bims-crepig 2025-04-13 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–04–13
28 papers selected by
Connor Rogerson, University of Cambridge

DNA-guided transcription factor interactions extend human gene regulatory code.
DUX-mediated configuration of p300/CBP drives minor zygotic genome activation independent of its catalytic activity.
Active regulatory elements recruit cohesin to establish cell specific chromatin domains.
Single-cell 5-hydroxymethylcytosine landscapes of mouse early embryos at single-base resolution.
Estradiol (E2) concentration shapes the chromatin binding landscape of estrogen receptor alpha.
Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans.
A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters.
dFLASH; dual FLuorescent transcription factor activity sensor for histone integrated live-cell reporting and high-content screening.
A transcription coupling model for how enhancers communicate with their target genes.
Dynamic O-GlcNAcylation and phosphorylation attract and expel proteins from RNA polymerase II to regulate mRNA maturation.
TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data.
The regulatory architecture of the primed pluripotent cell state.
STAT3 signaling enhances tissue expansion during postimplantation mouse development.
The transcription factor Traffic jam orchestrates the somatic piRNA pathway in Drosophila ovaries.
Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signaling.
Structure of the nucleosome-bound human BCL7A.
Acetylation of METTL3: A negative regulator of m6A deposition on chromatin-associated regulatory RNAs.
Spatial multi-omics reveals cell-type-specific nuclear compartments.
Perturb-tracing enables high-content screening of multi-scale 3D genome regulators.
Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.
Two transcription factors play critical roles in mediating epigenetic regulation of fruit ripening in tomato.
Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasis.
k-mer manifold approximation and projection for visualizing DNA sequences.
TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.
An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs.
Nuclear pores safeguard the integrity of the nuclear envelope.
Molecular insights into the overall architecture of human rixosome.
MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles.

Nature. 2025 Apr 09.

DNA-guided transcription factor interactions extend human gene regulatory code.

Zhiyuan Xie, Ilya Sokolov, Maria Osmala, Xue Yue, Grace Bower, J Patrick Pett, Yinan Chen, Kai Wang, Ayse Derya Cavga, Alexander Popov, Sarah A Teichmann, Ekaterina Morgunova, Evgeny Z Kvon, Yimeng Yin, Jussi Taipale.

In the same way that the mRNA-binding specificities of transfer RNAs define the genetic code, the DNA-binding specificities of transcription factors (TFs) form the molecular basis of the gene regulatory code1,2. The human gene regulatory code is much more complex than the genetic code, in particular because there are more than 1,600 TFs that commonly interact with each other. TF-TF interactions are required for specifying cell fate and executing cell-type-specific transcriptional programs. Despite this, the landscape of interactions between DNA-bound TFs is poorly defined. Here we map the biochemical interactions between DNA-bound TFs using CAP-SELEX, a method that can simultaneously identify individual TF binding preferences, TF-TF interactions and the DNA sequences that are bound by the interacting complexes. A screen of more than 58,000 TF-TF pairs identified 2,198 interacting TF pairs, 1,329 of which preferentially bound to their motifs arranged in a distinct spacing and/or orientation. We also discovered 1,131 TF-TF composite motifs that were markedly different from the motifs of the individual TFs. In total, we estimate that the screen identified between 18% and 47% of all human TF-TF motifs. The novel composite motifs we found were enriched in cell-type-specific elements, active in vivo and more likely to be formed between developmentally co-expressed TFs. Furthermore, TFs that define embryonic axes commonly interacted with different TFs and bound to distinct motifs, explaining how TFs with a similar specificity can define distinct cell types along developmental axes.

DOI: https://doi.org/10.1038/s41586-025-08844-z
Cell Rep. 2025 Apr 08. pii: S2211-1247(25)00315-8. [Epub ahead of print]44(4): 115544

DUX-mediated configuration of p300/CBP drives minor zygotic genome activation independent of its catalytic activity.

Lieying Xiao, Hao Jin, Yanna Dang, Panpan Zhao, Shuang Li, Yan Shi, Shaohua Wang, Kun Zhang.

  Maternal-deposited factors initiate zygotic genome activation (ZGA), driving the maternal-to-zygotic transition; however, the coordination between maternal coactivators and transcription factors (TFs) in this process remains unclear. In this study, by profiling the dynamic landscape of p300 during mouse ZGA, we reveal its role in promoting RNA polymerase II (Pol II) pre-configuration at ZGA gene regions and sequentially establishing enhancer activity and regulatory networks. Moreover, p300/CBP-catalyzed acetylation drives Pol II elongation and minor ZGA gene expression by inducing pivotal TFs such as Dux. Remarkably, the supplementation of exogenous Dux rescues ZGA failure and developmental defects caused by the loss of p300/CBP acetylation. DUX functions as a pioneer factor, guiding p300 and Pol II to minor ZGA gene regions and activating them in a manner dependent on the non-catalytic functions of p300/CBP. Together, our findings reveal a mutual dependency between p300/CBP and DUX, highlighting their coordinated role in regulating minor ZGA activation.

Keywords:  CP: Developmental biology; DUX; RNA polymerase II; ZGA; acetylation; embryo; enhancer; minor ZGA; p300/CBP; preimplantation

DOI:  https://doi.org/10.1016/j.celrep.2025.115544
Sci Rep. 2025 Apr 06. 15(1): 11780

Active regulatory elements recruit cohesin to establish cell specific chromatin domains.

