bims-crepig 2025-06-01 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–06–01
thirty-one papers selected by
Connor Rogerson, University of Cambridge

Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation.
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis.
FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate.
DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape.
The nucleolar granular component mediates genome-nucleolus interactions and establishes their repressive chromatin states.
CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly.
Bystander activation across a TAD boundary supports a cohesin-dependent transcription cluster model for enhancer function.
Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B.
CUT&Tag for Transcription Factor Binding Profiles During Mammalian Zygotic Genome Activation.
Quantifying Transcription Factor Enrichment at Target Loci in Live Embryos.
SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes.
Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells.
Methyl-Micro-C: simultaneous characterization of chromatin accessibility, interactions, and DNA methylation.
HMGA2 and protein leucine methylation drive pancreatic cancer lineage plasticity.
Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.
Histone variant H2A.W7 represses meiotic crossover formation in Arabidopsis heterochromatin.
Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation.
A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA.
scNucMap: mapping the nucleosome landscapes at single-cell resolution.
Donor embryonic stem cells displace host cells of 8-cell stage chimeras to the extraembryonic lineages by spatial crowding and FGF4 signalling.
Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.
Transcriptomic insights into fate choice of pallial versus subpallial GABAergic neurons.
Discovery of candidate functional non-coding mutations in acute myeloid leukemia using single-cell chromatin accessibility sequencing.
FOXA2 promotes metastatic competence in small cell lung cancer.
Ethanol induction of FGF21 in the liver is dependent on histone acetylation and ligand activation of ChREBP by glycerol-3-phosphate.
Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer.
The fire ant social chromosome exerts a major influence on genome regulation.
Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes.
Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus.
Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation.
Structural plasticity of the FOXO-DBD:p53-TAD interaction.

Mol Cell. 2025 May 22. pii: S1097-2765(25)00414-9. [Epub ahead of print]

Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation.

Audrey J Marsh, Sergei Pirogov, Yadwinder Kaur, Abby J Ruffridge, Suresh Sajwan, Tyler J Gibson, George Hunt, Melissa M Harrison, Mattias Mannervik.

  Immediately after fertilization, the genome is transcriptionally quiescent. Maternally encoded pioneer factors reprogram the chromatin state and facilitate transcription of the zygotic genome. In Drosophila, transcription is initiated by the pioneer factor Zelda. While Zelda-occupied sites are enriched with histone acetylation, a post-translational mark associated with active cis-regulatory regions, the functional relationship between Zelda and histone acetylation remained unclear. We show that Zelda-mediated recruitment of the histone acetyltransferase CREB-binding protein (CBP) is essential for zygotic transcription. CBP catalytic activity is necessary for the release of RNA polymerase II (RNA Pol II) into elongation and for embryonic development. However, CBP also activates transcription independent of acetylation through RNA Pol II recruitment. Neither CBP-mediated acetylation nor CBP itself is required for the pioneering function of Zelda. Our data suggest that pioneer-factor-mediated recruitment of CBP is a conserved mechanism required to activate zygotic transcription but is separable from the function of pioneer factors in restructuring chromatin accessibility.

Keywords:  Drosophila; RNA polymerase; histone acetyltransferase; pioneer factor; transcription; zygotic genome activation

DOI:  https://doi.org/10.1016/j.molcel.2025.05.009
Nat Commun. 2025 May 28. 16(1): 4724

Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis.

Tomoya Kujirai, Junko Kato, Kyoka Yamamoto, Seiya Hirai, Takeru Fujii, Kazumitsu Maehara, Akihito Harada, Lumi Negishi, Mitsuo Ogasawara, Yuki Yamaguchi, Yasuyuki Ohkawa, Yoshimasa Takizawa, Hitoshi Kurumizaka.

RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how RNAPII functions in the human genome, we isolate transcribing RNAPII complexes from human nuclei by chromatin immunopurification, and determine the cryo-electron microscopy structures of RNAPII elongation complexes (ECs) associated with genomic DNA in distinct forms, without or with the elongation factors SPT4/5, ELOF1, and SPT6. This ChIP-cryoEM method also reveals the two EC-nucleosome complexes corresponding nucleosome disassembly/reassembly processes. In the structure of EC-downstream nucleosome, EC paused at superhelical location (SHL) -5 in the nucleosome, suggesting that SHL(-5) pausing occurs in a sequence-independent manner during nucleosome disassembly. In the structure of the EC-upstream nucleosome, EC directly contacts the nucleosome through the nucleosomal DNA-RPB4/7 stalk and the H2A-H2B dimer-RPB2 wall interactions, suggesting that EC may be paused during nucleosome reassembly. These representative EC structures transcribing the human genome provide mechanistic insights into understanding RNAPII transcription on chromatin.

DOI: https://doi.org/10.1038/s41467-025-59580-x
Mol Cell. 2025 May 15. pii: S1097-2765(25)00407-1. [Epub ahead of print]

FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate.

Francesca Burgos-Bravo, Alexander B Tong, Chen Li, César Díaz-Celis, Craig D Kaplan, Gary LeRoy, Danny Reinberg, Carlos Bustamante.

  Transcription of yeast RNA polymerase II through nucleosomes requires the assistance of the histone chaperone FACT (facilitates chromatin transcription). Yet, how FACT modulates the nucleosomal mechanical barrier to affect the polymerase's elongation dynamics is poorly understood. Using high-resolution single-molecule optical tweezers, we show that FACT greatly decreases the magnitude of the barrier by favoring the unwrapping of DNA from the distal H2A-H2B dimer, which, in turn, weakens the contacts near the dyad, significantly reducing the enzyme's crossing time. We show that barrier crossing depends on the asymmetric flexibility of the nucleosome arms, an asymmetry we find across the genome. Mechanical unwrapping of Cy3-H2A nucleosomes reveals that FACT reduces their unwrapping force and stabilizes a hexasome-like intermediate that retains both labeled dimers during successive unwrapping cycles. This intermediate is also observed after transcription. In conclusion, FACT facilitates nucleosomal transcription by weakening the barrier and actively assisting the maintenance of nucleosomal integrity after enzyme passage.

