bims-crepig 2022-02-13 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022‒02‒13
twenty-five papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit

Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler.
Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development.
Pluripotency factors determine gene expression repertoire at zygotic genome activation.
Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation.
CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters.
Integrative analysis reveals multiple modes of LXR transcriptional regulation in liver.
Human transcription factor protein interaction networks.
A Mediator-cohesin axis controls heterochromatin domain formation.
Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity.
Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program.
Klf4 methylated by Prmt1 restrains the commitment of primitive endoderm.
The renal cancer risk allele at 14q24.2 activates a novel hypoxia-inducible transcription factor-binding enhancer of DPF3 expression.
GLI transcriptional repression is inert prior to Hedgehog pathway activation.
Bivalent-histone-marked immediate-early gene regulation is vital for VEGF-responsive angiogenesis.
METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis.
SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence.
Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development.
The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7.
HiCmapTools: a tool to access HiC contact maps.
Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level.
Sox9 is involved in the thyroid differentiation program and is regulated by crosstalk between TSH, TGFβ and thyroid transcription factors.
Mesenchymal-epithelial crosstalk shapes intestinal regionalisation via Wnt and Shh signalling.
Histone H3K4me3 modification is a transgenerational epigenetic signal for lipid metabolism in Caenorhabditis elegans.
MYCL-mediated reprogramming expands pancreatic insulin-producing cells.
Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.

Nat Neurosci. 2022 Feb;25(2): 154-167

Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler.

Florian Noack, Silvia Vangelisti, Gerald Raffl, Madalena Carido, Jeisimhan Diwakar, Faye Chong, Boyan Bonev.

How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, to systematically map the regulatory landscape of neural differentiation in the mouse neocortex, we profiled gene expression and chromatin accessibility in single cells and integrated these data with measurements of enhancer activity, DNA methylation and three-dimensional genome architecture in purified cell populations. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex.

DOI: https://doi.org/10.1038/s41593-021-01002-4
Nat Commun. 2022 Feb 09. 13(1): 773

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development.

Dominic D G Owens, Giorgio Anselmi, A Marieke Oudelaar, Damien J Downes, Alessandro Cavallo, Joe R Harman, Ron Schwessinger, Akin Bucakci, Lucas Greder, Sara de Ornellas, Danuta Jeziorska, Jelena Telenius, Jim R Hughes, Marella F T R de Bruijn.

The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.

DOI: https://doi.org/10.1038/s41467-022-28376-8
Nat Commun. 2022 Feb 10. 13(1): 788

Pluripotency factors determine gene expression repertoire at zygotic genome activation.

Meijiang Gao, Marina Veil, Marcus Rosenblatt, Aileen Julia Riesle, Anna Gebhard, Helge Hass, Lenka Buryanova, Lev Y Yampolsky, Björn Grüning, Sergey V Ulianov, Jens Timmer, Daria Onichtchouk.

Awakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyze chromatin accessibility and time-resolved transcription in single and double mutant zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that two factors modify chromatin in a largely independent manner. We distinguish four types of direct enhancers by differential requirements for Pou5f3 or Sox19b. We demonstrate that changes in chromatin accessibility of enhancers underlie the changes in zygotic expression repertoire in the double mutants. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. The genes regulating mesendodermal and dorsal fates are primed for activation independently of Pou5f3 and Sox19b. Strikingly, simultaneous loss of Pou5f3 and Sox19b leads to premature expression of genes, involved in regulation of organogenesis and differentiation.

DOI: https://doi.org/10.1038/s41467-022-28434-1
Nucleic Acids Res. 2022 Feb 07. pii: gkac051. [Epub ahead of print]

Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation.

Courtney W Hanna, Jiahao Huang, Christian Belton, Susanne Reinhardt, Andreas Dahl, Simon Andrews, A Francis Stewart, Andrea Kranz, Gavin Kelsey.

