC013 gears transcriptional regulation.

Elise Delaforge, Amanda D Due, Frederik Friis Theisen, Nicolas Morffy, Charlotte O'Shea, Martin Blackledge, Lucia C Strader, Karen Skriver, Birthe B Kragelund.

Transcriptional regulation involves interactions between transcription factors, coregulators, and DNA. Intrinsic disorder is a major player in this regulation, but mechanisms driven by disorder remain elusive. Here, we address molecular communication within the stress-regulating Arabidopsis thaliana transcription factor ANAC013. Through high-throughput screening of ANAC013 for transcriptional activation activity, we identify three activation domains within its C-terminal intrinsically disordered region. Two of these overlap with acidic islands and form dynamic interactions with the DNA-binding domain and are released, not only upon binding of target promoter DNA, but also by nonspecific DNA. We show that independently of DNA binding, the RST (RCD--SRO--TAF4) domain of the negative regulator RCD1 (Radical-induced Cell Death1) scavenges the two acidic activation domains positioned vis-à-vis through allovalent binding, leading to dynamic occupation at enhanced affinity. We propose an allovalency model for transcriptional regulation, where sequentially close activation domains in both DNA-bound and DNA-free states allow for efficient regulation. The model is likely relevant for many transcription factor systems, explaining the functional advantage of carrying sequentially close activation domains.

DOI: https://doi.org/10.1093/nar/gkaf065
Nat Commun. 2025 Feb 16. 16(1): 1691

Topological identification and interpretation for single-cell epigenetic regulation elucidation in multi-tasks using scAGDE.

Gaoyang Hao, Yi Fan, Zhuohan Yu, Yanchi Su, Haoran Zhu, Fuzhou Wang, Xingjian Chen, Yuning Yang, Guohua Wang, Ka-Chun Wong, Xiangtao Li.

Single-cell ATAC-seq technology advances our understanding of single-cell heterogeneity in gene regulation by enabling exploration of epigenetic landscapes and regulatory elements. However, low sequencing depth per cell leads to data sparsity and high dimensionality, limiting the characterization of gene regulatory elements. Here, we develop scAGDE, a single-cell chromatin accessibility model-based deep graph representation learning method that simultaneously learns representation and clustering through explicit modeling of data generation. Our evaluations demonstrated that scAGDE outperforms existing methods in cell segregation, key marker identification, and visualization across diverse datasets while mitigating dropout events and unveiling hidden chromatin-accessible regions. We find that scAGDE preferentially identifies enhancer-like regions and elucidates complex regulatory landscapes, pinpointing putative enhancers regulating the constitutive expression of CTLA4 and the transcriptional dynamics of CD8A in immune cells. When applied to human brain tissue, scAGDE successfully annotated cis-regulatory element-specified cell types and revealed functional diversity and regulatory mechanisms of glutamatergic neurons.

DOI: https://doi.org/10.1038/s41467-025-57027-x
Curr Biol. 2025 Feb 19. pii: S0960-9822(25)00074-0. [Epub ahead of print]

A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes.

Toyonori Sakata, Shoin Tei, Kosuke Izumi, Ian D Krantz, Masashige Bando, Katsuhiko Shirahige.

  The cohesin protein complex is essential for the formation of topologically associating domains (TADs) and chromatin loops on interphase chromosomes.1,2,3,4,5 For the loading onto chromosomes, cohesin requires the cohesin loader complex formed by NIPBL6,7,8 and MAU2.9 Cohesin localizes at enhancers and gene promoters with NIPBL in mammalian cells10,11,12,13,14 and forms enhancer-promoter loops.15,16 Cornelia de Lange syndrome (CdLS) is a rare, genetically heterogeneous disorder affecting multiple organs and systems during development,17,18 caused by mutations in the cohesin loader NIPBL gene (>60% of patients),19,20,21,22,23 as well as in genes encoding cohesin, a chromatin regulator, BRD4, and cohesin-related factors.24,25,26,27 We also reported CHOPS syndrome that phenotypically overlaps with CdLS28,29 and is caused by gene mutations of a super elongation complex (SEC) core component, AFF4. Although these syndromes are associated with transcriptional dysregulation,24,28,30,31,32 the underlying mechanism remains unclear. In this study, we provide the first comprehensive analysis of chromosome architectural changes caused by these mutations using cell lines derived from CdLS and CHOPS syndrome patients. In both patient cells, we found a decrease in cohesin, NIPBL, BRD4, and acetylation of lysine 27 on histone H3 (H3K27ac)33,34,35 in most enhancers with enhancer-promoter loop attenuation. By contrast, TADs were maintained in both patient cells. These findings reveal a shared molecular mechanism in these syndromes and highlight unexpected roles for cohesin, cohesin loaders, and the SEC in maintaining the enhancer complexes. These complexes are crucial for recruiting transcriptional regulators, sustaining active histone modifications, and facilitating enhancer-promoter looping.

Keywords:  3D genome structure; AFF4; BRD4; CHOPS syndrome; CdLS; H3K27ac; NIPBL; SEC; cohesin; enhancer

DOI:  https://doi.org/10.1016/j.cub.2025.01.044
Sci Adv. 2025 Feb 21. 11(8): eadr1453

Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability.

Leonie Kollenstart, Alva Biran, Nicolas Alcaraz, Nazaret Reverón-Gómez, Victor Solis-Mezarino, Moritz Völker-Albert, Fion Jenkinson, Valentin Flury, Anja Groth.

