bims-crepig 2025-05-11 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–05–11
29 papers selected by
Connor Rogerson, University of Cambridge

Structural basis of human CHD1 nucleosome recruitment and pausing.
Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation.
LEC2 induces somatic cell reprogramming through epigenetic activation of plant cell totipotency regulators.
Extensive folding variability between homologous chromosomes in mammalian cells.
Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper.
Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations.
Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.
Comparative analysis of gene regulation in single cells using Compass.
Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila.
The developmental factor TBX3 engages with the Wnt/β-catenin transcriptional complex in colorectal cancer to regulate metastasis genes.
Design principles of cell-state-specific enhancers in hematopoiesis.
Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors.
A distal enhancer with ETV4 binding is critical for UCP1 expression and thermogenesis in brown fat.
Native nucleosomes intrinsically encode genome organization principles.
The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription.
ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types.
Cis-Regulation of the CFTR Gene in Pancreatic Cells.
Human DNA replication initiation sites are specified epigenetically by oxidation of 5-methyl-deoxycytidine.
Chromatin state origins of uterine leiomyoma.
VGLL2 and TEAD1 fusion proteins identified in human sarcoma drive YAP/TAZ-independent tumorigenesis by engaging EP300.
Chromatin loops are an ancestral hallmark of the animal regulatory genome.
Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells.
CORESH: a gene signature-based search engine for public gene expression datasets.
The multilayered transcriptional architecture of glioblastoma ecosystems.
IVA Prime: automated primer design for in vivo assembly cloning.
DUX4 activates common and context-specific intergenic transcripts and isoforms.
The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution.
Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics.
Retroelement co-option disrupts the cancer transcriptional programme.

Mol Cell. 2025 May 02. pii: S1097-2765(25)00362-4. [Epub ahead of print]

Structural basis of human CHD1 nucleosome recruitment and pausing.

Allison M James, Lucas Farnung.

  Chromatin remodelers regulate gene expression and genome maintenance by controlling nucleosome positioning, but the structural basis for their regulated and directional activity remains poorly understood. Here, we present three cryoelectron microscopy (cryo-EM) structures of human chromodomain helicase DNA-binding protein 1 (CHD1) bound to nucleosomes that reveal previously unobserved recruitment and regulatory states. We identify a structural element, termed the "anchor element," that connects the CHD1 ATPase motor to the nucleosome entry-side acidic patch. The anchor element coordinates with other regulatory modules, including the gating element, which undergoes a conformational switch critical for remodeling. Our structures demonstrate how the DNA-binding region of CHD1 binds entry- and exit-side DNA during remodeling to achieve directional sliding. The observed structural elements are conserved across chromatin remodelers, suggesting a unified mechanism for nucleosome recognition and remodeling. Our findings show how chromatin remodelers couple nucleosome recruitment to regulated DNA translocation, providing a framework for understanding chromatin remodeler mechanisms beyond DNA translocation.

Keywords:  chromatin remodeling; cryo-EM; gene expression; genome organization; histone methylation; histone modification; nucleosome; nucleosome sliding; structural biology; transcription

DOI:  https://doi.org/10.1016/j.molcel.2025.04.020
BMC Genomics. 2025 May 08. 26(1): 454

Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation.

Mingzhu Fu, Long Pang, Zhenwei Wu, Mei Wang, Jin Jin, Shanshan Ai, Xin Li.

  Gastrulation represents a crucial stage in embryonic development and is tightly controlled by a complex network involving epigenetic reprogramming. However, the molecular coordination among distinct epigenetic layers entailing the progressive restriction of lineage potency remains unclear. Here, we present a multi-omics map of H3K27ac and H3K4me1 single-cell ChIP-seq profiles of mouse embryos collected at six sequential time points. Significant epigenetic priming, as reflected by H3K27ac signals, is evident, yet asynchronous cell fate commitment of each germ layer at distinct histone modification levels are observed. Integrated scRNA-seq and single-cell ChIP-seq analysis unveil a "time lag" transition pattern between enhancer activation and gene expression during germ-layer specification. Notably, by utilizing the H3K27ac and H3K4me1 co-marked active enhancers, we construct a gene regulatory network centered on pivotal transcription factors, highlighting the potential critical role of Cdkn1c in mesoderm lineage specification. Together, our study broadens the current understanding of intricate epigenetic regulatory networks governing mouse gastrulation and sheds light on their relevance to congenital diseases.

Keywords:  Cell fate; Enhancer; Epigenetic; Gastrulation; Single-cell

DOI:  https://doi.org/10.1186/s12864-025-11619-5
Nat Commun. 2025 May 06. 16(1): 4185

LEC2 induces somatic cell reprogramming through epigenetic activation of plant cell totipotency regulators.

Jing Peng, Qi Zhang, Li Ping Tang, Biao Jie Xu, Thomas Laux, Xian Sheng Zhang, Ying Hua Su.

Many plant species can develop embryos from somatic cells without fertilization. During this process, known as somatic embryogenesis, changes in the DNA methylation patterns are characteristic of reprogramming somatic cells into an embryogenic state. However, the underlying mechanisms connecting DNA methylation and activating totipotency-regulating genes have remained largely unknown. Here, we show that during somatic embryogenesis induced by overexpressing the totipotency-regulating transcription factor LEAFY COTYLEDON2 (LEC2) in Arabidopsis, CHH hypermethylation is deposited by the LEC2-activated RNA-directed DNA methylation (RdDM) pathway. A reader complex composed of SU(VAR)3-9 HOMOLOGS (SUVH) and its chaperone SUVH-INTERACTING DNAJ DOMAIN-CONTAINING PROTEIN (SDJ) binds to the CHH hypermethylated regions and recruits AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) chromatin modification proteins to increase chromatin accessibility, resulting in the transcriptional activation of totipotency-regulating genes. Our work reveals a molecular framework of how epigenetic modifications mediate somatic cell reprogramming, offering a pathway toward enhancing somatic embryogenesis in agricultural regeneration biology.

