bims-crepig 2023-05-07 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023–05–07
twenty papers selected by
Connor Rogerson, University of Cambridge

Loop stacking organizes genome folding from TADs to chromosomes.
Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting.
Landscape and significance of human super enhancer-driven core transcription regulatory circuitry.
Shared enhancer gene regulatory networks between wound and oncogenic programs.
GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells.
Changes in locus wide repression underlie the evolution of Drosophila abdominal pigmentation.
Functional interplay between Mediator and RSC chromatin remodeling complex controls nucleosome-depleted region maintenance at promoters.
Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors.
Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.
Screening for functional regulatory variants in open chromatin using GenIE-ATAC.
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency.
A single N-terminal amino acid determines the distinct roles of histones H3 and H3.3 in the Drosophila male germline stem cell lineage.
Loops and the activity of loop extrusion factors constrain chromatin dynamics.
Transcription factor induction of vascular blood stem cell niches in vivo.
Epigenetic programming defines haematopoietic stem cell fate restriction.
Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster.
TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors.
β-catenin-driven differentiation is a tissue-specific epigenetic vulnerability in adrenal cancer.
Bromodomain protein BRD8 regulates cell cycle progression in colorectal cancer cells through a TIP60-independent regulation of the pre-RC complex.
Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation.

Mol Cell. 2023 May 04. pii: S1097-2765(23)00252-6. [Epub ahead of print]83(9): 1377-1392.e6

Loop stacking organizes genome folding from TADs to chromosomes.

Antonina Hafner, Minhee Park, Scott E Berger, Sedona E Murphy, Elphège P Nora, Alistair N Boettiger.

  Although population-level analyses revealed significant roles for CTCF and cohesin in mammalian genome organization, their contributions at the single-cell level remain incompletely understood. Here, we used a super-resolution microscopy approach to measure the effects of removal of CTCF or cohesin in mouse embryonic stem cells. Single-chromosome traces revealed cohesin-dependent loops, frequently stacked at their loop anchors forming multi-way contacts (hubs), bridging across TAD boundaries. Despite these bridging interactions, chromatin in intervening TADs was not intermixed, remaining separated in distinct loops around the hub. At the multi-TAD scale, steric effects from loop stacking insulated local chromatin from ultra-long range (>4 Mb) contacts. Upon cohesin removal, the chromosomes were more disordered and increased cell-cell variability in gene expression. Our data revise the TAD-centric understanding of CTCF and cohesin and provide a multi-scale, structural picture of how they organize the genome on the single-cell level through distinct contributions to loop stacking.

Keywords:  3D genome organization; CTCF; chromosome tracing; cohesin; loop extrusion; multiplexed imaging; single-cell gene expression; single-chromosome chromatin folding

DOI:  https://doi.org/10.1016/j.molcel.2023.04.008
Nat Struct Mol Biol. 2023 May 01.

Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting.

Ineke Brouwer, Emma Kerklingh, Fred van Leeuwen, Tineke L Lenstra.

Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by the remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in Saccharomyces cerevisiae to measure how bursting changes upon combined perturbations of chromatin remodelers, the transcription factor Gal4 and preinitiation complex components. Using dynamic epistasis analysis, we reveal how the remodeling of different nucleosomes regulates transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC and Gal4 binding synergistically facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. At canonical TATA boxes, the nucleosomes are displaced by TBP binding to allow for transcription activation even in the absence of remodelers. Overall, our results reveal how promoter nucleosome remodeling together with Gal4 and preinitiation complex binding regulates transcriptional bursting.

DOI: https://doi.org/10.1038/s41594-023-00981-1
Mol Ther Nucleic Acids. 2023 Jun 13. 32 385-401

Landscape and significance of human super enhancer-driven core transcription regulatory circuitry.

Chenchen Feng, Chao Song, Yong Jiang, Jun Zhao, Jian Zhang, Yuezhu Wang, Mingxue Yin, Jiang Zhu, Bo Ai, Qiuyu Wang, Fengcui Qian, Yuexin Zhang, Desi Shang, Jiaqi Liu, Chunquan Li.