In the process of DNA replication, the first steps in restoring the chromatin landscape involve parental histone recycling and new histone deposition. Disrupting histone recycling to either the leading or lagging strand induces asymmetric histone inheritance, affecting epigenome maintenance and cellular identity. However, the order and kinetics of these effects remain elusive. Here, we use inducible mutants to dissect the early and late consequences of impaired histone recycling. Simultaneous disruption of both leading (POLE4) and lagging strand (MCM2-2A) recycling pathways impairs the transmission of parental histones to newly synthesized DNA, releasing some parental histones to the soluble pool. Subsequently, H3K27me3 accumulates aberrantly during chromatin restoration in a manner preceding gene expression changes. Loss of histone inheritance and the ensuing chromatin restoration defects alter gene expression in embryonic stem cells and challenge differentiation programs and cell viability. Our findings demonstrate the importance of efficient transmission of histone-based information during DNA replication for maintaining chromatin landscapes, differentiation potential, and cellular viability.

DOI: https://doi.org/10.1126/sciadv.adr1453
EMBO J. 2025 Feb 19.

Synergistic and antagonistic activities of IRF8 and FOS enhancer pairs during an immune-cell fate switch.

Antonios Klonizakis, Marc Alcoverro-Bertran, Pere Massó, Joanna Thomas, Luisa de Andrés-Aguayo, Xiao Wei, Vassiliki Varamogianni-Mamatsi, Christoforos Nikolaou, Thomas Graf.

  Cell fate instructive genes tend to be regulated by large clusters of enhancers. Whether and how individual enhancers within such clusters cooperate in regulating gene expression is poorly understood. We have previously developed a computational method, SEGCOND, which identifies hubs that we termed Putative Transcriptional Condensates (PTCs), consisting of enhancer clusters and associated target genes. Here, we use SEGCOND to identify PTCs in a CEBPA-induced B-cell-to-macrophage transdifferentiation system. We find that PTCs are enriched for highly expressed, lineage-restricted genes and associate with BRD4, a component of transcriptional condensates. Further, we performed single and combinatorial deletions of enhancers within two PTCs active during induced transdifferentiation, harboring IRF8 and FOS. Two enhancers within the IRF8 PTC were found to provide a backup mechanism when combined, safeguarding IRF8 expression and efficient transdifferentiation. Unexpectedly, two individual enhancers within the FOS PTC antagonize each other on day 1 of transdifferentiation, delaying the conversion of B-cells into macrophages and reducing FOS expression, while on day 7, they cooperate to increase FOS levels induced cells. Our results reveal complex, differentiation-stage-specific interactions between individual enhancers within enhancer clusters.

Keywords:  Cell Reprogramming; Enhancer Clusters; Enhancer Interactions; Enhancer Synergy; Transcription Factors

DOI:  https://doi.org/10.1038/s44318-025-00380-w
Cell Stem Cell. 2025 Feb 12. pii: S1934-5909(25)00010-4. [Epub ahead of print]

PSPC1 exerts an oncogenic role in AML by regulating a leukemic transcription program in cooperation with PU.1.

Juyeong Hong, Pinpin Sui, Ying Li, Kerryn Y Xu, Ji-Hoon Lee, Juan Wang, Shi Chen, Peng Zhang, Noah Wingate, Asra Noor, Yaxia Yuan, Robert Hromas, Hongwei Zhou, Karina Hamamoto, Rui Su, C Cameron Yin, Fengxi Ye, Andrés E Quesada, Jianjun Chen, Suming Huang, Daohong Zhou, M James You, Feng-Chun Yang, Jianlong Wang, Mingjiang Xu.

  Acute myeloid leukemia (AML) is an aggressive hematopoietic malignancy characterized by the blockage of myeloid cell differentiation and uncontrolled proliferation of immature myeloid cells. Here, we show that paraspeckle component 1 (PSPC1) is aberrantly overexpressed and associated with poor survival in AML patients. Using human AML cells and mouse models, we demonstrate that PSPC1 is not required for normal hematopoiesis, but it is critical and essential for AML cells to maintain their leukemic characteristics. PSPC1 loss induces robust differentiation, suppresses proliferation, and abolishes leukemogenesis in diverse AML cells. Mechanistically, PSPC1 exerts a pro-leukemia effect by regulating a unique leukemic transcription program via cooperative chromatin binding with PU.1 and activation of tumor-promoting genes, including NDC1, which is not previously implicated in AML. Our findings uncover a unique and crucial role of PSPC1 dependency in AML and highlight its potential as a promising therapeutic target for AML.

Keywords:  AML; NDC1; PSPC1; PU.1; hematopoiesis; leukemia

DOI:  https://doi.org/10.1016/j.stem.2025.01.010
Nat Commun. 2025 Feb 21. 16(1): 1833

Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis.

Jonas Coßmann, Pavel I Kos, Vassiliki Varamogianni-Mamatsi, Devin S Assenheimer, Tobias A Bischof, Timo Kuhn, Thomas Vomhof, Argyris Papantonis, Luca Giorgetti, J Christof M Gebhardt.

The three-dimensional folding of chromosomes is essential for nuclear functions such as DNA replication and gene regulation. The emergence of chromatin architecture is thus an important process during embryogenesis. To shed light on the molecular and kinetic underpinnings of chromatin architecture formation, we characterized biophysical properties of cohesin and CTCF binding to chromatin and their changes upon cofactor depletion using single-molecule imaging in live developing zebrafish embryos. We found that chromatin-bound fractions of both cohesin and CTCF increased significantly between the 1000-cell and shield stages, which we could explain through changes in both their association and dissociation rates. Moreover, increasing binding of cohesin restricted chromatin motion, potentially via loop extrusion, and showed distinct stage-dependent nuclear distribution. Polymer simulations with experimentally derived parameters recapitulated the experimentally observed gradual emergence of chromatin architecture. Our findings reveal molecular kinetics underlying chromatin architecture formation during zebrafish embryogenesis.

