bims-crepig 2025-07-20 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–07–20
twenty-six papers selected by
Connor Rogerson, University of Cambridge

Specificity in clustering of gene-specific transcription factors is encoded in the genome.
TRIM33 loss reduces androgen receptor transcriptional output and H2BK120 ubiquitination.
Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes.
HELLS is required for maintaining proper DNA modification at human satellite repeats.
TAF1 is required for fetal but not adult hematopoiesis in mice.
Non-canonical activating roles of RCoR2 sustain transcription in adrenergic neuroblastoma.
Leveraging transcription factor physical proximity for enhancing gene regulation inference.
Direct genetic transformation bypasses tumor-associated DNA methylation alterations.
Master transcription-factor binding sites constitute the core of early replication control elements.
CRISPR-based screening identifies the role of KRAB-containing transcription factors ZIM3 and ZNF394 in human major zygotic genome activation.
The Mgv1-Rlm1 axis orchestrates SAGA and SWI/SNF complexes at target promoters.
Histone marks enable formation of immiscible phase-separated chromatin compartments.
Retrograde signals control dynamic changes to the chromatin state at photosynthesis-associated loci.
A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq.
HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data.
Recruitment, rewiring and deep conservation in flowering plant gene regulation.
Chromatin heterogeneity modulates nuclear condensate dynamics and phase behavior.
Identification of functional non-coding variants associated with orofacial cleft.
Gene regulatory networks and essential transcription factors for de novo-originated genes.
Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.
Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing.
Deep learning-based high-resolution time inference for deciphering dynamic gene regulation from fixed embryos.
Higher resolution pooled genome-wide CRISPR knockout screening in Drosophila cells using integration and anti-CRISPR (IntAC).
Differential control of growth and identity by HNF4α isoforms in pancreatic ductal adenocarcinoma.
Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.
Time is encoded by methylation changes at clustered CpG sites.

Nucleic Acids Res. 2025 Jul 08. pii: gkaf625. [Epub ahead of print]53(13):

Specificity in clustering of gene-specific transcription factors is encoded in the genome.

Shivali Dongre, Nadine L Vastenhouw.

Gene-specific transcription factors (TFs) often form clusters in the nucleus. Such clusters can facilitate transcription, but it remains unclear how they form. It has been suggested that clusters are seeded by the sequence-specific binding of TFs to DNA and grow by interactions between intrinsically disordered regions (IDRs) that bring in more TFs. In this model, specificity in TF clustering must be provided by the IDRs. To investigate this model, we studied TF clustering by quantitative imaging of Nanog, Pou5f3, and Sox19b in zebrafish embryos. Using mutant TFs, we show that the formation of a TF cluster requires the DNA-binding domain (DBD) as well as at least one of its IDRs. Importantly, IDRs are not sufficient to join a pre-existing cluster. Rather, both IDR and DBD are needed. Finally, using chimeric TFs, we show that while IDRs are required to join a cluster, they are quite promiscuous, and it is the DBD that provides specificity to the clustering of a TF. Thus, for any TF to join a cluster, motif recognition is required, which explains the specificity in TF cluster formation. Taken together, our work provides an alternative model for how specificity is achieved in the organization of transcriptional machinery in the nucleus.

DOI: https://doi.org/10.1093/nar/gkaf625
Commun Biol. 2025 Jul 11. 8(1): 1043

TRIM33 loss reduces androgen receptor transcriptional output and H2BK120 ubiquitination.

Nils Eickhoff, Janina Janetzko, Nuno Padrão, Sebastian Gregoricchio, Joseph C Siefert, Liesbeth Hoekman, Simon Linder, Onno Bleijerveld, Andries M Bergman, Wilbert Zwart.

The Androgen Receptor (AR) is a ligand-dependent transcription factor that drives prostate cancer development and progression. Although, a detailed effect on AR biology has been described for a number of interacting proteins, many AR coregulators remain to be characterized in relation to their distinct impact on AR function. Here, we describe TRIM33 as a conserved AR-interactor across multiple prostate cancer cell lines. We observed that TRIM33 and AR share overall chromatin interaction profiles, in which TRIM33 is involved in downstream responsive transcriptomic output. In contrast to prior reports, we show that TRIM33 does not impact AR protein stability, but instead propose a model in which TRIM33 facilitates maximal AR activity by interfering with H2BK120 ubiquitination levels.

DOI: https://doi.org/10.1038/s42003-025-08449-2
Genome Res. 2025 Jul 14.

Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes.

Rachel M Petersen, Christopher M Vockley, Amanda J Lea.