  A core transcription regulatory circuitry (CRC) is an interconnected self-regulatory circuitry that is formed by a group of core transcription factors (TFs). These core TFs collectively regulate gene expression by binding not only to their own super enhancers (SEs) but also to the SEs of one another. For most human tissue/cell types, a global view of CRCs and core TFs has not been generated. Here, we identified numerous CRCs using two identification methods and detailed the landscape of the CRCs driven by SEs in large cell/tissue samples. The comprehensive biological analyses, including sequence conservation, CRC activity and genome binding affinity were conducted for common TFs, moderate TFs, and specific TFs, which exhibit different biological features. The local module located from the common CRC network highlighted the essential functions and prognostic performance. The tissue-specific CRC network was highly related to cell identity. Core TFs in tissue-specific CRC networks exhibited disease markers, and had regulatory potential for cancer immunotherapy. Moreover, a user-friendly resource named CRCdb (http://www.licpathway.net/crcdb/index.html) was developed, which contained the detailed information of CRCs and core TFs used in this study, as well as other interesting results, such as the most representative CRC, frequency of TFs, and indegree/outdegree of TFs.

Keywords:  MT: Bioinformatics; core transcription regulatory circuitry; network analysis; platform; super enhancer; transcription factor

DOI:  https://doi.org/10.1016/j.omtn.2023.03.014
Elife. 2023 May 03. pii: e81173. [Epub ahead of print]12

Shared enhancer gene regulatory networks between wound and oncogenic programs.

Swann Floc'hlay, Ramya Balaji, Dimitrije Stanković, Valerie M Christiaens, Carmen Bravo González-Blas, Seppe De Winter, Gert J Hulselmans, Maxime De Waegeneer, Xiaojiang Quan, Duygu Koldere, Mardelle Atkins, Georg Halder, Mirka Uhlirova, Anne Classen, Stein Aerts.

  Wound response programs are often activated during neoplastic growth in tumors. In both wound repair and tumor growth, cells respond to acute stress and balance the activation of multiple programs including apoptosis, proliferation, and cell migration. Central to those responses are the activation of the JNK/MAPK and JAK/STAT signaling pathways. Yet, to what extent these signaling cascades interact at the cis-regulatory level, and how they orchestrate different regulatory and phenotypic responses is still unclear. Here, we aim to characterize the regulatory states that emerge and cooperate in the wound response, using the Drosophila melanogaster wing disc as a model system, and compare these with cancer cell states induced by rasV12scrib-/- in the eye disc. We used single-cell multiome profiling to derive enhancer Gene Regulatory Networks (eGRNs) by integrating chromatin accessibility and gene expression signals. We identify a 'proliferative' eGRN, active in the majority of wounded cells and controlled by AP-1 and STAT. In a smaller, but distinct population of wound cells, a 'senescent' eGRN is activated and driven by C/EBP-like transcription factors (Irbp18, Xrp1, Slow border, and Vrille) and Scalloped. These two eGRN signatures are found to be active in tumor cells, at both gene expression and chromatin accessibility levels. Our single-cell multiome and eGRNs resource offers an in-depth characterisation of the senescence markers, together with a new perspective on the shared gene regulatory programs acting during wound response and oncogenesis.

Keywords:  D. melanogaster; computational biology; genetics; genomics; systems biology

DOI:  https://doi.org/10.7554/eLife.81173
Cell Stem Cell. 2023 May 04. pii: S1934-5909(23)00130-3. [Epub ahead of print]30(5): 722-740.e11

GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells.

Sven Turkalj, Niels Asger Jakobsen, Angus Groom, Marlen Metzner, Simone G Riva, E Ravza Gür, Batchimeg Usukhbayar, Mirian Angulo Salazar, Lance D Hentges, Gerda Mickute, Kevin Clark, Paul Sopp, James O J Davies, Jim R Hughes, Paresh Vyas.

  Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.

Keywords:  acute myeloid leukemia; cancer evolution; chromatin accessibility; clonal tracking; epigenomics; leukemia stem cells; single-cell ATAC-seq; single-cell technologies; somatic mutation; tumor heterogeneity

DOI:  https://doi.org/10.1016/j.stem.2023.04.012
PLoS Genet. 2023 May 03. 19(5): e1010722

Changes in locus wide repression underlie the evolution of Drosophila abdominal pigmentation.

Iván D Méndez-González, Thomas M Williams, Mark Rebeiz.