Histone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 (KMT2B) are essential for oogenesis. We investigated changes in H3K4me3 in Setd1b conditional knockout (cKO) oocytes using ultra-low input ChIP-seq, with comparisons to DNA methylation and gene expression analyses. H3K4me3 was redistributed in Setd1b cKO oocytes showing losses at active gene promoters associated with downregulated gene expression. Remarkably, many regions also gained H3K4me3, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich, which are hallmarks of MLL2 targets. Consequently, loss of SETD1B disrupts the balance between MLL2 and de novo DNA methyltransferases in determining the epigenetic landscape during oogenesis. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to gene expression and MLL2 to CpG content.

DOI: https://doi.org/10.1093/nar/gkac051
Nat Genet. 2022 Feb;54(2): 202-212

CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters.

Havva Ortabozkoyun, Pin-Yao Huang, Hyunwoo Cho, Varun Narendra, Gary LeRoy, Edgar Gonzalez-Buendia, Jane A Skok, Aristotelis Tsirigos, Esteban O Mazzoni, Danny Reinberg.

CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.

DOI: https://doi.org/10.1038/s41588-021-01008-5
Proc Natl Acad Sci U S A. 2022 Feb 15. pii: e2122683119. [Epub ahead of print]119(7):

Integrative analysis reveals multiple modes of LXR transcriptional regulation in liver.

Lara Bideyan, Wenxin Fan, Karolina Elżbieta Kaczor-Urbanowicz, Christina Priest, David Casero, Peter Tontonoz.

  The nuclear receptors liver X receptor (LXR) α and β play crucial roles in hepatic metabolism. Many genes induced in response to pharmacologic LXR agonism have been defined; however, the transcriptional consequences of loss of LXR binding to its genomic targets are less well characterized. Here, we addressed how deletion of both LXRα and LXRβ from mouse liver (LXR double knockout [DKO]) affects the transcriptional regulatory landscape by integrating changes in LXR binding, chromatin accessibility, and gene expression. Many genes involved in fatty acid metabolism showed reduced expression and chromatin accessibility at their intergenic and intronic regions in LXRDKO livers. Genes that were up-regulated with LXR deletion had increased chromatin accessibility at their promoter regions and were enriched for functions not linked to lipid metabolism. Loss of LXR binding in liver reduced the activity of a broad set of hepatic transcription factors, inferred through changes in motif accessibility. By contrast, accessibility at promoter nuclear factor Y (NF-Y) motifs was increased in the absence of LXR. Unexpectedly, we also defined a small set of LXR targets for direct ligand-dependent repression. These genes have LXR-binding sites but showed increased expression in LXRDKO liver and reduced expression in response to the LXR agonist. In summary, the binding of LXRs to the hepatic genome has broad effects on the transcriptional landscape that extend beyond its canonical function as an activator of lipid metabolic genes.

Keywords:  LXR; nuclear receptor; transcription

DOI:  https://doi.org/10.1073/pnas.2122683119
Nat Commun. 2022 Feb 09. 13(1): 766

Human transcription factor protein interaction networks.

Helka Göös, Matias Kinnunen, Kari Salokas, Zenglai Tan, Xiaonan Liu, Leena Yadav, Qin Zhang, Gong-Hong Wei, Markku Varjosalo.

Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein-protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription.

DOI: https://doi.org/10.1038/s41467-022-28341-5
Nat Commun. 2022 Feb 08. 13(1): 754

A Mediator-cohesin axis controls heterochromatin domain formation.

Judith H I Haarhuis, Robin H van der Weide, Vincent A Blomen, Koen D Flach, Hans Teunissen, Laureen Willems, Thijn R Brummelkamp, Benjamin D Rowland, Elzo de Wit.