A major goal in evolutionary biology and biomedicine is to understand the complex interactions between genetic variants, the epigenome, and gene expression. However, the causal relationships between these factors remain poorly understood. mSTARR-seq, a methylation-sensitive massively parallel reporter assay, is capable of identifying methylation-dependent regulatory activity at many thousands of genomic regions simultaneously and allows for the testing of causal relationships between DNA methylation and gene expression on a region-by-region basis. Here, we develop a multiplexed mSTARR-seq protocol to assay naturally occurring human genetic variation from 25 individuals from 10 localities in Europe and Africa. We identify 6957 regulatory elements in either the unmethylated or methylated state, and this set was enriched for enhancer and promoter chromatin annotations, as expected. The expression of 58% of these regulatory elements is modulated by methylation, which is generally associated with decreased transcription. Within our set of regulatory elements, we use allele-specific expression analyses to identify 8020 sites with genetic effects on gene regulation; further, we find that 42.3% of these genetic effects vary in direction or magnitude between methylated and unmethylated states. Sites exhibiting methylation-dependent genetic effects are enriched for GWAS and EWAS annotations, implicating them in human disease. Compared with data sets that assay DNA from a single European ancestry individual, our multiplexed assay is able to uncover more genetic effects and methylation-dependent genetic effects, highlighting the importance of including diverse genomes in assays that aim to understand gene regulatory processes.

DOI: https://doi.org/10.1101/gr.279957.124
Genome Biol. 2025 Jul 17. 26(1): 211

HELLS is required for maintaining proper DNA modification at human satellite repeats.

Philine Guckelberger, Leah Haut, Rosaria Tornisiello, Helene Kretzmer, Alexander Meissner.

  DNA methylation regulation involves multi-layered chromatin interactions that require remodeling proteins like the helicase, lymphoid-specific (HELLS). Here, we generate HELLS and DNA methyltransferase 3A and B (DNMT3A/B) knockout human pluripotent stem cells and report telomere-to-telomere maps of whole genome bisulfite sequencing data combined with ATAC-sequencing. Disrupting HELLS induces a global loss of DNA methylation that is distinct from the DNMTs, in particular over peri/centromeric satellite repeats as defined in the telomere-to-telomere genome assembly. However, HELLS appears dispensable for local enhancer remodeling and the potential to differentiate into the three embryonic germ layers. Taken together, our results further clarify the genomic targets and role of HELLS in human cells.

Keywords:  Centromeres; Chromatin remodeling; DNA methylation; HELLS; Satellite repeats; T2T

DOI:  https://doi.org/10.1186/s13059-025-03681-9
Dev Cell. 2025 Jul 14. pii: S1534-5807(25)00405-8. [Epub ahead of print]

TAF1 is required for fetal but not adult hematopoiesis in mice.

Fan Liu, Jingyin Yue, Francesco Tamiro, Jun Sun, Pradeep Kumar Reddy Cingaram, Krystal Lisa Hossack, Concepcion Martinez Caja, Ye Xu, Chuan Chen, Felipe Beckedorff, Ramin Shiekhattar, Stephen D Nimer.

  While many sequence-specific transcription factors (TFs) have been identified as key regulators of hematopoietic stem cell (HSC) lineage determination, the function of general TFs in HSC behavior is poorly understood. To evaluate the function of the TFIID subunit TAF1 in normal hematopoiesis, we generated Taf1 conditional knockout (cKO) mice and identified an essential role of TAF1 in fetal hematopoiesis. Surprisingly, TAF1 deletion in adult mice was not lethal to hematopoiesis; rather, we observed a marked expansion of the hematopoietic stem and progenitor cell (HSPC) compartment, with increased self-renewal and impaired differentiation capacity of these cells. TAF1-null HSPCs failed to produce mature blood cells in chimeric mice; these cells also failed to upregulate key differentiation genes when induced to differentiate in vitro. TAF1 loss not only disrupted TFIID chromatin recruitment but also reduced RNA polymerase II (RNAPII) promoter-proximal pausing. Thus, HSPCs utilize distinct transcriptional regulatory mechanisms to undergo differentiation versus maintaining self-renewal.

Keywords:  HSPC differentiation; RNAPII pausing; TAF1; TFIID; fetal and adult hematopoiesis; transcription regulation

DOI:  https://doi.org/10.1016/j.devcel.2025.06.027
Cell Rep. 2025 Jul 07. pii: S2211-1247(25)00722-3. [Epub ahead of print] 115951

Non-canonical activating roles of RCoR2 sustain transcription in adrenergic neuroblastoma.

Sara Aloisi, Martina Santulli, Marco Russo, Suleman K Zadran, Alberto Rigamonti, Diana H Chin, Marta Palombo, Leonardo Cimadom, Lorenzo Scrofani, Roberto Bernardoni, Giovanni Capranico, Berkley E Gryder, Giovanni Perini, Giorgio Milazzo.

  CoREST complexes (LSD1, HDAC1/2, and RCoR1/2/3) are pivotal in neurodevelopment and have long been recognized as transcriptional repressors across various cancers. However, distinct roles of RCoR factors remain underexplored. Here, we unveil non-canonical functions of RCoR2 in MYCN-amplified neuroblastoma (NB), underscoring its unique significance compared to its paralogs. This insight shifts the paradigm, highlighting RCoR2 as a key determinant of the NB chromatin landscape. Our findings demonstrate that RCoR2 is a super-enhancer-driven gene, which, unlike RCoR1, acts as a positive regulator of gene expression as a partner of the adrenergic NB core regulatory circuitry (CRC). We propose a model in which RCoR2 facilitates interactions between CRC-bound enhancers and their associated transcription start sites, thereby sustaining the expression of genes critical for NB cell survival. Thus, we identify RCoR2 as a critical vulnerability in high-risk NBs and a promising target for cancer therapeutics.

