bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2024–02–18
24 papers selected by
Connor Rogerson, University of Cambridge
  1. DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2.
  2. RNA polymerase II promotes the organization of chromatin following DNA replication.
  3. Nuclear morphology is shaped by loop-extrusion programs.
  4. Leveraging chromatin state transitions for the identification of regulatory networks orchestrating heart regeneration.
  5. Persistence of backtracking by human RNA polymerase II.
  6. The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis.
  7. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility.
  8. Mutation of the SWI/SNF complex component Smarce1 decreases nucleosome stability in ES cells and impairs differentiation.
  9. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis.
  10. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition.
  11. Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function.
  12. Identification of a core transcriptional program driving the human renal mesenchymal-to-epithelial transition.
  13. Tissue-location-specific transcription programs drive tumor dependencies in colon cancer.
  14. Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression.
  15. Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions.
  16. Multifaceted effects on even-skipped transcriptional dynamics upon Krüppel dosage changes.
  17. A single-cell time-lapse of mouse prenatal development from gastrula to birth.
  18. Biphasic regulation of epigenetic state by matrix stiffness during cell reprogramming.
  19. Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils.
  20. A methylation-phosphorylation switch controls EZH2 stability and hematopoiesis.
  21. Single-cell analysis reveals the spatial-temporal expression of genes associated with esophageal malformations.
  22. Oncoprotein SET-associated transcription factor ZBTB11 triggers lung cancer metastasis.
  23. Nuclear Factor I A (Nfia) and Nuclear Factor I B (Nfib) are jointly required for mouse postnatal neural stem cell self-renewal.
  24. Hypoxia-inducible PRMT2 addiction in glioblastomas.
  1. Nat Commun. 2024 Feb 16. 15(1): 1445
    DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2.
    Sveinn Bjarnason, Jordan A P McIvor, Andreas Prestel, Kinga S Demény, Jakob T Bullerjahn, Birthe B Kragelund, Davide Mercadante, Pétur O Heidarsson.
      More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
    DOI:  https://doi.org/10.1038/s41467-024-45847-2
  2. EMBO Rep. 2024 Feb 12.
    RNA polymerase II promotes the organization of chromatin following DNA replication.
    Susanne Bandau, Vanesa Alvarez, Hao Jiang, Sarah Graff, Ramasubramanian Sundaramoorthy, Marek Gierlinski, Matt Toman, Tom Owen-Hughes, Simone Sidoli, Angus Lamond, Constance Alabert.
      Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
    Keywords:  ATP-dependent Chromatin Remodellers; DNA Repair; DNA Replication; Transcription; Transcription Factor
    DOI:  https://doi.org/10.1038/s44319-024-00085-x
  3. Nature. 2024 Feb 14.
    Nuclear morphology is shaped by loop-extrusion programs.
    Indumathi Patta, Maryam Zand, Lindsay Lee, Shreya Mishra, Alexandra Bortnick, Hanbin Lu, Arpita Prusty, Sara McArdle, Zbigniew Mikulski, Huan-You Wang, Christine S Cheng, Kathleen M Fisch, Ming Hu, Cornelis Murre.
      It is well established that neutrophils adopt malleable polymorphonuclear shapes to migrate through narrow interstitial tissue spaces1-3. However, how polymorphonuclear structures are assembled remains unknown4. Here we show that in neutrophil progenitors, halting loop extrusion-a motor-powered process that generates DNA loops by pulling in chromatin5-leads to the assembly of polymorphonuclear genomes. Specifically, we found that in mononuclear neutrophil progenitors, acute depletion of the loop-extrusion loading factor nipped-B-like protein (NIPBL) induced the assembly of horseshoe, banded, ringed and hypersegmented nuclear structures and led to a reduction in nuclear volume, mirroring what is observed during the differentiation of neutrophils. Depletion of NIPBL also induced cell-cycle arrest, activated a neutrophil-specific gene program and conditioned a loss of interactions across topologically associating domains to generate a chromatin architecture that resembled that of differentiated neutrophils. Removing NIPBL resulted in enrichment for mega-loops and interchromosomal hubs that contain genes associated with neutrophil-specific enhancer repertoires and an inflammatory gene program. On the basis of these observations, we propose that in neutrophil progenitors, loop-extrusion programs produce lineage-specific chromatin architectures that permit the packing of chromosomes into geometrically confined lobular structures. Our data also provide a blueprint for the assembly of polymorphonuclear structures, and point to the possibility of engineering de novo nuclear shapes to facilitate the migration of effector cells in densely populated tumorigenic environments.