Changes in gene regulation represent an important path to generate developmental differences affecting anatomical traits. Interspecific divergence in gene expression often results from changes in transcription-stimulating enhancer elements. While gene repression is crucial for precise spatiotemporal expression patterns, the relative contribution of repressive transcriptional silencers to regulatory evolution remains to be addressed. Here, we show that the Drosophila pigmentation gene ebony has mainly evolved through changes in the spatial domains of silencers patterning its abdominal expression. By precisely editing the endogenous ebony locus of D. melanogaster, we demonstrate the requirement of two redundant abdominal enhancers and three silencers that repress the redundant enhancers in a patterned manner. We observe a role for changes in these silencers in every case of ebony evolution observed to date. Our findings suggest that negative regulation by silencers likely has an under-appreciated role in gene regulatory evolution.

DOI: https://doi.org/10.1371/journal.pgen.1010722
Cell Rep. 2023 May 02. pii: S2211-1247(23)00476-X. [Epub ahead of print]42(5): 112465

Functional interplay between Mediator and RSC chromatin remodeling complex controls nucleosome-depleted region maintenance at promoters.

Kévin M André, Nathalie Giordanengo Aiach, Veronica Martinez-Fernandez, Leo Zeitler, Adriana Alberti, Arach Goldar, Michel Werner, Cyril Denby Wilkes, Julie Soutourina.

  Chromatin organization is crucial for transcriptional regulation in eukaryotes. Mediator is an essential and conserved co-activator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. Here, we provide evidence in the yeast Saccharomyces cerevisiae that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. We determine the role of Mediator-RSC interaction in their chromatin binding, nucleosome occupancy, and transcription on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and TSS-associated +1 nucleosome stability. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.

Keywords:  CP: Molecular biology; Mediator; RNA polymerase II; RSC; genome-wide distribution; nucleosome-depleted region; transcription; yeast Saccharomyces cerevisiae

DOI:  https://doi.org/10.1016/j.celrep.2023.112465
Nat Commun. 2023 May 05. 14(1): 2600

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors.

Miaomiao Li, Tao Yao, Wanru Lin, Will E Hinckley, Mary Galli, Wellington Muchero, Andrea Gallavotti, Jin-Gui Chen, Shao-Shan Carol Huang.

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

DOI: https://doi.org/10.1038/s41467-023-38096-2
Mol Cell. 2023 Apr 24. pii: S1097-2765(23)00254-X. [Epub ahead of print]

Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.

Zlata Gvozdenov, Zeno Barcutean, Kevin Struhl.

  We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of random-sequence RNAs are comparable to yeast mRNAs, although transcription and decay rates are higher. Transcriptional initiation from random-sequence DNA occurs at numerous sites, indicating very low intrinsic specificity of the RNA Pol II machinery. In contrast, poly(A) profiles of random-sequence RNAs are roughly comparable to those of yeast mRNAs, suggesting limited evolutionary restraints on poly(A) site choice. Random-sequence RNAs show higher cell-to-cell variability than yeast mRNAs, suggesting that functional elements limit variability. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.

Keywords:  biological function; biological noise; chromatin; polyadenylation; transcription

DOI:  https://doi.org/10.1016/j.molcel.2023.04.010
Nucleic Acids Res. 2023 May 01. pii: gkad332. [Epub ahead of print]

Screening for functional regulatory variants in open chromatin using GenIE-ATAC.

Sarah Cooper, Jeremy Schwartzentruber, Eve L Coomber, Qianxin Wu, Andrew Bassett.

Understanding the effects of genetic variation in gene regulatory elements is crucial to interpreting genome function. This is particularly pertinent for the hundreds of thousands of disease-associated variants identified by GWAS, which frequently sit within gene regulatory elements but whose functional effects are often unknown. Current methods are limited in their scalability and ability to assay regulatory variants in their endogenous context, independently of other tightly linked variants. Here, we present a new medium-throughput screening system: genome engineering based interrogation of enhancers assay for transposase accessible chromatin (GenIE-ATAC), that measures the effect of individual variants on chromatin accessibility in their endogenous genomic and chromatin context. We employ this assay to screen for the effects of regulatory variants in human induced pluripotent stem cells, validating a subset of causal variants, and extend our software package (rgenie) to analyse these new data. We demonstrate that this methodology can be used to understand the impact of defined deletions and point mutations within transcription factor binding sites. We thus establish GenIE-ATAC as a method to screen for the effect of gene regulatory element variation, allowing identification and prioritisation of causal variants from GWAS for functional follow-up and understanding the mechanisms of regulatory element function.

DOI: https://doi.org/10.1093/nar/gkad332
Bioinformatics. 2023 May 04. pii: btad299. [Epub ahead of print]

HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency.

