bims-crepig 2025-01-26 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2025–01–26
seventeen papers selected by
Connor Rogerson, University of Cambridge

Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis.
NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit.
Mature chromatin packing domains persist after RAD21 depletion in 3D.
BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells.
Multiscale footprints reveal the organization of cis-regulatory elements.
SMC motor proteins extrude DNA asymmetrically and can switch directions.
Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes.
MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model.
Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.
Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy.
TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites.
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development.
FOXF2 expression triggered by endocrine therapy orchestrates therapeutic resistance through reorganization of chromatin architecture in breast cancer.
Mapping cells through time and space with moscot.
Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation.
Characterizing the regulatory effects of H2A.Z and SWR1-C on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae.
Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3.

Nat Commun. 2025 Jan 22. 16(1): 929

Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis.

Alireza Lorzadeh, George Ye, Sweta Sharma, Unmesh Jadhav.

Transcription factors guide tissue development by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of transcription factors. However, how transcription factors navigate chromatin features to selectively bind a small subset of all the possible genomic target loci remains poorly understood. Here we show that Cdx2-a lineage defining transcription factor that binds distinct targets in developing versus adult intestinal epithelial cells-has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic Cdx2 targets and methylated state of the CpG during development enables selective Cdx2 binding and activation of developmental enhancers and genes. In adult cells, demethylation at these enhancers prevents ectopic Cdx2 binding, instead directing Cdx2 to its canonical motif without a CpG. This shift in Cdx2 binding facilitates Ctcf and Hnf4 recruitment, establishing super-enhancers during development and homeostatic enhancers in adult cells, respectively. Induced DNA methylation in adult mouse epithelium or cultured cells recruits Cdx2 to developmental targets, promoting corecruitment of partner transcription factors. Thus, Cdx2's differential CpG motif preferences enable it to navigate distinct DNA methylation profiles, activating genes specific to appropriate developmental stages.

DOI: https://doi.org/10.1038/s41467-025-56187-0
Nat Commun. 2025 Jan 17. 16(1): 791

NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit.

Zhenlong Kang, Chen Xu, Shuai Lu, Jie Gong, Ruoyu Yan, Gan Luo, Yuanyuan Wang, Qing He, Yifei Wu, Yitong Yan, Baomei Qian, Shenglin Han, Zhiwen Bu, Jinwen Zhang, Xian Xia, Liang Chen, Zhibin Hu, Mingyan Lin, Zheng Sun, Yayun Gu, Lan Ye.

Transcription elongation, especially RNA polymerase II (Pol II) pause-release, is less studied than transcription initiation in regulating gene expression during meiosis. It is also unclear how transcription elongation interplays with transcription initiation. Here, we show that depletion of NKAPL, a testis-specific protein distantly related to RNA splicing factors, causes male infertility in mice by blocking the meiotic exit and downregulating haploid genes. NKAPL binds to promoter-associated nascent transcripts and co-localizes with DNA-RNA hybrid R-loop structures at GAA-rich loci to enhance R-loop formation and facilitate Pol II pause-release. NKAPL depletion prolongs Pol II pauses and stalls the SOX30/HDAC3 transcription initiation complex on the chromatin. Genetic variants in NKAPL are associated with azoospermia in humans, while mice carrying an NKAPL frameshift mutation (M349fs) show defective meiotic exit and transcriptomic changes similar to NKAPL depletion. These findings identify NKAPL as an R-loop-recognizing factor that regulates transcription elongation, which coordinates the meiotic-to-postmeiotic transcriptome switch in alliance with the SOX30/HDAC3-mediated transcription initiation.

DOI: https://doi.org/10.1038/s41467-024-55579-y
Sci Adv. 2025 Jan 24. 11(4): eadp0855

Mature chromatin packing domains persist after RAD21 depletion in 3D.

Wing Shun Li, Lucas M Carter, Luay Matthew Almassalha, Ruyi Gong, Emily M Pujadas-Liwag, Tiffany Kuo, Kyle L MacQuarrie, Marcelo Carignano, Cody Dunton, Vinayak Dravid, Masato T Kanemaki, Igal Szleifer, Vadim Backman.

