bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–03–16
twenty papers selected by
Connor Rogerson, University of Cambridge
  1. Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.
  2. Molecular model of TFIIH recruitment to the transcription-coupled repair machinery.
  3. Chromatin remodeling protein BPTF mediates chromatin accessibility at gene promoters in planarian stem cells.
  4. Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex.
  5. Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cells.
  6. Ectopic expression of testis-specific transcription elongation factor in driving cancer.
  7. Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag.
  8. Proliferation history and transcription factor levels drive direct conversion to motor neurons.
  9. Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction.
  10. Protocol to identify transcription factor target genes using TargetOrtho2.
  11. Targeted DamID detects cell-type-specific histone modifications in intact tissues or organisms.
  12. Phosphatase PHLPP1 is an alveolar-macrophage-intrinsic transcriptional checkpoint controlling pulmonary fibrosis.
  13. TET2 suppresses vascular calcification by forming inhibitory complex with HDAC1/2 and SNIP1 independent of demethylation.
  14. SNPeBoT: a tool for predicting transcription factor allele specific binding.
  15. Atlas of imprinted and allele-specific DNA methylation in the human body.
  16. SUV39H1 maintains cancer stem cell chromatin state and properties in glioblastoma.
  17. Cell type-dependent directional transcription at enhancers.
  18. Secure and scalable gene expression quantification with pQuant.
  19. Pancreatic alpha and beta cell fate choice is directed by apical-basal polarity dynamics.
  20. GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis.
  1. Proc Natl Acad Sci U S A. 2025 Mar 18. 122(11): e2413112122
    Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.
    Andrea Papale, Julie Segueni, Hanae El Maroufi, Daan Noordermeer, David Holcman.
      Topologically associating domains (TADs) are sub-Megabase regions in vertebrate genomes with enriched intradomain interactions that restrict enhancer-promoter contacts across their boundaries. However, the mechanisms that separate TADs remain incompletely understood. Most boundaries between TADs contain CTCF binding sites (CBSs), which individually contribute to the blocking of Cohesin-mediated loop extrusion. Using genome-wide classification, here we show that the width of TAD boundaries forms a continuum from narrow to highly extended and correlates with CBSs distribution, chromatin features, and gene regulatory elements. To investigate how these boundary widths emerge, we modified the random crosslinker polymer model to incorporate specific boundary configurations, enabling us to evaluate the differential impact of boundary composition on TAD insulation. Our analysis, using three generic boundary categories, identifies differential influence on TAD insulation, with varying local and distal effects on neighboring domains. Notably, we find that increasing boundary width reduces long-range inter-TAD contacts, as confirmed by Hi-C data. While blocking loop extrusion at boundaries indirectly promotes spurious intermingling of neighboring TADs, extended boundaries counteract this effect, emphasizing their role in establishing genome organization. In conclusion, TAD boundary width not only enhances the efficiency of loop extrusion blocking but may also modulate enhancer-promoter contacts over long distances across TAD boundaries, providing a further mechanism for transcriptional regulation.
    Keywords:  TAD; boundary; classification; loop extrusion; polymer modeling
    DOI:  https://doi.org/10.1073/pnas.2413112122
  2. Nat Commun. 2025 Mar 08. 16(1): 2341
    Molecular model of TFIIH recruitment to the transcription-coupled repair machinery.
    Tanmoy Paul, Chunli Yan, Jina Yu, Susan E Tsutakawa, John A Tainer, Dong Wang, Ivaylo Ivanov.
      Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In our model, CSB, CSA, UVSSA, elongation factor 1 (ELOF1), and specific Pol II and UVSSA-bound ubiquitin moieties come together to provide interaction interfaces needed for TFIIH recruitment. STK19 acts as a linchpin of the assembly, orienting the incoming TFIIH and bridging Pol II to core TCR factors and DNA. Molecular simulations of the TCR-associated CRL4CSA ubiquitin ligase complex unveil the interplay of segmental DDB1 flexibility, continuous Cullin4A flexibility, and the key role of ELOF1 for Pol II ubiquitination that enables TCR. Collectively, these findings elucidate the coordinated assembly of repair proteins in early TCR.