Keywords:  CP: Cancer; CP: Molecular biology; CoREST; HDAC; LSD1; MYCN; RCOR1; RCOR2; adrenergic; core regulatory circuitry; neuroblastoma; pediatric cancer

DOI:  https://doi.org/10.1016/j.celrep.2025.115951
Bioinformatics. 2025 Jul 01. 41(Supplement_1): i533-i541

Leveraging transcription factor physical proximity for enhancing gene regulation inference.

Xiaoqing Huang, Aamir R Hullur, Elham Jafari, Kaushik Shridhar, Mu Zhou, Kenneth Mackie, Kun Huang, Yijie Wang.

MOTIVATION: Gene regulation inference, a key challenge in systems biology, is crucial for understanding cell function, as it governs processes such as differentiation, cell state maintenance, signal transduction, and stress response. Leading methods utilize gene expression, chromatin accessibility, transcription factor (TF) DNA binding motifs, and prior knowledge. However, they overlook the fact that TFs must be in physical proximity to facilitate transcriptional gene regulation.
RESULTS: To fill the gap, we develop GRIP-Gene Regulation Inference by considering TF Proximity-a gene regulation inference method that directly considers the physical proximity between regulating TFs. Specifically, we use the distance in a protein-protein interaction (PPI) network to estimate the physical proximity between TFs. We design a novel Boolean convex program, which can identify TFs that not only can explain the gene expression of target genes (TGs) but also stay close in the PPI network. We propose an efficient algorithm to solve the Boolean relaxation of the proposed model with a theoretical tightness guarantee. We compare our GRIP with state-of-the-art methods (SCENIC+, DirectNet, Pando, and CellOracle) on inferring cell-type-specific (CD4, CD8, and CD 14) gene regulation using the PBMC 3k scMultiome-seq data and demonstrate its out-performance in terms of the predictive power of the inferred TFs, the physical distance between the inferred TFs, and the agreement between the inferred gene regulation and PCHiC data.
AVAILABILITY AND IMPLEMENTATION: https://github.com/EJIUB/GRIP.

DOI: https://doi.org/10.1093/bioinformatics/btaf186
Genome Biol. 2025 Jul 17. 26(1): 212

Direct genetic transformation bypasses tumor-associated DNA methylation alterations.

Sara Hetzel, Eran Hodis, Elena Torlai Triglia, Alexander Kovacsovics, Kathleen Steinmann, Andreas Gnirke, Meiying Cui, Daniel McQuaid, Raha Weigert, Georg Pohl, Mandar D Muzumdar, Serge Leyvraz, Ulrich Keilholz, Marie-Laure Yaspo, Aviv Regev, Helene Kretzmer, Zachary D Smith, Alexander Meissner.

   BACKGROUND: Tumors represent dynamically evolving populations of mutant cells, and many advances have been made in understanding the biology of their progression. However, there are key unresolved questions about the conditions that support a cell's initial transformation, which cannot be easily captured in patient populations and are instead modeled using transgenic cellular or animal systems.
RESULTS: Here, we use extensive patient atlas data to define common features of the tumor DNA methylation landscape as they compare to healthy human cells and apply this benchmark to evaluate 21 engineered human and mouse models for their ability to reproduce these patterns. Notably, we find that genetically induced cellular transformation rarely recapitulates the widespread de novo methylation of Polycomb regulated promoter sequences as found in clinical samples, but can trigger global changes in DNA methylation levels that are consistent with extensive proliferation in vitro.
CONCLUSIONS: Our results raise pertinent questions about the relationship between genetic and epigenetic aspects of tumorigenesis as well as provide an important molecular reference for evaluating existing and emerging tumor models.

Keywords:  Cancer; DNA methylation; Disease models; Epigenetics; Genetically engineered mouse models

DOI:  https://doi.org/10.1186/s13059-025-03650-2
EMBO J. 2025 Jul 17.

Master transcription-factor binding sites constitute the core of early replication control elements.

Jesse L Turner, Laura Hinojosa-Gonzalez, Takayo Sasaki, Satoshi Uchino, Athanasios Vouzas, Mariella S Soto, Abhijit Chakraborty, Karen E Alexander, Cheryl A Fitch, Amber N Brown, Ferhat Ay, David M Gilbert.

  Eukaryotic genomes replicate in a defined temporal order called the replication timing (RT) program. RT is developmentally regulated with the potential to drive cell fate transitions, but mechanisms controlling RT remain elusive. We previously identified "Early Replication Control Elements" (ERCEs), cis-acting elements necessary for early RT, domain-wide transcription, 3D chromatin architecture and compartmentalization in mouse embryonic stem cells (mESCs), but deletions identifying ERCEs were large and encompassed many putative regulatory elements. Here, we show that ERCEs are compound elements, whose RT activity can largely be accounted for by multiple binding sites for diverse master transcription factors (subERCEs). While deletion of subERCEs had large effects on both transcription and replication timing, deleting transcription start sites eliminated nearly all transcription with only moderate effects on replication timing. Our results suggest a model in which subERCEs are a class of transcriptional enhancers that can also organize chromatin domains structurally to support early replication timing, potentially providing a feed-forward loop to drive robust epigenomic change during cell fate transitions.