Understanding chromatin organization requires integrating measurements of genome connectivity and physical structure. It is well established that cohesin is essential for TAD and loop connectivity features in Hi-C, but the corresponding change in physical structure has not been studied using electron microscopy. Pairing chromatin scanning transmission electron tomography with multiomic analysis and single-molecule localization microscopy, we study the role of cohesin in regulating the conformationally defined chromatin nanoscopic packing domains. Our results indicate that packing domains are not physical manifestation of TADs. Using electron microscopy, we found that only 20% of packing domains are lost upon RAD21 depletion. The effect of RAD21 depletion is restricted to small, poorly packed (nascent) packing domains. In addition, we present evidence that cohesin-mediated loop extrusion generates nascent domains that undergo maturation through nucleosome posttranslational modifications. Our results demonstrate that a 3D genomic structure, composed of packing domains, is generated through cohesin activity and nucleosome modifications.

DOI: https://doi.org/10.1126/sciadv.adp0855
Brief Bioinform. 2024 Nov 22. pii: bbaf013. [Epub ahead of print]26(1):

BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells.

Lan Cao, Wenhao Zhang, Fan Yang, Shengquan Chen, Xiaobing Huang, Feng Zeng, Ying Wang.

  Understanding cell destiny requires unraveling the intricate mechanism of gene regulation, where transcription factors (TFs) play a pivotal role. However, the actual contribution of TFs, that is TF activity, is not only determined by TF expression, but also accessibility of corresponding chromatin regions. Therefore, we introduce BIOTIC, an advanced Bayesian model with a well-established gene regulation structure that harnesses the power of single-cell multi-omics data to model the gene expression process under the control of regulatory elements, thereby defining the regulatory activity of TFs with variational inference. We demonstrated that the TF activity inferred by BIOTIC can serve as a characterization of cell identity, and outperforms baseline methods for the tasks of cell typing, cell development tracking, and batch effect correction. Additionally, BIOTIC trained on multi-omics data can flexibly be applied to the scenario where merely single-cell transcriptome sequencing is available, to infer TF activity and annotate the cell type by mapping the query cell into the reference TF activity space, as an emerging application of cell atlases. The structure of BIOTIC has been determined to be adaptable for the inclusion of additional biological factors, allowing for flexible and more comprehensive gene regulation analysis. BIOTIC introduces a pioneering biological-mechanism-driven framework to infer TF activity and elucidate cell identity states at gene regulatory level, paving the way for a deeper understanding of the complex interplay between TFs and gene expression in living systems.

Keywords:  TF activity; gene regulatory; multi-omics; single-cell; transcriptional factor; variational inference

DOI:  https://doi.org/10.1093/bib/bbaf013
Nature. 2025 Jan 22.

Multiscale footprints reveal the organization of cis-regulatory elements.

Yan Hu, Max A Horlbeck, Ruochi Zhang, Sai Ma, Rojesh Shrestha, Vinay K Kartha, Fabiana M Duarte, Conrad Hock, Rachel E Savage, Ajay Labade, Heidi Kletzien, Alia Meliki, Andrew Castillo, Neva C Durand, Eugenio Mattei, Lauren J Anderson, Tristan Tay, Andrew S Earl, Noam Shoresh, Charles B Epstein, Amy J Wagers, Jason D Buenrostro.

Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time1. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size. Using these multiscale footprints, we created the seq2PRINT framework, which uses deep learning to allow precise inference of transcription factor and nucleosome binding and interprets regulatory logic at CREs. Applying seq2PRINT to single-cell chromatin accessibility data from human bone marrow, we observe sequential establishment and widening of CREs centred on pioneer factors across haematopoiesis. We further discover age-associated alterations in the structure of CREs in murine haematopoietic stem cells, including widespread reduction of nucleosome footprints and gain of de novo identified Ets composite motifs. Collectively, we establish a method for obtaining rich insights into DNA-binding protein dynamics from chromatin accessibility data, and reveal the architecture of regulatory elements across differentiation and ageing.

DOI: https://doi.org/10.1038/s41586-024-08443-4
Cell. 2025 Jan 10. pii: S0092-8674(24)01433-8. [Epub ahead of print]

SMC motor proteins extrude DNA asymmetrically and can switch directions.

Roman Barth, Iain F Davidson, Jaco van der Torre, Michael Taschner, Stephan Gruber, Jan-Michael Peters, Cees Dekker.