DOI: https://doi.org/10.1038/s41467-025-56889-5
J Exp Med. 2025 Apr 07. pii: e20231349. [Epub ahead of print]222(4):

Native stem cell transcriptional circuits define cardinal features of high-risk leukemia.

Qing Wang, Francesco Boccalatte, Jason Xu, Giovanni Gambi, Bettina Nadorp, Fatema Akter, Carea Mullin, Ashley F Melnick, Elizabeth Choe, Anna C McCarter, Nicole A Jerome, Siyi Chen, Karena Lin, Sarah Khan, Rohan Kodgule, Jonathan H Sussman, Petri Pölönen, Javier Rodriguez-Hernaez, Sonali Narang, Kleopatra Avrampou, Bryan King, Aristotelis Tsirigos, Russell J H Ryan, Charles G Mullighan, David T Teachey, Kai Tan, Iannis Aifantis, Mark Y Chiang.

While the mutational landscape across early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) and ETP-like leukemia is known, establishing a unified framework that activates stem cell genes characteristic of these tumors remains elusive. Using complementary mouse and human models, chromatin mapping, and enhancer profiling, we show that the coactivator ZMIZ1 promotes normal and malignant ETP population growth by inducing the transcription factor MYB in feedforward circuits to convergently activate oncogenes (MEF2C, MYCN, and BCL2) through essential enhancers. A key superenhancer, the N-Myc regulating enhancer (NMRE), drives malignant ETP population growth but is dispensable for normal lymphopoiesis. This network of stem cell superenhancers identifies treatment-resistant tumors and poor survival outcomes; unifies diverse ETP-ALLs; and contributes to cardinal features of the recently genomically identified high-risk bone marrow progenitor-like (BMP-like) ETP-ALL tumor-stem cell/myeloid gene expression, inhibited NOTCH1-induced T-cell development, aggressive clinical behavior, and venetoclax sensitivity. Since ZMIZ1 is dispensable for essential homeostasis, it might be possible to safely target this network to treat high-risk diseases.

DOI: https://doi.org/10.1084/jem.20231349
Nucleic Acids Res. 2025 Feb 08. pii: gkaf056. [Epub ahead of print]53(4):

Biomolecular condensation of human IDRs initiates endogenous transcription via intrachromosomal looping or high-density promoter localization.

Jing Li, Shizhe Liu, Sunghwan Kim, Jacob Goell, Zachary Allen Drum, John Patrick Flores, Alex J Ma, Barun Mahata, Mario Escobar, Alex Raterink, Jeong Hyun Ahn, Erik R Terán, Rosa Selenia Guerra-Resendez, Yuhao Zhou, Bo Yu, Michael R Diehl, Gang Greg Wang, Anna-Karin Gustavsson, Douglas H Phanstiel, Isaac B Hilton.

Protein intrinsically disordered regions (IDRs) are critical gene-regulatory components and aberrant fusions between IDRs and DNA-binding/chromatin-associating domains cause diverse human cancers. Despite this importance, how IDRs influence gene expression, and how aberrant IDR fusion proteins provoke oncogenesis, remains incompletely understood. Here we develop a series of synthetic dCas9-IDR fusions to establish that locus-specific recruitment of IDRs can be sufficient to stimulate endogenous gene expression. Using dCas9 fused to the paradigmatic leukemogenic NUP98 IDR, we also demonstrate that IDRs can activate transcription via localized biomolecular condensation and in a manner that is dependent upon overall IDR concentration, local binding density, and amino acid composition. To better clarify the oncogenic role of IDRs, we construct clinically observed NUP98 IDR fusions and show that, while generally non-overlapping, oncogenic NUP98-IDR fusions convergently drive a core leukemogenic gene expression program in donor-derived human hematopoietic stem cells. Interestingly, we find that this leukemic program arises through differing mechanistic routes based upon IDR fusion partner; either distributed intragenic binding and intrachromosomal looping, or dense binding at promoters. Altogether, our studies clarify the gene-regulatory roles of IDRs and, for the NUP98 IDR, connect this capacity to pathological cellular programs, creating potential opportunities for generalized and mechanistically tailored therapies.

DOI: https://doi.org/10.1093/nar/gkaf056
Elife. 2025 Feb 19. pii: RP87742. [Epub ahead of print]12

SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state.

Ruben Sebastian-Perez, Shoma Nakagawa, Xiaochuan Tu, Sergi Aranda, Martina Pesaresi, Pablo Aurelio Gomez-Garcia, Marc Alcoverro-Bertran, Jose Luis Gomez-Vazquez, Davide Carnevali, Eva Borràs, Eduard Sabidó, Laura Martin, Malka Nissim-Rafinia, Eran Meshorer, Maria Victoria Neguembor, Luciano Di Croce, Maria Pia Cosma.

  Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but the factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment in mice, we generated an inducible system to convert embryonic stem cells (ESCs) to 2C-like cells. This conversion is marked by a global reorganization and dispersion of H3K9me3-heterochromatin foci, which are then reversibly formed upon re-entry into pluripotency. By profiling the chromatin-bound proteome (chromatome) through genome capture of ESCs transitioning to 2C-like cells, we uncover chromatin regulators involved in de novo heterochromatin formation. We identified TOPBP1 and investigated its binding partner SMARCAD1. SMARCAD1 and TOPBP1 associate with H3K9me3-heterochromatin in ESCs. Interestingly, the nuclear localization of SMARCAD1 is lost in 2C-like cells. SMARCAD1 or TOPBP1 depletion in mouse embryos leads to developmental arrest, reduction of H3K9me3, and remodeling of heterochromatin foci. Collectively, our findings contribute to comprehending the maintenance of chromocenters during early development.