DOI: https://doi.org/10.1038/s41467-025-59335-8
Mol Syst Biol. 2025 May 06.

Extensive folding variability between homologous chromosomes in mammalian cells.

Ibai Irastorza-Azcarate, Alexander Kukalev, Rieke Kempfer, Christoph J Thieme, Guido Mastrobuoni, Julia Markowski, Gesa Loof, Thomas M Sparks, Emily Brookes, Kedar Nath Natarajan, Stephan Sauer, Amanda G Fisher, Mario Nicodemi, Bing Ren, Roland F Schwarz, Stefan Kempa, Ana Pombo.

  Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single-nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, and with Polycomb occupancy. We show that histone genes are expressed with allelic imbalance in mESCs, and are involved in haplotype-specific chromatin contacts marked by H3K27me3. Conditional knockouts of Polycomb enzymatic subunits, Ezh2 or Ring1, show that one-third of ASE genes, including histone genes, is regulated through Polycomb repression. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.

Keywords:  Allele-specific Expression; Gene Regulation; Genome Structure; Histone Locus; Polycomb

DOI:  https://doi.org/10.1038/s44320-025-00107-3
Genome Biol. 2025 May 08. 26(1): 121

Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper.

Hongji Yang, Guorong Yu, Zhidong Lv, Tonghui Li, Xi Wang, Ying Fu, Zhangsheng Zhu, Guangjun Guo, Hang He, Ming Wang, Guochen Qin, Feng Liu, Zhenhui Zhong, Yan Xue.

   BACKGROUND: Pepper (Capsicum annuum) is one of the earliest and most widely cultivated vegetable crops worldwide. While the large and complex genome of pepper severely hampered the understanding of its functional genome, it also indicates a rich yet unexplored reservoir of regulatory elements (REs). In fact, variations in the REs represent a major driving force in evolution and domestication in both plants and animals. However, identification of the REs remains difficult especially for plants with complex genomes.
RESULTS: Here, we present a comprehensive epigenomic landscape of Capsicum annuum, Zhangshugang (ST-8), including chromatin accessibility, histone modifications, DNA methylation, and transcriptome. We also develop comparative crosslinked immunoprecipitation mass spectrometry to reveal the proteome associated with certain chromatin features. Through integrated analysis of these epigenetic features, we profile promoters and enhancers involved in development, heat stress and cucumber mosaic virus challenges. We generate stress responsive expression networks composed of potential transcription activators and their target genes. Through population genetics analysis, we demonstrate that some regulatory elements show lower nucleotide diversity compare to other genomic regions during evolution.
CONCLUSIONS: We demonstrate that variations in the REs may contribute to more diversified and agronomically desired phenotypes. Our study provides a foundation not only for studying gene regulation, but also for targeted genetic and epigenetic manipulation for pepper improvement.

Keywords:   Cis-regulatory element; Development; Disease; Enhancer; Epigenome; Heat stress; Pepper (Capsicum spp.); Promoter; Proteome; Transcriptional regulation

DOI:  https://doi.org/10.1186/s13059-025-03595-6
Genome Biol. 2025 May 09. 26(1): 124

Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations.

Sebastian Gregoricchio, Aleksandar Kojic, Marlous Hoogstraat, Karianne Schuurman, Suzan Stelloo, Tesa M Severson, Tracy A O'Mara, Marjolein Droog, Abhishek A Singh, Dylan M Glubb, Lodewyk F A Wessels, Michiel Vermeulen, Flora E van Leeuwen, Wilbert Zwart.

   BACKGROUND: The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERα) for proliferation, but little is known about its transcriptional regulation in these tumors.
RESULTS: We generate epigenomics, transcriptomics, and Hi-C datastreams in healthy and tumor endometrial tissues, identifying robust ERα reprogramming and profound alterations in 3D genome organization that lead to a gain of tumor-specific enhancer activity during EC development. Integration with endometrial cancer risk single-nucleotide polymorphisms and whole-genome sequencing data from primary tumors and metastatic samples reveals a striking enrichment of risk variants and non-coding somatic mutations at tumor-enriched ERα sites. Through machine learning-based predictions and interaction proteomics analyses, we identify an enhancer mutation which alters 3D genome conformation, impairing recruitment of the transcriptional repressor EHMT2/G9a/KMT1C, thereby alleviating transcriptional repression of ESR1 in EC.
CONCLUSIONS: In summary, we identify a complex genomic-epigenomic interplay in EC development and progression, altering 3D genome organization to enhance expression of the critical driver ERα.

Keywords:  3D genome organization; Endometrial cancer; Epigenetic plasticity in tumor development; Estrogen receptor; Gene regulation; Non-coding somatic mutations

DOI:  https://doi.org/10.1186/s13059-025-03596-5
Nat Commun. 2025 May 07. 16(1): 4255

Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli.

Patrick Lally, Laura Gómez-Romero, Víctor H Tierrafría, Patricia Aquino, Claire Rioualen, Xiaoman Zhang, Sunyoung Kim, Gabriele Baniulyte, Jonathan Plitnick, Carol Smith, Mohan Babu, Julio Collado-Vides, Joseph T Wade, James E Galagan.