The genome consists of regions of transcriptionally active euchromatin and more silent heterochromatin. We reveal that the formation of heterochromatin domains requires cohesin turnover on DNA. Stabilization of cohesin on DNA through depletion of its release factor WAPL leads to a near-complete loss of heterochromatin domains. We observe the opposite phenotype in cells deficient for subunits of the Mediator-CDK module, with an almost binary partition of the genome into dense H3K9me3 domains, and regions devoid of H3K9me3 spanning the rest of the genome. We suggest that the Mediator-CDK module might contribute to gene expression by limiting the formation of dense heterochromatin domains. WAPL deficiency prevents the formation of heterochromatin domains, and allows for gene expression even in the absence of the Mediator-CDK subunit MED12. We propose that cohesin and Mediator affect heterochromatin in different ways to enable the correct distribution of epigenetic marks, and thus to ensure proper gene expression.

DOI: https://doi.org/10.1038/s41467-022-28377-7
Dev Cell. 2022 Feb 07. pii: S1534-5807(22)00006-5. [Epub ahead of print]57(3): 310-328.e9

Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity.

Preetish Kadur Lakshminarasimha Murthy, Rui Xi, Diana Arguijo, Jeffrey I Everitt, Dewran D Kocak, Yoshihiko Kobayashi, Aline Bozec, Silvestre Vicent, Shengli Ding, Gregory E Crawford, David Hsu, Purushothama Rao Tata, Timothy Reddy, Xiling Shen.

  Oncogenic Kras induces a hyper-proliferative state that permits cells to progress to neoplasms in diverse epithelial tissues. Depending on the cell of origin, this also involves lineage transformation. Although a multitude of downstream factors have been implicated in these processes, the precise chronology of molecular events controlling them remains elusive. Using mouse models, primary human tissues, and cell lines, we show that, in Kras-mutant alveolar type II cells (AEC2), FOSL1-based AP-1 factor guides the mSWI/SNF complex to increase chromatin accessibility at genomic loci controlling the expression of genes necessary for neoplastic transformation. We identified two orthogonal processes in Kras-mutant distal airway club cells. The first promoted their transdifferentiation into an AEC2-like state through NKX2.1, and the second controlled oncogenic transformation through the AP-1 complex. Our results suggest that neoplasms retain an epigenetic memory of their cell of origin through cell-type-specific transcription factors. Our analysis showed that a cross-tissue-conserved AP-1-dependent chromatin remodeling program regulates carcinogenesis.

Keywords:  ATAC-seq; Fosl1; KRAS; NSCLC; adenocarcinoma; alveolar type II cell; club cell; epigenetics; intestinal stem cell; lung

DOI:  https://doi.org/10.1016/j.devcel.2022.01.006
Nucleic Acids Res. 2022 Feb 07. pii: gkac042. [Epub ahead of print]

Transcription factor Zfp276 drives oligodendroglial differentiation and myelination by switching off the progenitor cell program.

Tim Aberle, Sandra Piefke, Simone Hillgärtner, Ernst R Tamm, Michael Wegner, Melanie Küspert.

In oligodendrocytes of the vertebrate central nervous system a complex network of transcriptional regulators is required to ensure correct and timely myelination of neuronal axons. Here we identify Zfp276, the only mammalian ZAD-domain containing zinc finger protein, as a transcriptional regulator of oligodendrocyte differentiation and central myelination downstream of Sox10. In the central nervous system, Zfp276 is exclusively expressed in mature oligodendrocytes. Oligodendroglial deletion of Zfp276 led to strongly reduced expression of myelin genes in the early postnatal mouse spinal cord. Retroviral overexpression of Zfp276 in cultured oligodendrocyte precursor cells induced precocious expression of maturation markers and myelin genes, further supporting its role in oligodendroglial differentiation. On the molecular level, Zfp276 directly binds to and represses Sox10-dependent gene regulatory regions of immaturity factors and functionally interacts with the transcriptional repressor Zeb2 to enable fast transition of oligodendrocytes to the myelinating stage.

DOI: https://doi.org/10.1093/nar/gkac042
Nucleic Acids Res. 2022 Feb 07. pii: gkac054. [Epub ahead of print]

Klf4 methylated by Prmt1 restrains the commitment of primitive endoderm.