Keywords:  2C-like cells; chromatin; developmental biology; embryonic stem cells; mouse; proteomics; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.87742
Cell Stem Cell. 2025 Feb 13. pii: S1934-5909(25)00011-6. [Epub ahead of print]

Sustained NF-κB activation allows mutant alveolar stem cells to co-opt a regeneration program for tumor initiation.

Frances J England, Ignacio Bordeu, Minn-E Ng, JaeHak Bang, Bumsoo Kim, Jinwook Choi, Erik C Cardoso, Bon-Kyoung Koo, Benjamin D Simons, Joo-Hyeon Lee.

  Disruptions to regulatory signals governing stem cell fate open the pathway to tumorigenesis. To determine how these programs become destabilized, we fate-map thousands of murine wild-type and KrasG12D-mutant alveolar type II (AT2) stem cells in vivo and find evidence for two independent AT2 subpopulations marked by distinct tumorigenic capacities. By combining clonal analyses with single-cell transcriptomics, we unveil striking parallels between lung regeneration and tumorigenesis that implicate Il1r1 as a common activator of AT2 reprogramming. We show that tumor evolution proceeds through the acquisition of lineage infidelity and reversible transitions between mutant states, which, in turn, modulate wild-type AT2 dynamics. Finally, we discover how sustained nuclear factor κB (NF-κB) activation sets tumorigenesis apart from regeneration, allowing mutant cells to subvert differentiation in favor of tumor growth.

Keywords:  AT2 clone dynamics; NF-κB activation; cell fate plasticity; cell plasticity; clonal modeling; lineage tracing; lung cancer; lung stem cells; regeneration program; stem cell competition; tumor ecosystem dynamics; tumor evolution

DOI:  https://doi.org/10.1016/j.stem.2025.01.011
Nucleic Acids Res. 2025 Feb 08. pii: gkaf058. [Epub ahead of print]53(4):

A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators.

Sunil Guharajan, Vinuselvi Parisutham, Robert C Brewster.

Transcription factors (TFs) are often classified as activators or repressors, yet these context-dependent labels are inadequate to predict quantitative profiles that emerge across different promoters. A mechanistic understanding of how different regulatory sequences shape TF function is challenging due to the lack of systematic genetic control in endogenous genes. To address this, we use a library of Escherichia coli strains with precise control of TF copy number, measuring the quantitative regulatory input-output function of 90 TFs on synthetic promoters that isolate the contributions of TF binding sequence, location, and basal promoter strength to gene expression. We interpret the measured regulation of these TFs using a thermodynamic model of gene expression and uncover stabilization of RNA polymerase as a pervasive regulatory mechanism, common to both activating and repressing TFs. This property suggests ways to tune the dynamic range of gene expression through the interplay of stabilizing TF function and RNA polymerase basal occupancy, a phenomenon we confirm by measuring fold change for stabilizing TFs across synthetic promoter sequences spanning over 100-fold basal expression. Our work deconstructs TF function at a mechanistic level, providing foundational principles on how gene expression is realized across different promoter contexts, with implications for decoding the relationship between sequence and gene expression.

DOI: https://doi.org/10.1093/nar/gkaf058
Nucleic Acids Res. 2025 Feb 08. pii: gkaf092. [Epub ahead of print]53(4):

Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.

Lingjie Liu, Yixin Zhao, Rebecca Hassett, Shushan Toneyan, Peter K Koo, Adam Siepel.

Rates of transcription elongation vary within and across eukaryotic gene bodies. Here, we introduce new methods for predicting elongation rates from nascent RNA sequencing data. First, we devise a probabilistic model that predicts nucleotide-specific elongation rates as a generalized linear function of nearby genomic and epigenomic features. We validate this model with simulations and apply it to public PRO-seq (Precision Run-On Sequencing) and epigenomic data for four cell types, finding that reductions in local elongation rate are associated with cytosine nucleotides, DNA methylation, splice sites, RNA stem-loops, CTCF (CCCTC-binding factor) binding sites, and several histone marks, including H3K36me3 and H4K20me1. By contrast, increases in local elongation rate are associated with thymines, A+T-rich and low-complexity sequences, and H3K79me2 marks. We then introduce a convolutional neural network that improves our local rate predictions. Our analysis is the first to permit genome-wide predictions of relative nucleotide-specific elongation rates.

DOI: https://doi.org/10.1093/nar/gkaf092
Nat Struct Mol Biol. 2025 Feb 21.

CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association.

Ruofan Yu, Shelby Roseman, Allison P Siegenfeld, Zachary Gardner, Son C Nguyen, Khoa A Tran, Eric F Joyce, Rajan Jain, Brian B Liau, Ian D Krantz, Katherine A Alexander, Shelley L Berger.

Recent findings indicate that nuclear speckles, a distinct type of nuclear body, interact with certain chromatin regions in a ground state. Here, we report that the chromatin structural factors CTCF and cohesin are required for full ground-state association between DNA and nuclear speckles. We identified a putative speckle-targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association, disruption of which also impaired induction of speckle-associated genes. Depletion of the cohesin-releasing factor WAPL, which stabilizes cohesin on chromatin, resulted in reinforcement of DNA-speckle contacts and enhanced inducibility of speckle-associated genes. Additionally, we observed disruption of chromatin-nuclear speckle association in patient-derived cells with Cornelia de Lange syndrome, a congenital neurodevelopmental disorder involving defective cohesin pathways. In summary, our findings reveal a mechanism for establishing the ground state of chromatin-speckle association and promoting gene inducibility, with relevance to human disease.