The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs using ChIP-Seq. We use these data to train BoltzNet, a novel neural network that predicts TF binding energy from DNA sequence. BoltzNet mirrors a quantitative biophysical model and provides directly interpretable predictions genome-wide at nucleotide resolution. We use BoltzNet to quantitatively design novel binding sites, which we validate with biophysical experiments on purified protein. We generate models for 124 TFs that provide insight into global features of TF binding, including clustering of sites, the role of accessory bases, the relevance of weak sites, and the background affinity of the genome. Our paper provides new paradigms for studying TF-DNA binding and for the development of biophysically motivated neural networks.

DOI: https://doi.org/10.1038/s41467-025-58862-8
Cell Rep Methods. 2025 Apr 30. pii: S2667-2375(25)00071-2. [Epub ahead of print] 101035

Comparative analysis of gene regulation in single cells using Compass.

Changxin Wan, Yilong Qu, Zhiyou Ye, Tianbei Zhang, Huifang Ma, Ming Chen, Wenpin Hou, Zhicheng Ji.

  Single-cell multi-omics is a transformative technology that measures both gene expression and chromatin accessibility in individual cells. However, most studies concentrate on a single tissue and are unable to determine whether a gene is regulated by a cis-regulatory element (CRE) in just one tissue or across multiple tissues. We developed Compass for comparative analysis of gene regulation across a large number of human and mouse tissues. Compass consists of a database, CompassDB, and an open-source R software package, CompassR. CompassDB contains processed single-cell multi-omics data of more than 2.8 million cells from hundreds of cell types. Building upon CompassDB, CompassR enables visualization and comparison of gene regulation across multiple tissues. We demonstrated that CompassR can identify CRE-gene linkages specific to a tissue type and their associated transcription factors in real examples.

Keywords:  CP: Systems biology; cis-regulatory elements; gene regulation; single-cell ATAC-seq; single-cell multi-omics

DOI:  https://doi.org/10.1016/j.crmeth.2025.101035
Genome Biol. 2025 May 08. 26(1): 116

Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila.

Sandrine Denaud, Gonzalo Sabarís, Marco Di Stefano, Giorgio-Lucio Papadopoulos, Bernd Schuettengruber, Giacomo Cavalli.

  The tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation and structure. By either deleting or shifting key regulatory elements needed to establish the epigenetic signature of Polycomb TADs, we show that the epigenome is not a major driving force for the establishment of TADs. On the other hand, physical domains have an important impact on the formation of epigenetic domains, as they can restrict the spreading of repressive histone marks and looping between cis-regulatory elements.

Keywords:   Drosophila ; Chromatin; Epigenome; Genome organization; PcG proteins; TADs

DOI:  https://doi.org/10.1186/s13059-025-03587-6
Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2419691122

The developmental factor TBX3 engages with the Wnt/β-catenin transcriptional complex in colorectal cancer to regulate metastasis genes.

Amaia Jauregi-Miguel, Simon Söderholm, Tamina Weiss, Anna Nordin, Valeria Ghezzi, Salome M Brütsch, Pierfrancesco Pagella, Yorick van de Grift, Gianluca Zambanini, Jacopo Ulisse, Alessandro Mattia, Ruslan Deviatiiarov, Elena Faustini, Lavanya Moparthi, Wenjing Zhong, Bergthor Björnsson, Per Sandström, Erik Lundqvist, Francisca Lottersberger, Stefan Koch, Andreas E Moor, Xiao-Feng Sun, Eleonore von Castelmur, Guojun Sheng, Claudio Cantù.

  Wnt signaling orchestrates gene expression in a plethora of processes during development and adult cell homeostasis via the action of nuclear β-catenin. Yet, little is known about how β-catenin generates context-specific transcriptional outcomes. Understanding this will reveal how aberrant Wnt/β-catenin signaling causes neoplasia specifically of the colorectal epithelium. We have previously identified the transcription factor TBX3 as a tissue-specific component of the Wnt/β-catenin nuclear complex during mouse forelimb development. In this study, we show that TBX3 is functionally active in human colorectal cancer (CRC). Here, genome-wide binding and transcriptomics analyses reveal that TBX3 regulates cancer metastasis genes in cooperation with Wnt/β-catenin. Proteomics proximity labeling performed across Wnt pathway activation shows that TBX3 engages with several transcription factors and chromatin remodeling complexes found at Wnt responsive elements (WRE). Protein sequence and structure analysis of TBX3 revealed short motifs, including an exposed Asn-Pro-Phe (NPF), that mediate these interactions. Deletion of these motifs abrogates TBX3's proximity to its protein partners and its ability to enhance the Wnt-dependent transcription. TBX3 emerges as a key modulator of the oncogenic activity of Wnt/β-catenin in CRC, and its mechanism of action exposes protein-interaction surfaces as putative druggable targets.

Keywords:  CUT&RUN; TBX3; Wnt signaling; proximity proteomics; β-catenin

DOI:  https://doi.org/10.1073/pnas.2419691122
Cell. 2025 May 07. pii: S0092-8674(25)00449-0. [Epub ahead of print]

Design principles of cell-state-specific enhancers in hematopoiesis.

Robert Frömel, Julia Rühle, Aina Bernal Martinez, Chelsea Szu-Tu, Felix Pacheco Pastor, Rosa Martinez-Corral, Lars Velten.

  During cellular differentiation, enhancers transform overlapping gradients of transcription factors (TFs) to highly specific gene expression patterns. However, the vast complexity of regulatory DNA impedes the identification of the underlying cis-regulatory rules. Here, we characterized 64,400 fully synthetic DNA sequences to bottom-up dissect design principles of cell-state-specific enhancers in the context of the differentiation of blood stem cells to seven myeloid lineages. Focusing on binding sites for 38 TFs and their pairwise interactions, we found that identical sites displayed both repressive and activating function as a consequence of cell state, site combinatorics, or simply predicted occupancy of a TF on an enhancer. Surprisingly, combinations of activating sites frequently neutralized one another or gained repressive function. These negative synergies convert quantitative imbalances in TF expression into binary activity patterns. We exploit this principle to automatically create enhancers with specificity to user-defined combinations of hematopoietic progenitor cell states from scratch.