Zhen-Yu Zuo, Guang-Hui Yang, Hai-Yu Wang, Shu-Yu Liu, Yan-Jun Zhang, Yun Cai, Fei Chen, Hui Dai, Yi Xiao, Mo-Bin Cheng, Yue Huang, Ye Zhang.

The second cell fate decision in the early stage of mammalian embryonic development is pivotal; however, the underlying molecular mechanism is largely unexplored. Here, we report that Prmt1 acts as an important regulator in primitive endoderm (PrE) formation. First, Prmt1 depletion promotes PrE gene expression in mouse embryonic stem cells (ESCs). Single-cell RNA sequencing and flow cytometry assays demonstrated that Prmt1 depletion in mESCs contributes to an emerging cluster, where PrE genes are upregulated significantly. Furthermore, the efficiency of extraembryonic endoderm stem cell induction increased in Prmt1-depleted ESCs. Second, the pluripotency factor Klf4 methylated at Arg396 by Prmt1 is required for recruitment of the repressive mSin3a/HDAC complex to silence PrE genes. Most importantly, an embryonic chimeric assay showed that Prmt1 inhibition and mutated Klf4 at Arg 396 induce the integration of mouse ESCs into the PrE lineage. Therefore, we reveal a regulatory mechanism for cell fate decisions centered on Prmt1-mediated Klf4 methylation.

DOI: https://doi.org/10.1093/nar/gkac054
J Biol Chem. 2022 Feb 08. pii: S0021-9258(22)00139-9. [Epub ahead of print] 101699

The renal cancer risk allele at 14q24.2 activates a novel hypoxia-inducible transcription factor-binding enhancer of DPF3 expression.

Johanna Protze, Stephanie Naas, René Krüger, Christine Stöhr, Andre Kraus, Steffen Grampp, Michael Wiesener, Mario Schiffer, Arndt Hartmann, Bernd Wullich, Johannes Schödel.

  Evolution of clear cell renal cell carcinoma (ccRCC) is guided by dysregulation of hypoxia-inducible transcription factor (HIF) pathways following loss of the von Hippel-Lindau tumor suppressor protein. RCC-associated polymorphisms influence HIF-DNA interactions at enhancers of important oncogenes thereby modulating the risk of developing renal cancer. A strong signal of genome-wide association with RCC was determined for the single-nucleotide polymorphism (SNP) rs4903064, located on chr14q.24.2 within an intron of DPF3, encoding for Double PHD Fingers 3, a member of chromatin remodeling complexes; however, it is unclear how the risk allele operates in renal cells. In this study we used tissue specimens and primary renal cells from a large cohort of RCC patients to examine the function of this polymorphism. In ccRCC tissue, isolated tumor cells as well as in primary renal tubular cells, in which HIF was stabilized, we determined genotype-specific increases of DPF3 mRNA levels and identified that the risk SNP resides in an active enhancer region, creating a novel HIF-binding motif. We then confirmed allele-specific HIF-binding to this locus using chromatin immunoprecipitation of HIF subunits. Consequentially, HIF-mediated DPF3 regulation was dependent on the presence of the risk allele. Finally, we show that DPF3 deletion in proximal tubular cells retarded cell growth, indicating potential roles for DPF3 in cell proliferation. Our analyses suggest that the HIF pathway differentially operates on a SNP-induced hypoxia-response element at 14q24.2, thereby affecting DPF3 expression, which increases the risk of developing renal cancer.

Keywords:  ATAC-seq; HIF; Renal Cancer; enhancer; polymorphism

DOI:  https://doi.org/10.1016/j.jbc.2022.101699
Nat Commun. 2022 Feb 10. 13(1): 808

GLI transcriptional repression is inert prior to Hedgehog pathway activation.

Rachel K Lex, Weiqiang Zhou, Zhicheng Ji, Kristin N Falkenstein, Kaleigh E Schuler, Kathryn E Windsor, Joseph D Kim, Hongkai Ji, Steven A Vokes.