Keywords:  FACT; RNA polymerase II; histone chaperone; nucleosomal DNA flexibility; nucleosome; nucleosome integrity; nucleosome unwrapping; optical tweezers; single-molecule fluorescence; transcription

DOI:  https://doi.org/10.1016/j.molcel.2025.05.002
Nucleic Acids Res. 2025 May 22. pii: gkaf435. [Epub ahead of print]53(10):

DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape.

Stephanie Gehrs, Zuguang Gu, Joschka Hey, Dieter Weichenhan, Niklas Buckwalter, Moritz Jakab, Agnes Hotz-Wagenblatt, Kersten Breuer, Maria Llamazares Prada, Daniel Hübschmann, Katharina Schlereth, Christoph Plass, Hellmut Augustin.

DNA methylation plays a fundamental role in regulating transcription during development and differentiation. However, its functional role in the regulation of endothelial cell (EC) transcription during state transition, meaning the switch from an angiogenic to a quiescent cell state, has not been systematically studied. Here, we report the longitudinal changes of the DNA methylome over the lifetime of the murine pulmonary vasculature. We identified prominent alterations in hyper- and hypomethylation during the transition from angiogenic to quiescent ECs. Once a quiescent state was established, DNA methylation marks remained stable throughout EC aging. These longitudinal differentially methylated regions correlated with endothelial gene expression and highlighted the recruitment of de novo DNA methyltransferase 3a (DNMT3A), evidenced by its motif enrichment at transcriptional start sites of genes with methylation-dependent expression patterns. Loss-of-function studies in mice revealed that the absence of DNMT3A-dependent DNA methylation led to the loss of active enhancers, resulting in mild transcriptional changes, likely due to loss of active enhancer integrity. These results underline the importance of DNA methylation as a key epigenetic mechanism of EC function during state transition. Furthermore, we show that DNMT3A-dependent DNA methylation appears to be involved in establishing the histone landscape required for accurate transcriptome regulation.

DOI: https://doi.org/10.1093/nar/gkaf435
Mol Cell. 2025 May 17. pii: S1097-2765(25)00409-5. [Epub ahead of print]

The nucleolar granular component mediates genome-nucleolus interactions and establishes their repressive chromatin states.

Shivani Gupta, Cristiana Bersaglieri, Dominik Bär, Mathieu Raingeval, Luana Schaab, Raffaella Santoro.

  Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.

Keywords:  G9a; H3K9me2; NADs; NPM1; chromatin; genome organization; nucleolus

DOI:  https://doi.org/10.1016/j.molcel.2025.05.004
Nat Commun. 2025 May 30. 16(1): 5011

CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly.

Hanna Schwaemmle, Hadrien Soldati, Nikolaos M R Lykoskoufis, Mylène Docquier, Alexandre Hainard, Simon M G Braun.

The SWI/SNF (or BAF) complex is an essential chromatin remodeler, which is frequently mutated in cancer and neurodevelopmental disorders. These are often heterozygous loss-of-function mutations, indicating a dosage-sensitive role for SWI/SNF subunits. However, the molecular mechanisms regulating SWI/SNF subunit dosage to ensure complex assembly remain largely unexplored. We performed a CRISPR KO screen, using epigenome editing in mouse embryonic stem cells, and identified Mlf2 and Rbm15 as regulators of SWI/SNF complex activity. First, we show that MLF2, a poorly characterized chaperone protein, promotes SWI/SNF assembly and binding to chromatin. Rapid degradation of MLF2 reduces chromatin accessibility at sites that depend on high levels of SWI/SNF binding to maintain open chromatin. Next, we find that RBM15, part of the m6A writer complex, controls m6A modifications on specific SWI/SNF mRNAs to regulate subunit protein levels. Misregulation of m6A methylation causes overexpression of core SWI/SNF subunits leading to the assembly of incomplete complexes lacking the catalytic ATPase/ARP subunits. These data indicate that targeting modulators of SWI/SNF complex assembly may offer a potent therapeutic strategy for diseases associated with impaired chromatin remodeling.

DOI: https://doi.org/10.1038/s41467-025-60424-x
Genes Dev. 2025 May 28.

Bystander activation across a TAD boundary supports a cohesin-dependent transcription cluster model for enhancer function.

Iain Williamson, Katy A Graham, Matthew Woolf, Hannes Becher, Robert E Hill, Wendy A Bickmore, Laura A Lettice.

  Mammalian enhancers can regulate genes over large genomic distances, often skipping over other genes. Despite this, precise developmental regulation suggests that mechanisms exist to ensure enhancers only activate their correct targets. Sculpting of three-dimensional chromosome organization through cohesin-dependent loop extrusion is thought to be important for facilitating and constraining enhancer action. The boundaries of topologically associating domains (TADs) are thought to prevent enhancers acting on genes in adjacent TADs. However, there are examples where enhancers appear to act across TAD boundaries, but it has remained unclear whether a single enhancer can simultaneously activate genes in different TADs. Here we show that some Shh enhancers can activate transcription concurrently not only at Shh but also at Mnx1 located in an adjacent TAD. This occurs in the context of a chromatin conformation maintaining genes and enhancers in close proximity and is influenced by cohesin. To our knowledge, this is the first report of two endogenous mammalian genes transcribed concurrently under the control of the same enhancer and across a TAD boundary. These findings have implications for understanding the design rules of gene regulatory landscapes and are consistent with a transcription cluster model of enhancer-promoter communication.

Keywords:  3D genome; CTCF; DNA-FISH; RNA-FISH; cohesin; loop extrusion; sonic hedgehog; transcriptional hubs

DOI:  https://doi.org/10.1101/gad.352648.125
EMBO J. 2025 May 30.

Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B.

Munetaka Akatsu, Rina Hirano, Tomoya Kujirai, Mitsuo Ogasawara, Haruhiko Ehara, Shun-Ichi Sekine, Yoshimasa Takizawa, Hitoshi Kurumizaka.