Keywords:  MPRA; cellular differentiation; functional genomics; gene regulation; hematopoiesis; synthetic enhancers; transcription factors

DOI:  https://doi.org/10.1016/j.cell.2025.04.017
Nat Commun. 2025 May 09. 16(1): 4325

Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors.

Nikoletta Psatha, Pavel Sova, Grigorios Georgolopoulos, Kiriaki Paschoudi, Mineo Iwata, Jordan Bloom, Tatyana Ulyanova, Hao Wang, Alexandra Kirtsou, Ninos-Ioannis Vasiloudis, Matthew S Wilken, John A Stamatoyannopoulos, Evangelia Yannaki, Thalia Papayanopoulou, George Stamatoyannopoulos, Jeff Vierstra.

Gene expression during cell development and differentiation is orchestrated by distal regulatory elements that precisely modulate cell selective gene activity. Gene therapy vectors leverage these elements for precise spatiotemporal transgene expression. Here, we develop a one-shot approach to screen candidate regulatory sequences from large-scale epigenomics data for programmable transgene expression within gene therapy viral vectors. We assess a library of 15,000 short sequences derived from developmentally active elements during erythropoiesis using a clinically relevant reporter vector. These elements display a gradient of transcriptional enhancer activity in erythroid cells, with high cell type restriction and developmental stage specificity. Finally, replacing the canonical β-globin μLCR with a compact enhancer in a β-thalassemia lentiviral vector successfully corrects the thalassemic phenotype in patient-derived hematopoietic and stem and progenitor cells (HSPCs), while increasing viral titers and cell transducibility. Our approach provides further insights into enhancer biology with wider implications for human gene therapy.

DOI: https://doi.org/10.1038/s41467-025-59235-x
Genes Dev. 2025 May 05.

A distal enhancer with ETV4 binding is critical for UCP1 expression and thermogenesis in brown fat.

Pengya Xue, Nicholas Holloway, Alexander Tran, Frances Lin, Jennie Dinh, Caleb Yang, Yuhui Wang, Danielle Yi, Hei Sook Sul.

  Brown adipose tissue (BAT) dissipates energy as heat in maintaining body temperature, and BAT mass inversely correlates with adiposity. During thermogenesis, BAT generates heat by uncoupling respiration through UCP1, and the -2.5 kb enhancer of UCP1 gene is known to activate UCP1 expression upon cold or β-adrenergic stimulation. Here, we identify a critical UCP1 enhancer located at 12 kb upstream of the UCP1 gene locus that functions through chromatin looping and uncover its essential role in UCP1 activation and thermogenesis by CRISPR activation and CRISPR interference in mice. Importantly, we identify ETV4 as a key regulator of UCP1 expression by binding the -12 kb enhancer to promote chromatin accessibility and histone acetylation. Using gain- and loss-of-function approaches, we reveal that ETV4 enhances uncoupled respiration and thermogenesis, thereby protecting mice from diet-induced obesity and insulin resistance. The -12 kb enhancer and ETV4 can be potential therapeutic targets for combating obesity and improving metabolic health.

Keywords:  UCP1; brown fat; thermogenesis; transcription factor

DOI:  https://doi.org/10.1101/gad.352748.125
Nature. 2025 May 07.

Native nucleosomes intrinsically encode genome organization principles.

Sangwoo Park, Raquel Merino-Urteaga, Violetta Karwacki-Neisius, Gustavo Ezequiel Carrizo, Advait Athreya, Alberto Marin-Gonzalez, Nils A Benning, Jonghan Park, Michelle M Mitchener, Natarajan V Bhanu, Benjamin A Garcia, Bin Zhang, Tom W Muir, Erika L Pearce, Taekjip Ha.

The eukaryotic genome is packed into nucleosomes of 147 base pairs around a histone core and is organized into euchromatin and heterochromatin, corresponding to the A and B compartments, respectively1,2. Here we investigated whether individual nucleosomes contain sufficient information for 3D genomic organization into compartments, for example, in their biophysical properties. We purified native mononucleosomes to high monodispersity and used physiological concentrations of polyamines to determine their condensability. The chromosomal regions known to partition into A compartments have low condensability and those for B compartments have high condensability. Chromatin polymer simulations using condensability as the only input, without any trans factors, reproduced the A/B compartments. Condensability is also strongly anticorrelated with gene expression, particularly near the promoters and in a cell type-dependent manner. Therefore, mononucleosomes have biophysical properties associated with genes being on or off. Comparisons with genetic and epigenetic features indicate that nucleosome condensability is an emergent property, providing a natural axis on which to project the high-dimensional cellular chromatin state. Analysis using various condensing agents or histone modifications and mutations indicates that the genome organization principle encoded into nucleosomes is mostly electrostatic in nature. Polyamine depletion in mouse T cells, resulting from either knocking out or inhibiting ornithine decarboxylase, results in hyperpolarized condensability, indicating that when cells cannot rely on polyamines to translate the biophysical properties of nucleosomes to 3D genome organization, they accentuate condensability contrast, which may explain the dysfunction observed with polyamine deficiency3-5.

DOI: https://doi.org/10.1038/s41586-025-08971-7
Nat Commun. 2025 May 03. 16(1): 4133

The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription.

