bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2025–01–05
25 papers selected by
Connor Rogerson, University of Cambridge
  1. Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.
  2. Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains.
  3. Cohesin positions the epigenetic reader Phf2 within the genome.
  4. PhpCNF-Y transcription factor infiltrates heterochromatin to generate cryptic intron-containing transcripts crucial for small RNA production.
  5. H3K56 acetylation regulates chromatin maturation following DNA replication.
  6. The transcription factor GABPA is a master regulator of naive pluripotency.
  7. Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.
  8. Predicting CTCF cell type active binding sites in human genome.
  9. Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers.
  10. DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells.
  11. Regulation of meristem and hormone function revealed through analysis of directly-regulated SHOOT MERISTEMLESS target genes.
  12. ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.
  13. MTFAP: a comprehensive platform for predicting and analyzing master transcription factors.
  14. Nuclear speckles regulate functional programs in cancer.
  15. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.
  16. Hybrid exons evolved by coupling transcription initiation and splicing at the nucleotide level.
  17. DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.
  18. Structural insights into how Cas9 targets nucleosomes.
  19. Transcription factor clusters as information transfer agents.
  20. The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR.
  21. SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells.
  22. Reconstitution of pluripotency from mouse fibroblast through Sall4 overexpression.
  23. vmrseq: probabilistic modeling of single-cell methylation heterogeneity.
  24. Histone N-tails modulate sequence-specific positioning of nucleosomes.
  25. CLADES: A Programmable Cascade of Genes for Cell Lineage Analysis and Manipulation.
  1. Genome Biol. 2024 Dec 31. 25(1): 324
    Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.
    Dingyue Wang, Suxin Xiao, Jiayue Shu, Lingxiao Luo, Minqi Yang, Myriam Calonje, Hang He, Baoxing Song, Yue Zhou.
       BACKGROUND: Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete.
    RESULTS: Here, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes.
    CONCLUSIONS: We identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.
    DOI:  https://doi.org/10.1186/s13059-024-03465-7
  2. Mol Cell. 2024 Dec 20. pii: S1097-2765(24)00997-3. [Epub ahead of print]
    Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains.
    Elana Bryan, Devisree Valsakumar, Nwamaka J Idigo, Marie Warburton, Kimberly M Webb, Katy A McLaughlin, Christos Spanos, Simone Lenci, Viktoria Major, Christina Ambrosi, Simon Andrews, Tuncay Baubec, Juri Rappsilber, Philipp Voigt.
      Promoters of developmental genes in embryonic stem cells (ESCs) are marked by histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 in an asymmetric nucleosomal conformation, with each sister histone H3 carrying only one of the two marks. These bivalent domains are thought to poise genes for timely activation upon differentiation. Here, we show that asymmetric bivalent nucleosomes recruit repressive H3K27me3 binders but fail to enrich activating H3K4me3 binders, thereby promoting a poised state. Strikingly, the bivalent mark combination further promotes recruitment of specific chromatin proteins that are not recruited by each mark individually, including the lysine acetyltransferase (KAT) complex KAT6B. Knockout of KAT6B blocks neuronal differentiation, demonstrating that KAT6B is critical for proper bivalent gene expression during ESC differentiation. These findings reveal how readout of the bivalent histone marks directly promotes a poised state at developmental genes while highlighting how nucleosomal asymmetry is critical for histone mark readout and function.
    Keywords:  Polycomb; bivalent domains; chromatin; differentiation; embryonic stem cells; histone acetylation; histone methylation; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2024.12.002
  3. EMBO J. 2025 Jan 02.
    Cohesin positions the epigenetic reader Phf2 within the genome.
    Wen Tang, Lorenzo Costantino, Roman Stocsits, Gordana Wutz, Rene Ladurner, Otto Hudecz, Karl Mechtler, Jan-Michael Peters.
      Genomic DNA is assembled into chromatin by histones, and extruded into loops by cohesin. These mechanisms control important genomic functions, but whether histones and cohesin cooperate in genome regulation is poorly understood. Here we identify Phf2, a member of the Jumonji-C family of histone demethylases, as a cohesin-interacting protein. Phf2 binds to H3K4me3 nucleosomes at active transcription start sites (TSSs), but also co-localizes with cohesin. Cohesin depletion reduces Phf2 binding at sites lacking H3K4me3, and depletion of Wapl and CTCF re-positions Phf2 together with cohesin in the genome, resulting in the accumulation of both proteins in chromosomal regions called vermicelli and cohesin islands. Conversely, Phf2 depletion reduces cohesin binding at TSSs lacking CTCF and decreases the number of short cohesin loops, while increasing the length of heterochromatic B compartments. These results suggest that Phf2 is an 'epigenetic reader', which is translocated through the genome by cohesin-mediated DNA loop extrusion, and which recruits cohesin to active TSSs and limits the size of B compartments. These findings reveal an unexpected degree of cooperativity between epigenetic and architectural mechanisms of eukaryotic genome regulation.