  Structural maintenance of chromosomes (SMC) complexes organize the genome via DNA loop extrusion. Although some SMCs were reported to do so symmetrically, reeling DNA from both sides into the extruded DNA loop simultaneously, others perform loop extrusion asymmetrically toward one direction only. The mechanism underlying this variability remains unclear. Here, we examine the directionality of DNA loop extrusion by SMCs using in vitro single-molecule experiments. We find that cohesin and SMC5/6 do not reel in DNA from both sides, as reported before, but instead extrude DNA asymmetrically, although the direction can switch over time. Asymmetric DNA loop extrusion thus is the shared mechanism across all eukaryotic SMC complexes. For cohesin, direction switches strongly correlate with the turnover of the subunit NIPBL, during which DNA strand switching may occur. Apart from expanding by extrusion, loops frequently diffuse and shrink. The findings reveal that SMCs, surprisingly, can switch directions.

Keywords:  DNA loop extrusion; NIPBL; SMC complexes; SMC5/6; cohesin; condensin; single molecule visualization

DOI:  https://doi.org/10.1016/j.cell.2024.12.020
Genome Biol. 2025 Jan 17. 26(1): 10

Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes.

Yihan Wang, Daniel A Armendariz, Lei Wang, Huan Zhao, Shiqi Xie, Gary C Hon.

   BACKGROUND: Genetic studies have associated thousands of enhancers with breast cancer (BC). However, the vast majority have not been functionally characterized. Thus, it remains unclear how BC-associated enhancers contribute to cancer.
RESULTS: Here, we perform single-cell CRISPRi screens of 3513 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of > 500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of BC-associated enhancers disrupts breast cancer gene programs. We observe BC-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple BC-associated enhancers indirectly regulate TP53. Comparative studies illustrate subtype specific functions between enhancers in ER + and ER - cells. Finally, we develop the pySpade package to facilitate analysis of single-cell enhancer screens.
CONCLUSIONS: Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.

Keywords:  Breast cancer; Cancer genomics; Enhancers; Functional genomics; Perturb-seq; Regulatory networks; Single-cell

DOI:  https://doi.org/10.1186/s13059-025-03474-0
Nat Commun. 2025 Jan 17. 16(1): 788

MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model.

Yunhee Jeong, Clarissa Gerhäuser, Guido Sauter, Thorsten Schlomm, Karl Rohr, Pavlo Lutsik.

DNA methylation (DNAm) is a key epigenetic mark that shows profound alterations in cancer. Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose MethylBERT, a Transformer-based model for read-level methylation pattern classification. MethylBERT identifies tumour-derived sequence reads based on their methylation patterns and local genomic sequence, and estimates tumour cell fractions within bulk samples. In our evaluation, MethylBERT outperforms existing deconvolution methods and demonstrates high accuracy regardless of methylation pattern complexity, read length and read coverage. Moreover, we show its applicability to cell-type deconvolution as well as non-invasive early cancer diagnostics using liquid biopsy samples. MethylBERT represents a significant advancement in read-level methylome analysis and enables accurate tumour purity estimation. The broad applicability of MethylBERT will enhance studies on both tumour and non-cancerous bulk methylomes.

DOI: https://doi.org/10.1038/s41467-025-55920-z
Nucleic Acids Res. 2025 Jan 11. pii: gkaf006. [Epub ahead of print]53(2):

Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.

Irina V Zhegalova, Sergey V Ulianov, Aleksandra A Galitsyna, Ilya A Pletenev, Olga V Tsoy, Artem V Luzhin, Petr A Vasiluev, Egor S Bulavko, Dmitry N Ivankov, Alexey A Gavrilov, Ekaterina E Khrameeva, Mikhail S Gelfand, Sergey V Razin.

Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into positionally conserved, largely consecutive, non-hierarchical and weakly insulated loops at the onset of multicellular development. The transcription level within the loop interior tends to be higher than in adjacent regions. Loop interiors frequently contain functionally linked genes and genes which coherently change expression level during development. Loop anchors are predominantly positioned by the genes in convergent orientation. Results of polymer simulations and Hi-C-based observations suggest that the loop profile may arise from the interplay between transcription and extrusion-driven chromatin folding. In this scenario, a convergent gene pair serves as a bidirectional extrusion barrier or a 'diode' that controls passage of the cohesin extruder by relative transcription level of paired genes.

DOI: https://doi.org/10.1093/nar/gkaf006
Elife. 2025 Jan 20. pii: RP97438. [Epub ahead of print]13

Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy.