Katharine Umphred-Wilson, Shashikala Ratnayake, Qianzi Tang, Rui Wang, Sneha Ghosh Chaudhary, Devaiah N Ballachanda, Josephine Trichka, Jan Wisniewski, Lan Zhou, Qingrong Chen, Daoud Meerzaman, Dinah S Singer, Stanley Adoro.

Addiction to oncogene-rewired transcriptional networks is a therapeutic vulnerability in cancer cells, underscoring a need to better understand mechanisms that relay oncogene signals to the transcriptional machinery. Here, using human and mouse T cell acute lymphoblastic leukemia (T-ALL) models, we identify an essential requirement for the endosomal sorting complex required for transport protein CHMP5 in T-ALL epigenetic and transcriptional programming. CHMP5 is highly expressed in T-ALL cells where it mediates recruitment of the coactivator BRD4 and the histone acetyl transferase p300 to enhancers and super-enhancers that enable transcription of T-ALL genes. Consequently, CHMP5 depletion causes severe downregulation of critical T-ALL genes, mitigates chemoresistance and impairs T-ALL initiation by oncogenic NOTCH1 in vivo. Altogether, our findings uncover a non-oncogene dependency on CHMP5 that enables T-ALL initiation and maintenance.

DOI: https://doi.org/10.1038/s41467-025-59504-9
Genome Biol. 2025 May 09. 26(1): 123

ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types.

Tevfik Umut Dincer, Jason Ernst.

  We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genomewide predictions of regulatory activity associated with each functional characterization dataset across many cell types based on available epigenomic data. It then for each cell type produces ChromScoreHMM genome annotations based on the combinatorial and spatial patterns within these predictions and ChromScore tracks of overall predicted regulatory activity. ChromActivity provides a resource for analyzing and interpreting the human regulatory genome across diverse cell types.

Keywords:  CRISPR screens; Epigenome; Gene regulation; Genome annotation; Hidden Markov model; Machine learning; Massively parallel reporter assays

DOI:  https://doi.org/10.1186/s13059-025-03579-6
Int J Mol Sci. 2025 Apr 17. pii: 3788. [Epub ahead of print]26(8):

Cis-Regulation of the CFTR Gene in Pancreatic Cells.

Clara Blotas, Anaïs Le Nabec, Mégane Collobert, Mattijs Bulcaen, Marianne S Carlon, Claude Férec, Stéphanie Moisan.

  Genome organization is essential for precise spatial and temporal gene expression and relies on interactions between promoters and distal cis-regulatory elements (CREs), which constitute ~8% of the human genome. For the cystic fibrosis transmembrane conductance regulator (CFTR) gene, tissue-specific expression, especially in the pancreas, remains poorly understood. Unraveling its regulation could clarify the clinical heterogeneity observed in cystic fibrosis and CFTR-related disorders. To understand the role of 3D chromatin architecture in establishing tissue-specific expression of the CFTR gene, we mapped chromatin interactions and epigenomic regulation in Capan-1 pancreatic cells. Candidate CREs are validated by luciferase reporter assay and CRISPR knock-out. We identified active CREs not only around the CFTR gene but also outside the topologically associating domain (TAD). We demonstrate the involvement of multiple CREs upstream and downstream of the CFTR gene and reveal a cooperative effect of the -44 kb, -35 kb, +15.6 kb, and +37.7 kb regions, which share common predicted transcription factor (TF) motifs. We also extend our analysis to compare 3D chromatin conformation in intestinal and pancreatic cells, providing valuable insights into the tissue specificity of CREs in regulating CFTR gene expression.

Keywords:  3D genome; 4C; ATAC; CFTR; CRISPR/Cas9; H3K27ac; chromatin; cis-regulatory element (CRE); pancreas; tissue specificity

DOI:  https://doi.org/10.3390/ijms26083788
Nucleic Acids Res. 2025 Apr 22. pii: gkaf362. [Epub ahead of print]53(8):

Human DNA replication initiation sites are specified epigenetically by oxidation of 5-methyl-deoxycytidine.

Torsten Krude, Jiaming Bi, Rachel Doran, Rebecca A Jones, James C Smith.

DNA replication initiates at tens of thousands of sites on the human genome during each S phase. However, no consensus DNA sequence has been found that specifies the locations of these replication origins. Here, we investigate modifications of human genomic DNA by density equilibrium centrifugation and DNA sequencing. We identified short discrete sites with increased density during quiescence and G1 phase that overlap with DNA replication origins before their activation in S phase. The increased density is due to the oxidation of 5-methyl-deoxycytidines by ten-eleven-translocation DNA dioxygenase (TET) enzymes at GC-rich domains. Reversible inhibition of de novo methylation and of subsequent oxidation of deoxycytidines results in a reversible inhibition of DNA replication and of cell proliferation. Our findings suggest a mechanism for the epigenetic specification and semiconservative inheritance of DNA replication origin sites in human cells that also provides a stable integral DNA replication licence to support once-per-cell cycle control of origin activation.

DOI: https://doi.org/10.1093/nar/gkaf362
Nat Commun. 2025 May 08. 16(1): 4307

Chromatin state origins of uterine leiomyoma.

FinnGen

Aberrations in the regulatory genome play a pivotal role in population-level disease predisposition. Annotation of the regulatory regions using appropriate primary tissues - instead of cell lines affected by selection and other confounding factors - could shed new light into mechanisms underlying common conditions. We test this approach in uterine leiomyomas, highly prevalent benign neoplasms of the myometrium, by creating 15-state chromatin annotations for myometrium and uterine leiomyomas. Integration with RNA-seq, ATAC-seq, HiChIP and methylation data enables us to compare the epigenomes of myometrium and ULs with distinct driver mutations, highlighting the role of bivalent regions in the neoplastic process. Subsequently, a genome wide association study meta-analysis is performed, using three different cohorts. Disease association loci are enriched at active chromatin, especially at enhancers, and harbor tumor- and driver mutation-specific chromatin states. At SATB2 locus we show the effect of the risk genotype already in the normal tissue. Integration of genome-wide association studies and deep regulatory genomics data from the correct tissue type represents a powerful approach in understanding population-level disease predisposition.