Emily Georgiades, Caroline Harrold, Nigel Roberts, Mira Kassouf, Simone G Riva, Edward Sanders, Damien Downes, Helena S Francis, Joseph Blayney, A Marieke Oudelaar, Thomas A Milne, Douglas Higgs, Jim R Hughes.

As the 3D structure of the genome is analysed at ever increasing resolution it is clear that there is considerable variation in the 3D chromatin architecture across different cell types. It has been proposed that this may, in part, be due to increased recruitment of cohesin to activated cis-elements (enhancers and promoters) leading to cell-type specific loop extrusion underlying the formation of new sub-TADs. Here we show that cohesin correlates well with the presence of active enhancers and that this varies in an allele-specific manner with the presence or absence of polymorphic enhancers which vary from one individual to another. Using the alpha globin cluster as a model, we show that when all enhancers are removed, peaks of cohesin disappear from these regions and the erythroid specific sub-TAD is no longer formed. Re-insertion of the major alpha globin enhancer (R2) is associated with re-establishment of recruitment and increased interactions. In complementary experiments insertion of the R2 enhancer element into a "neutral" region of the genome recruits cohesin, induces transcription and creates a new large (75 kb) erythroid-specific domain. Together these findings support the proposal that active enhancers recruit cohesin, stimulate loop extrusion and promote the formation of cell specific sub-TADs.

DOI: https://doi.org/10.1038/s41598-025-96248-4
Cell Rep. 2025 Apr 03. pii: S2211-1247(25)00291-8. [Epub ahead of print]44(4): 115520

Single-cell 5-hydroxymethylcytosine landscapes of mouse early embryos at single-base resolution.

Dongsheng Bai, Jinmin Yang, Xiaohui Xue, Yun Gao, Yan Wang, Mengge Cui, Bo He, Hu Zeng, Huifen Xiang, Zijian Guo, Lan Zhu, Juan Gao, Chenxu Zhu, Fuchou Tang, Chengqi Yi.

  DNA methylation and hydroxymethylation are extensively reprogrammed during mammalian early embryogenesis, and studying their regulatory functions requires comprehensive DNA hydroxymethylation maps at base resolution. Here, we develop single-cell 5-hydroxymethylcytosine (5hmC) chemical-assisted C-to-T conversion-enabled sequencing (schmC-CATCH), a method leveraging selective 5hmC labeling for a quantitative, base-resolution, genome-wide landscape of the DNA hydroxymethylome in mouse gametes and preimplantation embryos spanning from the zygote to blastocyst stage. We revealed that, in addition to late zygotic stages, onset of ten-eleven translocation (TET)-mediated DNA hydroxymethylation initiates immediately after fertilization and is characterized by the distinct 5hmC patterns on the parental genomes shaped by TET3 demethylase. We identified persistent clusters of 5hmC hotspots throughout early embryonic stages, which are highly associated with young retroelements. 5hmC is also associated with different regulatory elements, indicating a potential regulatory function during early embryogenesis. Collectively, our work elucidates the dynamics of active DNA demethylation during mouse preimplantation development and provides a valuable resource for functional studies of epigenetic reprogramming in early embryos.

Keywords:  CP: Developmental biology; CP: Molecular biology; DNA hydroxymethylation; TET3; bisulfite-free method; mammalian early embryo; single cell sequencing

DOI:  https://doi.org/10.1016/j.celrep.2025.115520
J Biol Chem. 2025 Apr 09. pii: S0021-9258(25)00348-5. [Epub ahead of print] 108499

Estradiol (E2) concentration shapes the chromatin binding landscape of estrogen receptor alpha.

Amy L Han, Kiran Vinod-Paul, Satyanarayan Rao, Heather M Brechbuhl, Carol A Sartorius, Srinivas Ramachandran, Peter Kabos.

  How transcription factors (TF) selectively occupy a minute subset of their binding sites from a sizeable pool of putative sites in large mammalian genomes remains an important unanswered question. In part, nucleosomes help by creating formidable barriers to TF binding. TF concentration itself plays a crucial role in the competition between TFs and nucleosomes. With nuclear receptors, the ligand adds another layer of complexity. Estrogen receptor alpha (ER) is a classic example where its main ligand estradiol (E2) can modulate ER binding on chromatin. Here, we show a shift in ER binding as a function of E2 concentration. As E2 concentration increases by two orders of magnitude, ER levels decrease, and ER binding localizes to promoter-distal sites with strong ER motifs. At low E2 levels, abundant levels of ER are present in the nucleus, and ER binding occurs mostly at sites without a canonical ER binding motif, in cooperation with other TFs like STAT1. We propose that E2's effect on ER activity plays a major role in defining genome-wide ER binding profiles. Thus, variations in E2 concentrations in ER-positive breast tumors could be a significant factor driving heterogeneity in tumor phenotype, treatment response, and potentially drug resistance.

Keywords:  Breast cancer; STAT1; chromatin biology; estradiol; estrogen receptor

DOI:  https://doi.org/10.1016/j.jbc.2025.108499
Genome Res. 2025 Apr 10.

Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans.

Jun Kim, Haoyu Wang, Sevinç Ercan.