    DOI:  https://doi.org/10.1038/s41586-024-07086-9
  4. Nucleic Acids Res. 2024 Feb 14. pii: gkae085. [Epub ahead of print]
    Leveraging chromatin state transitions for the identification of regulatory networks orchestrating heart regeneration.
    Julio Cordero, Adel Elsherbiny, Yinuo Wang, Lonny Jürgensen, Florian Constanty, Stefan Günther, Melanie Boerries, Joerg Heineke, Arica Beisaw, Florian Leuschner, David Hassel, Gergana Dobreva.
      The limited regenerative capacity of the human heart contributes to high morbidity and mortality worldwide. In contrast, zebrafish exhibit robust regenerative capacity, providing a powerful model for studying how to overcome intrinsic epigenetic barriers maintaining cardiac homeostasis and initiate regeneration. Here, we present a comprehensive analysis of the histone modifications H3K4me1, H3K4me3, H3K27me3 and H3K27ac during various stages of zebrafish heart regeneration. We found a vast gain of repressive chromatin marks one day after myocardial injury, followed by the acquisition of active chromatin characteristics on day four and a transition to a repressive state on day 14, and identified distinct transcription factor ensembles associated with these events. The rapid transcriptional response involves the engagement of super-enhancers at genes implicated in extracellular matrix reorganization and TOR signaling, while H3K4me3 breadth highly correlates with transcriptional activity and dynamic changes at genes involved in proteolysis, cell cycle activity, and cell differentiation. Using loss- and gain-of-function approaches, we identified transcription factors in cardiomyocytes and endothelial cells influencing cardiomyocyte dedifferentiation or proliferation. Finally, we detected significant evolutionary conservation between regulatory regions that drive zebrafish and neonatal mouse heart regeneration, suggesting that reactivating transcriptional and epigenetic networks converging on these regulatory elements might unlock the regenerative potential of adult human hearts.
    DOI:  https://doi.org/10.1093/nar/gkae085
  5. Mol Cell. 2024 Feb 06. pii: S1097-2765(24)00055-8. [Epub ahead of print]
    Persistence of backtracking by human RNA polymerase II.
    Kevin B Yang, Aviram Rasouly, Vitaly Epshtein, Criseyda Martinez, Thao Nguyen, Ilya Shamovsky, Evgeny Nudler.
      RNA polymerase II (RNA Pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome-wide distribution of more persistent backtracking are unknown. Consequently, we developed a method to directly sequence the extruded, "backtracked" 3' RNA. Our data show that RNA Pol II slides backward more than 20 nt in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where RNA Pol II pauses near promoters and intron-exon junctions and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking can potentially affect diverse gene expression programs.
    Keywords:  RNA polymerase II; backtracking; gene regulation; histone genes; transcription elongation
    DOI:  https://doi.org/10.1016/j.molcel.2024.01.019
  6. Dev Cell. 2024 Feb 07. pii: S1534-5807(24)00041-8. [Epub ahead of print]
    The BAS chromatin remodeler determines brassinosteroid-induced transcriptional activation and plant growth in Arabidopsis.
    Tao Zhu, Chuangqi Wei, Yaoguang Yu, Zhenzhen Zhang, Jiameng Zhu, Zhenwei Liang, Xin Song, Wei Fu, Yuhai Cui, Zhi-Yong Wang, Chenlong Li.
      Brassinosteroid (BR) signaling leads to the nuclear accumulation of the BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor, which plays dual roles in activating or repressing the expression of thousands of genes. BZR1 represses gene expression by recruiting histone deacetylases, but how it activates transcription of BR-induced genes remains unclear. Here, we show that BR reshapes the genome-wide chromatin accessibility landscape, increasing the accessibility of BR-induced genes and reducing the accessibility of BR-repressed genes in Arabidopsis. BZR1 physically interacts with the BRAHMA-associated SWI/SNF (BAS)-chromatin-remodeling complex on the genome and selectively recruits the BAS complex to BR-activated genes. Depletion of BAS abrogates the capacities of BZR1 to increase chromatin accessibility, activate gene expression, and promote cell elongation without affecting BZR1's ability to reduce chromatin accessibility and expression of BR-repressed genes. Together, these data identify that BZR1 recruits the BAS complex to open chromatin and to mediate BR-induced transcriptional activation of growth-promoting genes.