DOI: https://doi.org/10.1038/s41594-024-01465-6
Biol Open. 2025 Feb 15. pii: BIO061751. [Epub ahead of print]14(2):

The combinatorial binding syntax of transcription factors in forebrain-specific enhancers.

Fatima Batool, Huma Shireen, Muhammad Faizan Malik, Muhammad Abrar, Amir Ali Abbasi.

  Tissue-specific gene regulation in mammals involves the coordinated binding of multiple transcription factors (TFs). Using the forebrain as a model, we investigated the syntax of TF occupancy to determine tissue-specific enhancer regions. We analyzed forebrain-exclusive enhancers from the VISTA Enhancer Browser and a curated set of 23 TFs relevant to forebrain development and disease. Our findings revealed multiple distinct patterns of combinatorial TF binding, with the HES5-FOXP2-GATA3 triad being the most frequent in forebrain-specific enhancers. This syntactic structure was detected in 2614 enhancers from a genome-wide catalog of 25,000 predicted human forebrain enhancers. Notably, this catalog represents a computationally predicted dataset, distinct from the in vivo validated set of enhancers obtained from the VISTA Enhancer Browser. The shortlisted 2614 enhancers were further analyzed using genome-wide epigenetic data and evaluated for evolutionary conservation and disease relevance. Our findings highlight the value of these 2614 enhancers in forebrain-specific gene regulation and provide a framework for discovering tissue-specific enhancers, enhancing the understanding of enhancer function.

Keywords:  Enhancers; Epigenetics; Forebrain; Gene regulation; Transcription factors; Zebrafish

DOI:  https://doi.org/10.1242/bio.061751
Nucleic Acids Res. 2025 Feb 08. pii: gkaf048. [Epub ahead of print]53(4):

The epigenetic landscape shapes smoking-induced mutagenesis by modulating DNA damage susceptibility and repair efficiency.

Elisheva E Heilbrun, Dana Tseitline, Hana Wasserman, Ayala Kirshenbaum, Yuval Cohen, Raluca Gordan, Sheera Adar.

Lung cancer sequencing efforts have uncovered mutational signatures that are attributed to exposure to the cigarette smoke carcinogen benzo[a]pyrene. Benzo[a]pyrene metabolizes in cells to benzo[a]pyrene diol epoxide (BPDE) and reacts with guanine nucleotides to form bulky BPDE adducts. These DNA adducts block transcription and replication, compromising cell function and survival, and are repaired in human cells by the nucleotide excision repair pathway. Here, we applied high-resolution genomic assays to measure BPDE-induced damage formation and mutagenesis in human cells. We integrated the new damage and mutagenesis data with previous repair, DNA methylation, RNA expression, DNA replication, and chromatin component measurements in the same cell lines, along with lung cancer mutagenesis data. BPDE damage formation is significantly enhanced by DNA methylation and in accessible chromatin regions, including transcribed and early-replicating regions. Binding of transcription factors is associated primarily with reduced, but also enhanced damage formation, depending on the factor. While DNA methylation does not appear to influence repair efficiency, this repair was significantly elevated in accessible chromatin regions, which accumulated fewer mutations. Thus, when damage and repair drive mutagenesis in opposing directions, the final mutational patterns appear to be dictated by the efficiency of repair rather than the frequency of underlying damages.

DOI: https://doi.org/10.1093/nar/gkaf048
J Biol Chem. 2025 Feb 19. pii: S0021-9258(25)00182-6. [Epub ahead of print] 108333

Colorectal cancer hot spot mutations attenuate the ASXL-MLL4 interaction.

Soumi Biswas, Ji-Eun Lee, Guojia Xie, Louis Masclef, Zhizhong Ren, Jacques Côté, El Bachir Affar, Kai Ge, Tatiana G Kutateladze.

  Human additional sex combs like (ASXL) proteins are involved in the maintenance of both transcriptional activation and repression through their ability to bind multiple chromatin regulators, including two tumor suppressors: deubiquitinase BAP1 and methyltransferase MLL4 (KMT2D). The ASXL genes are often altered in colorectal cancer (CRC), and ASXL1 is one of the four hub genes related to the pathogenesis of CRC. Here, we show that MLL4 and BAP1 interdependently target specific genomic regions and positively or negatively regulate expression of a subset of genes in the human colon carcinoma HCT116 cells. MLL4 and BAP1 colocalize on a subset of enhancers and promoters in an interdependent manner. Genomic distribution of BAP1 in CRC cells differs from that in ESCs, with substantially more BAP1 binding sites identified on enhancers and promoters in HCT116 cells. MLL4 occupancy on MLL4+ BAP1+ genomic regions depends on functional ASXLs that interact with both MLL4 and BAP1, and CRC relevant mutations attenuate formation of the MLL4-ASXL complex. Mutational analysis and binding assays identified CRC hot spot mutations in ASXLs. Our findings suggest that alterations in genomic distribution of the MLL4-ASXL-BAP1 axis and CRC hot spot mutations in ASXLs perturb normal transcriptional programs and may trigger pathogenic events in colon cancer.