The Hedgehog (HH) pathway regulates a spectrum of developmental processes through the transcriptional mediation of GLI proteins. GLI repressors control tissue patterning by preventing sub-threshold activation of HH target genes, presumably even before HH induction, while lack of GLI repression activates most targets. Despite GLI repression being central to HH regulation, it is unknown when it first becomes established in HH-responsive tissues. Here, we investigate whether GLI3 prevents precocious gene expression during limb development. Contrary to current dogma, we find that GLI3 is inert prior to HH signaling. While GLI3 binds to most targets, loss of Gli3 does not increase target gene expression, enhancer acetylation or accessibility, as it does post-HH signaling. Furthermore, GLI repression is established independently of HH signaling, but after its onset. Collectively, these surprising results challenge current GLI pre-patterning models and demonstrate that GLI repression is not a default state for the HH pathway.

DOI: https://doi.org/10.1038/s41467-022-28485-4
Cell Rep. 2022 Feb 08. pii: S2211-1247(22)00048-1. [Epub ahead of print]38(6): 110332

Bivalent-histone-marked immediate-early gene regulation is vital for VEGF-responsive angiogenesis.

Yasuharu Kanki, Masashi Muramatsu, Yuri Miyamura, Kenta Kikuchi, Yoshiki Higashijima, Ryo Nakaki, Jun-Ichi Suehiro, Yuji Sasaki, Yoshiaki Kubota, Haruhiko Koseki, Hiroshi Morioka, Tatsuhiko Kodama, Mitsuyoshi Nakao, Daisuke Kurotaki, Hiroyuki Aburatani, Takashi Minami.

  Endothelial cells (ECs) are phenotypically heterogeneous, mainly due to their dynamic response to the tissue microenvironment. Vascular endothelial cell growth factor (VEGF), the best-known angiogenic factor, activates calcium-nuclear factor of activated T cells (NFAT) signaling following acute angiogenic gene transcription. Here, we evaluate the global mapping of VEGF-mediated dynamic transcriptional events, focusing on major histone-code profiles using chromatin immunoprecipitation sequencing (ChIP-seq). Remarkably, the gene loci of immediate-early angiogenic transcription factors (TFs) exclusively acquire bivalent H3K4me3-H3K27me3 double-positive histone marks after the VEGF stimulus. Moreover, NFAT-associated Pax transactivation domain-interacting protein (PTIP) directs bivalently marked TF genes transcription through a limited polymerase II running. The non-canonical polycomb1 variant PRC1.3 specifically binds to and allows the transactivation of PRC2-enriched bivalent angiogenic TFs until conventional PRC1-mediated gene silencing is achieved. Knockdown of these genes abrogates post-natal aberrant neovessel formation via the selective inhibition of indispensable bivalent angiogenic TF gene transcription. Collectively, the reported dynamic histone mark landscape may uncover the importance of immediate-early genes and the development of advanced anti-angiogenic strategies.

Keywords:  ChIP-seq; NFAT, transcription; PTIP; VEGF; angiogenesis; bivalent histone marks; endothelial cells; immediate-early genes; noncanonical polycomb

DOI:  https://doi.org/10.1016/j.celrep.2022.110332
Nat Cell Biol. 2022 Feb 10.

METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis.

Rui Su, Lei Dong, Yangchan Li, Min Gao, P Cody He, Wei Liu, Jiangbo Wei, Zhicong Zhao, Lei Gao, Li Han, Xiaolan Deng, Chenying Li, Emily Prince, Brandon Tan, Ying Qing, Xi Qin, Chao Shen, Meilin Xue, Keren Zhou, Zhenhua Chen, Jianhuang Xue, Wei Li, Hanjun Qin, Xiwei Wu, Miao Sun, Yunsun Nam, Chun-Wei Chen, Wendong Huang, David Horne, Steven T Rosen, Chuan He, Jianjun Chen.