    DOI:  https://doi.org/10.1038/s41467-025-57593-0
  3. BMC Genomics. 2025 Mar 11. 26(1): 232
    Chromatin remodeling protein BPTF mediates chromatin accessibility at gene promoters in planarian stem cells.
    Prince Verma, John M Allen, Alejandro Sánchez Alvarado, Elizabeth M Duncan.
       BACKGROUND: The regulation of chromatin accessibility is essential in eukaryotic cells as one of several mechanisms that ensure gene activation occurs at appropriate times and in appropriate cell types. Accordingly, mutations in chromatin remodeling proteins are linked to many different developmental disorders and cancers. One example of a chromatin protein that has been linked to both developmental abnormalities and cancer is BPTF/NURF301, the largest subunit of the Nucleosome Remodeling Factor (NuRF) complex. The BPTF subunit is not only important for the formation of NuRF but also helps direct its activity to particular regions of chromatin by preferentially binding histone H3 lysine four trimethylation (H3K4me3). Notably, defects caused by knockdown of bptf in Xenopus embryos mimic those caused by knockdown of wdr5, a core subunit of all H3K4me3 methyltransferase complexes. However, the mechanistic details of how and where BPTF/NuRF is recruited to regulate gene expression vary between studies and have been largely tested in vitro and/or in cultured cells. Improving our understanding of how this chromatin remodeling complex targets specific gene loci and regulates their expression in an organismal context will provide important insight into how pathogenic mutations disrupt its normal, in vivo, cellular functions.
    RESULTS: Here, we report our findings on the role of BPTF in maintaining chromatin accessibility and essential function in planarian (Schmidtea mediterranea) stem cells. We find that depletion of planarian BPTF primarily affects accessibility at gene promoters near transcription start sites (TSSs). BPTF-dependent loss of accessibility did not correlate with decreased gene expression when we considered all affected loci. However, we found that genes marked by Set1-dependent H3K4me3, but not MLL1/2-dependent H3K4me3, showed increased sensitivity to the loss of BPTF-dependent accessibility. In addition, knockdown of bptf (Smed-bptf) produces loss-of-function phenotypes similar to those caused by knockdown of Smed-set1.
    CONCLUSIONS: The S.mediterranea homolog of NuRF protein BPTF (SMED-BPTF) is essential for normal homeostasis in planarian tissues, potentially through its role in maintaining chromatin accessibility at a specific subset of gene promoters in planarian stem cells. By identifying loci that lose both chromatin accessibility and gene expression after depletion of BPTF, we have identified a cohort of genes that may have important functions in stem cell biology.
    Keywords:  Chromatin remodeling; Planarians; Stem cells; Transcription
    DOI:  https://doi.org/10.1186/s12864-025-11405-3
  4. Mol Cell. 2025 Mar 05. pii: S1097-2765(25)00144-3. [Epub ahead of print]
    Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex.
    Tiffany Ge, Donna Garvey Brickner, Kara Zehr, D Jake VanBelzen, Wenzhu Zhang, Christopher Caffalette, Gavin C Moeller, Sara Ungerleider, Nikita Marcou, Alexis Jacob, Vu Q Nguyen, Brian Chait, Michael P Rout, Jason H Brickner.
      Nuclear pore proteins (nucleoporins [Nups]) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers, and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC and in vitro, Crm1 binds directly to both Gcn4 and Nup2. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-guanosine triphosphate (GTP) nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates the docking of transcription-factor-bound enhancers at the NPC.
    Keywords:  nuclear architecture; nuclear pore complex; transcription; transcription factor
    DOI:  https://doi.org/10.1016/j.molcel.2025.02.013
  5. Stem Cell Reports. 2025 Mar 07. pii: S2213-6711(25)00054-2. [Epub ahead of print] 102450
    Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cells.