    Keywords:  Chromatin; Compartments; DNA Loop Extrusion; Epigenetics; SMC Complexes
    DOI:  https://doi.org/10.1038/s44318-024-00348-2
  4. Nat Commun. 2025 Jan 02. 16(1): 268
    PhpCNF-Y transcription factor infiltrates heterochromatin to generate cryptic intron-containing transcripts crucial for small RNA production.
    Manjit Kumar Srivastav, H Diego Folco, Patroula Nathanailidou, Anupa T Anil, Drisya Vijayakumari, Shweta Jain, Jothy Dhakshnamoorthy, Maura O'Neill, Thorkell Andresson, David Wheeler, Shiv I S Grewal.
      The assembly of repressive heterochromatin in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. Paradoxically, transcription of repetitive elements within constitutive heterochromatin domains is required for RNA-based mechanisms, such as the RNAi pathway, to target heterochromatin assembly proteins. However, the mechanism by which heterochromatic repeats are transcribed has been unclear. Using fission yeast, we show that the conserved trimeric transcription factor (TF) PhpCNF-Y complex can infiltrate constitutive heterochromatin via its histone-fold domains to transcribe repeat elements. PhpCNF-Y collaborates with a Zn-finger containing TF to bind repeat promoter regions with CCAAT boxes. Mutating either the TFs or the CCAAT binding site disrupts the transcription of heterochromatic repeats. Although repeat elements are transcribed from both strands, PhpCNF-Y-dependent transcripts originate from only one strand. These TF-driven transcripts contain multiple cryptic introns which are required for the generation of small interfering RNAs (siRNAs) via a mechanism involving the spliceosome and RNAi machinery. Our analyses show that siRNA production by this TF-mediated transcription pathway is critical for heterochromatin nucleation at target repeat loci. This study reveals a mechanism by which heterochromatic repeats are transcribed, initiating their own silencing by triggering a primary cascade that produces siRNAs necessary for heterochromatin nucleation.
    DOI:  https://doi.org/10.1038/s41467-024-55736-3
  5. Nat Commun. 2025 Jan 02. 16(1): 134
    H3K56 acetylation regulates chromatin maturation following DNA replication.
    Shoufu Duan, Ilana M Nodelman, Hui Zhou, Toshio Tsukiyama, Gregory D Bowman, Zhiguo Zhang.
      Following DNA replication, the newly reassembled chromatin is disorganized and must mature to its steady state to maintain both genome and epigenome integrity. However, the regulatory mechanisms governing this critical process remain poorly understood. Here, we show that histone H3K56 acetylation (H3K56ac), a mark on newly-synthesized H3, facilitates the remodeling of disorganized nucleosomes in nascent chromatin, and its removal at the subsequent G2/M phase of the cell cycle marks the completion of chromatin maturation. In vitro, H3K56ac enhances the activity of ISWI chromatin remodelers, including yeast ISW1 and its human equivalent SNF2h. In vivo, a deficiency of H3K56ac in nascent chromatin results in the formation of closely packed di-nucleosomes and/or tetra-nucleosomes. In contrast, abnormally high H3K56ac levels disrupt chromatin maturation, leading to genome instability. These findings establish a central role of H3K56ac in chromatin maturation and reveal a mechanism regulating this critical aspect of chromosome replication.
    DOI:  https://doi.org/10.1038/s41467-024-55144-7
  6. Nat Cell Biol. 2025 Jan 02.
    The transcription factor GABPA is a master regulator of naive pluripotency.
    Chengjie Zhou, Meng Wang, Chunxia Zhang, Yi Zhang.
      The establishment of naive pluripotency is a continuous process starting with the generation of inner cell mass (ICM) that then differentiates into epiblast (EPI). Recent studies have revealed key transcription factors (TFs) for ICM formation, but which TFs initiate EPI specification remains unknown. Here, using a targeted rapid protein degradation system, we show that GABPA is not only a regulator of major ZGA, but also a master EPI specifier required for naive pluripotency establishment by regulating 47% of EPI genes during E3.5 to E4.5 transition. Chromatin binding dynamics analysis suggests that GABPA controls EPI formation at least partly by binding to the ICM gene promoters occupied by the pluripotency regulators TFAP2C and SOX2 at E3.5 to establish naive pluripotency at E4.5. Our study not only uncovers GABPA as a master pluripotency regulator, but also supports the notion that mammalian pluripotency establishment requires a dynamic and stepwise multi-TF regulatory network.