    Keywords:  BAS-chromatin-remodeling complexes; BZR1; Brassinosteroid; SWI/SNF; chromatin accessibility; growth and development; phytohormone
    DOI:  https://doi.org/10.1016/j.devcel.2024.01.021
  7. Nat Genet. 2024 Feb 15.
    Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility.
    Satoko Ishii, Taishi Kakizuka, Sung-Joon Park, Ayako Tagawa, Chiaki Sanbo, Hideyuki Tanabe, Yasuyuki Ohkawa, Mahito Nakanishi, Kenta Nakai, Yusuke Miyanari.
      Chromatin accessibility is a hallmark of active regulatory regions and is functionally linked to transcriptional networks and cell identity. However, the molecular mechanisms and networks that govern chromatin accessibility have not been thoroughly studied. Here we conducted a genome-wide CRISPR screening combined with an optimized ATAC-see protocol to identify genes that modulate global chromatin accessibility. In addition to known chromatin regulators like CREBBP and EP400, we discovered a number of previously unrecognized proteins that modulate chromatin accessibility, including TFDP1, HNRNPU, EIF3D and THAP11 belonging to diverse biological pathways. ATAC-seq analysis upon their knockouts revealed their distinct and specific effects on chromatin accessibility. Remarkably, we found that TFDP1, a transcription factor, modulates global chromatin accessibility through transcriptional regulation of canonical histones. In addition, our findings highlight the manipulation of chromatin accessibility as an approach to enhance various cell engineering applications, including genome editing and induced pluripotent stem cell reprogramming.
    DOI:  https://doi.org/10.1038/s41588-024-01658-1
  8. J Cell Sci. 2024 Feb 15. pii: jcs.260467. [Epub ahead of print]
    Mutation of the SWI/SNF complex component Smarce1 decreases nucleosome stability in ES cells and impairs differentiation.
    Katsunobu Kashiwagi, Junko Yoshida, Hiroshi Kimura, Keiko Shinjo, Yutaka Kondo, Kyoji Horie.
      The SWI/SNF chromatin remodeling complex consists of more than 10 component proteins that form a large protein complex of>1 MDa. The catalytic proteins Smarca4 or Smarca2 work in concert with the component proteins to form a chromatin platform suitable for transcriptional regulation. However, the mechanism by which each component protein works synergistically with the catalytic proteins remains largely unknown. Here, we report on the function of Smarce1, a component of the SWI/SNF complex, through the phenotypic analysis of homozygous mutant embryonic stem (ES) cells. Disruption of Smarce1 induced the dissociation of other complex components from the SWI/SNF complex. Histone binding to DNA was loosened in homozygous mutant ES cells, indicating that disruption of Smarce1 decreased nucleosome stability. Sucrose gradient sedimentation analysis suggested an ectopic genomic distribution of the SWI/SNF complex, accounting for the misregulation of chromatin conformations. Unstable nucleosomes remained during ES cell differentiation, impairing the heterochromatin formation that is characteristic of the differentiation process. These results suggest that Smarce1 guides the SWI/SNF complex to the appropriate genomic regions to generate chromatin structures adequate for transcriptional regulation.
    Keywords:  BAF; Chromatin; Embryonic stem cells; Nucleosome; SWI/SNF; Smarce1
    DOI:  https://doi.org/10.1242/jcs.260467
  9. Nucleic Acids Res. 2024 Feb 14. pii: gkae095. [Epub ahead of print]
    The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis.
    Qiushi Xu, Yunlong Zhang, Wei Xu, Dong Liu, Wenfei Jin, Xi Chen, Ni Hong.
      Chromatin accessibility plays a critical role in the regulation of cell fate decisions. Although gene expression changes have been extensively profiled at the single-cell level during early embryogenesis, the dynamics of chromatin accessibility at cis-regulatory elements remain poorly studied. Here, we used a plate-based single-cell ATAC-seq method to profile the chromatin accessibility dynamics of over 10 000 nuclei from zebrafish embryos. We investigated several important time points immediately after zygotic genome activation (ZGA), covering key developmental stages up to dome. The results revealed key chromatin signatures in the first cell fate specifications when cells start to differentiate into enveloping layer (EVL) and yolk syncytial layer (YSL) cells. Finally, we uncovered many potential cell-type specific enhancers and transcription factor motifs that are important for the cell fate specifications.
