bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–01–02
fourteen papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer.
  2. TRACE generates fluorescent human reporter cell lines to characterize epigenetic pathways.
  3. Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells.
  4. RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins.
  5. Cobolt: integrative analysis of multimodal single-cell sequencing data.
  6. Histone variant H3.3 maintains adult haematopoietic stem cell homeostasis by enforcing chromatin adaptability.
  7. Genomic environments scale the activities of diverse core promoters.
  8. Epigenetic features improve TALE target prediction.
  9. The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication.
  10. Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin.
  11. HiCORE: Hi-C Analysis for Identification of Core Chromatin Looping Regions with Higher Resolution.
  12. Cell type-aware analysis of RNA-seq data.
  13. Single-cell chromatin accessibility and lipid profiling reveals SCD1-dependent metabolic shift in adipocytes induced by bariatric surgery.
  14. A transcription factor signature predicts the survival of patients with adrenocortical carcinoma.
  1. Genes Dev. 2021 Dec 30.
    Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer.
    Harshabad Singh, Davide Seruggia, Shariq Madha, Madhurima Saxena, Ankur K Nagaraja, Zhong Wu, Jin Zhou, Aaron J Huebner, Adrianna Maglieri, Juliette Wezenbeek, Konrad Hochedlinger, Stuart H Orkin, Adam J Bass, Jason L Hornick, Ramesh A Shivdasani.
      Barrett's esophagus (BE) and gastric intestinal metaplasia are related premalignant conditions in which areas of human stomach epithelium express mixed gastric and intestinal features. Intestinal transcription factors (TFs) are expressed in both conditions, with unclear causal roles and cis-regulatory mechanisms. Ectopic CDX2 reprogrammed isogenic mouse stomach organoid lines to a hybrid stomach-intestinal state transcriptionally similar to clinical metaplasia; squamous esophageal organoids resisted this CDX2-mediated effect. Reprogramming was associated with induced activity at thousands of previously inaccessible intestine-restricted enhancers, where CDX2 occupied DNA directly. HNF4A, a TF recently implicated in BE pathogenesis, induced weaker intestinalization by binding a novel shadow Cdx2 enhancer and hence activating Cdx2 expression. CRISPR/Cas9-mediated germline deletion of that cis-element demonstrated its requirement in Cdx2 induction and in the resulting activation of intestinal genes in stomach cells. dCas9-conjugated KRAB repression mapped this activity to the shadow enhancer's HNF4A binding site. Altogether, we show extensive but selective recruitment of intestinal enhancers by CDX2 in gastric cells and that HNF4A-mediated ectopic CDX2 expression in the stomach occurs through a conserved shadow cis-element. These findings identify mechanisms for TF-driven intestinal metaplasia and a likely pathogenic TF hierarchy.
    Keywords:  Barrett's esophagus; CDX2; HNF4A; gastric intestinal metaplasia; transcriptional control of cell identity
    DOI:  https://doi.org/10.1101/gad.348983.121
  2. Mol Cell. 2021 Dec 16. pii: S1097-2765(21)01037-6. [Epub ahead of print]
    TRACE generates fluorescent human reporter cell lines to characterize epigenetic pathways.
    Iva A Tchasovnikarova, Sharon K Marr, Manashree Damle, Robert E Kingston.
      Genetically encoded biosensors are powerful tools to monitor cellular behavior, but the difficulty in generating appropriate reporters for chromatin factors hampers our ability to dissect epigenetic pathways. Here, we present TRACE (transgene reporters across chromatin environments), a high-throughput, genome-wide technique to generate fluorescent human reporter cell lines responsive to manipulation of epigenetic factors. By profiling GFP expression from a large pool of individually barcoded lentiviral integrants in the presence and absence of a perturbation, we identify reporters responsive to pharmacological inhibition of the histone lysine demethylase LSD1 and genetic ablation of the PRC2 subunit SUZ12. Furthermore, by manipulating the HIV-1 host factor LEDGF through targeted deletion or fusion to chromatin reader domains, we alter lentiviral integration site preferences, thus broadening the types of chromatin examined by TRACE. The phenotypic reporters generated through TRACE will allow the genetic interrogation of a broad range of epigenetic pathways, furthering our mechanistic understanding of chromatin biology.