  H2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that the RNA polymerase II elongation complex (EC) transcribes the nucleosome containing H2A.B more efficiently than that with canonical H2A in vitro. Our cryo-electron microscopy analysis of the H2A.B nucleosome during transcription revealed that the proximal H2A.B-H2B dimer is released from the nucleosome as the EC transcribes the proximal half of the nucleosomal DNA. This dissociation, which is not observed in the canonical H2A nucleosome, likely enhances the EC elongation efficiency in the H2A.B nucleosome. Mutational analyses suggested that the unique short C-terminal region of H2A.B alone enhances EC elongation efficiency when substituted for its counterpart in canonical H2A. Additionally, other regions of H2A.B contribute to this enhancement. These structural and biochemical findings provide new insights into the role of H2A.B in regulating gene expression.

Keywords:  Chromatin; H2A.B; Histone Variant; Nucleosome; Transcription

DOI:  https://doi.org/10.1038/s44318-025-00473-6
Methods Mol Biol. 2025 ;2923 77-87

CUT&Tag for Transcription Factor Binding Profiles During Mammalian Zygotic Genome Activation.

Wataru Kobayashi, Kikuë Tachibana.

  Zygotic genome activation (ZGA) triggered by transcription factors (TFs) is a critical event to facilitate subsequent embryonic development. However, the paucity of material poses a challenge for mapping TF binding profiles in mammalian embryos. Here, we describe a low-input Cleavage Under Targets & Tagmentation (CUT&Tag) protocol optimized for TF binding using ~300 mouse two-cell embryos to investigate ZGA. This version of CUT&Tag is an immunostaining-based protocol with manual cell transfer by pipette to avoid loss of samples and gentle washing of fragile preimplantation embryos protected by the zona pellucida.

Keywords:  CUT&Tag; Low-input sample; Mammalian preimplantation embryo; Transcription factor; Zygotic genome activation

DOI:  https://doi.org/10.1007/978-1-0716-4522-2_6
Methods Mol Biol. 2025 ;2923 119-141

Quantifying Transcription Factor Enrichment at Target Loci in Live Embryos.

Samantha Fallacaro, Apratim Mukherjee, Ernesto Gamauf, Mustafa Mir.

  The mechanisms by which transcription factors efficiently search for and occupy their target gene loci within the crowded nuclear environment remain poorly understood. Recent discoveries made using high-resolution live imaging methods have revealed that transcription factors and other nuclear regulatory proteins form high-local concentration assemblies within nuclei. These assemblies, referred to as hubs, condensates, clusters, or foci, enhance how frequently factors bind to chromatin and can thus lead to robust occupancy or enrichment at target loci even in the face of low-affinity chromatin-protein interactions. However, quantifying the enrichment of transcription factors at target loci in live organisms is challenging. Here, we present a full workflow, from sample and microscope preparation to data analysis for calculating transcription factor enrichment at specific gene loci in live Drosophila embryos. In this method, the radial average fluorescence intensity of a tagged transcription factor centered at the transcription site is used to measure relative transcription factor enrichment. This chapter details how to acquire and analyze data using our pipeline while discussing common pitfalls, appropriate quality controls, and caveats. One key caveat we highlight is the confounding effect of using transcriptional sites too close to the nuclear periphery. For analysis, we present the Python package pyEnRICH, (PYthon framework for Enriched Radial Intensity Calculations for Hubs), and an accompanying tutorial complete with sample data to guide novices and experts through quantification of transcription factor enrichment at active gene loci.

Keywords:  Condensates; Gene activation; Lattice light-sheet microscopy; Live embryo imaging; Transcription factor enrichment; Transcription factor search; Transcriptional hubs; pyEnRICH; transcription factor dynamics

DOI:  https://doi.org/10.1007/978-1-0716-4522-2_8
Nucleic Acids Res. 2025 May 22. pii: gkaf431. [Epub ahead of print]53(10):

SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes.

Kulandaisamy Arulsamy, Bo Xia, Yang Yu, Hong Chen, William T Pu, Lili Zhang, Kaifu Chen.

Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and cell identity dysregulation involving diseases. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In alignment with recent reports that cell identity genes (CIGs) are regulated with unique epigenetic signatures, we found CIGs exhibit distinctive genetic sequence signatures, e.g. unique enrichment patterns of cis-regulatory elements. Using these genetic sequence signatures, along with gene expression information from single-cell RNA-seq data, SCIG uncovers the identity genes of a cell without a need for comparison to other cells. CIG score defined by SCIG surpassed expression value in network analysis to reveal the master transcription factors (TFs) regulating cell identity. Applying SCIG to the human endothelial cell atlas revealed that the tissue microenvironment is a critical supplement to master TFs for cell identity refinement. SCIG is publicly available at https://doi.org/10.5281/zenodo.14726426 , offering a valuable tool for advancing cell differentiation, development, and regenerative medicine research.

DOI: https://doi.org/10.1093/nar/gkaf431
Stem Cell Reports. 2025 May 20. pii: S2213-6711(25)00115-8. [Epub ahead of print] 102511

Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells.

Jielin Yan, Renhe Luo, Bess P Rosen, Dingyu Liu, Wilfred Wong, Christina S Leslie, Danwei Huangfu.

  Human embryonic stem cells (hESCs) are notable for their ability to self-renew and to differentiate into all tissue types in the body. NANOG is a core regulator of hESC identity, and dynamic control of its expression is crucial to maintain the balance between self-renewal and differentiation. Transcriptional regulation depends on enhancers, but NANOG enhancers in hESCs are not well characterized. Here, we report two NANOG enhancers discovered from a CRISPR interference screen in hESCs. Deletion of a single copy of either enhancer significantly reduced NANOG expression, compromising self-renewal and increasing differentiation propensity. Interestingly, these two NANOG enhancers are involved in a tandem duplication event found in certain primates including humans but not in mice. However, the duplicated counterparts do not regulate NANOG expression. This work expands our knowledge of functional enhancers in hESCs and highlights the sensitivity of the hESC state to the dosage of core regulators and their enhancers.

Keywords:  CRISPRi screens; NANOG; enhancer deletions; enhancer duplications; enhancers; genome architecture; hESC differentiation; hESCs; human embryonic stem cells; transcriptional regulation

DOI:  https://doi.org/10.1016/j.stemcr.2025.102511
NAR Genom Bioinform. 2025 Jun;7(2): lqaf060

Methyl-Micro-C: simultaneous characterization of chromatin accessibility, interactions, and DNA methylation.