    C Parikh, R A Glenn, Y Shi, K Chatterjee, K Kasliwal, E E Swanzey, S Singer, S C Do, Y Zhan, Y Furuta, M Tahiliani, E Apostolou, A Polyzos, R Koche, J G Mezey, T Vierbuchen, M Stadtfeld.
      Naive pluripotent stem cells (nPSCs) frequently undergo pathological loss of DNA methylation at imprinted gene loci, posing a hurdle for biomedical applications and underscoring the need to identify underlying causes. We show that nPSCs from inbred mouse strains exhibit strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming and upon exposure to a mitogen-activated protein kinase (MAPK) inhibitor, a common approach to maintain naive pluripotency. Analysis of genetically diverse nPSCs from the Diversity Outbred (DO) stock confirms the impact of genetic variation on epigenome stability, which we leverage to identify trans-acting quantitative trait loci (QTLs) that modulate DNA methylation levels at specific targets or genome-wide. Analysis of multi-target QTLs on chromosomes 4 and 17 suggests candidate transcriptional regulators contributing to DNA methylation maintenance in nPSCs. We propose that genetic variants represent biomarkers to identify pluripotent cell lines with desirable properties and may allow the targeted engineering of nPSCs with stable epigenomes.
    Keywords:  DNA methylation; QTL mapping; diversity outbred mice; epigenetic instability; genomic imprinting; naive pluripotency
    DOI:  https://doi.org/10.1016/j.stemcr.2025.102450
  6. Sci Adv. 2025 Mar 14. 11(11): eads4200
    Ectopic expression of testis-specific transcription elongation factor in driving cancer.
    Bin Zheng, Marta Iwanaszko, Shimaa Hassan AbdelAziz Soliman, Yukitomo Ishi, Sarah Gold, Ruxuan Qiu, Benjamin Charles Howard, Madhurima Das, Zibo Zhao, Rintaro Hashizume, Lu Wang, Ali Shilatifard.
      The testis-specific BET protein BRDT structurally resembles the ubiquitous BRD4 and is misexpressed in cancer, and we show that BRDT misexpression may affect lung cancer progression. BRDT knockdown in lung cancer cells slowed tumor growth and prolonged survival in a xenograft model. Comparative characterization of PTEFb complex participation and chromatin binding indicates BRD4-redundant and BRD4-distinct BRDT functions. Unlike dual depletion, individual BRD4 or BRDT knockdown did not impair transcriptional responses to hypoxia in BRDT-expressing cells, consistent with redundant function. However, BRD4 depletion/BRDT complementation revealed that BRDT can also release paused RNA polymerase II independently of its bromodomains as we previously demonstrated not to be required for Pol II pause/release function of BRD4, underscoring the functional importance of the C-terminal domains in both BRD4 and BRDT and their potential as therapeutic targets in solid tumors. Based on this study, future investigations should explore BRD4-distinct BRDT functions and BRDT misexpression driving cancer pathogenesis.
    DOI:  https://doi.org/10.1126/sciadv.ads4200
  7. Mol Cell. 2025 Mar 05. pii: S1097-2765(25)00143-1. [Epub ahead of print]
    Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag.
    Nadiya Khyzha, Kami Ahmad, Steven Henikoff.
      Nuclear compartments are membrane-less regions enriched in functionally related molecules. RNA is a major component of many nuclear compartments, but the identity and dynamics of transcripts within nuclear compartments are poorly understood. Here, we applied reverse transcribe and tagment (RT&Tag) to human cell lines to identify the transcript populations of Polycomb domains and nuclear speckles. We also developed SLAM-RT&Tag, which combines RNA metabolic labeling with RT&Tag, to quantify transcript dynamics within nuclear compartments. We observed unique transcript populations with differing structures and dynamics within each compartment. Intriguingly, exceptionally long genes are transcribed adjacent to Polycomb domains and are transiently associated with chromatin. By contrast, nuclear speckles act as quality control checkpoints that transiently confine incompletely spliced polyadenylated transcripts and facilitate their post-transcriptional splicing. In summary, we demonstrate that transcripts at Polycomb domains and nuclear speckles undergo distinct RNA processing mechanisms, highlighting the pivotal role of compartmentalization in RNA maturation.