METTL16 has recently been identified as an RNA methyltransferase responsible for the deposition of N6-methyladenosine (m6A) in a few transcripts. Whether METTL16 methylates a large set of transcripts, similar to METTL3 and METTL14, remains unclear. Here we show that METTL16 exerts both methyltransferase activity-dependent and -independent functions in gene regulation. In the cell nucleus, METTL16 functions as an m6A writer to deposit m6A into hundreds of its specific messenger RNA targets. In the cytosol, METTL16 promotes translation in an m6A-independent manner. More specifically, METTL16 directly interacts with the eukaryotic initiation factors 3a and -b as well as ribosomal RNA through its Mtase domain, thereby facilitating the assembly of the translation-initiation complex and promoting the translation of over 4,000 mRNA transcripts. Moreover, we demonstrate that METTL16 is critical for the tumorigenesis of hepatocellular carcinoma. Collectively, our studies reveal previously unappreciated dual functions of METTL16 as an m6A writer and a translation-initiation facilitator, which together contribute to its essential function in tumorigenesis.

DOI: https://doi.org/10.1038/s41556-021-00835-2
Elife. 2022 Feb 07. pii: e70344. [Epub ahead of print]11

SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence.

J Ignacio Gutierrez, Gregory P Brittingham, Yonca B Karadeniz, Kathleen D Tran, Arnob Dutta, Alex S Holehouse, Craig L Peterson, Liam J Holt.

  It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, were required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC lead to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that that pH changes are a second messenger for transcriptional reprogramming during carbon starvation, and that the SNF5 QLC acts as a pH-sensor.

Keywords:  S. cerevisiae; biochemistry; chemical biology; chromosomes; gene expression

DOI:  https://doi.org/10.7554/eLife.70344
Development. 2022 Feb 01. pii: dev200250. [Epub ahead of print]149(3):

Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development.

Aditi Singh, Arun Mahesh, Florian Noack, Beatriz Cardoso de Toledo, Federico Calegari, Vijay K Tiwari.

  Corticogenesis consists of a series of synchronised events, including fate transition of cortical progenitors, neuronal migration, specification and connectivity. NeuroD1, a basic helix-loop-helix (bHLH) transcription factor (TF), contributes to all of these events, but how it coordinates these independently is still unknown. Here, we demonstrate that NeuroD1 expression is accompanied by a gain of active chromatin at a large number of genomic loci. Interestingly, transcriptional activation of these loci relied on a high local density of adjacent bHLH TFs motifs, including, predominantly, Tcf12. We found that activity and expression levels of Tcf12 were high in cells with induced levels of NeuroD1 that spanned the transition of cortical progenitors from proliferative to neurogenic divisions. Moreover, Tcf12 forms a complex with NeuroD1 and co-occupies a subset of NeuroD1 target loci. This Tcf12-NeuroD1 cooperativity is essential for gaining active chromatin and targeted expression of genes involved in cell migration. By functional manipulation in vivo, we further show that Tcf12 is essential during cortical development for the correct migration of newborn neurons and, hence, for proper cortical lamination.

Keywords:  Cortical development; Epigenetics; Gene regulation; Genomics; Neurogenesis; Transcription factors

DOI:  https://doi.org/10.1242/dev.200250
Nucleic Acids Res. 2022 Feb 07. pii: gkac083. [Epub ahead of print]

The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7.

Mara Maldotti, Andrea Lauria, Francesca Anselmi, Ivan Molineris, Annalaura Tamburrini, Guohua Meng, Isabelle Laurence Polignano, Mirko Giuseppe Scrivano, Fabiola Campestre, Lisa Marie Simon, Stefania Rapelli, Edoardo Morandi, Danny Incarnato, Salvatore Oliviero.

The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.

DOI: https://doi.org/10.1093/nar/gkac083
BMC Bioinformatics. 2022 Feb 10. 23(1): 64

HiCmapTools: a tool to access HiC contact maps.