Leonardo Gonzalez-Smith, Claire Stevens, Huan Cao, Zexun Wu, Suhn K Rhie.

Epigenomes, characterized by patterns of different signatures such as chromatin accessibility, chromatin interactions, and DNA methylation, vary across cell types and play a pivotal role in regulating gene expression. By mapping these signatures, the underlying mechanisms of development and diseases can be uncovered. However, many canonical epigenetic methods focus on mapping only one signature. Simultaneous measurement of epigenetic signatures from the same cell or tissue provides significant benefits for research, especially when resources are limited, and precise analysis is essential. Here, we report a technique called Methyl-Micro-C (MMC), which simultaneously profiles chromatin accessibility, chromatin interactions, and DNA methylation in the same sample. MMC enhances the resolution of chromatin interactions and the coverage of CpGs by combining MNase-mediated fragmentation with enzymatic conversion. This technique allows for the profiling of three-dimensional epigenomes, capturing consistent chromatin accessibility, chromatin interactions, and DNA methylation signals in an efficient manner. It is also relatively straightforward, allowing researchers to implement and apply it easily.

DOI: https://doi.org/10.1093/nargab/lqaf060
Nat Commun. 2025 May 26. 16(1): 4866

HMGA2 and protein leucine methylation drive pancreatic cancer lineage plasticity.

Stephanie Dobersch, Naomi Yamamoto, Aidan Schutter, Sarah M Cavender, Tess M Robertson, Nithya Kartha, Annie N Samraj, Ben Doron, Lisa A Poole, Cynthia L Wladyka, Amy Zhang, Gun Ho Jang, Aswanth H Mahalingam, Guillermo Barreto, Srivatsan Raghavan, Goutham Narla, Faiyaz Notta, Robert N Eisenman, Andrew C Hsieh, Sita Kugel.

Basal pancreatic ductal adenocarcinoma (PDAC) has the worst overall survival and is the only subtype that serves as an independent poor prognostic factor. We identify elevated levels of LIN28B and its downstream target, HMGA2, in basal PDAC. Notably, LIN28B significantly accelerates KRAS-driven PDAC progression in a mouse model. Here, we show that HMGA2 promotes basal PDAC pathogenesis by enhancing mRNA translation downstream of LIN28B. Mechanistically, HMGA2 suppresses leucine carboxyl methyltransferase 1 (LCMT1) at the chromatin level, reducing PP2A methylation and activity. This leads to increased phosphorylation of S6K and eIF4B, boosting mRNA translation. Additionally, HMGA2 downregulates B56α (PPP2R5A), disrupting functional PP2A holoenzyme assembly and further sustaining phosphorylated S6K levels. Impaired PP2A function mimics HMGA2's effects, reinforcing increased mRNA translation and basal lineage features. This work uncovers a critical link between the LIN28B/HMGA2 axis, protein synthesis, and PDAC lineage specificity via LCMT1-mediated PP2A methylation and B56α-PP2A disruption.

DOI: https://doi.org/10.1038/s41467-025-60129-1
Nat Methods. 2025 May 26.

Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.

Sara Lobato-Moreno, Umut Yildiz, Annique Claringbould, Nila H Servaas, Evi P Vlachou, Christian Arnold, Hanke Gwendolyn Bauersachs, Víctor Campos-Fornés, Minyoung Kim, Ivan Berest, Karin D Prummel, Kyung-Min Noh, Mikael Marttinen, Judith B Zaugg.

Enhancers and transcription factors (TFs) are crucial in regulating cellular processes. Current multiomic technologies to study these elements in gene regulatory mechanisms lack multiplexing capability and scalability. Here we present single-cell ultra-high-throughput multiplexed sequencing (SUM-seq) for co-assaying chromatin accessibility and gene expression in single nuclei. SUM-seq enables profiling hundreds of samples at the million cell scale and outperforms current high-throughput single-cell methods. We demonstrate the capability of SUM-seq to (1) resolve temporal gene regulation of macrophage M1 and M2 polarization to bridge TF regulatory networks and immune disease genetic variants, (2) define the regulatory landscape of primary T helper cell subsets and (3) dissect the effect of perturbing lineage TFs via arrayed CRISPR screens in spontaneously differentiating human induced pluripotent stem cells. SUM-seq offers a cost-effective, scalable solution for ultra-high-throughput single-cell multiomic sequencing, accelerating the unraveling of complex gene regulatory networks in cell differentiation, responses to perturbations and disease studies.

DOI: https://doi.org/10.1038/s41592-025-02700-8
Proc Natl Acad Sci U S A. 2025 Jun 03. 122(22): e2414166122

Histone variant H2A.W7 represses meiotic crossover formation in Arabidopsis heterochromatin.

Pallas Kuo, Andrew J Tock, Xuexia Liu, Stephanie D Topp, Zhenhui Zhong, Ian R Henderson, Christophe Lambing.

  In eukaryotic genomes, DNA is packaged into nucleosomes to form chromatin. The incorporation of canonical or variant histones into nucleosomes confers different properties and influences chromatin structure to regulate cellular processes, including recombination. During meiosis, DNA double-strand breaks (DSBs) are formed and repaired as interhomolog crossovers. Nucleosome occupancy is generally associated with low crossover frequency, but it remains unclear which histone variants are involved in this process. In Arabidopsis, three variants of H2A coexist: H2A.X, H2A.Z, and H2A.W. Here, we show that H2A.W7 has a suppressive role on meiotic recombination. Genome-wide mapping of the crossover landscape revealed increased centromere-proximal recombination in h2a.w7. Moreover, H2A.W7 can be recruited to the 3a crossover hotspot via 21-24-nucleotide siRNAs during RNA-directed DNA methylation, causing increased nucleosome occupancy and decreased crossover frequency. Cytological analysis reveals that H2A.W7 restricts heterochromatin clustering during meiosis, which can form a mechanism to limit interhomolog recombination. Conversely, the linker histone H1, of which its loading is known to be restricted by H2A.W, promotes heterochromatin clustering and crossover on a heterochromatic genetic interval. Our study reveals a role for H2A.W7 in repressing crossover formation in Arabidopsis.