DOI: https://doi.org/10.1038/s41467-025-59646-w
Elife. 2025 May 08. pii: RP98386. [Epub ahead of print]13

VGLL2 and TEAD1 fusion proteins identified in human sarcoma drive YAP/TAZ-independent tumorigenesis by engaging EP300.

Susu Guo, Xiaodi Hu, Jennifer L Cotton, Lifang Ma, Qi Li, Jiangtao Cui, Yongjie Wang, Ritesh P Thakare, Zhipeng Tao, Y Tony Ip, Xu Wu, Jiayi Wang, Junhao Mao.

  Studies on Hippo pathway regulation of tumorigenesis largely center on YAP and TAZ, the transcriptional co-regulators of TEADs. Here, we present an oncogenic mechanism involving VGLL and TEAD fusions that is Hippo pathway-related but YAP/TAZ-independent. We characterize two recurrent fusions, VGLL2-NCOA2 and TEAD1-NCOA2, recently identified in human spindle cell rhabdomyosarcoma. We demonstrate that in contrast to VGLL2 and TEAD1 the fusion proteins are potent activators of TEAD-dependent transcription, and the function of these fusion proteins does not require YAP/TAZ. Furthermore, we identify that VGLL2 and TEAD1 fusions engage specific epigenetic regulation by recruiting histone acetyltransferase EP300 to control TEAD-mediated transcriptional and epigenetic landscapes. We show that small-molecule EP300 inhibition can suppress fusion protein-induced oncogenic transformation both in vitro and in vivo in mouse models. Overall, our study reveals a molecular basis for VGLL involvement in cancer and provides a framework for targeting tumors carrying VGLL, TEAD, or NCOA translocations.

Keywords:  EP300; HIPPO; NCOA2; TEAD; VGLL2; YAP; cancer biology; developmental biology; human

DOI:  https://doi.org/10.7554/eLife.98386
Nature. 2025 May 07.

Chromatin loops are an ancestral hallmark of the animal regulatory genome.

Iana V Kim, Cristina Navarrete, Xavier Grau-Bové, Marta Iglesias, Anamaria Elek, Grygoriy Zolotarov, Nikolai S Bykov, Sean A Montgomery, Ewa Ksiezopolska, Didac Cañas-Armenteros, Joan J Soto-Angel, Sally P Leys, Pawel Burkhardt, Hiroshi Suga, Alex de Mendoza, Marc A Marti-Renom, Arnau Sebé-Pedrós.

In bilaterian animals, gene regulation is shaped by a combination of linear and spatial regulatory information. Regulatory elements along the genome are integrated into gene regulatory landscapes through chromatin compartmentalization1,2, insulation of neighbouring genomic regions3,4 and chromatin looping that brings together distal cis-regulatory sequences5. However, the evolution of these regulatory features is unknown because the three-dimensional genome architecture of most animal lineages remains unexplored6,7. To trace the evolutionary origins of animal genome regulation, here we characterized the physical organization of the genome in non-bilaterian animals (sponges, ctenophores, placozoans and cnidarians)8,9 and their closest unicellular relatives (ichthyosporeans, filastereans and choanoflagellates)10 by combining high-resolution chromosome conformation capture11,12 with epigenomic marks and gene expression data. Our comparative analysis showed that chromatin looping is a conserved feature of genome architecture in ctenophores, placozoans and cnidarians. These sequence-determined distal contacts involve both promoter-enhancer and promoter-promoter interactions. By contrast, chromatin loops are absent in the unicellular relatives of animals. Our findings indicate that spatial genome regulation emerged early in animal evolution. This evolutionary innovation introduced regulatory complexity, ultimately facilitating the diversification of animal developmental programmes and cell type repertoires.

DOI: https://doi.org/10.1038/s41586-025-08960-w
Stem Cell Reports. 2025 Apr 25. pii: S2213-6711(25)00103-1. [Epub ahead of print] 102499

Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells.

Youjun Wu, Aaron Zhong, Alessandro Evangelisti, Mega Sidharta, Huangfu Danwei, Lorenz Studer, Ting Zhou.

  Verification of genome editing in human pluripotent stem cells (hPSCs), particularly at silent loci, is desirable but challenging, as it often requires complex and time-intensive differentiation to induce their expression. Here, we establish a rapid and effective workflow for verifying genome-edited hPSC lines targeting unexpressed genes using CRISPR-mediated transcriptional activation (CRISPRa). We systematically compared the efficiency of various CRISPRa systems and identified the synergistic activation mediator (SAM) system as the most potent for activating silent genes in hPSCs. Furthermore, combining SAM with TET1, a demethylation module, enhanced the activation of methylated genes. By inducing targeted gene activation in undifferentiated hPSCs using CRISPRa, we successfully verified single- and dual-reporter lines, functionally tested degradation tag (dTAG) knockins, and validated silent gene knockouts within 48 h. This approach bypasses the need to induce target gene expression through differentiation, providing a rapid and effective assay for verifying silent gene editing at the hPSC stage.

Keywords:  CRISPR-mediated transcriptional activation; dTAG system; human pluripotent stem cells; knockins; knockouts; reporter lines; silent gene editing

DOI:  https://doi.org/10.1016/j.stemcr.2025.102499
Nucleic Acids Res. 2025 May 05. pii: gkaf372. [Epub ahead of print]

CORESH: a gene signature-based search engine for public gene expression datasets.