In mammals, cohesin and CTCF organize the 3D genome into topologically associating domains (TADs) to regulate communication between cis-regulatory elements. Many organisms, including S. cerevisiae, C. elegans, and A. thaliana contain cohesin but lack CTCF. Here, we used C. elegans to investigate the function of cohesin in 3D genome organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features called "fountains," which have also been reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20-40 kb in C. elegans Hi-C analysis upon cohesin and WAPL-1 depletion supports the idea that cohesin is preferentially loaded at sites bound by the C. elegans ortholog of NIPBL and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains suggest that cohesin processivity is unequal on each side, possibly owing to collision with cohesin loaded from surrounding sites. The putative cohesin loading sites are closest to active enhancers, and fountain strength is associated with transcription. Compared with mammals, the average processivity of C. elegans cohesin is about 10-fold shorter, and the binding of NIPBL ortholog does not depend on cohesin. We propose that preferential loading and loop extrusion by cohesin is an evolutionarily conserved mechanism that regulates the 3D interactions of enhancers in animal genomes.

DOI: https://doi.org/10.1101/gr.279365.124
Nucleic Acids Res. 2025 Apr 10. pii: gkaf276. [Epub ahead of print]53(7):

A two-step regulatory mechanism dynamically controls histone H3 acetylation by SAGA complex at growth-related promoters.

Sevil Zencir, Daniel Dilg, Maria Jessica Bruzzone, Françoise Stutz, Julien Soudet, David Shore, Benjamin Albert.

Acetylation of histone H3 at residue K9 (H3K9ac) is a dynamically regulated mark associated with transcriptionally active promoters in eukaryotes. However, our understanding of the relationship between H3K9ac and gene expression remains mostly correlative. In this study, we identify a large suite of growth-related (GR) genes in yeast that undergo a particularly strong down-regulation of both transcription and promoter-associated H3K9ac upon stress, and delineate the roles of transcriptional activators (TAs), repressors, SAGA (Spt-Ada-Gcn5 acetyltransferase) histone acetyltransferase, and RNA-polymerase II in this response. We demonstrate that H3K9 acetylation states are orchestrated by a two-step mechanism driven by the dynamic binding of transcriptional repressors (TRs) and activators, that is independent of transcription. In response to stress, promoter release of TAs at GR genes is a prerequisite for rapid reduction of H3K9ac, whereas binding of TRs is required to establish a hypo-acetylated, strongly repressed state.

DOI: https://doi.org/10.1093/nar/gkaf276
Nat Commun. 2025 Apr 07. 16(1): 3298

dFLASH; dual FLuorescent transcription factor activity sensor for histone integrated live-cell reporting and high-content screening.

Timothy P Allen, Alison E Roennfeldt, Moganalaxmi Reckdharajkumar, Adrienne E Sullivan, Miaomiao Liu, Ronald J Quinn, Darryl L Russell, Daniel J Peet, Murray L Whitelaw, David C Bersten.

Live-cell transcription factor (TF) activity reporting is crucial for synthetic biology, drug discovery and functional genomics. Here we present dFLASH (dual FLuorescent transcription factor Activity Sensor for Histone-integrated live-cell reporting), a modular, genome-integrated TF sensor. dFLASH homogeneously and specifically detects endogenous Hypoxia Inducible Factor (HIF) and Progesterone Receptor (PGR) activities, as well as coactivator recruitment to synthetic TFs. The dFLASH system produces dual-color nuclear fluorescence, enabling normalized, dynamic, live-cell TF activity sensing with strong signal-to-noise ratios and robust screening performance (Z' = 0.61-0.74). We validate dFLASH for functional genomics and drug screening, demonstrating HIF regulation via CRISPRoff and application to whole-genome CRISPR KO screening. Additionally, we apply dFLASH for drug discovery, identifying HIF pathway modulators from a 1600-compound natural product library using high-content imaging. Together, this versatile platform provides a powerful tool for studying TF activity across diverse applications.

DOI: https://doi.org/10.1038/s41467-025-58488-w
Nat Struct Mol Biol. 2025 Apr 11.

A transcription coupling model for how enhancers communicate with their target genes.

Elisabeth Altendorfer, Stefan Mundlos, Andreas Mayer.

How enhancers communicate with their target genes to influence transcription is an unresolved question of fundamental importance. Current models of the mechanism of enhancer-target gene or enhancer-promoter (E-P) communication are transcription-factor-centric and underappreciate major findings, including that enhancers are themselves transcribed by RNA polymerase II, which correlates with enhancer activity. In this Perspective, we posit that enhancer transcription and its products, enhancer RNAs, are elementary components of enhancer-gene communication. Specifically, we discuss the possibility that transcription at enhancers and at their cognate genes are linked and that this coupling is at the basis of how enhancers communicate with their targets. This model of transcriptional coupling between enhancers and their target genes is supported by growing experimental evidence and represents a synthesis of recent key discoveries.

DOI: https://doi.org/10.1038/s41594-025-01523-7
J Biomed Sci. 2025 Apr 04. 32(1): 39

Dynamic O-GlcNAcylation and phosphorylation attract and expel proteins from RNA polymerase II to regulate mRNA maturation.

Aishwarya Gondane, Harri M Itkonen.