Keywords:  H2A.W; crossover; epigenetics; meiosis; nucleosomes

DOI:  https://doi.org/10.1073/pnas.2414166122
EMBO J. 2025 May 27.

Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation.

Simon Zhongyuan Tian, Yang Yang, Duo Ning, Ting Yu, Tong Gao, Yuqing Deng, Ke Fang, Yewen Xu, Kai Jing, Guangyu Huang, Gengzhan Chen, Pengfei Yin, Yiming Li, Fuxing Zeng, Ruilin Tian, Meizhen Zheng.

  The three-dimensional (3D) chromatin structure of Epstein-Barr virus (EBV) within host cells and the underlying mechanisms of chromatin interaction and gene regulation, particularly those involving EBV's noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques of 3D genome mapping, including protein-associated chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), RNA-associated chromatin interaction technique (RDD), and super-resolution microscopy, to delineate the spatial architecture of EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E-E), EBV-to-host (E-H), and host-to-host (H-H) interactions linked to host proteins and EBV RNAs. Our findings reveal that EBV utilizes host CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) to form distinct chromatin contact domains (CCDs) and RNAPII-associated interaction domains (RAIDs). The anchors of these chromatin domains serve as platforms for extensive interactions with host chromatin, thus modulating host gene expression. Notably, EBV ncRNAs, especially Epstein-Barr-encoded RNAs (EBERs), target and interact with less accessible regions of host chromatin to repress a subset of genes via the inhibition of RNAPII-associated chromatin loops. This process involves the cofactor nucleolin (NCL) and its RNA recognition motifs, and depletion of either NCL or EBERs alters expression of genes crucial for host infection control, immune response, and cell cycle regulation. These findings unveil a sophisticated interplay between EBV and host chromatin.

Keywords:  3D Genome Mapping; EBV; Host–Virus Interactions; Spatial Architecture; ncRNA

DOI:  https://doi.org/10.1038/s44318-025-00466-5
Nat Struct Mol Biol. 2025 May 28.

A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA.

Ilana M Nodelman, Heather J Folkwein, Wesley S Glime, Jean-Paul Armache, Gregory D Bowman.

The Chd1 chromatin remodeler repositions nucleosomes into evenly spaced arrays, a characteristic of most eukaryotic genes. Here we show that the yeast Chd1 remodeler requires two activating segments to distort nucleosomal DNA into an A-form-like conformation, a critical first step in nucleosome sliding. As shown by cryo-electron microscopy, these two activating segments together pack against the ATPase motor, where they are poised to stabilize the central ATPase cleft. These activating elements contact the ATPase at locations that are incompatible with binding of NegC, an autoinhibitory segment located between the two activators. NegC inhibits sliding by antagonizing the activators through steric competition and constraining activator placement, giving rise to directional nucleosome sliding. Given that activator reinforcement of the ATPase cleft is needed for DNA distortion, this first step in remodeling appears to provide a natural checkpoint for regulation of chromatin remodeler activity.

DOI: https://doi.org/10.1038/s41594-025-01556-y
Bioinformatics. 2025 May 27. pii: btaf324. [Epub ahead of print]

scNucMap: mapping the nucleosome landscapes at single-cell resolution.

Qianming Xiang, Binbin Lai.

MOTIVATION: Nucleosome depletion around cis-regulatory elements (CREs) is associated with CRE activity and implies the underlying gene regulatory network. Single-cell micrococcal nuclease sequencing (scMNase-seq) enables the simultaneous measurement of nucleosome positioning and chromatin accessibility at single-cell resolution, thereby capturing cellular heterogeneity in epigenetic regulation. However, there is currently no computational tool specifically designed to decode scMNase-seq data, impeding the generation of more precise and context-dependent insights into chromatin dynamics and gene regulation.
RESULTS: Here, we present scNucMap, a tool designed to leverage the unique characteristics of scMNase-seq data to map the landscapes of candidate nucleosome-free regions (NFRs). scNucMap demonstrated superior performance and robustness in cell clustering on scMNase-seq data compared to Signac and chromVAR across diverse sample compositions and data complexities, achieving higher overall accuracy and Kappa coefficients. Additionally, scNucMap identified significant TFs associated with nucleosome depletion at CREs at both single-cell and cell-cluster levels, thereby facilitating cell-type annotation and regulatory network inference. When applied to scATAC-seq, scNucMap enriched standard analyses with complementary insights into nucleosome architecture, underscoring its cross‑modality versatility. Overall, scNucMap exhibits both high reliability and adaptability, making it an effective tool for analyzing scMNase-seq data and supporting multimodal studies, thereby illuminating the intricate relationship between regulatory networks and nucleosome positioning at single-cell resolution.
AVAILABILITY AND IMPLEMENTATION: scNucMap is available at https://github.com/qianming-bioinfo/scNucMap.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btaf324
Development. 2025 May 30. pii: dev.204518. [Epub ahead of print]

Donor embryonic stem cells displace host cells of 8-cell stage chimeras to the extraembryonic lineages by spatial crowding and FGF4 signalling.

Stanley E Strawbridge, Anna Katharina Schrattel, Peter Humphreys, Kenneth A Jones, Jérôme Artus, Anna-Katerina Hadjantonakis, Alexander G Fletcher, Jennifer Nichols.

  Following mouse embryo compaction, outer cells become trophectoderm, while inner cells form the inner cell mass (ICM), later differentiating into primitive endoderm and epiblast during blastocyst formation. Trophectoderm specification is driven by position-governed polarisation, while primitive endoderm specification is positively regulated by FGF4 signalling from the unspecified ICM and epiblast. When injected into an 8-cell stage morula, Embryonic stem cells (ESCs, derived from preimplantation epiblast cells in vitro) can exclude host cells from the epiblast, leading to mice derived entirely from these cells. While evidence suggests roles for ESC-produced FGF4 and physical crowding in host cell displacement from the ICM, the interplay between these possible mechanisms has yet to be dissected, in part due to the lack of studies using Fgf4-/- ESCs. Here, we combine chimera titration assays with mathematical modelling to study these mechanisms of host cell displacement. Both Fgf4+/+ and Fgf4-/- ESCs displaced host cells from the epiblast, while only Fgf4-/- injected embryos reduced primitive endoderm and increased trophectoderm, indicating sequential exclusion by displacement crowding followed by FGF4 signalling.