    DOI:  https://doi.org/10.1038/s41556-024-01554-0
  7. Nat Commun. 2024 Dec 30. 15(1): 10922
    Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.
    Xiaokun Liu, Hanhan Wei, Qifan Zhang, Na Zhang, Qingqing Wu, Chenhuan Xu.
      The proximity ligation-based Hi-C and derivative methods are the mainstream tools to study genome-wide chromatin interactions. These methods often fragment the genome using enzymes functionally irrelevant to the interactions per se, restraining the efficiency in identifying structural features and the underlying regulatory elements. Here we present Footprint-C, which yields high-resolution chromatin contact maps built upon intact and genuine footprints protected by transcription factor (TF) binding. When analyzed at one-dimensional level, the billions of chromatin contacts from Footprint-C enable genome-wide analysis at single footprint resolution, and reveal preferential modes of local TF co-occupancy. At pairwise contact level, Footprint-C exhibits higher efficiency in identifying chromatin structural features when compared with other Hi-C methods, segregates chromatin interactions emanating from adjacent TF footprints, and uncovers multiway interactions involving different TFs. Altogether, Footprint-C results suggest that rich regulatory modes of TF may underlie both local residence and distal chromatin interactions, in terms of TF identity, valency, and conformational configuration.
    DOI:  https://doi.org/10.1038/s41467-024-55403-7
  8. Sci Rep. 2024 Dec 30. 14(1): 31744
    Predicting CTCF cell type active binding sites in human genome.
    Lu Chai, Jie Gao, Zihan Li, Hao Sun, Junjie Liu, Yong Wang, Lirong Zhang.
      The CCCTC-binding factor (CTCF) is pivotal in orchestrating diverse biological functions across the human genome, yet the mechanisms driving its cell type-active DNA binding affinity remain underexplored. Here, we collected ChIP-seq data from 67 cell lines in ENCODE, constructed a unique dataset of cell type-active CTCF binding sites (CBS), and trained convolutional neural networks (CNN) to dissect the patterns of CTCF binding activity. Our analysis reveals that transcription factors RAD21/SMC3 and chromatin accessibility are more predictive compared to sequence motifs and histone modifications. Integrating them together achieved AUPRC values consistently above 0.868, highlighting their utility in deciphering CTCF transcription factor binding dynamics. This study provides a deeper understanding of the regulatory functions of CTCF via machine learning framework.
    Keywords:  CTCF binding site; Chromatin accessibility; Convolutional neural networks; RAD21; SMC3
    DOI:  https://doi.org/10.1038/s41598-024-82238-5
  9. Nat Commun. 2025 Jan 02. 16(1): 131
    Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers.
    James A Oo, Timothy Warwick, Katalin Pálfi, Frederike Lam, Francois McNicoll, Cristian Prieto-Garcia, Stefan Günther, Can Cao, Yinuo Zhou, Alexey A Gavrilov, Sergey V Razin, Alfredo Cabrera-Orefice, Ilka Wittig, Soni Savai Pullamsetti, Leo Kurian, Ralf Gilsbach, Marcel H Schulz, Ivan Dikic, Michaela Müller-McNicoll, Ralf P Brandes, Matthias S Leisegang.
      The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central role in cell type- and context-dependent gene expression. Despite the absence of a defined DNA recognition motif, SWI/SNF binds lineage specific enhancers genome-wide where it actively maintains open chromatin state. It does so while retaining the ability to respond dynamically to cellular signals. However, the mechanisms that guide SWI/SNF to specific genomic targets have remained elusive. Here we demonstrate that trans-acting long non-coding RNAs (lncRNAs) direct the SWI/SNF complex to cell type-specific enhancers. SWI/SNF preferentially binds lncRNAs and these predominantly bind DNA targets in trans. Together they localize to enhancers, many of which are cell type-specific. Knockdown of SWI/SNF- and enhancer-bound lncRNAs causes the genome-wide redistribution of SWI/SNF away from enhancers and a concomitant differential expression of spatially connected target genes. These lncRNA-SWI/SNF-enhancer networks support an enhancer hub model of SWI/SNF genomic targeting. Our findings reveal that lncRNAs competitively recruit SWI/SNF, providing a specific and dynamic layer of control over chromatin accessibility, and reinforcing their role in mediating enhancer activity and gene expression.
    DOI:  https://doi.org/10.1038/s41467-024-55539-6
  10. Nat Commun. 2024 Dec 30. 15(1): 10803
    DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells.