Jia-Ming Chang, Yi-Fu Weng, Wei-Ting Chang, Fu-An Lin, Giacomo Cavalli.

  BACKGROUND: With the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool to query contact maps in order to extract biological information from HiC datasets.RESULTS: We present HiCmapTools, a tool for biologists to efficiently calculate and analyze HiC maps. The complete program provides multi-query modes and analysis tools. We have validated its utility on two real biological questions: TAD loop and TAD intra-density.
CONCLUSIONS: HiCmapTools supports seven access options so that biologists can quantify contact frequency of the interest sites. The tool has been implemented in C++ and R and is freely available at https://github.com/changlabtw/hicmaptools and documented at https://hicmaptools.readthedocs.io/ .

Keywords:  3D genome; Hi-C; Juicer; Topologically Associating Domains (TADs); hicpipe

DOI:  https://doi.org/10.1186/s12859-022-04589-y
Science. 2022 Feb 11. 375(6581): 681-686

Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level.

Yanxiang Deng, Marek Bartosovic, Petra Kukanja, Di Zhang, Yang Liu, Graham Su, Archibald Enninful, Zhiliang Bai, Gonçalo Castelo-Branco, Rong Fan.

Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.

DOI: https://doi.org/10.1126/science.abg7216
Sci Rep. 2022 Feb 09. 12(1): 2144

Sox9 is involved in the thyroid differentiation program and is regulated by crosstalk between TSH, TGFβ and thyroid transcription factors.

Arístides López-Márquez, Carlos Carrasco-López, Andrea Martínez-Cano, Pascale Lemoine, Christophe E Pierreux, Pilar Santisteban.

While the signaling pathways and transcription factors involved in the differentiation of thyroid follicular cells, both in embryonic and adult life, are increasingly well understood, the underlying mechanisms and potential crosstalk between the thyroid transcription factors Nkx2.1, Foxe1 and Pax8 and inductive signals remain unclear. Here, we focused on the transcription factor Sox9, which is expressed in Nkx2.1-positive embryonic thyroid precursor cells and is maintained from embryonic development to adulthood, but its function and control are unknown. We show that two of the main signals regulating thyroid differentiation, TSH and TGFβ, modulate Sox9 expression. Specifically, TSH stimulates the cAMP/PKA pathway to transcriptionally upregulate Sox9 mRNA and protein expression, a mechanism that is mediated by the binding of CREB to a CRE site within the Sox9 promoter. Contrastingly, TGFβ signals through Smad proteins to inhibit TSH-induced Sox9 transcription. Our data also reveal that Sox9 transcription is regulated by the thyroid transcription factors, particularly Pax8. Interestingly, Sox9 significantly increased the transcriptional activation of Pax8 and Foxe1 promoters and, consequently, their expression, but had no effect on Nkx2.1. Our study establishes the involvement of Sox9 in thyroid follicular cell differentiation and broadens our understanding of transcription factor regulation of thyroid function.

DOI: https://doi.org/10.1038/s41598-022-06004-1
Nat Commun. 2022 Feb 07. 13(1): 715

Mesenchymal-epithelial crosstalk shapes intestinal regionalisation via Wnt and Shh signalling.

Martti Maimets, Marianne Terndrup Pedersen, Jordi Guiu, Jes Dreier, Malte Thodberg, Yasuko Antoku, Pawel J Schweiger, Leonor Rib, Raul Bardini Bressan, Yi Miao, K Christopher Garcia, Albin Sandelin, Palle Serup, Kim B Jensen.