    DOI:  https://doi.org/10.1093/nar/gkae095
  10. Nat Genet. 2024 Feb 15.
    Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition.
    Sedona Eve Murphy, Alistair Nicol Boettiger.
      Polycomb group proteins have a critical role in silencing transcription during development. It is commonly proposed that Polycomb-dependent changes in genome folding, which compact chromatin, contribute directly to repression by blocking the binding of activating complexes. Recently, it has also been argued that liquid-liquid demixing of Polycomb proteins facilitates this compaction and repression by phase-separating target genes into a membraneless compartment. To test these models, we used Optical Reconstruction of Chromatin Architecture to trace the Hoxa gene cluster, a canonical Polycomb target, in thousands of single cells. Across multiple cell types, we find that Polycomb-bound chromatin frequently explores decompact states and partial mixing with neighboring chromatin, while remaining uniformly repressed, challenging the repression-by-compaction or phase-separation models. Using polymer simulations, we show that these observed flexible ensembles can be explained by 'spatial feedback'-transient contacts that contribute to the propagation of the epigenetic state (epigenetic memory), without inducing a globular organization.
    DOI:  https://doi.org/10.1038/s41588-024-01661-6
  11. Nat Struct Mol Biol. 2024 Feb 16.
    Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function.
    Tyler J Gibson, Elizabeth D Larson, Melissa M Harrison.
      Chromatin is a barrier to the binding of many transcription factors. By contrast, pioneer factors access nucleosomal targets and promote chromatin opening. Despite binding to target motifs in closed chromatin, many pioneer factors display cell-type-specific binding and activity. The mechanisms governing pioneer factor occupancy and the relationship between chromatin occupancy and opening remain unclear. We studied three Drosophila transcription factors with distinct DNA-binding domains and biological functions: Zelda, Grainy head and Twist. We demonstrated that the level of chromatin occupancy is a key determinant of pioneering activity. Multiple factors regulate occupancy, including motif content, local chromatin and protein concentration. Regions outside the DNA-binding domain are required for binding and chromatin opening. Our results show that pioneering activity is not a binary feature intrinsic to a protein but occurs on a spectrum and is regulated by a variety of protein-intrinsic and cell-type-specific features.
    DOI:  https://doi.org/10.1038/s41594-024-01231-8
  12. Dev Cell. 2024 Feb 02. pii: S1534-5807(24)00031-5. [Epub ahead of print]
    Identification of a core transcriptional program driving the human renal mesenchymal-to-epithelial transition.
    John-Poul Ng-Blichfeldt, Benjamin J Stewart, Menna R Clatworthy, Julie M Williams, Katja Röper.
      During kidney development, nephron epithelia arise de novo from fate-committed mesenchymal progenitors through a mesenchymal-to-epithelial transition (MET). Downstream of fate specification, transcriptional mechanisms that drive establishment of epithelial morphology are poorly understood. We used human iPSC-derived renal organoids, which recapitulate nephrogenesis, to investigate mechanisms controlling renal MET. Multi-ome profiling via snRNA-seq and ATAC-seq of organoids identified dynamic changes in gene expression and chromatin accessibility driven by activators and repressors throughout MET. CRISPR interference identified that paired box 8 (PAX8) is essential for initiation of MET in human renal organoids, contrary to in vivo mouse studies, likely by activating a cell-adhesion program. While Wnt/β-catenin signaling specifies nephron fate, we find that it must be attenuated to allow hepatocyte nuclear factor 1-beta (HNF1B) and TEA-domain(TEAD) transcription factors to drive completion of MET. These results identify the interplay between fate commitment and morphogenesis in the developing human kidney, with implications for understanding both developmental kidney diseases and aberrant epithelial plasticity following adult renal tubular injury.
    Keywords:  epithelial polarity; kidney development; mesenchymal-to-epithelial transition; organoids; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.devcel.2024.01.011
  13. Nat Commun. 2024 Feb 15. 15(1): 1384
    Tissue-location-specific transcription programs drive tumor dependencies in colon cancer.
    Lijing Yang, Lei Tu, Shilpa Bisht, Yiqing Mao, Daniel Petkovich, Sara-Jayne Thursby, Jinxiao Liang, Nibedita Patel, Ray-Whay Chiu Yen, Tina Largent, Cynthia Zahnow, Malcolm Brock, Kathy Gabrielson, Kevan J Salimian, Stephen B Baylin, Hariharan Easwaran.