   BACKGROUND: Phosphorylation and O-GlcNAcylation are the key modifications regulating RNA Polymerase II (RNA Pol II)-driven transcription. Transcriptional kinases, cyclin-dependent kinase 7 (CDK7), CDK9 and CDK12 phosphorylate RNA Pol II, whereas O-GlcNAcylation is added by O-GlcNAc transferase (OGT) and removed by O-GlcNAcase (OGA). Currently, no study has systematically evaluated how inhibiting each of these enzyme activities impacts the assembly of the appropriate protein complexes on the polymerase and the maturation of mRNA.
METHODS: Here, we systematically evaluate remodeling of RNA Pol II interactome and effects on the nascent mRNA maturation by using mass spectrometry and SLAM-seq, respectively. For validation, we rely predominantly on analysis of intronic polyadenylation (IPA) sites, mitochondrial flux assays (Seahorse), western blotting and patient data.
RESULTS: We show that OGT / OGA inhibition reciprocally affect protein recruitment to RNA Pol II, and appropriate O-GlcNAcylation levels are required for optimal function of the RNA Pol II complex. These paradoxical effects are explained through IPA, because despite being prematurely poly-adenylated, these mRNAs are scored as mature in SLAM-seq. Unlike previously proposed, we show that, similar to inhibition of CDK12, also targeting CDK9 stimulates transcription of short genes at the cost of long genes. However, our systematic proteomic- and IPA-analysis revealed that these effects are mediated by distinct molecular mechanisms: CDK9 inhibition leads to a failure of recruiting Integrator complex to RNA Pol II, and we then show that depletion of Integrator subunits phenocopy the gene length-dependent effects. In contrast, CDK12 inhibition triggers IPA. Finally, we show that dynamic O-GlcNAcylation predominantly interplays with CDK9: OGT inhibition augments CDK9 inhibitor effects on mRNA maturation due to defects in transcription elongation, while OGA inhibition rescues mRNA maturation failure caused by targeting CDK9, but induces IPA.
CONCLUSION: We show that dynamic O-GlcNAcylation is a negative regulator of mRNA biosynthesis and propose that the addition and removal of the modification serve as quality control-steps to ascertain successful generation of mature mRNAs. Our work identifies unprecedented redundancy in the regulation of RNA Pol II, which increases resilience towards transcriptional stress, and also underscores the difficulty of targeting transcription to control cancer.

Keywords:  Cyclin-dependent kinase; Intronic poly-adenylation; Nascent transcription; O-GlcNAc transferase; SLAM-seq; mRNA maturation

DOI:  https://doi.org/10.1186/s12929-025-01135-9
Genome Res. 2025 Apr 10. pii: gr.279955.124. [Epub ahead of print]

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data.

Chen Li, Sijie Chen, Yixin Chen, Haiyang Bian, Minsheng Hao, Lei Wei, Xuegong Zhang.

Reprogramming cell state transitions provides the potential for cell engineering and regenerative therapy for many diseases. Finding the reprogramming transcription factors (TFs) and their combinations that can direct the desired state transition is crucial for the task. Computational methods have been developed to identify such reprogramming TFs. However, most of them can only generate a ranked list of individual TFs and ignore the identification of TF combinations. Even for individual reprogramming TF identification, current methods often fail to put the real effective reprogramming TFs at the top of their rankings. To address these challenges, we developed TFcomb, a computational method that leverages single-cell multiomics data to identify reprogramming TFs and TF combinations that can direct cell state transitions. We modeled the task of finding reprogramming TFs and their combinations as an inverse problem to enable searching for answers in very high dimensional space, and used Tikhonov regularization to guarantee the generalization ability of solutions. For the coefficient matrix of the model, we designed a graph attention network to augment gene regulatory networks built with single-cell RNA-seq and ATAC-seq data. Benchmarking experiments on data of human embryonic stem cells demonstrated superior performance of TFcomb against existing methods for identifying individual TFs. We curated datasets of multiple cell reprogramming cases and demonstrated that TFcomb can efficiently identify reprogramming TF combinations from a vast pool of potential combinations. We applied TFcomb on a dataset of mouse hair follicle development and found key TFs in cell differentiation. All experiments showed that TFcomb is powerful in identifying reprogramming TFs and TF combinations from single-cell datasets to empower future cell engineering.

DOI: https://doi.org/10.1101/gr.279955.124
Nat Commun. 2025 Apr 09. 16(1): 3351

The regulatory architecture of the primed pluripotent cell state.

Bo I Li, Mariano J Alvarez, Hui Zhao, Napon Chirathivat, Andrea Califano, Michael M Shen.

Despite extensive research, the gene regulatory architecture governing mammalian cell states remains poorly understood. Here we present an integrative systems biology approach to elucidate the network architecture of primed state pluripotency. Using an unbiased methodology, we identified and experimentally confirmed 132 transcription factors as master regulators (MRs) of mouse epiblast stem cell (EpiSC) pluripotency, many of which were further validated by CRISPR-mediated functional assays. To assemble a comprehensive regulatory network, we silenced each of the 132 MRs to assess their effects on the other MRs and their transcriptional targets, yielding a network of 1273 MR → MR interactions. Network architecture analyses revealed four functionally distinct MR modules (communities), and identified key Speaker and Mediator MRs based on their hierarchical rank and centrality. Our findings elucidate the de-centralized logic of a "communal interaction" model in which the balanced activities of four MR communities maintain primed state pluripotency.

DOI: https://doi.org/10.1038/s41467-025-57894-4
Cell Rep. 2025 Apr 05. pii: S2211-1247(25)00277-3. [Epub ahead of print]44(4): 115506

STAT3 signaling enhances tissue expansion during postimplantation mouse development.

Takuya Azami, Bart Theeuwes, Mai-Linh Nu Ton, William Mansfield, Luke Harland, Masaki Kinoshita, Berthold Gottgens, Jennifer Nichols.