Carmina Lichauco, Eric J Foss, Tonibelle Gatbonton-Schwager, Nelson F Athow, Brandon Lofts, Robin Acob, Erin Taylor, James J Marquez, Uyen Lao, Shawna Miles, Antonio Bedalov.

  The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA (rDNA) arrays. We have previously reported that in the absence of SIR2, a de-repressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler.

Keywords:  DNA replication; Fun30; S. cerevisiae; Sir2; chromatin; chromatin remodeling enzyme; chromosomes; gene expression; silencing

DOI:  https://doi.org/10.7554/eLife.97438
J Mol Biol. 2025 Feb 01. pii: S0022-2836(24)00551-5. [Epub ahead of print]437(3): 168921

TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites.

Julien Minniti, Frédéric Checler, Eric Duplan, Cristine Alves da Costa.

  Transcription is a key cell process that consists of synthesizing several copies of RNA from a gene DNA sequence. This process is highly regulated and closely linked to the ability of transcription factors to bind specifically to DNA. TFinder is an easy-to-use Python web portal allowing the identification of Individual Motifs (IM) such as Transcription Factor Binding Sites (TFBS). Using the NCBI API, TFinder extracts either promoter or gene terminal regulatory regions, through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species for an unlimited number of genes. TFinder searches for Individual Motifs in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows de novo generations of a Position Weight Matrix (PWM) and the use of already established PWM. Finally, the data are provided in a tabular and a graph format showing the relevance and the P-value of the Individual Motifs found as well as their location relative to the Transcription Start Site (TSS) or the terminal region of the gene. The results are then sent by email to users facilitating the subsequent data analysis and sharing. TFinder is written in Python and freely available on GitHub under the MIT license: https://github.com/Jumitti/TFinder. It can be accessed as a web application implemented in Streamlit at https://tfinder-ipmc.streamlit.app. Resources are available on Streamlit "Resources" tab. TFINDER strength is that it relies on an all-in-one intuitive tool allowing users inexperienced with bioinformatics tools to retrieve gene regulatory regions sequences in multiple species and to search for individual motifs in a huge number of genes.

Keywords:  prediction; promoter; software; transcription factor binding sites

DOI:  https://doi.org/10.1016/j.jmb.2024.168921
Cell. 2025 Jan 16. pii: S0092-8674(24)01426-0. [Epub ahead of print]

An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development.

Marlies E Oomen, Diego Rodriguez-Terrones, Mayuko Kurome, Valeri Zakhartchenko, Lorenza Mottes, Kilian Simmet, Camille Noll, Tsunetoshi Nakatani, Carlos Michel Mourra-Diaz, Irene Aksoy, Pierre Savatier, Jonathan Göke, Eckhard Wolf, Henrik Kaessmann, Maria-Elena Torres-Padilla.

  Transcriptional activation of the embryonic genome (EGA) is a major developmental landmark enabling the embryo to become independent from maternal control. The magnitude and control of transcriptional reprogramming during this event across mammals remains poorly understood. Here, we developed Smart-seq+5' for high sensitivity, full-length transcript coverage and simultaneous capture of 5' transcript information from single cells and single embryos. Using Smart-seq+5', we profiled 34 developmental stages in 5 mammalian species and provide an extensive characterization of the transcriptional repertoire of early development before, during, and after EGA. We demonstrate widespread transposable element (TE)-driven transcription across species, including, remarkably, of DNA transposons. We identify 19,657 TE-driven genic transcripts, suggesting extensive TE co-option in early development over evolutionary timescales. TEs display similar expression dynamics across species and species-specific patterns, suggesting shared and divergent regulation. Our work provides a powerful resource for understanding transcriptional regulation of mammalian development.

Keywords:  TSS; ZGA; evolutionary conservation; evolutionary genomics; mammalian preimplantation development; transcriptomics; transposable elements

DOI:  https://doi.org/10.1016/j.cell.2024.12.013
Cancer Lett. 2025 Jan 17. pii: S0304-3835(25)00027-8. [Epub ahead of print] 217463

FOXF2 expression triggered by endocrine therapy orchestrates therapeutic resistance through reorganization of chromatin architecture in breast cancer.

Rui Zhang, Wen-Jing Jiang, Shuai Zhao, Li-Juan Kang, Qing-Shan Wang, Yu-Mei Feng.