Organs are anatomically compartmentalised to cater for specialised functions. In the small intestine (SI), regionalisation enables sequential processing of food and nutrient absorption. While several studies indicate the critical importance of non-epithelial cells during development and homeostasis, the extent to which these cells contribute to regionalisation during morphogenesis remains unexplored. Here, we identify a mesenchymal-epithelial crosstalk that shapes the developing SI during late morphogenesis. We find that subepithelial mesenchymal cells are characterised by gradients of factors supporting Wnt signalling and stimulate epithelial growth in vitro. Such a gradient impacts epithelial gene expression and regional villus formation along the anterior-posterior axis of the SI. Notably, we further provide evidence that Wnt signalling directly regulates epithelial expression of Sonic Hedgehog (SHH), which, in turn, acts on mesenchymal cells to drive villi formation. Taken together our results uncover a mechanistic link between Wnt and Hedgehog signalling across different cellular compartments that is central for anterior-posterior regionalisation and correct formation of the SI.

DOI: https://doi.org/10.1038/s41467-022-28369-7
Nat Commun. 2022 Feb 09. 13(1): 768

Histone H3K4me3 modification is a transgenerational epigenetic signal for lipid metabolism in Caenorhabditis elegans.

Qin-Li Wan, Xiao Meng, Chongyang Wang, Wenyu Dai, Zhenhuan Luo, Zhinan Yin, Zhenyu Ju, Xiaodie Fu, Jing Yang, Qunshan Ye, Zhan-Hui Zhang, Qinghua Zhou.

As a major risk factor to human health, obesity presents a massive burden to people and society. Interestingly, the obese status of parents can cause progeny's lipid accumulation through epigenetic inheritance in multiple species. To date, many questions remain as to how lipid accumulation leads to signals that are transmitted across generations. In this study, we establish a nematode model of C. elegans raised on a high-fat diet (HFD) that leads to measurable lipid accumulation, which can transmit the lipid accumulation signal to their multigenerational progeny. Using this model, we find that transcription factors DAF-16/FOXO and SBP-1/SREBP, nuclear receptors NHR-49 and NHR-80, and delta-9 desaturases (fat-5, fat-6, and fat-7) are required for transgenerational lipid accumulation. Additionally, histone H3K4 trimethylation (H3K4me3) marks lipid metabolism genes and increases their transcription response to multigenerational obesogenic effects. In summary, this study establishes an interaction between a network of lipid metabolic genes and chromatin modifications, which work together to achieve transgenerational epigenetic inheritance of obesogenic effects.

DOI: https://doi.org/10.1038/s41467-022-28469-4
Nat Metab. 2022 Feb 10.

MYCL-mediated reprogramming expands pancreatic insulin-producing cells.

Michitada Hirano, Yusei So, Shin Tsunekawa, Mio Kabata, Sho Ohta, Hiroshi Sagara, Nao Sankoda, Jumpei Taguchi, Yosuke Yamada, Tomoyo Ukai, Makoto Kato, Jiro Nakamura, Manabu Ozawa, Takuya Yamamoto, Yasuhiro Yamada.

β cells have a limited capacity for regeneration, which predisposes towards diabetes. Here, we show that, of the MYC family members, Mycl plays a key role in proliferation of pancreatic endocrine cells. Genetic ablation of Mycl causes a reduction in the proliferation of pancreatic endocrine cells in neonatal mice. By contrast, the expression of Mycl in adult mice stimulates the proliferation of β and α cells, and the cells persist after withdrawal of Mycl expression. A subset of the expanded α cells give rise to insulin-producing cells after this withdrawal. Transient Mycl expression in vivo is sufficient to normalize the hyperglycaemia of diabetic mice. In vitro expression of Mycl similarly provokes active replication in islet cells, even in those from aged mice. Finally, we show that MYCL stimulates the division of human adult cadaveric islet cells. Our results demonstrate that the induction of Mycl alone expands the functional β-cell population, which may provide a regenerative strategy for β cells.

DOI: https://doi.org/10.1038/s42255-022-00530-y
Sci Data. 2022 Feb 10. 9(1): 47

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.

Ana Mota, Maud Schweitzer, Erik Wernersson, Nicola Crosetto, Magda Bienko.

Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.

DOI: https://doi.org/10.1038/s41597-022-01139-2