  Signal transducer and activator of transcription (STAT)3 signaling has been studied extensively using mouse embryonic stem cells. Zygotic deletion of Stat3 enables embryo implantation, but thereafter, mutants resemble non-affected littermates from the previous day until around mid-gestation. This probably results from the loss of serine-phosphorylated STAT3, the predominant form in early postimplantation embryonic tissues associated with mitochondrial activity. Bulk RNA sequencing of isolated mouse epiblasts confirmed developmental delay transcriptionally. Single-cell RNA sequencing revealed the exclusion of derivatives of Stat3 null embryonic stem cells exclusively from the erythroid lineage of mid-gestation chimeras. We show that Stat3 null embryonic stem cells can differentiate into erythroid and hematopoietic lineages in vitro but become outcompeted when mixed with wild-type cells. Our results implicate a role for STAT3 in the temporal control of embryonic progression, particularly in tissues requiring rapid cell division, such as postimplantation epiblast and hematopoietic lineages. Interestingly, mutations in STAT3 are associated with short stature in humans.

Keywords:  CP: Developmental biology; RNA sequencing; STAT3 signaling; chimeras; developmental delay; erythroid differentiation; pluripotent stem cells

DOI:  https://doi.org/10.1016/j.celrep.2025.115506
Cell Rep. 2025 Apr 06. pii: S2211-1247(25)00224-4. [Epub ahead of print] 115453

The transcription factor Traffic jam orchestrates the somatic piRNA pathway in Drosophila ovaries.

Azad Alizada, Aline Martins, Nolwenn Mouniée, Julia V Rodriguez Suarez, Benjamin Bertin, Nathalie Gueguen, Vincent Mirouse, Anna-Maria Papameletiou, Austin J Rivera, Nelson C Lau, Abdou Akkouche, Stéphanie Maupetit-Méhouas, Gregory J Hannon, Benjamin Czech Nicholson, Emilie Brasset.

  The PIWI-interacting RNA (piRNA) pathway is essential for transposable element (TE) silencing in animal gonads. While the transcriptional regulation of piRNA pathway components in germ cells has been documented in mice and flies, their control in somatic cells of Drosophila ovaries remains unresolved. Here, we demonstrate that Traffic jam (Tj), the Drosophila ortholog of large Maf transcription factors in mammals, is a master regulator of the somatic piRNA pathway. Tj binds to regulatory regions of somatic piRNA factors and the major piRNA cluster flamenco, which carries a Tj-bound enhancer downstream of its promoter. Depletion of Tj in somatic follicle cells causes downregulation of piRNA factors, loss of flamenco expression, and derepression of gypsy-family TEs. We propose that the arms race between the host and TEs led to the co-evolution of promoters in piRNA pathway genes as well as TE regulatory regions, which both rely on a shared transcription factor.

Keywords:  CP: Developmental biology; CP: Molecular biology; Drosophila; oogenesis; piRNA pathway; transcription factors; transposable elements

DOI:  https://doi.org/10.1016/j.celrep.2025.115453
Nat Struct Mol Biol. 2025 Apr 04.

Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signaling.

Pawel Mikulski, Sahar S H Tehrani, Anna Kogan, Izma Abdul-Zani, Emer Shell, Louise James, Brent J Ryan, Lars E T Jansen.

Interferon-γ (IFNγ) transiently activates genes related to inflammation and innate immunity. A subset of targets retain a mitotically heritable memory of prior IFNγ exposure, resulting in hyperactivation upon re-exposure through poorly understood mechanisms. Here, we discover that the transcriptionally permissive chromatin marks H3K4me1, H3K14ac and H4K16ac are established during IFNγ priming and are selectively maintained on a cluster of guanylate-binding protein (GBP) genes in dividing human cells in the absence of transcription. The histone acetyltransferase KAT7 is required for H3K14ac deposition at GBP genes and for accelerated GBP reactivation upon re-exposure to IFNγ. In naive cells, the GBP cluster is maintained in a low-level repressive chromatin state, marked by H3K27me3, limiting priming through a PRC2-dependent mechanism. Unexpectedly, IFNγ priming results in transient accumulation of this repressive mark despite active gene expression. However, during the memory phase, H3K27 methylation is selectively depleted from primed GBP genes, facilitating hyperactivation. Furthermore, we identified a cis-regulatory element that forms transient, long-range contacts across the GBP cluster and acts as a repressor, curbing hyperactivation of previously IFNγ-primed cells. Our results provide insight into the chromatin basis for the long-term transcriptional memory of IFNγ signaling, which might contribute to enhanced innate immunity.

DOI: https://doi.org/10.1038/s41594-025-01522-8
Nucleic Acids Res. 2025 Apr 10. pii: gkaf273. [Epub ahead of print]53(7):

Structure of the nucleosome-bound human BCL7A.

Franck Martin, Asgar Abbas Kazrani, Julie Lafouge, Dana Mariel Diaz-Jimenez, Stéphanie Siebert, Leonie Fabbro-Burtschell, Emma Maillard, Karine Lapouge, Haydyn David Thomas Mertens, Claude Sauter, Alexander Leitner, Françoise Ochsenbein, Alexandre Blais, Elisa Bergamin.

Proteins of the BCL7 family (BCL7A, BCL7B, and BCL7C) are among the most recently identified subunits of the mammalian SWI/SNF chromatin remodeler complex and are absent from the unicellular version of this complex. Their function in the complex is unknown, and very limited structural information is available, despite the fact that they are mutated in several cancer types, most notably blood malignancies and hence medically relevant. Here, using cryo-electron microscopy in combination with biophysical and biochemical approaches, we show that BCL7A forms a stable, high-affinity complex with the nucleosome core particle (NCP) through binding of BCL7A with the acidic patch of the nucleosome via an arginine anchor motif. This interaction is impaired by BCL7A mutations found in cancer. Further, we determined that BCL7A contributes to the remodeling activity of the mSWI/SNF complex and we examined its function at the genomic level. Our findings reveal how BCL7 proteins interact with the NCP and help rationalize the impact of cancer-associated mutations. By providing structural information on the positioning of BCL7 on the NCP, our results broaden the understanding of the mechanism by which SWI/SNF recognizes the chromatin fiber.