      Cancers of the same tissue-type but in anatomically distinct locations exhibit different molecular dependencies for tumorigenesis. Proximal and distal colon cancers exemplify such characteristics, with BRAFV600E predominantly occurring in proximal colon cancers along with increased DNA methylation phenotype. Using mouse colon organoids, here we show that proximal and distal colon stem cells have distinct transcriptional programs that regulate stemness and differentiation. We identify that the homeobox transcription factor, CDX2, which is silenced by DNA methylation in proximal colon cancers, is a key mediator of the differential transcriptional programs. Cdx2-mediated proximal colon-specific transcriptional program concurrently is tumor suppressive, and Cdx2 loss sufficiently creates permissive state for BRAFV600E-driven transformation. Human proximal colon cancers with CDX2 downregulation showed similar transcriptional program as in mouse proximal organoids with Cdx2 loss. Developmental transcription factors, such as CDX2, are thus critical in maintaining tissue-location specific transcriptional programs that create tissue-type origin specific dependencies for tumor development.
    DOI:  https://doi.org/10.1038/s41467-024-45605-4
  14. Nucleic Acids Res. 2024 Feb 13. pii: gkae088. [Epub ahead of print]
    Lineage-determining transcription factor-driven promoters regulate cell type-specific macrophage gene expression.
    Gergely Nagy, Dóra Bojcsuk, Petros Tzerpos, Tímea Cseh, László Nagy.
      Mammalian promoters consist of multifarious elements, which make them unique and support the selection of the proper transcript variants required under diverse conditions in distinct cell types. However, their direct DNA-transcription factor (TF) interactions are mostly unidentified. Murine bone marrow-derived macrophages (BMDMs) are a widely used model for studying gene expression regulation. Thus, this model serves as a rich source of various next-generation sequencing data sets, including a large number of TF cistromes. By processing and integrating the available cistromic, epigenomic and transcriptomic data from BMDMs, we characterized the macrophage-specific direct DNA-TF interactions, with a particular emphasis on those specific for promoters. Whilst active promoters are enriched for certain types of typically methylatable elements, more than half of them contain non-methylatable and prototypically promoter-distal elements. In addition, circa 14% of promoters-including that of Csf1r-are composed exclusively of 'distal' elements that provide cell type-specific gene regulation by specialized TFs. Similar to CG-rich promoters, these also contain methylatable CG sites that are demethylated in a significant portion and show high polymerase activity. We conclude that this unusual class of promoters regulates cell type-specific gene expression in macrophages, and such a mechanism might exist in other cell types too.
    DOI:  https://doi.org/10.1093/nar/gkae088
  15. Nat Commun. 2024 Feb 10. 15(1): 1274
    Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions.
    Tianxin Liu, Qian Zhu, Yan Kai, Trevor Bingham, Stacy Wang, Hye Ji Cha, Stuti Mehta, Thorsten M Schlaeger, Guo-Cheng Yuan, Stuart H Orkin.
      Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Changes in chromatin occupancy by Matr3 also correlated with these alterations. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture.
    DOI:  https://doi.org/10.1038/s41467-024-45386-w
  16. Development. 2024 Feb 12. pii: dev.202132. [Epub ahead of print]
    Multifaceted effects on even-skipped transcriptional dynamics upon Krüppel dosage changes.
    Shufan Lin, Bomyi Lim.
      Although fluctuations in transcription factor (TF) dosage are often well tolerated, TF dosage modulation can change the target gene expression dynamics and result in significant non-lethal developmental phenotypes. Using MS2/MCP-mediated quantitative live imaging in early Drosophila embryos, we analyzed how changing the gap gene Krüppel (Kr) level affects transcriptional dynamics of the pair-rule gene even-skipped (eve). Halving the Kr dosage leads to a transient posterior expansion of the eve stripe 2 and an anterior shift of stripe 5. Surprisingly, the most significant changes are observed in eve stripes 3 and 4, whose enhancers do not contain Kr binding sites. In Kr heterozygous embryos, both stripes 3 and 4 display narrower widths, anteriorly shifted boundaries, and reduced mRNA production levels. We show that Kr dosage indirectly affects stripe 3 and 4 dynamics by modulating other gap gene dynamics. We quantitatively correlate moderate body segment phenotypes of Kr heterozygotes with spatiotemporal changes in eve expression. Our results indicate that nonlinear relationships between TF dosage and phenotypes underlie direct TF-DNA and indirect TF-TF interactions.