    Xianle Shi, Yanjing Li, Hongwei Zhou, Xiukun Hou, Jihong Yang, Vikas Malik, Francesco Faiola, Junjun Ding, Xichen Bao, Miha Modic, Weiyu Zhang, Lingyi Chen, Syed Raza Mahmood, Effie Apostolou, Feng-Chun Yang, Mingjiang Xu, Wei Xie, Xin Huang, Yong Chen, Jianlong Wang.
      Pluripotent stem cells possess a unique nuclear architecture characterized by a larger nucleus and more open chromatin, which underpins their ability to self-renew and differentiate. Here, we show that the nucleolus-specific RNA helicase DDX18 is essential for maintaining the pluripotency of human embryonic stem cells. Using techniques such as Hi-C, DNA/RNA-FISH, and biomolecular condensate analysis, we demonstrate that DDX18 regulates nucleolus phase separation and nuclear organization by interacting with NPM1 in the granular nucleolar component, driven by specific nucleolar RNAs. Loss of DDX18 disrupts nucleolar substructures, impairing centromere clustering and perinucleolar heterochromatin (PNH) formation. To probe this further, we develop NoCasDrop, a tool enabling precise nucleolar targeting and controlled liquid condensation, which restores centromere clustering and PNH integrity while modulating developmental gene expression. This study reveals how nucleolar phase separation dynamics govern chromatin organization and cell fate, offering fresh insights into the molecular regulation of stem cell pluripotency.
    DOI:  https://doi.org/10.1038/s41467-024-55054-8
  11. Sci Rep. 2025 Jan 02. 15(1): 240
    Regulation of meristem and hormone function revealed through analysis of directly-regulated SHOOT MERISTEMLESS target genes.
    Tamara Lechon, Nicholas A Kent, James A H Murray, Simon Scofield.
      The Arabidopsis Knotted1-like homeobox (KNOX) gene SHOOT MERISTEMLESS (STM) encodes a homeodomain transcription factor that operates as a central component of the gene regulatory network (GRN) controlling shoot apical meristem formation and maintenance. It regulates the expression of target genes that include transcriptional regulators associated with meristem function, particularly those involved in pluripotency and cellular differentiation, as well as genes involved in hormone metabolism and signaling. Previous studies have identified KNOX-regulated genes and their associated cis-regulatory elements in several plant species. However, little is known about STM-DNA interactions in the regulatory regions of target genes in Arabidopsis. Here, we identify and map STM binding sites in the Arabidopsis genome using global ChIP-seq analysis to reveal potential directly-regulated STM target genes. We show that in the majority of target loci, STM binds within 1 kb upstream of the TSS, with other loci showing STM binding at more distal enhancer sites, and we reveal enrichment of DNA motifs containing a TGAC and/or TGAT core in STM-bound target gene cis-regulatory elements. We further demonstrate that many STM-bound genes are transcriptionally responsive to altered levels of STM activity, and show that among these, transcriptional regulators with key roles in meristem and hormone function are highly represented. Finally, we use a subset of these target genes to perform Bayesian network analysis to infer gene regulatory associations and to construct a refined GRN for STM-mediated control of meristem function.
    DOI:  https://doi.org/10.1038/s41598-024-83985-1
  12. Nat Commun. 2025 Jan 02. 16(1): 317
    ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.
    Wouter Saelens, Olga Pushkarev, Bart Deplancke.
      Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw accessibility data, without peak-calling or windows, to link regions to gene expression and determine differentially accessible chromatin. We show how ChromatinHD consistently outperforms existing peak and window-based approaches and find that this is due to a large number of uniquely captured, functional accessibility changes within and outside of putative cis-regulatory regions. Furthermore, ChromatinHD can delineate collaborating regulatory regions, including their preferential genomic conformations, that drive gene expression. Finally, our models also use changes in ATAC-seq fragment lengths to identify dense binding of transcription factors, a feature not captured by footprinting methods. Altogether, ChromatinHD, available at https://chromatinhd.org , is a suite of computational tools that enables a data-driven understanding of chromatin accessibility at various scales and how it relates to gene expression.
    DOI:  https://doi.org/10.1038/s41467-024-55447-9
  13. Sci Rep. 2024 Dec 30. 14(1): 32012
    MTFAP: a comprehensive platform for predicting and analyzing master transcription factors.
    Jianyuan Zhou, Haojie Yu, Chunhui Lou, Min Yang, Yanshang Li, Qian Yang, Shuhan Li, Chunwang Ji, Song Li, Shuang Wang, Haotian Cao, Xuecang Li, Lian Liu.