Zixuan Wang, Shuwen Xiong, Yun Yu, Jiliu Zhou, Yongqing Zhang.

MOTIVATION: Transcription factor (TF) binds to conservative DNA binding sites in different cellular environments and development stages by physical interaction with interdependent nucleotides. However, systematic computational characterization of the relationship between higher-order nucleotide dependency and TF-DNA binding mechanism in diverse cell types remains challenging.
RESULTS: Here, we propose a novel multi-task learning framework HAMPLE to simultaneously predict TF binding sites (TFBS) in distinct cell types by characterizing higher-order nucleotide dependencies. Specifically, HAMPLE first represents a DNA sequence through three higher-order nucleotide dependencies, including k-mer encoding, DNA shape and histone modification. Then, HAMPLE employs the customized gate control and the channel attention convolutional architecture to further capture cell-type-specific and cell-type-shared DNA binding motifs and epigenomic languages. Finally, HAMPLE exploits the joint loss function to optimize the TFBS prediction for different cell types in an end-to-end manner. Extensive experimental results on seven datasets demonstrate that HAMPLE significantly outperforms the state-of-the-art approaches in terms of auROC. In addition, feature importance analysis illustrates that k-mer encoding, DNA shape and histone modification have predictive power for TF-DNA binding in different cellular environments and are complementary to each other. Furthermore, ablation study and interpretable analysis validate the effectiveness of the customized gate control and the channel attention convolutional architecture in characterizing higher-order nucleotide dependencies.
AVAILABILITY: The source code is available at https://github.com/ZhangLab312/Hample.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btad299
PLoS Biol. 2023 May 01. 21(5): e3002098

A single N-terminal amino acid determines the distinct roles of histones H3 and H3.3 in the Drosophila male germline stem cell lineage.

Chinmayi Chandrasekhara, Rajesh Ranjan, Jennifer A Urban, Brendon E M Davis, Wai Lim Ku, Jonathan Snedeker, Keji Zhao, Xin Chen.

Adult stem cells undergo asymmetric cell divisions to produce 2 daughter cells with distinct cell fates: one capable of self-renewal and the other committed for differentiation. Misregulation of this delicate balance can lead to cancer and tissue degeneration. During asymmetric division of Drosophila male germline stem cells (GSCs), preexisting (old) and newly synthesized histone H3 are differentially segregated, whereas old and new histone variant H3.3 are more equally inherited. However, what underlies these distinct inheritance patterns remains unknown. Here, we report that the N-terminal tails of H3 and H3.3 are critical for their inheritance patterns, as well as GSC maintenance and proper differentiation. H3 and H3.3 differ at the 31st position in their N-termini with Alanine for H3 and Serine for H3.3. By swapping these 2 amino acids, we generated 2 mutant histones (i.e., H3A31S and H3.3S31A). Upon expressing them in the early-stage germline, we identified opposing phenotypes: overpopulation of early-stage germ cells in the H3A31S-expressing testes and significant germ cell loss in testes expressing the H3.3S31A. Asymmetric H3 inheritance is disrupted in the H3A31S-expressing GSCs, due to misincorporation of old histones between sister chromatids during DNA replication. Furthermore, H3.3S31A mutation accelerates old histone turnover in the GSCs. Finally, using a modified Chromatin Immunocleavage assay on early-stage germ cells, we found that H3A31S has enhanced occupancy at promoters and transcription starting sites compared with H3, while H3.3S31A is more enriched at transcriptionally silent intergenic regions compared to H3.3. Overall, these results suggest that the 31st amino acids for both H3 and H3.3 are critical for their proper genomic occupancy and function. Together, our findings indicate a critical role for the different amino acid composition of the N-terminal tails between H3 and H3.3 in an endogenous stem cell lineage and provide insights into the importance of proper histone inheritance in specifying cell fates and regulating cellular differentiation.

DOI: https://doi.org/10.1371/journal.pbio.3002098
Mol Biol Cell. 2023 Apr 26. mbcE23040119

Loops and the activity of loop extrusion factors constrain chromatin dynamics.

Mary Lou P Bailey, Ivan Surovtsev, Jessica F Williams, Hao Yan, Tianyu Yuan, Kevin Li, Katherine Duseau, Simon G J Mochrie, Megan C King.