DOI: https://doi.org/10.1093/nar/gkaf273
Mol Cell. 2025 Apr 03. pii: S1097-2765(25)00195-9. [Epub ahead of print]85(7): 1251-1252

Acetylation of METTL3: A negative regulator of m6A deposition on chromatin-associated regulatory RNAs.

Yutao Zhao, Chuan He.

In this issue, Huang et al.1 report the acetylation of METTL3 as a negative regulator of m6A deposition of chromatin-associated regulatory RNAs from enhancers and promoters. This acetylation is mediated by p300 and positively regulated by PAK2.

DOI: https://doi.org/10.1016/j.molcel.2025.03.002
Nature. 2025 Apr 09.

Spatial multi-omics reveals cell-type-specific nuclear compartments.

Yodai Takei, Yujing Yang, Jonathan White, Isabel N Goronzy, Jina Yun, Meera Prasad, Lincoln J Ombelets, Simone Schindler, Prashant Bhat, Mitchell Guttman, Long Cai.

The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization1-3. Understanding their relationships rests on identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci and transcriptional levels in individual cells, all in complex tissues. Here, we introduce two-layer DNA seqFISH+, which enables simultaneous mapping of 100,049 genomic loci, together with the nascent transcriptome for 17,856 genes and subnuclear structures in single cells. These data enable imaging-based chromatin profiling of diverse subnuclear markers and can capture their changes at genomic scales ranging from 100-200 kilobases to approximately 1 megabase, depending on the marker and DNA locus. By using multi-omics datasets in the adult mouse cerebellum, we showed that repressive chromatin regions are more variable by cell type than are active regions across the genome. We also discovered that RNA polymerase II-enriched foci were locally associated with long, cell-type-specific genes (bigger than 200 kilobases) in a manner distinct from that of nuclear speckles. Furthermore, our analysis revealed that cell-type-specific regions of heterochromatin marked by histone H3 trimethylated at lysine 27 (H3K27me3) and histone H4 trimethylated at lysine 20 (H4K20me3) are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear structures, associated genomic loci and their effects on gene regulation, directly within complex tissues.

DOI: https://doi.org/10.1038/s41586-025-08838-x
Nat Methods. 2025 Apr 10.

Perturb-tracing enables high-content screening of multi-scale 3D genome regulators.

Yubao Cheng, Mengwei Hu, Bing Yang, Tyler B Jensen, Yuan Zhang, Tianqi Yang, Ruihuan Yu, Zhaoxia Ma, Jonathan S D Radda, Shengyan Jin, Chongzhi Zang, Siyuan Wang.

Three-dimensional (3D) genome organization becomes altered during development, aging and disease, but the factors regulating chromatin topology are incompletely understood and currently no technology can efficiently screen for new regulators of multi-scale chromatin organization. Here, we developed an image-based high-content screening platform (Perturb-tracing) that combines pooled CRISPR screens, a cellular barcode readout method (BARC-FISH) and chromatin tracing. We performed a loss-of-function screen in human cells, and visualized alterations to their 3D chromatin folding conformations, alongside perturbation-paired barcode readout in the same single cells. We discovered tens of new regulators of chromatin folding at different length scales, ranging from chromatin domains and compartments to chromosome territory. A subset of the regulators exhibited 3D genome effects associated with loop extrusion and A-B compartmentalization mechanisms, while others were largely unrelated to these known 3D genome mechanisms. Finally, we identified new regulators of nuclear architectures and found a functional link between chromatin compaction and nuclear shape. Altogether, our method enables scalable, high-content identification of chromatin and nuclear topology regulators that will stimulate new insights into the 3D genome.

DOI: https://doi.org/10.1038/s41592-025-02652-z
EMBO Rep. 2025 Apr 11.

Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer.

Jayita Roy, Aniket Kumar, Shouvik Chakravarty, Nidhan K Biswas, Srikanta Goswami, Anup Mazumder.

  Pancreatic ductal adenocarcinoma (PDAC) is one of the most prevalent and aggressive forms of pancreatic cancer with low survival rates and limited treatment options. Aberrant expression of the MYC oncogene promotes PDAC progression. Recent reports have established a role for enhancer RNAs (eRNAs), originating from active enhancers, in controlling gene transcription. Here we show that a novel MYC eRNA regulates MYC gene expression during chronic inflammatory conditions in pancreatic cancer cells. A higher amount of MYC eRNA is observed in chronic pancreatitis and in pancreatic cancer patients. We show that MYC eRNA interacts with YEATS2, a histone reader protein of the ATAC-HAT complex, and augments the association of YEATS2-containing ATAC complexes with MYC promoter/enhancer regions and thus increases MYC gene expression. TNF-α induced Tyrosine dephosphorylation of the YEATS domain increases MYC eRNA binding to the YEATS2 protein in pancreatic cancer cells. Our study adds another regulatory layer of MYC gene expression by enhancer-driven transcription.