Keywords:  Cell Cycle; Cell fate Transitions; Genome Architecture; Replication Timing; Transcription

DOI:  https://doi.org/10.1038/s44318-025-00501-5
Cell Rep. 2025 Jul 15. pii: S2211-1247(25)00786-7. [Epub ahead of print]44(8): 116015

CRISPR-based screening identifies the role of KRAB-containing transcription factors ZIM3 and ZNF394 in human major zygotic genome activation.

Jiayu Li, Liangfu Xie, Cheng Shi, Tiantian Zhang, Xiwen Lin, Haokun Da, Kongqianqian Sun, Chunsheng Han, Bing Zhu, Xi Chen, Hongkui Deng, Jun Xu.

  The initiation of major zygotic genome activation (ZGA) is crucial for human early embryogenesis. However, the transcription factors (TFs) regulating major ZGA in humans remain largely unknown. Here, we performed a CRISPR-based activation screen of 1,603 human TFs in human extended pluripotent stem cells (hEPSCs), which identified 132 candidates as potential regulators of major ZGA. Further evaluation of these candidates revealed that the KRAB-containing TFs ZIM3 and ZNF394 activated totipotent features in hEPSCs upon overexpression. Importantly, simultaneous knockdown of these two TFs arrested human embryo development prior to the eight-cell embryo stage. Mechanistically, the KRAB domains contributed to ZIM3- and ZNF394-mediated totipotency induction in vitro, accompanied by the suppression of a set of four-cell embryo enriched genes. Our study provided valuable resources for totipotency and major ZGA regulation, suggesting an un-reported role of KRAB-containing TFs in major ZGA in humans.

Keywords:  CP: Developmental biology; CP: Molecular biology; totipotency; transcription factors; zygotic genome activation

DOI:  https://doi.org/10.1016/j.celrep.2025.116015
Nucleic Acids Res. 2025 Jul 08. pii: gkaf653. [Epub ahead of print]53(13):

The Mgv1-Rlm1 axis orchestrates SAGA and SWI/SNF complexes at target promoters.

Chaoyun Xu, Yueqi Zhang, Chengqi Zhang, Li Chen, Yanni Yin, Yun Chen, Zunyong Liu, Zhonghua Ma.

The SWI/sucrose non-fermentable (SWI/SNF)-facilitated removal of nucleosomes and Spt-Ada-Gcn5 acetyltransferase (SAGA) complex-mediated histone acetylation are crucial for the activation of transcription initiation. However, the mechanism by which these two complexes coordinate to regulate gene expression involved in cell wall remodeling during infection process or in response to external stimuli remains largely unknown in plant pathogenic fungi. Here, we demonstrate that the cell wall integrity (CWI) pathway is activated under toxin (deoxynivalenol)-inducing conditions in the phytopathogenic fungus Fusarium graminearum. This treatment results in the phosphorylation and nuclear translocation of the mitogen-activated protein kinase FgMgv1 in the CWI signaling pathway. Once in the nucleus, the activated FgMgv1 phosphorylates the downstream transcription factor FgRlm1, which binds to a 12- or 14-bp cis-element in the promoters of target genes. Notably, FgMgv1 forms a polymer and interacts with FgRlm1 via its kinase domain. Crucially, this polymerization enables FgMgv1 to recruit both the SWI/SNF and SAGA complexes simultaneously through its C-terminal domain at the target promoters. This coordinated action among FgMgv1, FgRlm1, SWI/SNF, and SAGA ultimately facilitates the transcriptional activation of target genes. Collectively, these findings illuminate a regulatory framework in which Mgv1-Rlm1 axis serves as a key regulatory hub, integrating CWI signals with epigenetic modifications to ensure transcriptional responsiveness to external stimuli.

DOI: https://doi.org/10.1093/nar/gkaf653
Cell Rep. 2025 Jul 11. pii: S2211-1247(25)00774-0. [Epub ahead of print]44(7): 116003

Histone marks enable formation of immiscible phase-separated chromatin compartments.

Wenjing Sun, Jiacheng Wang, Wenqian Liu, Baixue Tang, Hongyuan Qu, Huanxing Su, Jianwei Wang, Haitao Li, Wei Xie, Pilong Li.