    Keywords:   Drosophila ; Krüppel ; even-skipped ; Live imaging; MS2; Transcriptional regulation
    DOI:  https://doi.org/10.1242/dev.202132
  17. Nature. 2024 Feb 14.
    A single-cell time-lapse of mouse prenatal development from gastrula to birth.
    Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure.
      The house mouse (Mus musculus) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans1,2. Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing transformation of a single-cell zygote into a free-living pup composed of more than 500 million cells. Here, to establish a global framework for exploring mammalian development, we applied optimized single-cell combinatorial indexing3 to profile the transcriptional states of 12.4 million nuclei from 83 embryos, precisely staged at 2- to 6-hour intervals spanning late gastrulation (embryonic day 8) to birth (postnatal day 0). From these data, we annotate hundreds of cell types and explore the ontogenesis of the posterior embryo during somitogenesis and of kidney, mesenchyme, retina and early neurons. We leverage the temporal resolution and sampling depth of these whole-embryo snapshots, together with published data4-8 from earlier timepoints, to construct a rooted tree of cell-type relationships that spans the entirety of prenatal development, from zygote to birth. Throughout this tree, we systematically nominate genes encoding transcription factors and other proteins as candidate drivers of the in vivo differentiation of hundreds of cell types. Remarkably, the most marked temporal shifts in cell states are observed within one hour of birth and presumably underlie the massive physiological adaptations that must accompany the successful transition of a mammalian fetus to life outside the womb.
    DOI:  https://doi.org/10.1038/s41586-024-07069-w
  18. Sci Adv. 2024 Feb 16. 10(7): eadk0639
    Biphasic regulation of epigenetic state by matrix stiffness during cell reprogramming.
    Yang Song, Jennifer Soto, Sze Yue Wong, Yifan Wu, Tyler Hoffman, Navied Akhtar, Sam Norris, Julia Chu, Hyungju Park, Douglas O Kelkhoff, Cheen Euong Ang, Marius Wernig, Andrea Kasko, Timothy L Downing, Mu-Ming Poo, Song Li.
      We investigate how matrix stiffness regulates chromatin reorganization and cell reprogramming and find that matrix stiffness acts as a biphasic regulator of epigenetic state and fibroblast-to-neuron conversion efficiency, maximized at an intermediate stiffness of 20 kPa. ATAC sequencing analysis shows the same trend of chromatin accessibility to neuronal genes at these stiffness levels. Concurrently, we observe peak levels of histone acetylation and histone acetyltransferase (HAT) activity in the nucleus on 20 kPa matrices, and inhibiting HAT activity abolishes matrix stiffness effects. G-actin and cofilin, the cotransporters shuttling HAT into the nucleus, rises with decreasing matrix stiffness; however, reduced importin-9 on soft matrices limits nuclear transport. These two factors result in a biphasic regulation of HAT transport into nucleus, which is directly demonstrated on matrices with dynamically tunable stiffness. Our findings unravel a mechanism of the mechano-epigenetic regulation that is valuable for cell engineering in disease modeling and regenerative medicine applications.
    DOI:  https://doi.org/10.1126/sciadv.adk0639
  19. Mol Cell. 2024 Jan 29. pii: S1097-2765(24)00006-6. [Epub ahead of print]
    Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils.
    Kristian Jeppsson, Biswajit Pradhan, Takashi Sutani, Toyonori Sakata, Miki Umeda Igarashi, Davide Giorgio Berta, Takaharu Kanno, Ryuichiro Nakato, Katsuhiko Shirahige, Eugene Kim, Camilla Björkegren.
      The structural maintenance of chromosomes (SMC) protein complexes-cohesin, condensin, and the Smc5/6 complex (Smc5/6)-are essential for chromosome function. At the molecular level, these complexes fold DNA by loop extrusion. Accordingly, cohesin creates chromosome loops in interphase, and condensin compacts mitotic chromosomes. However, the role of Smc5/6's recently discovered DNA loop extrusion activity is unknown. Here, we uncover that Smc5/6 associates with transcription-induced positively supercoiled DNA at cohesin-dependent loop boundaries on budding yeast (Saccharomyces cerevisiae) chromosomes. Mechanistically, single-molecule imaging reveals that dimers of Smc5/6 specifically recognize the tip of positively supercoiled DNA plectonemes and efficiently initiate loop extrusion to gather the supercoiled DNA into a large plectonemic loop. Finally, Hi-C analysis shows that Smc5/6 links chromosomal regions containing transcription-induced positive supercoiling in cis. Altogether, our findings indicate that Smc5/6 controls the three-dimensional organization of chromosomes by recognizing and initiating loop extrusion on positively supercoiled DNA.