Keywords:  ASXL1; BAP1; KMT2D; MLL4; PHD finger; colorectal carcinoma

DOI:  https://doi.org/10.1016/j.jbc.2025.108333
Nucleic Acids Res. 2025 Feb 08. pii: gkaf079. [Epub ahead of print]53(4):

An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters.

Yi-Hui Wang, Hannah L Hertz, Benjamin Pastore, Wen Tang.

In all three domains of life, genes with related functions can be organized into specific genomic regions known as gene clusters. In eukaryotes, histone, piRNA (Piwi-interacting RNA), and rDNA (ribosomal DNA) clusters are among the most notable clusters which play fundamental roles in chromatin formation, genome integrity, and translation, respectively. These clusters have long been thought to be regulated by distinct transcriptional mechanisms. In this study, using Caenorhabditis elegans as a model system we identify ATTF-6, a member of the AT-hook family, as a key factor for the expression of histone, piRNA, and 5S rDNA-SL1 (spliced leader 1) clusters. ATTF-6 is essential for C. elegans viability. It forms distinct nuclear foci at both piRNA and 5S rDNA-SL1 clusters. Loss of ATTF-6 leads to a depletion of histone mRNAs, SL1 transcripts, and piRNAs. Additionally, we demonstrate that ATTF-6 is required for the recruitment of USTC (Upstream Sequence Transcription Complex) to piRNA clusters, which is necessary for piRNA production. Collectively, our findings reveal a unifying role for an AT-hook transcription factor in promoting the expression of fundamental gene clusters.

DOI: https://doi.org/10.1093/nar/gkaf079
Mol Cell. 2025 Feb 11. pii: S1097-2765(25)00056-5. [Epub ahead of print]

Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens.

Varun Sood, Ronald Holewinski, Thorkell Andresson, Daniel R Larson, Tom Misteli.

  Stochastic transcriptional bursting is a universal property of active genes. While different genes exhibit distinct bursting patterns, the molecular mechanisms that govern gene-specific stochastic bursting are largely unknown. We have developed a high-throughput-imaging-based screening strategy to identify cellular factors that determine the bursting patterns of native genes in human cells. We identify protein acetylation as a prominent effector of burst frequency and burst size acting via decreasing off-times and gene-specific changes in the on-time. These effects are not correlated with promoter acetylation. Instead, we demonstrate acetylation of the Integrator complex as a key determinant of gene bursting that alters Integrator interactions with transcription elongation and RNA processing factors but without affecting pausing. Our results suggest a prominent role for non-histone acetylation of a transcription cofactors as a mechanism for modulation of bursting via a far-downstream checkpoint.

Keywords:  Integrator complex; acetylation; high-throughput imaging screen; live-cell imaging; single-molecule; stochastic gene bursting; transcription

DOI:  https://doi.org/10.1016/j.molcel.2025.01.022
Nat Struct Mol Biol. 2025 Feb 20.

Haspin kinase binds to a nucleosomal DNA supergroove.

Chad W Hicks, Colin R Gliech, Sanim Rahman, Xiangbin Zhang, Andrew S Eneim, Stacy J Vasquez, Andrew J Holland, Cynthia Wolberger.

Phosphorylation of histone H3 threonine 3 (H3T3) by Haspin recruits the chromosomal passenger complex to the inner centromere and ensures proper cell cycle progression through mitosis. The mechanism by which Haspin binds to nucleosomes to phosphorylate H3T3 is not known. Here we report cryogenic electron microscopy structures of the human Haspin kinase domain bound to a nucleosome. In contrast with previous structures of histone-modifying enzymes, Haspin solely contacts the nucleosomal DNA, inserting into a supergroove formed by apposing major grooves of two DNA gyres. This binding mode provides a plausible mechanism by which Haspin can bind to nucleosomes in a condensed chromatin environment to phosphorylate H3T3. We identify key basic residues in the Haspin kinase domain that are essential for phosphorylation of nucleosomal histone H3 and binding to mitotic chromatin. Our structural data provide notable insight into a histone-modifying enzyme that binds to nucleosomes solely through DNA contacts.

DOI: https://doi.org/10.1038/s41594-025-01502-y
PLoS Comput Biol. 2025 Feb 18. 21(2): e1012841

ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.

Laura M Gunsalus, Michael J Keiser, Katherine S Pollard.

The investigation of chromatin organization in single cells holds great promise for identifying causal relationships between genome structure and function. However, analysis of single-molecule data is hampered by extreme yet inherent heterogeneity, making it challenging to determine the contributions of individual chromatin fibers to bulk trends. To address this challenge, we propose ChromaFactor, a novel computational approach based on non-negative matrix factorization that deconvolves single-molecule chromatin organization datasets into their most salient primary components. ChromaFactor provides the ability to identify trends accounting for the maximum variance in the dataset while simultaneously describing the contribution of individual molecules to each component. Applying our approach to two single-molecule imaging datasets across different genomic scales, we find that these primary components demonstrate significant correlation with key functional phenotypes, including active transcription, enhancer-promoter distance, and genomic compartment. Also, we find that some bulk trends exist at the single-cell level, but only in a small fraction of cells, suggesting that critical changes in genome organization may be driven by specific rare subpopulations rather than occurring uniformly across all cells. ChromaFactor offers a robust tool for understanding the complex interplay between chromatin structure and function on individual DNA molecules, pinpointing which subpopulations drive functional changes and fostering new insights into cellular heterogeneity and its implications for bulk genomic phenomena.

DOI: https://doi.org/10.1371/journal.pcbi.1012841
Sci Adv. 2025 Feb 21. 11(8): eadu3194

Direct ionic stress sensing and mitigation by the transcription factor NFAT5.