    Keywords:  LEDGF; PRC2; Polycomb; SUZ12; TRACE; TRIP; chromatin; epigenetics; fluorescent reporter; lentiviral integration
    DOI:  https://doi.org/10.1016/j.molcel.2021.11.035
  3. Epigenetics Chromatin. 2021 Dec 27. 14(1): 58
    Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells.
    Claudia Baumann, Xiangyu Zhang, Ling Zhu, Yuhong Fan, Rabindranath De La Fuente.
      Directed differentiation of mouse embryonic stem cells (mESCs) or induced pluripotent stem cells (iPSCs) provides powerful models to dissect the molecular mechanisms leading to the formation of specific cell lineages. Treatment with histone deacetylase inhibitors can significantly enhance the efficiency of directed differentiation. However, the mechanisms are not well understood. Here, we use CUT&RUN in combination with ATAC-seq to determine changes in both histone modifications and genome-wide chromatin accessibility following valproic acid (VPA) exposure. VPA induced a significant increase in global histone H3 acetylation (H3K56ac), a core histone modification affecting nucleosome stability, as well as enrichment at loci associated with cytoskeletal organization and cellular morphogenesis. In addition, VPA altered the levels of linker histone H1 subtypes and the total histone H1/nucleosome ratio indicative of initial differentiation events. Notably, ATAC-seq analysis revealed changes in chromatin accessibility of genes involved in regulation of CDK serine/threonine kinase activity and DNA duplex unwinding. Importantly, changes in chromatin accessibility were evident at several key genomic loci, such as the pluripotency factor Lefty, cardiac muscle troponin Tnnt2, and the homeodomain factor Hopx, which play critical roles in cardiomyocyte differentiation. Massive parallel transcription factor (TF) footprinting also indicates an increased occupancy of TFs involved in differentiation toward mesoderm and endoderm lineages and a loss of footprints of POU5F1/SOX2 pluripotency factors following VPA treatment. Our results provide the first genome-wide analysis of the chromatin landscape following VPA-induced differentiation in mESCs and provide new mechanistic insight into the intricate molecular processes that govern departure from pluripotency and early lineage commitment.
    Keywords:  ATAC-seq; Chromatin accessibility; Differentiation; Embryonic stem cells; HDAC; HDACi; Next-generation sequencing; VPA
    DOI:  https://doi.org/10.1186/s13072-021-00432-5
  4. Proc Natl Acad Sci U S A. 2022 Jan 04. pii: e2116222119. [Epub ahead of print]119(1):
    RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins.
    Alexey A Gavrilov, Rinat I Sultanov, Mikhail D Magnitov, Aleksandra A Galitsyna, Erdem B Dashinimaev, Erez Lieberman Aiden, Sergey V Razin.
      Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA-DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA-chromatin interactions. Here, we introduce RedChIP, a technique combining RNA-DNA proximity ligation and chromatin immunoprecipitation for identifying RNA-chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of cis- and trans-acting ncRNAs enriched at Polycomb- and CTCF-binding sites in human cells, which may be involved in Polycomb-mediated gene repression and CTCF-dependent chromatin looping. By providing a protein-centric view of RNA-DNA interactions, RedChIP represents an important tool for studies of nuclear ncRNAs.
    Keywords:  CTCF; Polycomb; RNA–DNA interactome; cell nucleus; noncoding RNA
    DOI:  https://doi.org/10.1073/pnas.2116222119
  5. Genome Biol. 2021 Dec 28. 22(1): 351
    Cobolt: integrative analysis of multimodal single-cell sequencing data.
    Boying Gong, Yun Zhou, Elizabeth Purdom.
      A growing number of single-cell sequencing platforms enable joint profiling of multiple omics from the same cells. We present Cobolt, a novel method that not only allows for analyzing the data from joint-modality platforms, but provides a coherent framework for the integration of multiple datasets measured on different modalities. We demonstrate its performance on multi-modality data of gene expression and chromatin accessibility and illustrate the integration abilities of Cobolt by jointly analyzing this multi-modality data with single-cell RNA-seq and ATAC-seq datasets.