      Master transcription factors (MTFs) activate gene expression in pluripotent embryonic stem cells (ESCs) by binding to enhancers and super-enhancers, which precisely control ESC fate. Compelling evidence reveals a strong correlation between the operation of MTFs and the initiation and progression of cancer. Nevertheless, the challenge of identifying MTFs imposes a barrier for researchers. Therefore, we developed a master transcription factors prediction and analysis web resource (MTFAP). MTFAP is a comprehensive web tool designed to predict and analyze MTFs with different data types. To enhance user experience and facilitate exploration of interest MTFs, MTFAP offers search and browse functionalities. Furthermore, we have developed a Docker file to empower users with the capability to conduct localized analyses Additionally, MTFAP extends support for further analysis and data visualization for the MTFs identified by Coltron and CRCmapper. The platform is freely available at http://www.xiejjlab.bio/MTFAP/.
    Keywords:  Bulk RNA-seq; Core regulatory circuit; Master transcription factors; Single-cell RNA-seq
    DOI:  https://doi.org/10.1038/s41598-024-83686-9
  14. Nat Cell Biol. 2025 Jan 02.
    Nuclear speckles regulate functional programs in cancer.
    Katherine A Alexander, Ruofan Yu, Nicolas Skuli, Nathan J Coffey, Son Nguyen, Christine L Faunce, Hua Huang, Ian P Dardani, Austin L Good, Joan Lim, Catherine Y Li, Nicholas Biddle, Eric F Joyce, Arjun Raj, Daniel Lee, Brian Keith, M Celeste Simon, Shelley L Berger.
      Nuclear speckles are dynamic nuclear bodies characterized by high concentrations of factors involved in RNA production. Although the contents of speckles suggest multifaceted roles in gene regulation, their biological functions are unclear. Here we investigate speckle variation in human cancer, finding two main signatures. One speckle signature was similar to healthy adjacent tissues, whereas the other was dissimilar, and considered an aberrant cancer speckle state. Aberrant speckles show altered positioning within the nucleus, higher levels of the TREX RNA export complex and correlate with poorer patient outcomes in clear cell renal cell carcinoma (ccRCC), a cancer typified by hyperactivation of the HIF-2α transcription factor. We demonstrate that HIF-2α promotes physical association of certain target genes with speckles depending on HIF-2α protein speckle-targeting motifs, defined in this study. We identify homologous speckle-targeting motifs within many transcription factors, suggesting that DNA-speckle targeting may be a general gene regulatory mechanism. Integrating functional, genomic and imaging studies, we show that HIF-2α gene regulatory programs are impacted by speckle state and by abrogation of HIF-2α-driven speckle targeting. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of select HIF-2α-regulated target genes that, in turn, influence patient outcomes. Beyond ccRCC, tumour speckle states broadly correlate with altered functional pathways and expression of speckle-associated gene neighbourhoods, exposing a general link between nuclear speckles and gene expression dysregulation in human cancer.
    DOI:  https://doi.org/10.1038/s41556-024-01570-0
  15. Nat Commun. 2024 Dec 30. 15(1): 10854
    MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.
    Jonathan Cahn, Michael Regulski, Jason Lynn, Evan Ernst, Cristiane de Santis Alves, Srividya Ramakrishnan, Kapeel Chougule, Sharon Wei, Zhenyuan Lu, Xiaosa Xu, Umamaheswari Ramu, Jorg Drenkow, Melissa Kramer, Arun Seetharam, Matthew B Hufford, W Richard McCombie, Doreen Ware, David Jackson, Michael C Schatz, Thomas R Gingeras, Robert A Martienssen.
      Modern maize (Zea mays ssp. mays) was domesticated from Teosinte parviglumis (Zea mays ssp. parviglumis), with subsequent introgressions from Teosinte mexicana (Zea mays ssp. mexicana), yielding increased kernel row number, loss of the hard fruit case and dissociation from the cob upon maturity, as well as fewer tillers. Molecular approaches have identified transcription factors controlling these traits, yet revealed that a complex regulatory network is at play. MaizeCODE deploys ENCODE strategies to catalog regulatory regions in the maize genome, generating histone modification and transcription factor ChIP-seq in parallel with transcriptomics datasets in 5 tissues of 3 inbred lines which span the phenotypic diversity of maize, as well as the teosinte inbred TIL11. Transcriptomic analysis reveals that pollen grains share features with endosperm, and express dozens of "proto-miRNAs" potential vestiges of gene drive and hybrid incompatibility. Integrated analysis with chromatin modifications results in the identification of a comprehensive set of regulatory regions in each tissue of each inbred, and notably of distal enhancers expressing non-coding enhancer RNAs bi-directionally, reminiscent of "super enhancers" in animal genomes. Furthermore, the morphological traits selected during domestication are recapitulated, both in gene expression and within regulatory regions containing enhancer RNAs, while highlighting the conflict between enhancer activity and silencing of the neighboring transposable elements.