    Keywords:  H3K27me3; Polycomb domains; RNA dynamics; RNA localization; RNA metabolic labeling; RNA sequencing; RT&Tag; compartments; nuclear bodies; nuclear organization; nuclear speckles; post-transcriptional splicing
    DOI:  https://doi.org/10.1016/j.molcel.2025.02.012
  8. Cell Syst. 2025 Mar 11. pii: S2405-4712(25)00038-9. [Epub ahead of print] 101205
    Proliferation history and transcription factor levels drive direct conversion to motor neurons.
    Nathan B Wang, Brittany A Lende-Dorn, Adam M Beitz, Patrick Han, Honour O Adewumi, Timothy M O'Shea, Kate E Galloway.
      The sparse and stochastic nature of conversion has obscured our understanding of how transcription factors (TFs) drive cells to new identities. To overcome this limit, we develop a tailored, high-efficiency conversion system that increases the direct conversion of fibroblasts to motor neurons 100-fold. By tailoring the cocktail to a minimal set of transcripts, we reduce extrinsic variation, allowing us to examine how proliferation and TFs synergistically drive conversion. We show that cell state-as set by proliferation history-defines how cells interpret the levels of TFs. Controlling for proliferation history and titrating each TF, we find that conversion correlates with levels of the pioneer TF Ngn2. By isolating cells by both their proliferation history and Ngn2 levels, we demonstrate that levels of Ngn2 expression alone are insufficient to predict conversion rates. Rather, proliferation history and TF levels combine to drive direct conversion. Finally, increasing the proliferation rate of adult human fibroblasts generates morphologically mature induced human motor neurons at high rates.
    Keywords:  cell state; cell-fate transition; direct conversion; molecular systems biology; motor neurons; proliferation; reprogramming; synthetic biology; transcription factor
    DOI:  https://doi.org/10.1016/j.cels.2025.101205
  9. Elife. 2025 Mar 12. pii: RP95566. [Epub ahead of print]13
    Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction.
    James Boocock, Noah Alexander, Leslie Alamo Tapia, Laura Walter-McNeill, Shivani Prashant Patel, Chetan Munugala, Joshua S Bloom, Leonid Kruglyak.
      Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.
    Keywords:  S. cerevisiae; eQTL; evolutionary biology; gene expression; genetics; genomics; single-cell RNA sequencing
    DOI:  https://doi.org/10.7554/eLife.95566
  10. STAR Protoc. 2025 Mar 06. pii: S2666-1667(25)00086-3. [Epub ahead of print]6(1): 103680
    Protocol to identify transcription factor target genes using TargetOrtho2.
    Jonathan D Rumley, Jee Hun Kim, Oliver Hobert.
      TargetOrtho2 uses transcription factor binding site information to predict transcription factor targets in C. elegans, based on an in silico phylogenetic footprinting approach. Here, we present a protocol to identify transcription factor target genes using a new version of TargetOrtho2. We provide instructions for installing TargetOrtho2 and its required suite of programs, for predicting transcription factor target genes, and for updating and adding new genomes to TargetOrtho2.
    Keywords:  Bioinformatics; Gene Expression; Genomics; Model Organisms; Molecular Biology; Sequence analysis
    DOI:  https://doi.org/10.1016/j.xpro.2025.103680
  11. PLoS Biol. 2025 Mar 11. 23(3): e3002944
    Targeted DamID detects cell-type-specific histone modifications in intact tissues or organisms.
    Jelle van den Ameele, Manuel Trauner, Eva Hörmanseder, Alex P A Donovan, Oriol Llorà-Batlle, Seth W Cheetham, Robert Krautz, Rebecca Yakob, Anna Malkowska, John B Gurdon, Andrea H Brand.