  Patients with estrogen receptor-positive (ER+) breast cancer require long-term endocrine therapy. However, endocrine resistance remains a critical issue to be addressed. Herein, we show that ERα repressed FOXF2 transcription in ER+ breast cancer through H3K27me3 modification, therefore endocrine therapy triggered FOXF2 transcription via loss of H3K27me3. FOXF2 transactivation orchestrated endocrine resistance and bone metastasis. Mechanistically, FOXF2 globally activated enhancers of genes involved in epithelial-mesenchymal transition/epithelial-osteogenic transition, as well as super-enhancers of NCOA3 (a coactivator of FOXF2) and SP1 (an upstream transactivator of FOXF2) by recruiting the SWI/SNF complex that mediates the reorganization of chromatin architecture. Forthermore, FOXF2 systematically modulates the reorganization of chromatin architecture and gene expression by recruiting SMARCC1. Therefore, FOXF2 acts as a pioneer factor to orchestrate endocrine resistance through the reorganization of chromatin architecture. Additionally, FOXF2 expression levels in the tumors of ER+ breast cancer predicted response to endocrine therapeutic drugs and outcome of patients. Targeting BRD4, an essential transcriptional coactivator of FOXF2, significantly inhibited FOXF2-orchestrated endocrine-resistance and bone metastasis. Our findings uncover a mechanism underlying endocrine resistance and provide a promising strategy for managing endocrine-resistant breast cancer.

Keywords:  Endocrine-resistant breast cancer; Enhancer; FOXF2; SWI/SNF complex; Super-enhancer

DOI:  https://doi.org/10.1016/j.canlet.2025.217463
Nature. 2025 Jan 22.

Mapping cells through time and space with moscot.

Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Lama Saber, Changying Jing, Aimée Bastidas-Ponce, Perla Cota, Marta Tarquis-Medina, Shrey Parikh, Ilan Gold, Heiko Lickert, Mostafa Bakhti, Mor Nitzan, Marco Cuturi, Fabian J Theis.

Single-cell genomic technologies enable the multimodal profiling of millions of cells across temporal and spatial dimensions. However, experimental limitations hinder the comprehensive measurement of cells under native temporal dynamics and in their native spatial tissue niche. Optimal transport has emerged as a powerful tool to address these constraints and has facilitated the recovery of the original cellular context1-4. Yet, most optimal transport applications are unable to incorporate multimodal information or scale to single-cell atlases. Here we introduce multi-omics single-cell optimal transport (moscot), a scalable framework for optimal transport in single-cell genomics that supports multimodality across all applications. We demonstrate the capability of moscot to efficiently reconstruct developmental trajectories of 1.7 million cells from mouse embryos across 20 time points. To illustrate the capability of moscot in space, we enrich spatial transcriptomic datasets by mapping multimodal information from single-cell profiles in a mouse liver sample and align multiple coronal sections of the mouse brain. We present moscot.spatiotemporal, an approach that leverages gene-expression data across both spatial and temporal dimensions to uncover the spatiotemporal dynamics of mouse embryogenesis. We also resolve endocrine-lineage relationships of delta and epsilon cells in a previously unpublished mouse, time-resolved pancreas development dataset using paired measurements of gene expression and chromatin accessibility. Our findings are confirmed through experimental validation of NEUROD2 as a regulator of epsilon progenitor cells in a model of human induced pluripotent stem cell islet cell differentiation. Moscot is available as open-source software, accompanied by extensive documentation.

DOI: https://doi.org/10.1038/s41586-024-08453-2
Cell. 2025 Jan 15. pii: S0092-8674(24)01422-3. [Epub ahead of print]

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation.

Giuseppe Quarto, Andrea Li Greci, Martin Bizet, Audrey Penning, Irina Primac, Frédéric Murisier, Liliana Garcia-Martinez, Rodrigo L Borges, Qingzeng Gao, Pradeep K R Cingaram, Emilie Calonne, Bouchra Hassabi, Céline Hubert, Adèle Herpoel, Pascale Putmans, Frédérique Mies, Jérôme Martin, Louis Van der Linden, Gaurav Dube, Pankaj Kumar, Romuald Soin, Abhay Kumar, Anurag Misra, Jie Lan, Morgane Paque, Yogesh K Gupta, Arnaud Blomme, Pierre Close, Pierre-Olivier Estève, Elizabeth A Caine, Kristin M Riching, Cyril Gueydan, Danette L Daniels, Sriharsa Pradhan, Ramin Shiekhattar, Yael David, Lluis Morey, Jana Jeschke, Rachel Deplus, Evelyne Collignon, François Fuks.