Keywords:  Bayesian inference.; Epiblast; Mathematical modelling; Mouse embryo; Primitive endoderm; Trophectoderm

DOI:  https://doi.org/10.1242/dev.204518
Nat Genet. 2025 May 27.

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.

Mai H Q Phan, Tobias Zehnder, Fiona Puntieri, Andreas Magg, Blanka Majchrzycka, Milan Antonović, Hannah Wieler, Bai-Wei Lo, Damir Baranasic, Boris Lenhard, Ferenc Müller, Martin Vingron, Daniel M Ibrahim.

Developmental gene expression is a remarkably conserved process, yet most cis-regulatory elements (CREs) lack sequence conservation, especially at larger evolutionary distances. Some evidence suggests that CREs at the same genomic position remain functionally conserved independent of sequence conservation. However, the extent of such positional conservation remains unclear. Here, we profiled the regulatory genome in mouse and chicken embryonic hearts at equivalent developmental stages and found that most CREs lack sequence conservation. To identify positionally conserved CREs, we introduced the synteny-based algorithm interspecies point projection, which identifies up to fivefold more orthologs than alignment-based approaches. We termed positionally conserved orthologs 'indirectly conserved' and showed that they exhibited chromatin signatures and sequence composition similar to sequence-conserved CREs but greater shuffling of transcription factor binding sites between orthologs. Finally, we validated indirectly conserved chicken enhancers using in vivo reporter assays in mouse. By overcoming alignment-based limitations, we revealed widespread functional conservation of sequence-divergent CREs.

DOI: https://doi.org/10.1038/s41588-025-02202-5
Nat Commun. 2025 May 30. 16(1): 5032

Transcriptomic insights into fate choice of pallial versus subpallial GABAergic neurons.

Lijuan Sun, Feng Xiong, Feier Huang, Shuangshuang Dong, Pei Zhu, Pengfei Jiang, Baoshen Zhang, Xinxin Zhang, Jie Sun, Hanchuan Peng, Chunjie Zhao.

The activity of the telencephalon is shaped by pallial and subpallial GABAergic neurons, two large populations produced in the embryonic ganglionic eminence. However, knowledge about the fate specification of neuron subtypes is limited, especially whether there is a common mechanism directing the fate choice of pallial versus subpallial populations remains unknown, largely because each population comprises numerous subtypes. Here, using sc-RNA sequencing combined with loss-of-function we profile ganglion eminence lineages and find that Foxg1 deletion causes the pallial population to adopt subpallial fates in mice. We delineate developmental trajectories and reveal FOXG1-driven transcriptional programs that specify neuron subtypes in each GE lineage and transcription factors that direct lineage bifurcation decisions. We uncover a common mechanism that drives pallial fate over subpallial fate across ganglion eminence lineages. Our study illuminates the control of production between pallial and subpallial populations and offers transcriptomic insights into the pathogenesis of GABAergic neuron-related disorders.

DOI: https://doi.org/10.1038/s41467-025-60338-8
Commun Biol. 2025 May 26. 8(1): 808

Discovery of candidate functional non-coding mutations in acute myeloid leukemia using single-cell chromatin accessibility sequencing.

Ming Zhu, Jiali Zhu, Zhijuan Zhu, Yiding Yang, Jinxian Dai, Hua Li, Nainong Li, Jialiang Huang.

Mutations and gene rearrangements are crucial for the diagnosis and subtyping of acute myeloid leukemia (AML). However, the contribution of non-coding genetic variants, particularly those within cis-regulatory elements (CREs), to AML pathophysiology and heterogeneity remains poorly understood. In this study, we characterize the single-cell chromatin accessibility landscapes of 10 bone marrow samples from AML patients at diagnosis. Additionally, we develop eMut, an integrated computational pipeline for detecting, imputing, and functionally characterizing non-coding mutations in CREs at the single-cell level. Our analysis identifies 2878 potential somatic non-coding mutations, highlighting the extensive mutational heterogeneity in the non-coding genome of AML patients, with recurrent non-coding mutations displaying cell type-specific patterns. We show that mutated CREs are enriched with blood-related genetic variants, potentially linked to AML-associated genes, and harbor a higher abundance of functional CREs, suggesting their functional relevance in leukemogenesis. Importantly, we pinpoint candidate functional non-coding mutations that associate with alteration of target gene expression in AML. Collectively, our work provides a comprehensive resource of single-cell chromatin accessibility in AML and introduces an integrative approach to identify candidate functional non-coding mutations contributing to cellular heterogeneity in AML.

DOI: https://doi.org/10.1038/s42003-025-08257-8
Nat Commun. 2025 May 26. 16(1): 4865

FOXA2 promotes metastatic competence in small cell lung cancer.

Kenta Kawasaki, Sohrab Salehi, Yingqian A Zhan, Kevin Chen, Jun Ho Lee, Eralda Salataj, Hong Zhong, Parvathy Manoj, Dennis Kinyua, Barbara P Mello, Harsha Sridhar, Sam E Tischfield, Irina Linkov, Nicholas Ceglia, Matthew Zatzman, Eliyahu Havasov, Neil J Shah, Fanli Meng, Brian Loomis, Umesh K Bhanot, Esther Redin, Elisa de Stanchina, Pierre-Jacques Hamard, Richard P Koche, Andrew McPherson, Álvaro Quintanal-Villalonga, Sohrab P Shah, Joan Massagué, Charles M Rudin.

Small cell lung cancer (SCLC) is known for its high metastatic potential, with most patients demonstrating clinically evident metastases in multiple organs at diagnosis. The factors contributing to this exceptional metastatic capacity have not been defined. To bridge this gap, we compare gene expression in SCLC patient samples who never experienced metastasis or relapse throughout their clinical course, versus primary SCLC patient samples from more typical patients who had metastatic disease at diagnosis. This analysis identifies FOXA2 as a transcription factor strongly associated with SCLC metastasis. Subsequent analyses in experimental models demonstrates that FOXA2 induces a fetal neuroendocrine gene expression program and promotes multi-site metastasis. Moreover, we identify ASCL1, a transcription factor known for its initiating role in SCLC tumorigenesis, as a direct binder of the FOXA2 promoter and regulator of FOXA2 expression. Taken together, these data define the ASCL1-FOXA2 axis as a critical driver of multiorgan SCLC metastasis.