Keywords:   MYC ; Enhancer RNA (eRNA); Epigenetic Modification; Pancreatic Cancer; YEATS2

DOI:  https://doi.org/10.1038/s44319-025-00446-0
Proc Natl Acad Sci U S A. 2025 Apr 15. 122(15): e2422798122

Two transcription factors play critical roles in mediating epigenetic regulation of fruit ripening in tomato.

Qingfeng Niu, Yaping Xu, Huan Huang, Linzhu Li, Dengguo Tang, Siqun Wu, Ping Liu, Ruie Liu, Yu Ma, Bo Zhang, Jian-Kang Zhu, Zhaobo Lang.

  DNA methylation regulates fruit ripening in tomato, and disruption of the DNA demethylase DEMETER-LIKE 2 (DML2) results in genome-wide DNA hypermethylation and impaired ripening. We report here that the transcription factors Ripening Inhibitor (RIN) and FRUITFULL 1 (FUL1) play critical roles in mediating the effect of DNA methylation on tomato fruit ripening. RIN and FUL1 are silenced in dml2 mutant plants, and the defective ripening phenotype of dml2 is mimicked by the rin/ful1 double mutant. Restoration of RIN expression in dml2 partially rescues its ripening defects. DNA methylation controls ripening not only by regulating the expression of RIN and FUL1 but also by interfering with the genomic binding of RIN. In dml2 mutant plants, RIN cannot bind to some of its targets in vivo even though DNA methylation does not interfere with RIN binding in vitro; this inhibited binding in vivo is correlated with increased DNA methylation and histone H3 enrichment within 100 bp of the binding site. Our work uncovers the molecular mechanisms underlying DNA methylation control of fruit ripening in tomato.

Keywords:  DML2; DNA methylation; FUL1; RIN; demethylase

DOI:  https://doi.org/10.1073/pnas.2422798122
Mol Cell. 2025 Mar 28. pii: S1097-2765(25)00202-3. [Epub ahead of print]

Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasis.

Chuan Gao, Ang Gao, Yulong Jiang, Ronghui Gao, Yan Guo, Zirou Peng, Weiwei Jiang, Mengyao Zhang, Zirui Zhou, Chaojun Yan, Wentong Fang, Hankun Hu, Guangya Zhu, Jing Zhang.

  Hypoxia and dysregulated phase separation can both activate oncogenic transcriptomic profiles. However, whether hypoxia regulates transcription-associated phase separation remains unknown. Here, we find that zinc fingers and homeoboxes 2 (ZHX2) undergoes phase separation in response to hypoxia, promoting their occupancy on chromatin and activating a cluster of oncogene transcription that is enriched by metastatic genes distinct from the targets of hypoxia-inducible factor (HIF) and pathologically relevant to breast cancer. Hypoxia induces ZHX2 phase separation via a proline-rich intrinsically disordered region (IDR), enhancing phosphorylation of ZHX2 at S625 and S628 that incorporates CCCTC-binding factor (CTCF) in condensates to alter chromatin looping, consequently driving metastatic gene transcription and cancer metastasis. Our findings provide significant insight into oncogene activation and suggest a phase-separation-based therapeutic strategy for cancer.

Keywords:  CTCF; ZHX2; chromatin looping; hypoxia; metastasis; phase separation

DOI:  https://doi.org/10.1016/j.molcel.2025.03.009
Genome Res. 2025 Apr 10.

k-mer manifold approximation and projection for visualizing DNA sequences.

Chengbo Fu, Einari A Niskanen, Gong-Hong Wei, Zhirong Yang, Marta Sanvicente-García, Marc Güell, Lu Cheng.

Identifying and illustrating patterns in DNA sequences are crucial tasks in various biological data analyses. In this task, patterns are often represented by sets of k-mers, the fundamental building blocks of DNA sequences. To visually unveil these patterns, one could project each k-mer onto a point in two-dimensional (2D) space. However, this projection poses challenges owing to the high-dimensional nature of k-mers and their unique mathematical properties. Here, we establish a mathematical system to address the peculiarities of the k-mer manifold. Leveraging this k-mer manifold theory, we develop a statistical method named KMAP for detecting k-mer patterns and visualizing them in 2D space. We applied KMAP to three distinct data sets to showcase its utility. KMAP achieves a comparable performance to the classical method MEME, with ∼90% similarity in motif discovery from HT-SELEX data. In the analysis of H3K27ac ChIP-seq data from Ewing sarcoma (EWS), we find that BACH1, OTX2, and KNCH2 might affect EWS prognosis by binding to promoter and enhancer regions across the genome. We also observe potential colocalization of BACH1, OTX2, and the motif CCCAGGCTGGAGTGC in ∼70 bp windows in the enhancer regions. Furthermore, we find that FLI1 binds to the enhancer regions after ETV6 degradation, indicating competitive binding between ETV6 and FLI1. Moreover, KMAP identifies four prevalent patterns in gene editing data of the AAVS1 locus, aligning with findings reported in the literature. These applications underscore that KMAP can be a valuable tool across various biological contexts.

DOI: https://doi.org/10.1101/gr.279458.124
Genome Biol. 2025 Apr 09. 26(1): 92

TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks.

Taylor Jones, Rutendo F Sigauke, Lynn Sanford, Dylan J Taatjes, Mary A Allen, Robin D Dowell.

  TF Profiler is a method of inferring transcription factor (TF) regulatory activity, i.e., when a TF is present and actively participating in the regulation of transcription, directly from nascent sequencing assays such as PRO-seq and GRO-seq. While ChIP assays have measured DNA localization, they fall short of identifying when and where the effector domain of a transcription factor is active. Our method uses RNA polymerase activity to infer TF effector domain activity across hundreds of data sets and transcription factors. TF Profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.