  Eukaryotic chromatin is organized into compartments for gene expression regulation, but the underlying mechanisms remain unclear. Here, we demonstrate that multivalent H3K27me3 and its reader, the CBX7-PRC1 complex, regulate facultative heterochromatin via a phase separation mechanism. Facultative and constitutive heterochromatin represent distinct, coexisting condensates in nuclei. In vitro, H3K27me3- and H3K9me3-marked nucleosomal arrays and their reader complexes can phase separate into immiscible condensates that are analogous to the relationship between facultative and constitutive heterochromatin in vivo. Moreover, overexpression of CBX7-PRC1 causes aberrant chromatin compartmentalization as demonstrated by H3K9me3 CUT&Tag and up-regulation of genes related to cancer, such as acute myeloblastic leukemia (AML). Chromobox 7 (CBX7) inhibitor effectively inhibits cancer cell proliferation, possibly through phase-separation-mediated compartment reorganization. Our data demonstrate how the specificity of compartmentalization is achieved based on the formation of immiscible phase-separated condensates and offer potential epigenetic mechanistic insights into tumor development.

Keywords:  CBX7-PRC1; CP: Molecular biology; chromatin compartmentalization; constitutive heterochromatin; cooperativity; facultative heterochromatin; immiscible condensates; liquid-liquid phase separation; multivalence

DOI:  https://doi.org/10.1016/j.celrep.2025.116003
Nat Commun. 2025 Jul 15. 16(1): 6527

Retrograde signals control dynamic changes to the chromatin state at photosynthesis-associated loci.

Marti Quevedo, Ivona Kubalová, Alexis Brun, Luis Cervela-Cardona, Elena Monte, Åsa Strand.

Retrograde signalling networks originating in the organelles dictate nuclear gene expression and are essential for control and regulation of cellular energy metabolism. We investigate whether such plastid retrograde signals control nuclear gene expression by altering the chromatin state during the establishment of photosynthetic function in response to light. An Arabidopsis thaliana cell culture provides the required temporal resolution to map four histone modifications during the greening process. We uncover sequential and distinct epigenetic reprogramming events where an epigenetic switch from a histone methylation to an acetylation at photosynthesis-associated loci is dependent on a plastid retrograde signal. The transcription factors VIVIPAROUS1/ABI3-LIKE (VAL1), RELATIVE OF EARLY FLOWERING 6 (REF6) and GOLDEN2-LIKE FACTOR1/2 (GLKs) are linked to the H3K27ac deposition at photosynthesis associated loci that precedes full activation of the photosynthesis genes. Our work demonstrates that retrograde signals play a role in the epigenetic reprogramming essential to the establishment of photosynthesis in plant cells.

DOI: https://doi.org/10.1038/s41467-025-61831-w
Genome Res. 2025 Jul 11.

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq.

PsychENCODE Consortium

Genome-wide association studies (GWASs) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. Here, we perform capture STARR-sequencing of over 70,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We select candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWASs. Over 8000 regions demonstrate enhancer activity in the phNPCs, and we link these regions to over 2200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including neuronal system, nervous system development, and developmental delay. We functionally validate a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identify thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.

DOI: https://doi.org/10.1101/gr.279584.124
Brief Bioinform. 2025 Jul 02. pii: bbaf341. [Epub ahead of print]26(4):

HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data.

Bishal Shrestha, Zheng Wang.

  The 3D organization of chromatin is essential for the functioning of cellular processes, including transcriptional regulation, genome integrity, chromatin accessibility, and higher order nuclear architecture. However, detecting anomalous chromatin interactions in spatiotemporal Hi-C data remains a significant challenge. We present HiC4D-SPOT, an unsupervised deep-learning framework that models chromatin dynamics using a ConvLSTM-based autoencoder to identify structural anomalies. Benchmarking results demonstrate high reconstruction fidelity, with Pearson Correlation Coefficient and Spearman Correlation Coefficient values of 0.9, while accurately detecting deviations linked to temporal inconsistencies, topologically associating domain (TAD) and loop perturbations, and significant chromatin remodeling events. HiC4D-SPOT successfully identifies swapped time points in a time-swap experiment, captures simulated TAD and loop disruptions with high confidence scores and statistical significance of 0.01, and detects HERV-H boundary weakening during cardiomyocyte differentiation, as well as cohesin-mediated loop loss and recovery-aligning with experimentally observed chromatin remodeling events. These findings establish HiC4D-SPOT as an efficient tool for analyzing 3D chromatin dynamics, enabling the detection of biologically significant structural anomalies in spatiotemporal Hi-C data.

Keywords:  ConvLSTM; Hi-C; anomaly detection; spatiotemporal autoencoder; spatiotemporal dynamics

DOI:  https://doi.org/10.1093/bib/bbaf341
Nat Plants. 2025 Jul 15.

Recruitment, rewiring and deep conservation in flowering plant gene regulation.

Leo A Baumgart, Sharon I Greenblum, Abraham Morales-Cruz, Peng Wang, Yu Zhang, Lin Yang, Cindy Chen, David J Dilworth, Alexis C Garretson, Nicolas Grosjean, Guifen He, Emily Savage, Yuko Yoshinaga, Ian K Blaby, Chris G Daum, Ronan C O'Malley.