DOI: https://doi.org/10.1038/s41467-025-60141-5
Proc Natl Acad Sci U S A. 2025 Jun 03. 122(22): e2505263122

Ethanol induction of FGF21 in the liver is dependent on histone acetylation and ligand activation of ChREBP by glycerol-3-phosphate.

Mi Cheong Cheong, Bryan Mackowiak, Hyung Bum Kim, Genaro Hernandez, Tulip Nandu, Kevin Vale, Yuan Zhang, Lauren G Zacharias, Thomas P Mathews, Bin Gao, W Lee Kraus, Steven A Kliewer, David J Mangelsdorf.

  Ethanol rapidly stimulates the liver to synthesize the hormone fibroblast growth factor 21 (FGF21), which then acts on the brain to elicit a multifaceted protective response. We show that in mice, this induction of FGF21 occurs at the level of gene transcription and is regulated by two byproducts of ethanol metabolism, glycerol-3-phosphate (G3P) and acetyl-CoA. Using cell-based reporter and thermal shift binding assays, we show that G3P binds to a conserved domain and activates the transcription factor carbohydrate-responsive element-binding protein (ChREBP), which regulates the Fgf21 gene promoter. The stimulation of Fgf21 gene transcription by ethanol also requires its metabolism to acetyl-CoA and correlates with histone acetylation. Accordingly, a p300/CBP histone acetyltransferase inhibitor blocks histone acetylation, ChREBP recruitment, and transcriptional activation at the Fgf21 promoter. Together, these findings reveal a dual regulatory mechanism driven by both G3P and acetyl-CoA that explains ethanol's robust stimulatory effect on Fgf21 and possibly other ChREBP target genes in the liver.

Keywords:  ChREBP; FGF21; alcohol; liver; transcription

DOI:  https://doi.org/10.1073/pnas.2505263122
Cell Death Dis. 2025 May 25. 16(1): 414

Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer.

Bengisu Dayanc, Sude Eris, Nazife Ege Gulfirat, Gulden Ozden-Yilmaz, Ece Cakiroglu, Ozlem Silan Coskun Deniz, Gökhan Karakülah, Serap Erkek-Ozhan, Serif Senturk.

Osimertinib, a third-generation EGFR tyrosine kinase inhibitor (EGFR-TKI), has dramatically transformed the treatment landscape for patients with EGFR-mutant NSCLC. However, the long-term success of this therapy is often compromised by the onset of acquired resistance, with non-genetic mechanisms increasingly recognized as pivotal contributors. Here, we exploit a multi-omics approach to profile genome-wide chromatin accessibility and transcriptional landscapes between drug sensitive and resistant EGFR-mutant cells. Our findings reveal a robust concordance between epigenetic regulome and transcriptomic changes that characterize the osimertinib resistant state. Through CRISPR-based functional genomics screen targeting epigenetic regulators and transcription factors, we uncover a critical regulatory network featuring key members of the NuRD and PRC2 complexes that mediate resistance. Most critically, our screen identifies FOSL1 and JUN, two subunits of the AP-1 transcription factor within this network, as the most significant hits. Mechanistically, we demonstrate that cis-regulatory elements exhibiting altered chromatin accessibility in the resistant state are enriched for cognate AP-1 binding motifs, enabling AP-1 to orchestrate a gene expression program that underpins the druggable MEK/ERK signaling axis, potentially enhancing cell viability and fitness of resistant cells. Importantly, genetic depletion or pharmacological inhibition of AP-1 reinstates cellular and molecular sensitivity, and reverts resistance-associated phenotypes, such as epithelial-to-mesenchymal transition, upon anti-EGFR rechallenge by repressing AKT and ERK signaling. These findings provide novel insights into the epigenetic and transcriptional control of osimertinib resistance in EGFR-mutant NSCLC, highlighting AP-1 as a targetable vulnerability of resistance-related hallmarks and offering a promising avenue for developing resistance reversal strategies.

DOI: https://doi.org/10.1038/s41419-025-07711-z
Mol Biol Evol. 2025 May 24. pii: msaf112. [Epub ahead of print]

The fire ant social chromosome exerts a major influence on genome regulation.

Beryl M Jones, Alex H Waugh, Michael A Catto, Sasha Kay, Karl M Glastad, Michael A D Goodisman, Sarah D Kocher, Brendan G Hunt.

  Supergenes underlying complex trait polymorphisms ensure sets of coadapted alleles remain genetically linked. Despite their prevalence in nature, the mechanisms of supergene effects on genome regulation are poorly understood. In the fire ant Solenopsis invicta, a supergene containing over 500 individual genes influences trait variation in multiple castes to collectively underpin a colony level social polymorphism. Here, we present results of an integrative investigation of supergene effects on gene regulation. We present analyses of ATAC-seq data to investigate variation in chromatin accessibility by supergene genotype and STARR-seq data to characterize enhancer activity by supergene haplotype. Integration with gene co-expression analyses, newly mapped intact transposable elements (TEs), and previously identified copy number variants (CNVs), collectively reveal widespread effects of the supergene on chromatin structure, gene transcription, and regulatory element activity, with a genome-wide bias for open chromatin and increased expression in the presence of the derived supergene haplotype, particularly in regions that harbor intact TEs. Integrated consideration of CNVs and regulatory element divergence suggests each evolved in concert to shape the expression of supergene encoded factors, including several transcription factors that may directly contribute to the trans-regulatory footprint of a heteromorphic social chromosome. Overall, we show how genome structure in the form of a supergene has wide-reaching effects on gene regulation and gene expression.

Keywords:  epigenetics; evolution; gene regulation; supergenes; trait polymorphism

DOI:  https://doi.org/10.1093/molbev/msaf112
J Clin Invest. 2025 May 27. pii: e189266. [Epub ahead of print]

Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes.