Keywords:  Cellular regulation; Tissue specificity; Transcription factor

DOI:  https://doi.org/10.1186/s13059-025-03545-2
Nat Genet. 2025 Apr;57(4): 962-972

An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs.

Lishuan Wang, Wei Yuan, Amir Gamliel, Wubin Ma, Seowon Lee, Yuliang Tan, Zeyu Chen, Havilah Taylor, Kenneth Ohgi, Soohwan Oh, Aneel K Aggarwal, Michael G Rosenfeld.

The evidence that signal- and ligand-dependent pathways function by activating regulatory enhancer programs suggests that a 'checkpoint' strategy may underline activation of many diversely regulated enhancers. Here we report a molecular mechanism common to several acute signal- and ligand-dependent enhancer activation programs based on release of a shared enhancer RNA (eRNA) transcription checkpoint. It requires recruitment of a DNA-dependent protein kinase catalytic subunit (DNA-PKcs)-phosphorylated RING finger repressor (Krüppel-associated box)-associated protein 1 (KAP1) as a modulator, inhibiting its association with 7SK and E3 small ubiquitin-like modifier (SUMO) ligase activity on the CDK9 subunit of positive transcription elongation factor b (P-TEFb). This facilitates formation of an activated P-TEFb complex, licensing eRNA elongation. Overcoming this checkpoint for signal-dependent enhancer activation occurs in diverse pathways, including estrogen receptor-α, NF-κB-regulated proinflammatory stimulation, androgen receptor and neuronal depolarization. Therefore, a specific strategy required to convert a basal state enhancer P-TEFb complex to an active state to release a conserved checkpoint is apparently employed by several functionally important signal-regulated regulatory enhancers to implement the instructions of the endocrine and paracrine system.

DOI: https://doi.org/10.1038/s41588-025-02138-w
Nat Cell Biol. 2025 Apr 09.

Nuclear pores safeguard the integrity of the nuclear envelope.

Reiya Taniguchi, Clarisse Orniacki, Jan Philipp Kreysing, Vojtech Zila, Christian E Zimmerli, Stefanie Böhm, Beata Turoňová, Hans-Georg Kräusslich, Valérie Doye, Martin Beck.

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange, which is essential for eukaryotes. Mutations in the central scaffolding components of NPCs are associated with genetic diseases, but how they manifest only in specific tissues remains unclear. This is exemplified in Nup133-deficient mouse embryonic stem cells, which grow normally during pluripotency, but differentiate poorly into neurons. Here, using an innovative in situ structural biology approach, we show that Nup133-/- mouse embryonic stem cells have heterogeneous NPCs with non-canonical symmetries and missing subunits. During neuronal differentiation, Nup133-deficient NPCs frequently disintegrate, resulting in abnormally large nuclear envelope openings. We propose that the elasticity of the NPC scaffold has a protective function for the nuclear envelope and that its perturbation becomes critical under conditions that impose an increased mechanical load onto nuclei.

DOI: https://doi.org/10.1038/s41556-025-01648-3
Nat Commun. 2025 Apr 07. 16(1): 3288

Molecular insights into the overall architecture of human rixosome.

Ji Huang, Liang Tong.

Rixosome is a conserved, multi-subunit protein complex that has critical roles in ribosome biogenesis and silencing of Polycomb target genes. The subunits of human rixosome include PELP1, WDR18, TEX10, LAS1L and NOL9, with LAS1L providing the endoribonuclease activity and NOL9 the RNA 5' kinase activity. We report here cryo-EM structures of the human PELP1-WDR18-TEX10 and LAS1L-NOL9 complexes and a lower-resolution model of the human PELP1-WDR18-LAS1L complex. The structures reveal the overall organization of the human rixosome core scaffold of PELP1-WDR18-TEX10-LAS1L and indicate how the LAS1L-NOL9 endonuclease/kinase catalytic module is recruited to this core scaffold. Each TEX10 molecule has two regions of contact with WDR18, while the helix at the C terminus of WDR18 interacts with the helical domain of LAS1L. The structural observations are supported by our mutagenesis studies. Mutations in both WDR18-TEX10 contact regions can block the binding of TEX10, while truncation of the C-terminal helix of WDR18 can abolish the binding of LAS1L. The structures also reveal substantial conformational differences for TEX10 between the PELP1-WDR18-TEX10 complex alone and that in complex with pre-ribosome.

DOI: https://doi.org/10.1038/s41467-025-58732-3
Genome Biol. 2025 Apr 08. 26(1): 90

MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles.

Salvatore Milite, Giulio Caravagna, Andrea Sottoriva.

High-throughput multi-omic molecular profiling allows the probing of biological systems at unprecedented resolution. However, integrating and interpreting high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving new biological insights with current methods is difficult because they are not rooted in biological principles but prioritise tasks like dimensionality reduction. Here, we introduce a framework that combines archetypal analysis, an approach grounded in biological principles, with deep learning. Using archetypes based on evolutionary trade-offs and Pareto optimality, MIDAA finds extreme data points that define the geometry of the latent space, preserving the complexity of biological interactions while retaining an interpretable output. We demonstrate that these extreme points represent cellular programmes reflecting the underlying biology. Moreover, we show that, compared to alternative methods, MIDAA can identify parsimonious, interpretable, and biologically relevant patterns from real and simulated multi-omics.

DOI: https://doi.org/10.1186/s13059-025-03530-9