Transcription factors (TFs) are proteins that bind DNA to control where and when genes are expressed. In plants, dozens of TF families interact with distinct sets of binding sites (TFBSs) that reflect each TF's role in organismal function and species-specific adaptations. However, defining these roles and understanding broader patterns of regulatory evolution remain challenging, as predicted TFBSs may lack a clear impact on transcription, and experimentally derived TF binding maps to date are modest in scale or restricted to model organisms. Here we present a scalable TFBS assay that we leveraged to create an atlas of nearly 3,000 genome-wide binding site maps for 360 TFs in ten species spanning 150 million years of flowering plant evolution. We found that TF orthologues from distant species retain nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread. Within lineages, however, conserved TFBSs are over-represented and found in regions harbouring signatures of functional regulatory elements. Moreover, genes with conserved TFBSs showed striking enrichment for cell-type-specific expression in 14 single-nucleus RNA atlases, providing a robust marker of each TF's activity and developmental role. Finally, we compare distant lineages, illustrating how ancient regulatory modules were recruited and rewired to enable adaptations underlying the evolutionary success of grasses.

DOI: https://doi.org/10.1038/s41477-025-02047-0
Nat Commun. 2025 Jul 11. 16(1): 6406

Chromatin heterogeneity modulates nuclear condensate dynamics and phase behavior.

Jing Xia, Jessica Z Zhao, Amy R Strom, Clifford P Brangwynne.

The cell nucleus is a soft composite material with a shell-like nuclear cortex enclosing chromatin, comprised of roughly 2 meters of DNA and associated proteins. Assembling on and around chromatin are droplet-like structures known as biomolecular condensates, which form via phase separation, and facilitate vital roles in gene expression. From studies in non-living materials, the driving forces for phase separation are expected to be sensitive to the local mechanical environment, which often exhibits significant spatial heterogeneity. However, the relationship between chromatin heterogeneity and the phase equilibrium and dynamics of nuclear condensates remains unclear. Here, we investigate the interplay between chromatin organization and the formation, dynamics, and size of engineered model condensates and endogenous nuclear bodies in living cells. We demonstrate that decreasing chromatin heterogeneity with epigenetic modifying drugs correlates with decreased mobility of both endogenous and engineered condensates, and is associated with impaired condensate growth and shifts in the binodal phase boundary of engineered condensates. These findings illustrate how the cell nucleus behaves as a heterogeneous composite material with mechanically permissive chromatin micro-environments.

DOI: https://doi.org/10.1038/s41467-025-60771-9
Nat Commun. 2025 Jul 16. 16(1): 6545

Identification of functional non-coding variants associated with orofacial cleft.

Priyanka Kumari, Ryan Z Friedman, Sarah W Curtis, Lira Pi, Kitt Paraiso, Axel Visel, Lindsey Rhea, Martine Dunnwald, Anjali P Patni, Daniel Mar, Karol Bomsztyk, Julie Mathieu, Hannele Ruohola-Baker, Elizabeth J Leslie-Clarkson, Michael A White, Barak A Cohen, Robert A Cornell.

Oral facial cleft (OFC) comprises cleft lip with or without cleft palate (CL/P) or cleft palate only. Genome wide association studies (GWAS) of isolated OFC have identified common single nucleotide polymorphisms (SNPs) in many genomic loci where the presumed effector gene (for example, IRF6 in the 1q32 locus) is expressed in embryonic oral epithelium. To identify candidates for functional SNPs at eight such loci we conduct a massively parallel reporter assay in a fetal oral epithelial cell line, revealing SNPs with allele-specific effects on enhancer activity. We filter these SNPs against chromatin-mark evidence of enhancers and test a subset in traditional reporter assays, which support the candidacy of SNPs at loci containing FOXE1, IRF6, MAFB, TFAP2A, and TP63. For two SNPs near IRF6 and one near FOXE1, we engineer the genome of induced pluripotent stem cells, differentiate the cells into embryonic oral epithelium, and discover allele-specific effects on the levels of effector gene expression, and, in two cases, the binding affinity of transcription factors FOXE1 or ETS2. Conditional analyses of GWAS data suggest the two functional SNPs near IRF6 account for the majority of risk for CL/P at this locus. This study connects genetic variation associated with OFC to mechanisms of pathogenesis.

DOI: https://doi.org/10.1038/s41467-025-61734-w
Nat Ecol Evol. 2025 Jul 14.

Gene regulatory networks and essential transcription factors for de novo-originated genes.

Junhui Peng, Bing-Jun Wang, Nicolas Svetec, Li Zhao.

The regulation of gene expression is crucial for the functional integration of evolutionarily young genes, particularly those that emerge de novo. However, the regulatory programmes governing the expression of de novo genes remain unknown. To address this, we applied computational methods to single-cell RNA sequencing data, identifying key transcription factors probably instrumental in regulating de novo genes. We found that transcription factors do not have the same propensity for regulating de novo genes; some transcription factors regulate more de novo genes than others. Leveraging genetic and genomic tools in Drosophila, we further examined the role of two key transcription factors, achintya and vismay, and the regulatory architecture of new genes. Our findings identify key transcription factors associated with the expression of de novo genes and highlight how transcription factors, and possibly their duplications, are linked to the expressional regulation of de novo genes.