    DOI:  https://doi.org/10.1038/s41467-024-55195-w
  16. Nucleic Acids Res. 2024 Dec 31. pii: gkae1251. [Epub ahead of print]
    Hybrid exons evolved by coupling transcription initiation and splicing at the nucleotide level.
    Steven T Mick, Christine L Carroll, Maritere Uriostegui-Arcos, Ana Fiszbein.
      Exons within transcripts are traditionally classified as first, internal or last exons, each governed by different regulatory mechanisms. We recently described the widespread usage of 'hybrid' exons that serve as terminal or internal exons in different transcripts. Here, we employ an interpretable deep learning pipeline to dissect the sequence features governing the co-regulation of transcription initiation and splicing in hybrid exons. Using ENCODE data from human tissues, we identified 80 000 hybrid first-internal exons. These exons often possess a relaxed chromatin state, allowing transcription initiation within the gene body. Interestingly, transcription start sites of hybrid exons are typically centered at the 3' splice site, suggesting tight coupling between splicing and transcription initiation. We identified two subcategories of hybrid exons: the majority resemble internal exons, maintaining strong 3' splice sites, while a minority show enrichment in promoter elements, resembling first exons. Diving into the evolution of their sequences, we found that human hybrid exons with orthologous first exons in other species usually gained 3' splice sites or whole exons upstream, while those with orthologous internal exons often gained promoter elements. Overall, our findings unveil the intricate regulatory landscape of hybrid exons and reveal stronger connections between transcription initiation and RNA splicing than previously acknowledged.
    DOI:  https://doi.org/10.1093/nar/gkae1251
  17. Nat Commun. 2025 Jan 02. 16(1): 10
    DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts.
    Krzysztof Kuś, Loic Carrique, Tea Kecman, Marjorie Fournier, Sarah Sayed Hassanein, Ebru Aydin, Cornelia Kilchert, Jonathan M Grimes, Lidia Vasiljeva.
      Precursor messenger RNA (pre-mRNA) is processed into its functional form during RNA polymerase II (Pol II) transcription. Although functional coupling between transcription and pre-mRNA processing is established, the underlying mechanisms are not fully understood. We show that the key transcription termination factor, RNA exonuclease Xrn2 engages with Pol II forming a stable complex. Xrn2 activity is stimulated by Spt5 to ensure efficient degradation of nascent RNA leading to Pol II dislodgement from DNA. Our results support a model where Xrn2 first forms a stable complex with the elongating Pol II to achieve its full activity in degrading nascent RNA revising the current 'torpedo' model of termination, which posits that RNA degradation precedes Xrn2 engagement with Pol II. Spt5 is also a key factor that attenuates the expression of non-coding transcripts, coordinates pre-mRNA splicing and 3'-end processing. Our findings indicate that engagement with the transcribing Pol II is an essential regulatory step modulating the activity of RNA enzymes such as Xrn2, thus advancing our understanding of how RNA maturation is controlled during transcription.
    DOI:  https://doi.org/10.1038/s41467-024-55063-7
  18. Nat Commun. 2024 Dec 30. 15(1): 10744
    Structural insights into how Cas9 targets nucleosomes.
    Reina Nagamura, Tomoya Kujirai, Junko Kato, Yutaro Shuto, Tsukasa Kusakizako, Hisato Hirano, Masaki Endo, Seiichi Toki, Hiroaki Saika, Hitoshi Kurumizaka, Osamu Nureki.
      The CRISPR-associated endonuclease Cas9 derived from prokaryotes is used as a genome editing, which targets specific genomic loci by single guide RNAs (sgRNAs). The eukaryotes, the target of genome editing, store their genome DNA in chromatin, in which the nucleosome is a basic unit. Despite previous structural analyses focusing on Cas9 cleaving free DNA, structural insights into Cas9 targeting of DNA within nucleosomes are limited, leading to uncertainties in understanding how Cas9 operates in the eukaryotic genome. In the present study, we perform native-polyacrylamide gel electrophoresis (PAGE)  analyses and find that Cas9 targets the linker DNA and the entry-exit DNA region of the nucleosome but not the DNA tightly wrapped around the histone octamer. We further determine cryo-electron microscopy (cryo-EM) structure of the Cas9-sgRNA-nucleosome ternary complex that targets linker DNA in nucleosomes. The structure suggests interactions between Cas9 and nucleosomes at multiple sites. Mutants that reduce the interaction between nucleosomal DNA and Cas9 improve nucleosomal DNA cleavage activity in vitro, although inhibition by the interaction between Cas9 and nucleosomes is limited in vivo. These findings will contribute to the development of novel genome editing tools in chromatin.