The chromosomes - DNA polymers and their binding proteins - are compacted into a spatially organized, yet dynamic, three-dimensional structure. Recent genome-wide chromatin conformation capture experiments reveal a hierarchical organization of the DNA structure that is imposed, at least in part, by looping interactions arising from the activity of loop extrusion factors. The dynamics of chromatin reflects the response of the polymer to a combination of thermal fluctuations and active processes. However, how chromosome structure and enzymes acting on chromatin together define its dynamics remains poorly understood. To gain insight into the structure-dynamics relationship of chromatin, we combine high-precision microscopy in living Schizosaccharomyces pombe cells with systematic genetic perturbations and Rouse-model polymer simulations. We first investigated how the activity of two loop extrusion factors, the cohesin and condensin complexes, influences chromatin dynamics. We observed that deactivating cohesin, or to a lesser extent condensin, increased chromatin mobility, suggesting that loop extrusion constrains rather than agitates chromatin motion. Our corresponding simulations reveal that the introduction of loops is sufficient to explain the constraining activity of loop extrusion factors, highlighting that the conformation adopted by the polymer plays a key role in defining its dynamics. Moreover, we find that the number loops or residence times of loop extrusion factors influences the dynamic behavior of the chromatin polymer. Last, we observe that the activity of the INO80 chromatin remodeler, but not the SWI/SNF or RSC complexes, is critical for ATP-dependent chromatin mobility in fission yeast. Taken together we suggest that thermal and INO80-dependent activities exert forces that drive chromatin fluctuations, which are constrained by the organization of the chromosome into loops.

DOI: https://doi.org/10.1091/mbc.E23-04-0119
Dev Cell. 2023 Apr 25. pii: S1534-5807(23)00160-0. [Epub ahead of print]

Transcription factor induction of vascular blood stem cell niches in vivo.

Elliott J Hagedorn, Julie R Perlin, Rebecca J Freeman, Samuel J Wattrus, Tianxiao Han, Clara Mao, Ji Wook Kim, Inés Fernández-Maestre, Madeleine L Daily, Christopher D'Amato, Michael J Fairchild, Raquel Riquelme, Brian Li, Dana A V E Ragoonanan, Khaliun Enkhbayar, Emily L Henault, Helen G Wang, Shelby E Redfield, Samantha H Collins, Asher Lichtig, Song Yang, Yi Zhou, Balvir Kunar, Jesus Maria Gomez-Salinero, Thanh T Dinh, Junliang Pan, Karoline Holler, Henry A Feldman, Eugene C Butcher, Alexander van Oudenaarden, Shahin Rafii, J Philipp Junker, Leonard I Zon.

  The hematopoietic niche is a supportive microenvironment composed of distinct cell types, including specialized vascular endothelial cells that directly interact with hematopoietic stem and progenitor cells (HSPCs). The molecular factors that specify niche endothelial cells and orchestrate HSPC homeostasis remain largely unknown. Using multi-dimensional gene expression and chromatin accessibility analyses in zebrafish, we define a conserved gene expression signature and cis-regulatory landscape that are unique to sinusoidal endothelial cells in the HSPC niche. Using enhancer mutagenesis and transcription factor overexpression, we elucidate a transcriptional code that involves members of the Ets, Sox, and nuclear hormone receptor families and is sufficient to induce ectopic niche endothelial cells that associate with mesenchymal stromal cells and support the recruitment, maintenance, and division of HSPCs in vivo. These studies set forth an approach for generating synthetic HSPC niches, in vitro or in vivo, and for effective therapies to modulate the endogenous niche.

Keywords:  blood stem cell niche; hematopoietic development; niche endothelial cells; reprogramming; vascular endothelium; zebrafish

DOI:  https://doi.org/10.1016/j.devcel.2023.04.007
Nat Cell Biol. 2023 May 01.

Epigenetic programming defines haematopoietic stem cell fate restriction.

Yiran Meng, Joana Carrelha, Roy Drissen, Xiying Ren, Bowen Zhang, Adriana Gambardella, Simona Valletta, Supat Thongjuea, Sten Eirik Jacobsen, Claus Nerlov.