Srinivas Aluri, Te Ling, Ellen Fraint, Samarpana Chakraborty, Kevin Zhang, Aarif Ahsan, Leah Kravets, Gowri Poigaialwar, Rongbao Zhao, Kith Pradhan, Anitria Cotton, Kimo Bachiashvili, Jung-In Yang, Anjali Budhathoki, Beamon Agarwal, Shanisha Gordon-Mitchell, Milagros Carbajal, Srabani Sahu, Jacqueline Boultwood, Andrea Pellagatti, Ulrich Steidl, Amittha Wickrema, Satish Nandakumar, Aditi Shastri, Rajasekhar Nvs Suragani, Teresa V Bowman, John D Crispino, Sadanand Vodala, Amit Verma.

  Anemia is the primary clinical manifestation of myelodysplastic syndromes (MDS), but the molecular pathogenesis of ineffective erythropoiesis remains incompletely understood. Luspatercept, an activin receptor 2B (ACVRIIB-Fc) ligand trap, has been approved to treat anemia, however its molecular mechanism of action is unclear. We found that the ACVR2B, its ligand GDF11, and effector, SMAD2, are upregulated in MDS patient samples. GDF11 inhibited human erythropoiesis in vitro and caused anemia in zebrafish, effects that were abrogated by luspatercept. Upon GDF11 stimulation of human erythroid progenitors, SMAD2 binding occurred in the erythroid regulatory regions, including at GATA1 intron. Intronic SMAD2 binding led to skipping of exon 2 of GATA1, resulting in a shorter, hypomorphic isoform (GATA1s). CRISPR deletion of the SMAD2 binding intronic region decreased GATA1s production upon GDF11 stimulation. Expression of gata1s in a mouse model led to anemia, rescued by a murine ActRIIB-Fc (RAP-536). Finally, RNA-seq analysis of samples from the Phase 3 MEDALIST trial revealed that responders to Luspatercept had a higher proportion of GATA1s compared to non-responders. Moreover, the increase RBCs post-treatment was linked to a relative decrease in GATA1s isoform. Our study indicates that GDF11-mediated SMAD2 activation results in an increase in functionally impaired GATA1 isoforms, consequently contributing to anemia and influencing responses to Luspatercept in MDS.

Keywords:  Cell biology; Hematology; Hematopoietic stem cells

DOI:  https://doi.org/10.1172/JCI189266
Development. 2025 May 30. pii: dev.204524. [Epub ahead of print]

Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus.

Olga Lanzetta, Marchesa Bilio, Johannes Liebig, Katharina Jechow, Foo Wei Ten, Rosa Ferrentino, Ilaria Aurigemma, Elizabeth Illingworth, Christian Conrad, Soeren Lukassen, Claudia Angelini, Antonio Baldini.

  TBX1, a T-BOX transcription factor, is essential for pharyngeal apparatus development and marks cardiopharyngeal mesoderm (CPM) in various species. However, in mammals, we have an incomplete knowledge of the molecular pathways driving CPM diversification and of the role of TBX1 in this context. Using CPM relevant in vitro differentiation of WT and Tbx1-/- mouse embryonic stem cells, we performed simultaneous single-nucleus RNA-seq and ATAC-seq at two stages, validated findings in embryos, and found that TBX1 loss affects gene expression and chromatin remodeling in a cell subpopulation-specific manner. TBX1 regulates chromatin accessibility and gene expression of distinct and evolutionary conserved transcriptional modules for branchiomeric and cardiac development, and for tissue morphogenesis. Computational analyses predicted a feed-forward regulatory relationship between TBX1 and SIX factors. Notably, selected Tbx1 mutant CPM cell populations showed altered differentiation trajectory, exhibiting activation of a mesothelial-like transcriptional program. We also observed cell death later in development. Thus, TBX1 is crucial for maintaining CPM transcriptional identity.

Keywords:  Cardiopharyngeal mesoderm; Tbx1; differentiation robustness

DOI:  https://doi.org/10.1242/dev.204524
Science. 2025 May 29.

Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation.

Ajay S Labade, Zachary D Chiang, Caroline Comenho, Paul L Reginato, Andrew C Payne, Andrew S Earl, Rojesh Shrestha, Fabiana M Duarte, Ehsan Habibi, Ruochi Zhang, George M Church, Edward S Boyden, Fei Chen, Jason D Buenrostro.

Microscopy and genomics are used to characterize cell function, but approaches to connect the two types of information are lacking, particularly at subnuclear resolution. Here, we describe expansion in situ genome sequencing (ExIGS), a technology that enables sequencing of genomic DNA and superresolution localization of nuclear proteins in single cells. Applying ExIGS to progeria-derived fibroblasts revealed that lamin abnormalities are linked to hotspots of aberrant chromatin regulation that may erode cell identity. Lamin was found to generally repress transcription, suggesting variation in nuclear morphology may affect gene regulation across tissues and aged cells. These results demonstrate that ExIGS may serve as a generalizable platform to link nuclear abnormalities to gene regulation, offering insights into disease mechanisms.

DOI: https://doi.org/10.1126/science.adt2781
Nat Commun. 2025 May 27. 16(1): 4907

Structural plasticity of the FOXO-DBD:p53-TAD interaction.

Klara Kohoutova, Pavel Srb, Veronika Obsilova, Vaclav Veverka, Tomas Obsil.

The transcription factors FOXO4 and p53 regulate aging, and their deregulation has been linked to several diseases, including cancer. Under stress conditions, cellular senescence is promoted by p53 sequestration and senescence-associated protein p21 transcriptional upregulation induced by interactions between the FOXO4 Forkhead DNA-binding domain and the p53 transactivation domain. However, the molecular details of these interactions remain unclear. Here, we report that these interactions between p53 and FOXO4 domains are highly heterogeneous. The p53 transactivation domain primarily interacts with the region formed by the N-terminal helical bundle of the FOXO4 Forkhead domain but retains a substantial degree of flexibility in the complex. In addition, NMR data-driven molecular simulations suggest that p53 interacts with FOXO4 through multiple binding modes. Overall, our findings not only provide the structural insights into interactions between FOXO4 and p53 but also highlight their potential as targets for developing senolytic compounds.

DOI: https://doi.org/10.1038/s41467-025-59106-5