      Histone modifications play a key role in regulating gene expression and cell fate during development and disease. Current methods for cell-type-specific genome-wide profiling of histone modifications require dissociation and isolation of cells and are not compatible with all tissue types. Here we adapt Targeted DamID (TaDa) to recognize specific histone marks, by fusing chromatin-binding proteins or single-chain antibodies to Dam, an Escherichia coli DNA adenine methylase. When combined with TaDa, this enables cell-type-specific chromatin profiling in intact tissues or organisms. We first profiled H3K4me3, H3K9ac, H3K27me3 and H4K20me1 in vivo in neural stem cells of the developing Drosophila brain. Next, we mapped cell-type-specific H3K4me3, H3K9ac and H4K20me1 distributions in the developing mouse brain. Finally, we injected RNA encoding DamID constructs into 1-cell stage Xenopus embryos to profile H3K4me3 distribution during gastrulation and neurulation. These results illustrate the versatility of TaDa to profile cell-type-specific histone marks throughout the genome in diverse model systems.
    DOI:  https://doi.org/10.1371/journal.pbio.3002944
  12. Cell Rep. 2025 Mar 12. pii: S2211-1247(25)00170-6. [Epub ahead of print]44(3): 115399
    Phosphatase PHLPP1 is an alveolar-macrophage-intrinsic transcriptional checkpoint controlling pulmonary fibrosis.
    Yuyu Jiang, Yunkai Zhang, Xiaohui Wang, Yan Xiang, Zeting Wang, Bo Wang, Yingying Ding, Ying Gao, Bing Rui, Jie Bai, Yue Ding, Chang Chen, Zhenzhen Zhan, Xingguang Liu.
      Alveolar macrophages (AMs) are crucial for lung homeostasis, and their dysfunction causes uncontrolled fibrotic responses and pulmonary disorders. Protein phosphatases control multiple cellular events. However, whether nuclear phosphatases cooperate with histone modifiers to affect pulmonary fibrosis progress remains obscure. Here, we identified pleckstrin homology domain and leucine-rich repeat protein phosphatase 1 (PHLPP1) as a key protective factor for pulmonary fibrosis. Transcriptomics and epigenomics data confirmed that PHLPP1 selectively targeted Kruppel-like factor 4 (KLF4) for transcriptional inhibition in AMs. Nuclear PHLPP1 directly bound and dephosphorylated histone deacetylase 8 (HDAC8) at serine 39, thereby enhancing its deacetylase enzyme activity and subsequently suppressing KLF4 expression via the decreased histone acetylation and chromatin accessibility. Thus, loss of PHLPP1 amplified KLF4-centric profibrotic transcriptional program in AMs, while intratracheal administration of Klf4-short hairpin RNA (shRNA) adeno-associated virus ameliorated lung fibrosis in PHLPP1-deficient mice. Our study implies that targeting decreased PHLPP1 in AMs might be a promising therapeutic strategy for pulmonary fibrosis.
    Keywords:  CP: Immunology; CP: Molecular biology; KLF4; PHLPP1; alveolar macrophage; histone acetylation; protein phosphatase; pulmonary fibrosis
    DOI:  https://doi.org/10.1016/j.celrep.2025.115399
  13. J Clin Invest. 2025 Mar 11. pii: e186673. [Epub ahead of print]
    TET2 suppresses vascular calcification by forming inhibitory complex with HDAC1/2 and SNIP1 independent of demethylation.
    Dayu He, Jianshuai Ma, Ziting Zhou, Yanli Qi, Yaxin Lian, Feng Wang, Huiyong Yin, Huanji Zhang, Tingting Zhang, Hui Huang.