Haematopoietic stem cells (HSCs) are multipotent, but individual HSCs can show restricted lineage output in vivo. Currently, the molecular mechanisms and physiological role of HSC fate restriction remain unknown. Here we show that lymphoid fate is epigenetically but not transcriptionally primed in HSCs. In multi-lineage HSCs that produce lymphocytes, lymphoid-specific upstream regulatory elements (LymUREs) but not promoters are preferentially accessible compared with platelet-biased HSCs that do not produce lymphoid cell types, providing transcriptionally silent lymphoid lineage priming. Runx3 is preferentially expressed in multi-lineage HSCs, and reinstating Runx3 expression increases LymURE accessibility and lymphoid-primed multipotent progenitor 4 (MPP4) output in old, platelet-biased HSCs. In contrast, platelet-biased HSCs show elevated levels of epigenetic platelet-lineage priming and give rise to MPP2 progenitors with molecular platelet bias. These MPP2 progenitors generate platelets with faster kinetics and through a more direct cellular pathway compared with MPP2s derived from multi-lineage HSCs. Epigenetic programming therefore predicts both fate restriction and differentiation kinetics in HSCs.

DOI: https://doi.org/10.1038/s41556-023-01137-5
PLoS Genet. 2023 May 05. 19(5): e1010439

Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster.

Khoi Huynh, Brittny R Smith, Stuart J Macdonald, Anthony D Long.

We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred strain genetic backgrounds, seven associated with a reference quality genome assembly. We develop a method for the quantile normalization of ATAC-seq fragments and test for differences in coverage among genotypes, tissues, and their interaction at 44099 peaks throughout the euchromatic genome. For the strains with reference quality genome assemblies, we correct ATAC-seq profiles for read mis-mapping due to nearby polymorphic structural variants (SVs). Comparing coverage among genotypes without accounting for SVs results in a highly elevated rate (55%) of identifying false positive differences in chromatin state between genotypes. After SV correction, we identify 1050, 30383, and 4508 regions whose peak heights are polymorphic among genotypes, among tissues, or exhibit genotype-by-tissue interactions, respectively. Finally, we identify 3988 candidate causative variants that explain at least 80% of the variance in chromatin state at nearby ATAC-seq peaks.

DOI: https://doi.org/10.1371/journal.pgen.1010439
Gigascience. 2022 Dec 28. pii: giad026. [Epub ahead of print]12

TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors.

Markus Hoffmann, Nico Trummer, Leon Schwartz, Jakub Jankowski, Hye Kyung Lee, Lina-Liv Willruth, Olga Lazareva, Kevin Yuan, Nina Baumgarten, Florian Schmidt, Jan Baumbach, Marcel H Schulz, David B Blumenthal, Lothar Hennighausen, Markus List.

BACKGROUND: Eukaryotic gene expression is controlled by cis-regulatory elements (CREs), including promoters and enhancers, which are bound by transcription factors (TFs). Differential expression of TFs and their binding affinity at putative CREs determine tissue- and developmental-specific transcriptional activity. Consolidating genomic datasets can offer further insights into the accessibility of CREs, TF activity, and, thus, gene regulation. However, the integration and analysis of multimodal datasets are hampered by considerable technical challenges. While methods for highlighting differential TF activity from combined chromatin state data (e.g., chromatin immunoprecipitation [ChIP], ATAC, or DNase sequencing) and RNA sequencing data exist, they do not offer convenient usability, have limited support for large-scale data processing, and provide only minimal functionality for visually interpreting results.
RESULTS: We developed TF-Prioritizer, an automated pipeline that prioritizes condition-specific TFs from multimodal data and generates an interactive web report. We demonstrated its potential by identifying known TFs along with their target genes, as well as previously unreported TFs active in lactating mouse mammary glands. Additionally, we studied a variety of ENCODE datasets for cell lines K562 and MCF-7, including 12 histone modification ChIP sequencing as well as ATAC and DNase sequencing datasets, where we observe and discuss assay-specific differences.
CONCLUSION: TF-Prioritizer accepts ATAC, DNase, or ChIP sequencing and RNA sequencing data as input and identifies TFs with differential activity, thus offering an understanding of genome-wide gene regulation, potential pathogenesis, and therapeutic targets in biomedical research.

DOI: https://doi.org/10.1093/gigascience/giad026
Cancer Res. 2023 May 02. pii: CAN-22-2712. [Epub ahead of print]

β-catenin-driven differentiation is a tissue-specific epigenetic vulnerability in adrenal cancer.