DOI: https://doi.org/10.1038/s41559-025-02747-y
BMC Biol. 2025 Jul 15. 23(1): 211

Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.

Sisi Yuan, Pengyu Ni, Zhengchang Su.

   BACKGROUND: Cis-regulatory modules (CRMs) such as enhancers and silencers play critical roles in virtually all biological processes by enhancing and repressing, respectively, the transcription of their target genes in specific cell types. Although numerous CRMs have been predicted in genomes, identifying their target genes remains a challenge due to low quality of the predicted CRMs and the fact that CRMs often do not regulate their closest genes.
RESULTS: We developed a method - correlation and physical proximity (CAPP) by leveraging our recently predicted 1.2 M CRMs in the human genome. CAPP is able to not only predict the CRMs' target genes but also their functional types using only chromatin accessibility (CA) and RNA-seq data in a panel of cell/tissue types plus Hi-C data in a few cell types. Applying CAPP to a panel of only 107 cell/tissue types with CA and RNA-seq data available, we predict target genes for 14.3% of the 1.2 M CRMs, of which 1.4% are predicted as both enhancers and silencers (dual functional CRMs), 98.2% as exclusive enhancers, and 0.4% as exclusive silencers. Dual functional CRMs tend to regulate more distant genes than exclusive enhancers and silencers. Enhancers tend to cooperate with other enhancers, whereas silencers typically act independently. Silencers preferentially regulate genes expressed across many cell/tissue types, while enhancers are prone to regulate genes expressed in fewer cell/tissue types.
CONCLUSIONS: CAPP represents a significant advancement in predicting target genes and functional types of CRMs, especially dual functional CRMs, and different types of CRMs show distinct properties.

Keywords:   Cis-regulatory modules; Dual functional CRMs; Enhancers; Silencers; Target genes

DOI:  https://doi.org/10.1186/s12915-025-02313-9
Sci Adv. 2025 Jul 18. 11(29): eadt1644

Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing.

Gemma Valcárcel, Aleksey Lazarenkov, Anna V López-Rubio, Clara Berenguer, Josep Calafell-Segura, Javier Rodríguez-Ubreva, Esteban Ballestar, José Luis Sardina.

Immune cell differentiation and activation are associated with widespread DNA methylation changes; however, the causal relationship between these changes and their impact in shaping cell fate decisions still needs to be fully elucidated. Here, we conducted a genome-wide analysis to investigate the relationship between DNA methylation and gene expression at gene regulatory regions in human immune cells. By using CRISPR-dCas9-TET1 and -DNMT3A epigenome editing tools, we successfully established a cause-and-effect relationship between the DNA methylation levels of the promoter of the interleukin-1 receptor antagonist (IL1RN) gene and its expression. We observed that modifying the DNA methylation status of the IL1RN promoter is sufficient to alter human myeloid cell fate and change the cellular response to inflammatory and pathogenic stimuli. Collectively, our findings demonstrate the potential of targeting specific DNA methylation events to directly modulate immune and inflammatory responses, providing a proof of principle for intervening in a broad range of inflammation-related diseases.

DOI: https://doi.org/10.1126/sciadv.adt1644
Nat Commun. 2025 Jul 16. 16(1): 6565

Deep learning-based high-resolution time inference for deciphering dynamic gene regulation from fixed embryos.

Huihan Bao, Shihe Zhang, Zhiyang Yu, Heng Xu.

Embryo development is driven by the spatiotemporal dynamics of complex gene regulatory networks. Uncovering these dynamics requires simultaneous tracking of multiple fluctuating molecular species over time, which exceeds the capabilities of traditional live-imaging approaches. Fixed-embryo imaging offers the necessary sensitivity and capacity but lacks temporal resolution. Here, we present a multi-scale ensemble deep learning approach to precisely infer absolute developmental time with 1-minute resolution from nuclear morphology in fixed Drosophila embryo images. Applying this approach to quantitative imaging of fixed wild-type embryos, we resolve the spatiotemporal regulation of the endogenous segmentation gene Krüppel (Kr) by multiple transcription factors (TFs) during early development without genetic modification. Integrating a time-resolved theoretical model of single-molecule mRNA statistics, we further uncover the unsteady-state bursty kinetics of the endogenous segmentation gene, hunchback (hb), driven by dynamic TF binding. Our method provides a versatile framework for deciphering complex gene network dynamics in genetically unmodified organisms.

DOI: https://doi.org/10.1038/s41467-025-61907-7
Nat Commun. 2025 Jul 15. 16(1): 6498

Higher resolution pooled genome-wide CRISPR knockout screening in Drosophila cells using integration and anti-CRISPR (IntAC).

Raghuvir Viswanatha, Samuel Entwisle, Yanhui Hu, Ah-Ram Kim, Kelly Reap, Matthew Butnaru, Mujeeb Qadiri, Stephanie E Mohr, Norbert Perrimon.