      Osteogenic transdifferentiation of vascular smooth muscle cells (VSMCs) has been recognized as the principal mechanism underlying vascular calcification (VC). Runt-related transcription factor 2 (RUNX2) in VSMCs plays a pivotal role because it constitutes an essential osteogenic transcription factor for bone formation. As a key DNA demethylation enzyme, ten-eleven translocation 2 (TET2) is crucial in maintaining the VSMC phenotype. However, whether TET2 involves in VC progression remains elusive. Here we identified a substantial downregulation of TET2 in calcified human and mouse arteries, as well as human primary VSMCs. In vitro gain- and loss-of function experiments demonstrated TET2 regulated VC. Subsequently, in vivo knockdown of TET2 significantly exacerbated VC in both vitamin D3 and adenine-diet-induced chronic kidney disease (CKD) mice models. Mechanistically, TET2 binds to and suppresses the activity of the P2 promoter within the RUNX2 gene, whereas an enzymatic loss-of-function mutation of TET2 has a comparable effect. Furthermore, TET2 forms a complex with histone deacetylases 1/2 (HDAC1/2 ) to deacetylate H3K27ac on the P2 promoter, thereby inhibiting its transcription. Moreover, SNIP1 is indispensable for TET2 to interact with HDAC1/2 to exert inhibitory effect on VC, and knockdown of SNIP1 accelerated VC in mice. Collectively, our findings imply that TET2 might serve as a potential therapeutic target for VC.
    Keywords:  Cardiology; Cardiovascular disease; Vascular biology
    DOI:  https://doi.org/10.1172/JCI186673
  14. BMC Bioinformatics. 2025 Mar 10. 26(1): 81
    SNPeBoT: a tool for predicting transcription factor allele specific binding.
    Patrick Gohl, Baldo Oliva.
       BACKGROUND: Mutations in non-coding regulatory regions of DNA may lead to disease through the disruption of transcription factor binding. However, our understanding of binding patterns of transcription factors and the effects that changes to their binding sites have on their action remains limited. To address this issue we trained a Deep learning model to predict the effects of Single Nucleotide Polymorphisms (SNP) on transcription factor binding. Allele specific binding (ASB) data from Chromatin Immunoprecipitation sequencing (ChIP-seq) experiments were paired with high sequence-identity DNA binding Domains assessed in Protein Binding Microarray (PBM) experiments. For each transcription factor a paired DNA binding Domain was selected from which we derived E-score profiles for reference and alternate DNA sequences of ASB events. A Convolutional Neural Network (CNN) was trained to predict whether these profiles were indicative of ASB gain/loss or no change in binding. 18211 E-score profiles from 113 transcription factors were split into train, validation and test data. We compared the performance of the trained model with other available platforms for predicting the effect of SNP on transcription factor binding. Our model demonstrated increased accuracy and ASB recall in comparison to the best scoring benchmark tools.
    CONCLUSION: In this paper we present our model SNPeBoT (Single Nucleotide Polymorphism effect on Binding of Transcription Factors) in its standalone and web server form. The increased recovery and prediction accuracy of allele specific binding events could prove useful in discovering non-coding mutations relevant to disease.
    Keywords:  Gene regulation; Neural network; Transcription factor
    DOI:  https://doi.org/10.1186/s12859-025-06094-4
  15. Nat Commun. 2025 Mar 11. 16(1): 2141
    Atlas of imprinted and allele-specific DNA methylation in the human body.
    Jonathan Rosenski, Ayelet Peretz, Judith Magenheim, Netanel Loyfer, Ruth Shemer, Benjamin Glaser, Yuval Dor, Tommy Kaplan.
      Allele-specific DNA methylation reflects genetic variation and parentally-inherited changes, and is involved in gene regulation and pathologies. Yet, our knowledge of this phenomenon is largely limited to blood. Here we present a comprehensive atlas of allele-specific DNA methylation using deep whole-genome sequencing across 39 normal human cell types. We identified 325k regions, covering 6% of the genome and 11% of CpGs, that show a bimodal distribution of methylated and unmethylated molecules. In 34k of these regions, genetic variations at individual alleles segregate with methylation patterns, validating allele-specific methylation. We also identified 460 regions showing parental allele-specific methylation, the majority of which are novel, as well as 78 regions associated with known imprinted genes. Surprisingly, sequence-dependent and parental allele-dependent methylation is often restricted to specific cell types, revealing unappreciated variation of allele-specific methylation across the human body. Finally, we validate tissue-specific, maternal allele-specific methylation of CHD7, offering a potential mechanism for the paternal bias in the inheritance mode of CHARGE syndrome associated with this gene. The atlas provides a resource for studying allele-specific methylation and regulatory mechanisms underlying imprinted expression in specific human cell types.