Dipika R Mohan, Kleiton S Borges, Isabella Finco, Christopher R LaPensee, Juilee Rege, April L Solon, Donald W Little, Tobias Else, Madson Q Almeida, Derek Dang, James Haggerty-Skeans, April A Apfelbaum, Michelle Vinco, Alda Wakamatsu, Beatriz M P Mariani, Larissa Costa Amorim, Ana Claudia Latronico, Berenice B Mendonca, Maria Claudia N Zerbini, Elizabeth R Lawlor, Ryoma Ohi, Richard J Auchus, William E Rainey, Suely K N Marie, Thomas J Giordano, Sriram Venneti, Maria Candida Barisson Villares Fragoso, David T Breault, Antonio Marcondes Lerario, Gary D Hammer.

Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent β-catenin activating mutations. Here, we demonstrated that ACC differentiation is maintained by a balance between nuclear, tissue-specific β-catenin-containing complexes and the epigenome. On chromatin, β-catenin bound master adrenal transcription factor SF1 and hijacked the adrenocortical super-enhancer landscape to maintain differentiation in CIMP-high ACC; off chromatin, β-catenin bound histone methyltransferase EZH2. SF1/β-catenin and EZH2/β-catenin complexes present in normal adrenals persisted through all phases of ACC evolution. Pharmacologic EZH2 inhibition in CIMP-high ACC expelled SF1/β-catenin from chromatin and favored EZH2/β-catenin assembly, erasing differentiation and restraining cancer growth in vitro and in vivo. These studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-2712
iScience. 2023 Apr 21. 26(4): 106563

Bromodomain protein BRD8 regulates cell cycle progression in colorectal cancer cells through a TIP60-independent regulation of the pre-RC complex.

Kiyoshi Yamaguchi, Saya Nakagawa, Akari Saku, Yumiko Isobe, Rui Yamaguchi, Paul Sheridan, Kiyoko Takane, Tsuneo Ikenoue, Chi Zhu, Masashi Miura, Yuya Okawara, Satoru Nagatoishi, Hiroko Kozuka-Hata, Masaaki Oyama, Susumu Aikou, Yuka Ahiko, Dai Shida, Kouhei Tsumoto, Satoru Miyano, Seiya Imoto, Yoichi Furukawa.

  Bromodomain-containing protein 8 (BRD8) is a subunit of the NuA4/TIP60-histone acetyltransferase complex. Although BRD8 has been considered to act as a co-activator of the complex, its biological role remains to be elucidated. Here, we uncovered that BRD8 accumulates in colorectal cancer cells through the inhibition of ubiquitin-dependent protein degradation by the interaction with MRG domain binding protein. Transcriptome analysis coupled with genome-wide mapping of BRD8-binding sites disclosed that BRD8 transactivates a set of genes independently of TIP60, and that BRD8 regulates the expression of multiple subunits of the pre-replicative complex in concert with the activator protein-1. Depletion of BRD8 induced cell-cycle arrest at the G1 phase and suppressed cell proliferation. We have also shown that the bromodomain of BRD8 is indispensable for not only the interaction with histone H4 or transcriptional regulation but also its own protein stability. These findings highlight the importance of bromodomain as a therapeutic target.

Keywords:  Cancer systems biology; Cell biology; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2023.106563
Nat Plants. 2023 May 04.

Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation.

Xuemei Liu, Xiao Min Bie, Xuelei Lin, Menglu Li, Hongzhe Wang, Xiaoyu Zhang, Yiman Yang, Chunyan Zhang, Xian Sheng Zhang, Jun Xiao.

Genetic transformation is important for gene functional study and crop improvement. However, it is less effective in wheat. Here we employed a multi-omic analysis strategy to uncover the transcriptional regulatory network (TRN) responsible for wheat regeneration. RNA-seq, ATAC-seq and CUT&Tag techniques were utilized to profile the transcriptional and chromatin dynamics during early regeneration from the scutellum of immature embryos in the wheat variety Fielder. Our results demonstrate that the sequential expression of genes mediating cell fate transition during regeneration is induced by auxin, in coordination with changes in chromatin accessibility, H3K27me3 and H3K4me3 status. The built-up TRN driving wheat regeneration was found to be dominated by 446 key transcription factors (TFs). Further comparisons between wheat and Arabidopsis revealed distinct patterns of DNA binding with one finger (DOF) TFs in the two species. Experimental validations highlighted TaDOF5.6 (TraesCS6A02G274000) and TaDOF3.4 (TraesCS2B02G592600) as potential enhancers of transformation efficiency in different wheat varieties.

DOI: https://doi.org/10.1038/s41477-023-01406-z