Vladimir Sukhov, Aigul Nugmanova, Yury Vorontsov, Parul Mehrotra, Maksim Kleverov, Kodi Ravichandran, Maxim Artyomov, Alexey Sergushichev.

Public data repositories like Gene Expression Omnibus (GEO) contain an extensive amount of data from hundreds of thousands of experiments, making them a valuable resource for researchers. A common scenario for utilizing this resource is to show transcriptional similarity of one's own data to a public dataset as evidence of potentially similar biology. However, when searching for such datasets, researchers are usually limited to keyword-based search, which requires having a specific hypothesis and relies on the presence of high-quality metadata in public datasets. Here, we introduce CORESH, a web server designed to systematically find GEO datasets that match a user-provided gene signature-such as a list of top upregulated genes in response to a treatment-in a data-driven manner. CORESH operates on a compendium of >40 000 human and 40 000 mouse datasets and outputs a ranked list of datasets where the input genes exhibit similar expression patterns. The discovered datasets can then be used to identify experimental conditions associated with the activation of the query signature, offering insights into underlying biological mechanisms and guiding experimental validation. CORESH is freely accessible at https://alserglab.wustl.edu/coresh/, requires no login, and is regularly updated with the latest GEO data.

DOI: https://doi.org/10.1093/nar/gkaf372
Nat Genet. 2025 May 09.

The multilayered transcriptional architecture of glioblastoma ecosystems.

Masashi Nomura, Avishay Spitzer, Kevin C Johnson, Luciano Garofano, Djamel Nehar-Belaid, Noam Galili Darnell, Alissa C Greenwald, Lillian Bussema, Young Taek Oh, Frederick S Varn, Fulvio D'Angelo, Simon Gritsch, Kevin J Anderson, Simona Migliozzi, L Nicolas Gonzalez Castro, Tamrin ChowdhFury, Nicolas Robine, Catherine Reeves, Jong Bae Park, Anuja Lipsa, Frank Hertel, Anna Golebiewska, Simone P Niclou, Labeeba Nusrat, Sorcha Kellet, Sunit Das, Hyo Eun Moon, Sun Ha Paek, Franck Bielle, Alice Laurenge, Anna Luisa Di Stefano, Bertrand Mathon, Alberto Picca, Marc Sanson, Shota Tanaka, Nobuhito Saito, David M Ashley, Stephen T Keir, Keith L Ligon, Jason T Huse, W K Alfred Yung, Anna Lasorella, Roel G W Verhaak, Antonio Iavarone, Mario L Suvà, Itay Tirosh.

In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary and recurrent GBM samples from 59 patients using single-nucleus RNA sequencing and bulk tumor DNA sequencing to characterize GBM transcriptional heterogeneity. First, GBMs can be classified by their broad cellular composition, encompassing malignant and nonmalignant cell types. Second, in each cell type we describe the diversity of cellular states and their pathway activation, particularly an expanded set of malignant cell states, including glial progenitor cell-like, neuronal-like and cilia-like. Third, the remaining variation between GBMs highlights three baseline gene expression programs. These three layers of heterogeneity are interrelated and partially associated with specific genetic aberrations, thereby defining three stereotypic GBM ecosystems. This work provides an unparalleled view of the multilayered transcriptional architecture of GBM. How this architecture evolves during disease progression is addressed in the companion manuscript by Spitzer et al.

DOI: https://doi.org/10.1038/s41588-025-02167-5
Nucleic Acids Res. 2025 May 05. pii: gkaf386. [Epub ahead of print]

IVA Prime: automated primer design for in vivo assembly cloning.

Radu Cristian Leonte, Patrick David Fischer, Beatriz Herguedas, Javier García-Nafría, Sebastian Hiller.

Molecular cloning through in vivo assembly (IVA) is an efficient homology-based approach that can achieve complex cloning operations in a single step, bypassing the need for enzymes and reducing hands-on time and costs. However, primer design remains the most demanding task, requiring substantial expertise and a source of human error. Here, we introduce "IVA Prime," an intuitive online tool for automated primer design for IVA cloning, which reduces the workload and avoids errors. We describe how IVA Prime generates optimized primers for all cloning operations, i.e. mutagenesis, insertions, deletions, and subcloning. IVA Prime provides an intuitive interface and robust algorithms, thus mitigating the complexities associated with primer design into a single mouse click. A set of thoroughly tested default parameters allows both inexperienced users and experts to generate ready-to-order primer sequences for a standardized cloning protocol with high success rate. We describe the method and demonstrate its efficiency and reliability with example applications. IVA Prime is freely available at https://www.ivaprime.com.

DOI: https://doi.org/10.1093/nar/gkaf386
Sci Adv. 2025 May 09. 11(19): eadt5356

DUX4 activates common and context-specific intergenic transcripts and isoforms.

Dongxu Zheng, Anita van den Heuvel, Judit Balog, Iris M Willemsen, Susan Kloet, Stephen J Tapscott, Ahmed Mahfouz, Silvère M van der Maarel.

DUX4 regulates the expression of genic and nongenic elements and modulates chromatin accessibility during zygotic genome activation in cleavage stage embryos. Its misexpression in skeletal muscle causes facioscapulohumeral dystrophy (FSHD). By leveraging full-length RNA isoform sequencing with short-read RNA sequencing of DUX4-inducible myoblasts, we elucidate an isoform-resolved transcriptome featuring numerous unannotated isoforms from known loci and novel intergenic loci. While DUX4 activates similar programs in early embryos and FSHD muscle, the isoform usage of known DUX4 targets is notably distinct between the two contexts. DUX4 also activates hundreds of previously unannotated intergenic loci dominated by repetitive elements. The transcriptional and epigenetic profiles of these loci in myogenic and embryonic contexts indicate that the usage of DUX4-binding sites at these intergenic loci is influenced by the cellular environment. These findings demonstrate that DUX4 induces context-specific transcriptomic programs, enriching our understanding of DUX4-induced muscle pathology.