    DOI:  https://doi.org/10.1038/s41467-024-54768-z
  19. Sci Adv. 2025 Jan 03. 11(1): eadp3251
    Transcription factor clusters as information transfer agents.
    Rahul Munshi, Jia Ling, Sergey Ryabichko, Eric F Wieschaus, Thomas Gregor.
      Deciphering how genes interpret information from transcription factor (TF) concentrations within the cell nucleus remains a fundamental question in gene regulation. Recent advancements have revealed the heterogeneous distribution of TF molecules, posing challenges to precisely decoding concentration signals. Using high-resolution single-cell imaging of the fluorescently tagged TF Bicoid in living Drosophila embryos, we show that Bicoid accumulation in submicrometer clusters preserves the spatial information of the maternal Bicoid gradient. These clusters provide precise spatial cues through intensity, size, and frequency. We further discover that Bicoid target genes colocalize with these clusters in an enhancer-binding affinity-dependent manner. Our modeling suggests that clustering offers a faster sensing mechanism for global nuclear concentrations than freely diffusing TF molecules detected by simple enhancers.
    DOI:  https://doi.org/10.1126/sciadv.adp3251
  20. Nat Commun. 2024 Dec 30. 15(1): 10745
    The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR.
    Cauã Antunes Westmann, Leander Goldbach, Andreas Wagner.
      Transcription factor binding sites (TFBSs) are important sources of evolutionary innovations. Understanding how evolution navigates the sequence space of such sites can be achieved by mapping TFBS adaptive landscapes. In such a landscape, an individual location corresponds to a TFBS bound by a transcription factor. The elevation at that location corresponds to the strength of transcriptional regulation conveyed by the sequence. Here, we develop an in vivo massively parallel reporter assay to map the landscape of bacterial TFBSs. We apply this assay to the TetR repressor, for which few TFBSs are known. We quantify the strength of transcriptional repression for 17,765 TFBSs and show that the resulting landscape is highly rugged, with 2092 peaks. Only a few peaks convey stronger repression than the wild type. Non-additive (epistatic) interactions between mutations are frequent. Despite these hallmarks of ruggedness, most high peaks are evolutionarily accessible. They have large basins of attraction and are reached by around 20% of populations evolving on the landscape. Which high peak is reached during evolution is unpredictable and contingent on the mutational path taken. This in-depth analysis of a prokaryotic gene regulator reveals a landscape that is navigable but much more rugged than the landscapes of eukaryotic regulators.
    DOI:  https://doi.org/10.1038/s41467-024-54723-y
  21. Genome Biol. 2025 Jan 02. 26(1): 1
    SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells.
    Xin Wan, Jie Kong, Xiaodi Hu, Lulu Liu, Yuanping Yang, Hu Li, Gaoao Liu, Xingchen Niu, Fengling Chen, Dan Zhang, Dahai Zhu, Yong Zhang.
      We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurrent labeling of DNA and RNA across various cell types. Using SiCLAT, we accurately labeled chromatin loop anchor interactions and associated gene transcription during myogenic differentiation. This imaging system offers a novel means of directly observing cis-element interactions and the corresponding gene transcription in living primary cells, thus providing real-time imaging for comprehensive mechanistic investigations of dynamic enhancer-promoter or enhancer-enhancer interactions in regulating transcription activation within living cells.
    Keywords:  3D genome; CRISPR imaging; Enhancer and promoter interaction; Genetic mouse model; Living primary cell; Non-repetitive DNA and RNA imaging
    DOI:  https://doi.org/10.1186/s13059-024-03463-9
  22. Nat Commun. 2024 Dec 30. 15(1): 10787
    Reconstitution of pluripotency from mouse fibroblast through Sall4 overexpression.
    Lizhan Xiao, Zifen Huang, Zixuan Wu, Yongzheng Yang, Zhen Zhang, Manish Kumar, Haokaifeng Wu, Huiping Mao, Lihui Lin, Runxia Lin, Jingxian Long, Lihua Zeng, Jing Guo, Rongping Luo, Yi Li, Ping Zhu, Baojian Liao, Luqin Wang, Jing Liu.
      Somatic cells can be reprogrammed into pluripotent stem cells (iPSCs) by overexpressing defined transcription factors. Specifically, overexpression of OCT4 alone has been demonstrated to reprogram mouse fibroblasts into iPSCs. However, it remains unclear whether any other single factor can induce iPSCs formation. Here, we report that SALL4 alone, under an optimized reprogramming medium iCD4, is capable of reprogramming mouse fibroblasts into iPSCs. Mechanistically, SALL4 facilitates reprogramming by inhibiting somatic genes and activating pluripotent genes, such as Esrrb and Tfap2c. Furthermore, we demonstrate that co-overexpressing SALL4 and OCT4 synergistically enhances reprogramming efficiency. Specifically, the activation of Rsk1/Esrrb/Tfap2c by SALL4, alongside OCT4's activation of Sox2 and the suppression of Mndal by SALL4 and Sbsn by OCT4, cooperate to facilitate SALL4+OCT4-mediated reprogramming. Overall, our study not only establishes an efficient method for iPSCs induction using the SALL4 single factor but also provides insights into the synergistic effects of SALL4 and OCT4 in reprogramming.