    DOI:  https://doi.org/10.1038/s41467-025-57433-1
  16. JCI Insight. 2025 Mar 10. pii: e186344. [Epub ahead of print]10(5):
    SUV39H1 maintains cancer stem cell chromatin state and properties in glioblastoma.
    Chunying Li, Qiqi Xie, Sugata Ghosh, Bihui Cao, Yuanning Du, Giau V Vo, Timothy Y Huang, Charles Spruck, Richard L Carpenter, Y Alan Wang, Q Richard Lu, Kenneth P Nephew, Jia Shen.
      Glioblastoma (GBM) is the most lethal brain cancer, with GBM stem cells (GSCs) driving therapeutic resistance and recurrence. Targeting GSCs offers a promising strategy for preventing tumor relapse and improving outcomes. We identify SUV39H1, a histone-3, lysine-9 methyltransferase, as critical for GSC maintenance and GBM progression. SUV39H1 is upregulated in GBM compared with normal brain tissues, with single-cell RNA-seq showing its expression predominantly in GSCs due to super-enhancer-mediated activation. Knockdown of SUV39H1 in GSCs impaired their proliferation and stemness. Whole-cell RNA-seq analysis revealed that SUV39H1 regulates G2/M cell cycle progression, stem cell maintenance, and cell death pathways in GSCs. By integrating the RNA-seq data with ATAC-seq data, we further demonstrated that knockdown of SUV39H1 altered chromatin accessibility in key genes associated with these pathways. Chaetocin, an SUV39H1 inhibitor, mimics the effects of SUV39H1 knockdown, reducing GSC stemness and sensitizing cells to temozolomide, a standard GBM chemotherapy. In a patient-derived xenograft model, targeting SUV39H1 inhibits GSC-driven tumor growth. Clinically, high SUV39H1 expression correlates with poor glioma prognosis, supporting its relevance as a therapeutic target. This study identifies SUV39H1 as a crucial regulator of GSC maintenance and a promising therapeutic target to improve GBM treatment and patient outcomes.
    Keywords:  Cancer; Cell biology; Oncology; Stem cells
    DOI:  https://doi.org/10.1172/jci.insight.186344
  17. NAR Genom Bioinform. 2025 Mar;7(1): lqaf007
    Cell type-dependent directional transcription at enhancers.
    Saumya Agrawal, Emi Kanamaru, Yoriko Saito, Fumihiko Ishikawa, Michiel de Hoon.
      Enhancers are noncoding regulatory regions in the genome that play essential roles in modulating gene expression. Previous work showed that enhancers are not transcriptionally silent but are characterized by bidirectional expression of short capped noncoding RNAs. Balanced bidirectional expression has therefore been used as a key feature for the detection of enhancers from transcriptome data. Instead, by analyzing FANTOM5 and other deep cap analysis gene expression transcriptome datasets, we find enhancer transcription preferentially in one direction in individual cell types. As the preferred direction of transcription of an enhancer can switch between cell types, balanced bidirectional enhancer expression may appear if transcriptome data are aggregated over cell types. 5' single-cell RNA sequencing data showed that enhancers were almost exclusively expressed unidirectionally in a single cell. Reporter assay data demonstrated that the regulatory function of an enhancer does not depend on its preference for unidirectional or bidirectional expression. We conclude that requiring balanced bidirectional transcription for enhancer detection may discard most valid enhancers when applied to transcriptome data of a single cell type.
    DOI:  https://doi.org/10.1093/nargab/lqaf007
  18. Nat Commun. 2025 Mar 10. 16(1): 2380
    Secure and scalable gene expression quantification with pQuant.
    Seungwan Hong, Conor R Walker, Yoolim A Choi, Gamze Gürsoy.