    Keywords:  3D chromosome organization; ChIP-seq; DNA loop extrusion; DNA plectoneme; DNA supercoiling; Hi-C; Smc5/6; cohesin; convergent transcription; single-molecule analysis
    DOI:  https://doi.org/10.1016/j.molcel.2024.01.005
  20. Elife. 2024 Feb 12. pii: e86168. [Epub ahead of print]13
    A methylation-phosphorylation switch controls EZH2 stability and hematopoiesis.
    Pengfei Guo, Rebecca C Lim, Keshari Rajawasam, Tiffany Trinh, Hong Sun, Hui Zhang.
      The Polycomb Repressive Complex 2 (PRC2) methylates H3K27 to regulate development and cell fate by transcriptional silencing. Alteration of PRC2 is associated with various cancers. Here, we show that mouse Kdm1a deletion causes dramatic reduction of PRC2 proteins, whereas mouse null mutation of L3mbtl3 or Dcaf5 results in PRC2 accumulation and increased H3K27 trimethylation. The catalytic subunit of PRC2, EZH2, is methylated at lysine 20 (K20), promoting EZH2 proteolysis by L3MBTL3 and the CLR4DCAF5 ubiquitin ligase. KDM1A (LSD1) demethylates the methylated K20 to stabilize EZH2. K20 methylation is inhibited by AKT-mediated phosphorylation of serine 21 in EZH2. Mouse Ezh2K20R/K20R mutants develop hepatosplenomegaly associated with high GFI1B expression, and Ezh2K20R/K20R mutant bone marrows expand hematopoietic stem cells and downstream hematopoietic populations. Our studies reveal that EZH2 is regulated by methylation-dependent proteolysis, which is negatively controlled by AKT-mediated S21 phosphorylation to establish a methylation-phosphorylation switch to control the PRC2 activity and hematopoiesis.
    Keywords:  biochemistry; cancer biology; chemical biology; mouse
    DOI:  https://doi.org/10.7554/eLife.86168
  21. Sci Rep. 2024 02 14. 14(1): 3752
    Single-cell analysis reveals the spatial-temporal expression of genes associated with esophageal malformations.
    Carlo Maj, Antonia Eberts, Johannes Schumacher, Pouria Dasmeh.
      Understanding the molecular mechanisms of congenital diseases is challenging due to their occurrence within specific developmental stages. Esophageal malformations are examples of such conditions, characterized by abnormalities in the development of esophagus during embryogenesis. These developmental malformations encompass a range of anomalies, including esophageal atresia, and tracheoesophageal fistula. Here, we investigated the preferential expression of 29 genes that are implicated in such malformations and their immediate interactome (a total of 67 genes). We conducted our analyses across several single-cell atlases of embryonic development, encompassing approximately 150,000 cells from the mouse foregut, 180,000 cells from human embryos, and 500,000 cells from 24 human organs. Our study, spanning diverse mesodermal and endodermal cell populations and early developmental stages, shows that the genes associated with esophageal malformations show their highest cell-type specific expression in lateral plate mesoderm cells and at the developmental stage of E8.75-E9.0 days. In human embryos, these genes show a significant cell-type specific expression among subpopulations of epithelial cells, fibroblasts and progenitor cells including basal cells. Notably, members of the forkhead-box family of transcription factors, namely FOXF1, FOXC1, and FOXD1, as well as the SRY-box transcription factor, SOX2, demonstrate the most significant preferential expression in both mouse and human embryos. Overall, our findings provide insights into the temporal and cellular contexts contributing to esophageal malformations.
    DOI:  https://doi.org/10.1038/s41598-024-53098-w
  22. Nat Commun. 2024 Feb 14. 15(1): 1362
    Oncoprotein SET-associated transcription factor ZBTB11 triggers lung cancer metastasis.
    Wenbin Xu, Han Yao, Zhen Wu, Xiaojun Yan, Zishan Jiao, Yajing Liu, Meng Zhang, Donglai Wang.