DOI: https://doi.org/10.1126/sciadv.adt5356
Nat Cancer. 2025 May 08.

The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution.

Michael Tyler, Avishai Gavish, Chaya Barbolin, Roi Tschernichovsky, Rouven Hoefflin, Michael Mints, Sidharth V Puram, Itay Tirosh.

Recent years have seen a rapid proliferation of single-cell cancer studies, yet most of these studies profiled few tumors, limiting their statistical power. Combining data and results across studies holds great promise but also involves various challenges. We recently began to address these challenges by curating a large collection of cancer single-cell RNA-sequencing datasets, leveraging it for systematic analyses of tumor heterogeneity. Here we greatly extend this repository to 124 datasets for over 40 cancer types, together comprising 2,836 samples, with improved data annotations, visualizations and exploration. Using this vast cohort, we generate an updated map of recurrent expression programs in malignant cells and systematically quantify context-dependent gene expression and cell-cycle patterns across cell types and cancer types. These data, annotations and analysis results are all freely available for exploration and download through the Curated Cancer Cell Atlas, a central community resource that opens new avenues in cancer research.

DOI: https://doi.org/10.1038/s43018-025-00957-8
Nat Genet. 2025 May 09.

Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics.

Avishay Spitzer, Kevin C Johnson, Masashi Nomura, Luciano Garofano, Djamel Nehar-Belaid, Noam Galili Darnell, Alissa C Greenwald, Lillian Bussema, Young Taek Oh, Frederick S Varn, Fulvio D'Angelo, Simon Gritsch, Kevin J Anderson, Simona Migliozzi, L Nicolas Gonzalez Castro, Tamrin Chowdhury, Nicolas Robine, Catherine Reeves, Jong Bae Park, Anuja Lipsa, Frank Hertel, Anna Golebiewska, Simone P Niclou, Labeeba Nusrat, Sorcha Kellet, Sunit Das, Hyo-Eun Moon, Sun Ha Paek, Franck Bielle, Alice Laurenge, Anna Luisa Di Stefano, Bertrand Mathon, Alberto Picca, Marc Sanson, Shota Tanaka, Nobuhito Saito, David M Ashley, Stephen T Keir, Keith L Ligon, Jason T Huse, W K Alfred Yung, Anna Lasorella, Antonio Iavarone, Roel G W Verhaak, Itay Tirosh, Mario L Suvà.

The evolution of isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) after standard-of-care therapy remains poorly understood. Here we analyzed matched primary and recurrent GBMs from 59 patients using single-nucleus RNA sequencing and bulk DNA sequencing, assessing the longitudinal evolution of the GBM ecosystem across layers of cellular and molecular heterogeneity. The most consistent change was a lower malignant cell fraction at recurrence and a reciprocal increase in glial and neuronal cell types in the tumor microenvironment (TME). The predominant malignant cell state differed between most matched pairs, but no states were exclusive or highly enriched in either time point, nor was there a consistent longitudinal trajectory across the cohort. Nevertheless, specific trajectories were enriched in subsets of patients. Changes in malignant state abundances mirrored changes in TME composition and baseline profiles, reflecting the co-evolution of the GBM ecosystem. Our study provides a blueprint of GBM's diverse longitudinal trajectories and highlights the treatment and TME modifiers that shape them.

DOI: https://doi.org/10.1038/s41588-025-02168-4
Genome Med. 2025 May 07. 17(1): 48

Retroelement co-option disrupts the cancer transcriptional programme.

Jane Loong, Rachael Thompson, Callum Hall, Laura Doglio, Judith Pape, Tobias Plowman, George Kassiotis.

   BACKGROUND: Transcriptional activation of otherwise repressed retrotransposable elements (RTEs) is a hallmark of cancer, shaping tumour progression and immunogenicity by multifaceted, yet incompletely understood, mechanisms.
METHODS: We used an extended pan-cancer transcriptome assembly to identify potential effects of RTEs on the genes within which they have integrated or those in proximity. These were subsequently verified in test cases by further analysis of transcriptional profiles in cancer patient data, and by in vitro studies involving restoration of gene activity, and proliferation and migration assays in cancer cell lines.
RESULTS: We report that cancer-specific transcriptional activation of RTEs causes frequent reduction or loss of gene function. Exonisation and alternative splicing of RTEs creates non-functional RNA and protein isoforms and derepressed RTE promoter activity initiates antisense transcription, both at the expense of the canonical isoforms. Contrary to theoretical expectation, transcriptionally activated RTEs affect genes with established tumour-promoting functions, including the common essential RNGTT and the lung cancer-promoting CHRNA5 genes. Furthermore, the disruptive effect of RTE activation on adjacent tumour-promoting genes is associated with slower disease progression in clinical data, whereas experimental restoration of gene activity enhances tumour cell growth and invasiveness in vitro.
CONCLUSIONS: These findings underscore the gene-disruptive potential of seemingly innocuous germline RTE integrations, unleashed only by their transcriptional utilisation in cancer. They further suggest that such metastable RTE integrations are co-opted as sensors of the epigenetic and transcriptional changes occurring during cellular transformation and as executors that disrupt the function of tumour-promoting genes.

Keywords:  Cancer; Isoform switching; Retrotransposable elements; Transcriptional disruption

DOI:  https://doi.org/10.1186/s13073-025-01479-9