    DOI:  https://doi.org/10.1038/s41467-024-54924-5
  23. Genome Biol. 2024 Dec 30. 25(1): 321
    vmrseq: probabilistic modeling of single-cell methylation heterogeneity.
    Ning Shen, Keegan Korthauer.
      Single-cell DNA methylation measurements reveal genome-scale inter-cellular epigenetic heterogeneity, but extreme sparsity and noise challenges rigorous analysis. Previous methods to detect variably methylated regions (VMRs) have relied on predefined regions or sliding windows and report regions insensitive to heterogeneity level present in input. We present vmrseq, a statistical method that overcomes these challenges to detect VMRs with increased accuracy in synthetic benchmarks and improved feature selection in case studies. vmrseq also highlights context-dependent correlations between methylation and gene expression, supporting previous findings and facilitating novel hypotheses on epigenetic regulation. vmrseq is available at https://github.com/nshen7/vmrseq .
    Keywords:  DNA methylation; Epigenetic heterogeneity; Hidden Markov model; Single-cell bisulfite sequencing
    DOI:  https://doi.org/10.1186/s13059-024-03457-7
  24. J Biol Chem. 2024 Dec 26. pii: S0021-9258(24)02640-1. [Epub ahead of print] 108138
    Histone N-tails modulate sequence-specific positioning of nucleosomes.
    Tatiana Nikitina, Wilfried M Guiblet, Feng Cui, Victor B Zhurkin.
      Spatial organization of chromatin is essential for cellular functioning. However, the precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA still remain unknown in detail. Existing algorithms, taking into account the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo. To uncover additional factors responsible for the nucleosome positioning, we analyzed potential involvement of the histone N-tails in this process. To this aim, we reconstituted the H2A/H4 N-tailless nucleosomes on human BRCA1 DNA (∼100 kb) and compared their positions and sequences with those of the wild-type nucleosomes. We found that removal of the histone N-tails promoted displacement of the predominant positions of nucleosomes, accompanied by redistribution of the AT-rich and GC-rich motifs in nucleosome sequences. Importantly, most of these sequence changes occurred at superhelical locations (SHLs) ±4, ±1 and ±2, where the H2A and H4 N-tails interact with the DNA minor grooves. Furthermore, a substantial number of H4-tailless nucleosomes exhibit rotational setting opposite to that of the wild-type nucleosomes, the effect known to change the topological properties of chromatin fiber. Thus, the histone N-tails are operative in selection of nucleosome positions, which may have wide-ranging implications for epigenetic modulation of chromatin states.
    Keywords:  DNA endonuclease; DNA sequencing; DNA structure; electrostatics; epigenetics; histone modification; nucleosome; structure‐function
    DOI:  https://doi.org/10.1016/j.jbc.2024.108138
  25. Methods Mol Biol. 2025 ;2886 421-437
    CLADES: A Programmable Cascade of Genes for Cell Lineage Analysis and Manipulation.
    Inés González-Aspe, Beatriz Madariaga Puchol, Blanca López Arrabal, Brooke Bosonac, Jorge García-Marqués.
      In the Drosophila brain, neuronal diversity originates from approximately 100 neural stem cells, each dividing asymmetrically. Precise mapping of cell lineages at the single-cell resolution is crucial for understanding the mechanisms that direct neuronal specification. However, existing methods for high-resolution lineage tracing are notably time-consuming and labor-intensive. Here, we outline the best practices for lineage tracing using CLADES (cell lineage access driven by an edition sequence), a revolutionary approach to neuronal lineage tracing that addresses the limitations of previous methods. CLADES effectively traces the birth order of neurons using approximately 100 samples. The technique relies on a genetic cascade of reporter activations and deactivations that delineate lineage progression through color-coded markers. This system not only facilitates the detailed mapping of neuronal lineages but also holds the potential to be applied to tracking biological events and producing cell types for therapeutic purposes.
    Keywords:  CRISPR; CaSSA; Drosophila; Genetic cascades; Genetic tools; Lineage tracing; Neuronal specification
    DOI:  https://doi.org/10.1007/978-1-0716-4310-5_21
This page is being maintained by Thomas Krichel. It was last updated on 2025‒02‒17 at 14:25.