      Metastasis is the major cause of lung cancer-related death, but the mechanisms governing lung tumor metastasis remain incompletely elucidated. SE translocation (SET) is overexpressed in lung tumors and correlates with unfavorable prognosis. Here we uncover SET-associated transcription factor, zinc finger and BTB domain-containing protein 11 (ZBTB11), as a prometastatic regulator in lung tumors. SET interacts and collaborates with ZBTB11 to promote lung cancer cell migration and invasion, primarily through SET-ZBTB11 complex-mediated transcriptional activation of matrix metalloproteinase-9 (MMP9). Additionally, by transcriptional repression of proline-rich Gla protein 2 (PRRG2), ZBTB11 links Yes-associated protein 1 (YAP1) activation to drive lung tumor metastasis independently of SET-ZBTB11 complex. Loss of ZBTB11 suppresses distal metastasis in a lung tumor mouse model. Overexpression of ZBTB11 is recapitulated in human metastatic lung tumors and correlates with diminished survival. Our study demonstrates ZBTB11 as a key metastatic regulator and reveals diverse mechanisms by which ZBTB11 modulates lung tumor metastasis.
    DOI:  https://doi.org/10.1038/s41467-024-45585-5
  23. Stem Cells Dev. 2024 Feb 17.
    Nuclear Factor I A (Nfia) and Nuclear Factor I B (Nfib) are jointly required for mouse postnatal neural stem cell self-renewal.
    Christine E Campbell, Karstin Webber, Jonathan E Bard, Lee D Chaves, Jason M Osinski, Richard M Gronostajski.
      Mouse postnatal neural stem cells (pNSCs) can be expanded in vitro in the presence of EGF and FGF2 and upon removal of these factors cease proliferation and generate neurons, astrocytes and oligodendrocytes. The genetic requirements for self-renewal and lineage-commitment of pNSCs are incompletely understood. Here we show that the transcription factors NFIA and NFIB, previously shown individually to be essential for the normal commitment of pNSCs to the astrocytic lineage in vivo, are jointly required for normal self-renewal of pNSCs in vitro and in vivo. Using conditional knockout alleles of Nfia & Nfib we show that the simultaneous loss of these 2 genes under self-renewal conditions in vitro reduces the expression of the proliferation markers PCNA and Ki67, eliminates clonogenicity of the cells, reduces the number of cells in S phase and induces aberrant differentiation primarily into the neuroblast lineage. This phenotype requires the loss of both genes and is not seen upon loss of Nfia or Nfib alone, nor with combined loss of Nfia & Nfix or Nfib & Nfix. These data demonstrate a unique combined requirement for both Nfia and Nfib for pNSC self-renewal.
    DOI:  https://doi.org/10.1089/scd.2022.0204
  24. Cell Signal. 2024 Feb 08. pii: S0898-6568(24)00062-7. [Epub ahead of print]117 111094
    Hypoxia-inducible PRMT2 addiction in glioblastomas.
    Feng Dong, Xiaoyu Sun, Jiacheng Su, Qian Li, You He, Wei Li, Baofeng Wang, Bo Wang, Guogang Xu, Xudong Wu.
      Hypoxia-inducible transcription factors (HIFs) are key transcription factors for cellular response to low oxygen levels. However, the specific mediators responsible for activating downstream transcription are not well characterized. We previously identified Protein Arginine methyltransferase 2 (PRMT2), a highly expressed methyltransferase in glioblastoma multiforme, as a transcription co-activator. And we established a connection between PRMT2-mediated histone H3R8 asymmetric methylation (H3R8me2a) and transcription activation. Here we find that PRMT2 is activated by HIF1α under hypoxic conditions. And we demonstrate that PRMT2 and its H3R8me2a activity are required for the transcription activation of a significant subset of hypoxia-induced genes. Consequently, the inactivation of PRMT2 suppresses hypoxia-induced glioblastoma cell migration, attenuates tumor progression, and enhances chemotherapeutic sensitivity in mouse xenograft models. In addition, our analysis of clinical glioma specimens reveals a correlation between PRMT2 protein levels, HIF1α abundance, and an unfavorable prognosis. Our study establishes HIF1α-induced PRMT2 as a critical modulator in the activation of hypoxia-related transcriptional programs, ultimately driving malignant progression.
    Keywords:  Glioblastoma; Histone arginine methylation; Hypoxia; Protein arginine methyltransferase 2; Transcription
    DOI:  https://doi.org/10.1016/j.cellsig.2024.111094
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