Chandni B Khandwala, Parijat Sarkar, H Broder Schmidt, Mengxiao Ma, Ganesh V Pusapati, Frederic Lamoliatte, Maia Kinnebrew, Bhaven B Patel, Desiree Tillo, Andres M Lebensohn, Rajat Rohatgi.

Rising temperatures and water scarcity caused by climate change are increasingly exposing our cells and tissues to ionic stress, a consequence of elevated cytoplasmic ionic strength that can disrupt protein, organelle, and genome function. Here, we unveil a single-protein mechanism for ionic strength sensing and mitigation in animal cells, one that is notably different from the analogous high osmolarity glycerol kinase cascade in yeast. The Rel family transcription factor NFAT5 directly senses intracellular ionic strength using a C-terminal prion-like domain (PLD). In response to elevated intracellular ionic strength, this PLD is necessary and sufficient to coordinate an adaptive gene expression program by recruiting the transcriptional coactivator BRD4. The purified NFAT5 PLD forms condensates in response to elevated solution ionic strength in vitro, and human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic stress in yeast. We propose that ion-sensitive conformational changes in a PLD directly regulate transcription to maintain ionic strength homeostasis in animal cells.

DOI: https://doi.org/10.1126/sciadv.adu3194
Nat Commun. 2025 Feb 20. 16(1): 1787

Explainable artificial intelligence of DNA methylation-based brain tumor diagnostics.

Salvatore Benfatto, Martin Sill, David T W Jones, Stefan M Pfister, Felix Sahm, Andreas von Deimling, David Capper, Volker Hovestadt.

We have recently developed a machine learning classifier that enables fast, accurate, and affordable classification of brain tumors based on genome-wide DNA methylation profiles that is widely employed in the clinic. Neuro-oncology research would benefit greatly from understanding the underlying artificial intelligence decision process, which currently remains unclear. Here, we describe an interpretable framework to explain the classifier's decisions. We show that functional genomic regions of various sizes are predominantly employed to distinguish between different tumor classes, ranging from enhancers and CpG islands to large-scale heterochromatic domains. We detect a high degree of genomic redundancy, with many genes distinguishing individual tumor classes, explaining the robustness of the classifier and revealing potential targets for further therapeutic investigation. We anticipate that our resource will build up trust in machine learning in clinical settings, foster biomarker discovery and development of compact point-of-care assays, and enable further epigenome research of brain tumors. Our interpretable framework is accessible to the research community via an interactive web application ( https://hovestadtlab.shinyapps.io/shinyMNP/ ).

DOI: https://doi.org/10.1038/s41467-025-57078-0
Nat Commun. 2025 Feb 14. 16(1): 1640

Dynamic properties of transcriptional condensates modulate CRISPRa-mediated gene activation.

Yujuan Fu, Xiaoxuan Yang, Sihui Li, Chenyang Ma, Yao An, Tao Cheng, Ying Liang, Shengbai Sun, Tianyi Cheng, Yongyang Zhao, Jianghu Wang, Xiaoyue Wang, Pengfei Xu, Yafei Yin, Hongqing Liang, Nan Liu, Wei Zou, Baohui Chen.

CRISPR activation (CRISPRa) is a powerful tool for endogenous gene activation, yet the mechanisms underlying its optimal transcriptional activation remain unclear. By monitoring real-time transcriptional bursts, we find that CRISPRa modulates both burst duration and amplitude. Our quantitative imaging reveals that CRISPR-SunTag activators, with three tandem VP64-p65-Rta (VPR), form liquid-like transcriptional condensates and exhibit high activation potency. Although visible CRISPRa condensates are associated with some RNA bursts, the overall levels of phase separation do not correlate with transcriptional bursting or activation strength in individual cells. When the number of SunTag scaffolds is increased to 10 or more, solid-like condensates form, sequestering co-activators such as p300 and MED1. These condensates display low dynamicity and liquidity, resulting in ineffective gene activation. Overall, our studies characterize various phase-separated CRISPRa systems for gene activation, highlighting the foundational principles for engineering CRISPR-based programmable synthetic condensates with appropriate properties to effectively modulate gene expression.

DOI: https://doi.org/10.1038/s41467-025-56735-8
Commun Biol. 2025 Feb 20. 8(1): 272

The histone demethylase dLsd1 regulates organ size by silencing transposable elements.

Ines Selmi, Manuela Texier, Marion Aguirrenbegoa, Clémentine Merce, Laurence Fraisse-Lepourry, Bruno Mugat, Mourdas Mohamed, Séverine Chambeyron, David Cribbs, Luisa Di Stefano.

The specific role of chromatin modifying factors in the timely execution of transcriptional changes in gene expression to regulate organ size remains largely unknown. Here, we report that in Drosophila melanogaster depletion of the histone demethylase dLsd1 results in the reduction of wing size. dLsd1 depletion affects cell proliferation and causes an increase in DNA damage and cell death. Mechanistically, we have identified Transposable Elements (TEs) as critical dLsd1 targets for organ size determination. We found that upon dLsd1 loss many TE families are upregulated, and new TE insertions appear. By blocking this new TE activity, we could rescue the wing size phenotype. Collectively, our results reveal that the histone demethylase dLsd1 and maintenance of TE homeostasis are required to ensure proper wing size.

DOI: https://doi.org/10.1038/s42003-025-07724-6
Sci Adv. 2025 Feb 21. 11(8): eado2830

The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers.