  The marking of DNA, histones, and RNA is central to gene expression regulation in development and disease. Recent evidence links N6-methyladenosine (m6A), installed on RNA by the METTL3-METTL14 methyltransferase complex, to histone modifications, but the link between m6A and DNA methylation remains scarcely explored. This study shows that METTL3-METTL14 recruits the DNA methyltransferase DNMT1 to chromatin for gene-body methylation. We identify a set of genes whose expression is fine-tuned by both gene-body 5mC, which promotes transcription, and m6A, which destabilizes transcripts. We demonstrate that METTL3-METTL14-dependent 5mC and m6A are both essential for the differentiation of embryonic stem cells into embryoid bodies and that the upregulation of key differentiation genes during early differentiation depends on the dynamic balance between increased 5mC and decreased m6A. Our findings add a surprising dimension to our understanding of how epigenetics and epitranscriptomics combine to regulate gene expression and impact development and likely other biological processes.

Keywords:  DNA methylation; DNMT1; ESCs; METTL14; METTL3; differentiation; epigenetics; epitranscriptomics; gene expression; m(6)A

DOI:  https://doi.org/10.1016/j.cell.2024.12.009
PLoS Genet. 2025 Jan 21. 21(1): e1011566

Characterizing the regulatory effects of H2A.Z and SWR1-C on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae.

Hilary T Brewis, Peter C Stirling, Michael S Kobor.

Chromatin structure and DNA accessibility are partly modulated by the incorporation of histone variants. H2A.Z, encoded by the non-essential HTZ1 gene in S. cerevisiae, is an evolutionarily conserved H2A histone variant that is predominantly incorporated at transcription start sites by the SWR1-complex (SWR1-C). While H2A.Z has often been implicated in transcription regulation, htz1Δ mutants exhibit minimal changes in gene expression compared to wild-type. However, given that growth defects of htz1Δ mutants are alleviated by simultaneous deletion of SWR1-C subunits, previous work examining the role of H2A.Z in gene expression regulation may be confounded by deleterious activity caused by SWR1-C when missing its H2A.Z substrate (apo-SWR1-C). Furthermore, as H2A.Z mutants only display significant growth defects in genotoxic stress conditions, a more substantive role for H2A.Z in gene expression may only be uncovered after exposure to cellular stress. To explore this possibility, we generated mRNA transcript profiles for wild-type, htz1Δ, swr1Δ, and htz1Δswr1Δ mutants before and after exposure to hydroxyurea (HU), which induces DNA replication stress. Our data showed that H2A.Z played a more prominent role in gene activation than repression during HU exposure, and its incorporation was important for proper upregulation of several HU-induced genes. We also observed that apo-SWR1-C contributed to gene expression defects in the htz1Δ mutant, particularly for genes involved in phosphate homeostasis regulation. Furthermore, mapping H2A.Z incorporation before and after treatment with HU revealed that decreases in H2A.Z enrichment at transcription start sites was correlated with, but generally not required for, the upregulation of genes during HU exposure. Together this study characterized the regulatory effects of H2A.Z incorporation during the transcriptional response to HU.

DOI: https://doi.org/10.1371/journal.pgen.1011566
Genome Biol. 2025 Jan 20. 26(1): 11

Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3.

Valentin Hure, Florence Piron-Prunier, Tamara Yehouessi, Clémentine Vitte, Aleksandra E Kornienko, Gabrielle Adam, Magnus Nordborg, Angélique Déléris.

   BACKGROUND: The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation.
RESULTS: In this study, we show that TEs can also be solely targeted and silenced by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerate relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. We also show that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, a comparison of Arabidopsis natural accessions reveals the existence of a category of TEs-which we refer to as "bifrons"-that are marked by DNA methylation or H3K27me3 depending on the accession. This variation can be linked to intrinsic TE features and to trans-acting factors and reveals a change in epigenetic status across the TE lifespan.
CONCLUSIONS: Our study sheds light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.

Keywords:  DNA methylation; Epigenetics; Epigenomics; Natural variation; Polycomb (PcG); Transposable elements (TE)

DOI:  https://doi.org/10.1186/s13059-024-03466-6