      Next generation sequencing reads from RNA-seq studies expose private genotypes of individuals during computation. Here, we introduce pQuant, an algorithm that employs homomorphic encryption to ensure privacy-preserving quantification of gene expression from RNA-seq data across public and cloud servers. pQuant performs computations on encrypted data, allowing researchers to handle sensitive information without exposing it. Our evaluations demonstrate that pQuant achieves accuracy comparable to state-of-the-art non-secure algorithms like STAR and kallisto. pQuant is highly scalable and its runtime and memory do not depend on the number of reads. It also supports parallel processing to enhance efficiency regardless of the number of genes analyzed.
    DOI:  https://doi.org/10.1038/s41467-025-57393-6
  19. Dev Cell. 2025 Mar 04. pii: S1534-5807(25)00113-3. [Epub ahead of print]
    Pancreatic alpha and beta cell fate choice is directed by apical-basal polarity dynamics.
    Ulf Tiemann, Chenglei Tian, Florian Hermann, Martin Proks, Emilie Skovgaard, Ivan Kulik, Yilin Di, Jakub Sedzinski, Henrik Semb.
      A central question in cell and developmental biology is how extracellular cues control the differentiation of multipotent progenitors in a dynamically changing niche. Here, we identify apical-basal polarity as the main regulator of the differentiation of multipotent pancreatic Neurogenin3+ endocrine progenitors (EPs) into the beta or alpha cell fates. We show that human EPs dynamically change their apical-basal polarity status. Whereas polarized EPs are predisposed to differentiate into beta cells rather than alpha cells, inhibiting apical-basal polarity selectively suppresses beta cell differentiation. Single-cell RNA sequencing and complementary mechanistic data demonstrate that apical-basal polarity in human EPs promotes beta cell specification via cyclic AMP (cAMP)/PKA-cAMP response element binding protein (CREB)-EGR1-mediated inhibition of ARX expression, while reduced cAMP levels in non-polarized human EPs maintain expression of ARX, leading to alpha cell differentiation. These findings identify the apical-basal polarity status of multipotent EPs as a critical epithelial feature that determines their fate into the alpha or beta cell lineages.
    Keywords:  apical-basal polarity; cAMP; multipotent pancreatic endocrine progenitors; pancreas; pancreatic alpha cells; pancreatic beta cells
    DOI:  https://doi.org/10.1016/j.devcel.2025.02.008
  20. Elife. 2025 Mar 13. pii: RP100797. [Epub ahead of print]13
    GATA6 regulates WNT and BMP programs to pattern precardiac mesoderm during the earliest stages of human cardiogenesis.
    Joseph A Bisson, Miriam Gordillo, Ritu Kumar, Neranjan de Silva, Ellen Yang, Kelly M Banks, Zhong-Dong Shi, Kihyun Lee, Dapeng Yang, Wendy K Chung, Danwei Huangfu, Todd Evans.
      Haploinsufficiency for GATA6 is associated with congenital heart disease (CHD) with variable comorbidity of pancreatic or diaphragm defects, although the etiology of disease is not well understood. Here, we used cardiac directed differentiation from human embryonic stem cells (hESCs) as a platform to study GATA6 function during early cardiogenesis. GATA6 loss-of-function hESCs had a profound impairment in cardiac progenitor cell (CPC) specification and cardiomyocyte (CM) generation due to early defects during the mesendoderm and lateral mesoderm patterning stages. Profiling by RNA-seq and CUT&RUN identified genes of the WNT and BMP programs regulated by GATA6 during early mesoderm patterning. Furthermore, interactome analysis detected GATA6 binding with developmental transcription factors and chromatin remodelers, suggesting cooperative regulation of cardiac lineage gene accessibility. We show that modulating WNT and BMP inputs during the first 48 hr of cardiac differentiation is sufficient to partially rescue CPC and CM defects in GATA6 heterozygous and homozygous mutant hESCs. This study provides evidence of the regulatory functions for GATA6 directing human precardiac mesoderm patterning during the earliest stages of cardiogenesis to further our understanding of haploinsufficiency causing CHD and the co-occurrence of cardiac and other organ defects caused by human GATA6 mutations.
    Keywords:  cardiac progenitors; congenital heart disease; developmental biology; eomesodermin; heart development; human; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.100797
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