CRISPR screens enable systematic, scalable genotype-to-phenotype mapping. We previously developed a CRISPR screening method for Drosophila melanogaster and mosquito cell lines using plasmid transfection and site-specific integration to introduce single guide (sgRNA) libraries. The method relies on weak sgRNA promoters to avoid early CRISPR-Cas9 activity causing discrepancies between genome edits and integrated sgRNAs. To address this issue and utilize higher strength sgRNA expression, we introduce a method to co-transfect a plasmid expressing anti-CRISPR protein to suppress early CRISPR-Cas9 activity which we term "IntAC" (integrase with anti-CRISPR). IntAC dramatically improves precision-recall of fitness genes across the genome, allowing us to generate the most comprehensive list of cell fitness genes yet assembled for Drosophila. Drosophila fitness genes show strong correlation with human fitness genes and underscore the effects of paralogs on gene essentiality. We also perform a resistance screen to proaerolysin, a glycosylphosphatidylinositol-(GPI)-binding pore-forming toxin, retrieving 18/23 expected and one previously uncharacterized GPI synthesis gene. We also demonstrate that an IntAC sublibrary enables precise positive selection of a transporter under solute overload. IntAC represents a straightforward enhancement to existing Drosophila CRISPR screening methods, dramatically increasing accuracy, and might also be broadly applicable to virus-free CRISPR screens in other cell and species types.

DOI: https://doi.org/10.1038/s41467-025-61692-3
Mol Cancer Res. 2025 Jul 16.

Differential control of growth and identity by HNF4α isoforms in pancreatic ductal adenocarcinoma.

Pengshu Fang, Emily R Wilson, Sydney N Larsen, Walter A Orellana, Margaret A Hall, Chris Stubben, Acramul Haque Kabir, Kajsa Affolter, Richard A Moffitt, Xiaoyang Zhang, Eric L Snyder.

Although transcriptomic studies have stratified pancreatic ductal adenocarcinoma (PDAC) into clinically relevant subtypes, classical or basal-like, further research is needed to identify the transcriptional regulators of each subtype. Previous studies identified HNF4α as a key regulator of the classical subtype. Still, the distinct contributions of its isoforms (P1 and P2), which display dichotomous functions in normal development and gastrointestinal malignancies, remain unexplored. Here, we show that HNF4α-positive human PDAC tumors exhibit uniform expression of P2-isoforms but variable expression of P1 isoforms. To dissect the roles of each isoform in PDAC, we performed functional, transcriptomic, and epigenetic analysis after exogenous expression in HNF4α-negative models or CRISPRi-mediated knockdown of endogenous isoforms. We demonstrated that P1 isoforms are less compatible with growth and stronger transcriptional regulators than P2. Despite both isoforms sharing a common DNA-binding domain, P1 isoforms displayed stronger binding at HNF4α target genes, resulting in increased transcriptional activity. These findings provide a detailed characterization of HNF4α P1 and P2 isoforms and their distinct roles in PDAC biology. Implications: HNF4α isoforms exhibit heterogeneous expression in PDAC and have distinct effects on proliferation and gene expression, including markers of clinically relevant molecular subtypes.

DOI: https://doi.org/10.1158/1541-7786.MCR-25-0175
Science. 2025 Jul 17. 389(6757): eadr3831

Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.

Upneet Kaur, Hao Wu, Yifan Cheng, Geeta J Narlikar.

Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180° away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.

DOI: https://doi.org/10.1126/science.adr3831
Cell Rep. 2025 Jul 08. pii: S2211-1247(25)00729-6. [Epub ahead of print] 115958

Time is encoded by methylation changes at clustered CpG sites.

Bracha-Lea Ochana, Daniel Nudelman, Daniel Cohen, Ayelet Peretz, Sheina Piyanzin, Ofer Gal Rosenberg, Amit Horn, Netanel Loyfer, Miri Varshavsky, Ron Raisch, Ilona Shapiro, Yechiel Friedlander, Hagit Hochner, Benjamin Glaser, Yuval Dor, Tommy Kaplan, Ruth Shemer.

  Age-dependent changes in DNA methylation allow chronological and biological age inference, but the underlying mechanisms remain unclear. Using ultra-deep sequencing of >300 blood samples from healthy individuals, we show that age-dependent methylation changes occur regionally across clusters of CpG sites either stochastically or in a coordinated block-like manner. Deep learning of single-molecule patterns from two genomic loci predicts chronological age with a median accuracy of 1.36-1.7 years on held-out samples, dramatically improving current clocks. Predictions are robust to sex, smoking, BMI, and biological age measures. Longitudinal 10-year analysis shows that early deviations from predicted age persist throughout life, and subsequent changes faithfully record time. Strikingly, accurate chronological age predictions are possible using as few as 50 DNA molecules, suggesting that age is encoded by individual cells. Overall, DNA methylation changes in clustered CpG sites illuminate the principles of time measurement by cells and tissues and facilitate medical and forensic applications.

Keywords:  CP: Metabolism; CP: Molecular biology; DNA methylation; age prediction; aging; biological age; chronological age; computational biology; deep learning; epigenetics; forensics; neural networks

DOI:  https://doi.org/10.1016/j.celrep.2025.115958