Recep Bayraktar, Yitao Tang, Mihnea P Dragomir, Cristina Ivan, Xinxin Peng, Linda Fabris, Jianhua Zhang, Alessandro Carugo, Serena Aneli, Jintan Liu, Mei-Ju M Chen, Sanjana Srinivasan, Iman Sahnoune, Emine Bayraktar, Kadir C Akdemir, Meng Chen, Pranav Narayanan, Wilson Huang, Leonie Florence Ott, Agda Karina Eterovic, Oscar Eduardo Villarreal, Mohammad Moustaf Mohammad, Michael D Peoples, Danielle M Walsh, Jon Andrew Hernandez, Margaret B Morgan, Kenna R Shaw, Jennifer S Davis, David Menter, Constantine S Tam, Paul Yeh, Sarah-Jane Dawson, Laura Z Rassenti, Thomas J Kipps, Tanja Kunej, Zeev Estrov, Simon A Joosse, Luca Pagani, Catherine Alix-Panabières, Klaus Pantel, Alessandra Ferajoli, Andrew Futreal, Ignacio I Wistuba, Milan Radovich, Scott Kopetz, Michael J Keating, Giulio F Draetta, John S Mattick, Han Liang, George A Calin.

The mutational landscape of phylogenetically ultraconserved elements (UCEs), especially those in noncoding DNAs (ncUCEs), and their functional relevance in cancers remain poorly characterized. Here, we perform a systematic analysis of whole-genome and in-house targeted UCE sequencing datasets from more than 3000 patients with cancer of 13,736 UCEs and demonstrate that ncUCE somatic alterations are common. Using a multiplexed CRISPR knockout screen in colorectal cancer cells, we show that the loss of several altered ncUCEs significantly affects cell proliferation. In-depth functional studies in vitro and in vivo further reveal that specific ncUCEs can be enhancers of tumor suppressors (such as ARID1B) and silencers of oncogenic proteins (such as RPS13). Moreover, several miRNAs located in ncUCEs are recurrently mutated. Mutations in miR-142 locus can affect the Drosha-mediated processing of precursor miRNAs, resulting in the down-regulation of the mature transcript. These results provide systematic evidence that specific ncUCEs play diverse regulatory roles in cancer.

DOI: https://doi.org/10.1126/sciadv.ado2830
Nat Commun. 2025 Feb 18. 16(1): 1743

Cooperation between the Hippo and MAPK pathway activation drives acquired resistance to TEAD inhibition.

Sayantanee Paul, Thijs J Hagenbeek, Julien Tremblay, Vasumathi Kameswaran, Christy Ong, Chad Liu, Alissa D Guarnaccia, James A Mondo, Peter L Hsu, Noelyn M Kljavin, Bartosz Czech, Janina Smola, Dieu An H Nguyen, Jennifer A Lacap, Trang H Pham, Yuxin Liang, Robert A Blake, Luca Gerosa, Matthew Grimmer, Shiqi Xie, Bence Daniel, Xiaosai Yao, Anwesha Dey.

TEAD (transcriptional enhanced associate domain) transcription factors (TEAD1-4) serve as the primary effectors of the Hippo signaling pathway in various cancers. Targeted therapy leads to the emergence of resistance and the underlying mechanism of resistance to TEAD inhibition in cancers is less characterized. We uncover that upregulation of the AP-1 (activator protein-1) transcription factors, along with restored YAP (yes-associated protein) and TEAD activity, drives resistance to GNE-7883, a pan-TEAD inhibitor. Acute GNE-7883 treatment abrogates YAP-TEAD binding and attenuates FOSL1 (FOS like 1) activity. TEAD inhibitor resistant cells restore YAP and TEAD chromatin occupancy, acquire additional FOSL1 binding and exhibit increased MAPK (mitogen-activated protein kinase) pathway activity. FOSL1 is required for the chromatin binding of YAP and TEAD. This study describes a clinically relevant interplay between the Hippo and MAPK pathway and highlights the key role of MAPK pathway inhibitors in mitigating resistance to TEAD inhibition in Hippo pathway dependent cancers.

DOI: https://doi.org/10.1038/s41467-025-56634-y
Nat Genet. 2025 Feb 17.

Multiomic single-cell profiling identifies critical regulators of postnatal brain.

Tereza Clarence, Jaroslav Bendl, Xuan Cao, Xinyi Wang, Shiwei Zheng, Gabriel E Hoffman, Alexey Kozlenkov, Aram Hong, Marina Iskhakova, Manoj K Jaiswal, Sarah Murphy, Alexander Yu, Vahram Haroutunian, Stella Dracheva, Schahram Akbarian, John F Fullard, Guo-Cheng Yuan, Donghoon Lee, Panos Roussos.

Human brain development spans from embryogenesis to adulthood, with dynamic gene expression controlled by cell-type-specific cis-regulatory element activity and three-dimensional genome organization. To advance our understanding of postnatal brain development, we simultaneously profiled gene expression and chromatin accessibility in 101,924 single nuclei from four brain regions across ten donors, covering five key postnatal stages from infancy to late adulthood. Using this dataset and chromosome conformation capture data, we constructed enhancer-based gene regulatory networks to identify cell-type-specific regulators of brain development and interpret genome-wide association study loci for ten main brain disorders. Our analysis connected 2,318 cell-specific loci to 1,149 unique genes, representing 41% of loci linked to the investigated traits, and highlighted 55 genes influencing several disease phenotypes. Pseudotime analysis revealed distinct stages of postnatal oligodendrogenesis and their regulatory programs. These findings provide a comprehensive dataset of cell-type-specific gene regulation at critical timepoints in postnatal brain development.

DOI: https://doi.org/10.1038/s41588-025-02083-8