    Keywords:  Integration; Multi-omics; Single cell
    DOI:  https://doi.org/10.1186/s13059-021-02556-z
  6. Nat Cell Biol. 2021 Dec 27.
    Histone variant H3.3 maintains adult haematopoietic stem cell homeostasis by enforcing chromatin adaptability.
    Peipei Guo, Ying Liu, Fuqiang Geng, Andrew W Daman, Xiaoyu Liu, Liangwen Zhong, Arjun Ravishankar, Raphael Lis, José Gabriel Barcia Durán, Tomer Itkin, Fanying Tang, Tuo Zhang, Jenny Xiang, Koji Shido, Bi-Sen Ding, Duancheng Wen, Steven Z Josefowicz, Shahin Rafii.
      Histone variants and the associated post-translational modifications that govern the stemness of haematopoietic stem cells (HSCs) and differentiation thereof into progenitors (HSPCs) have not been well defined. H3.3 is a replication-independent H3 histone variant in mammalian systems that is enriched at both H3K4me3- and H3K27me3-marked bivalent genes as well as H3K9me3-marked endogenous retroviral repeats. Here we show that H3.3, but not its chaperone Hira, prevents premature HSC exhaustion and differentiation into granulocyte-macrophage progenitors. H3.3-null HSPCs display reduced expression of stemness and lineage-specific genes with a predominant gain of H3K27me3 marks at their promoter regions. Concomitantly, loss of H3.3 leads to a reduction of H3K9me3 marks at endogenous retroviral repeats, opening up binding sites for the interferon regulatory factor family of transcription factors, allowing the survival of rare, persisting H3.3-null HSCs. We propose a model whereby H3.3 maintains adult HSC stemness by safeguarding the delicate interplay between H3K27me3 and H3K9me3 marks, enforcing chromatin adaptability.
    DOI:  https://doi.org/10.1038/s41556-021-00795-7
  7. Genome Res. 2021 Dec 27.
    Genomic environments scale the activities of diverse core promoters.
    Clarice K Y Hong, Barak A Cohen.
      A classical model of gene regulation is that enhancers provide specificity whereas core promoters provide a modular site for the assembly of the basal transcriptional machinery. However, examples of core promoter specificity have led to an alternate hypothesis in which specificity is achieved by core promoters with different sequence motifs that respond differently to genomic environments containing different enhancers and chromatin landscapes. To distinguish between these models, we measured the activities of hundreds of diverse core promoters in four different genomic locations and, in a complementary experiment, six different core promoters at thousands of locations across the genome. Although genomic locations had large effects on expression, the intrinsic activities of different classes of promoters were preserved across genomic locations, suggesting that core promoters are modular regulatory elements whose activities are independently scaled up or down by different genomic locations. This scaling of promoter activities is nonlinear and depends on the genomic location and the strength of the core promoter. Our results support the classical model of regulation in which diverse core promoter motifs set the intrinsic strengths of core promoters, which are then amplified or dampened by the activities of their genomic environments.
    DOI:  https://doi.org/10.1101/gr.276025.121
  8. BMC Genomics. 2021 Dec 29. 22(1): 914
    Epigenetic features improve TALE target prediction.
    Annett Erkes, Stefanie Mücke, Maik Reschke, Jens Boch, Jan Grau.
       BACKGROUND: The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box.
    RESULTS: To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets.
    CONCLUSIONS: Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs.
    Keywords:  Chromatin; Computational prediction; DNA methylation; Transcription activator-like effector
    DOI:  https://doi.org/10.1186/s12864-021-08210-z
  9. Genes Dev. 2021 Dec 30.
    The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication.
    Jonathan P Karr, John J Ferrie, Robert Tjian, Xavier Darzacq.
      How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle-one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer-promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
    Keywords:  3D genome; coactivator; enhancer; gene regulation; p300; transcription
    DOI:  https://doi.org/10.1101/gad.349160.121
  10. Genome Res. 2021 Dec 28.
    Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin.
    Hossein Salari, Marco Di Stefano, Daniel Jost.
      Chromosome organization and dynamics are involved in regulating many fundamental processes such as gene transcription and DNA repair. Experiments unveiled that chromatin motion is highly heterogeneous inside cell nuclei, ranging from a liquid-like, mobile state to a gel-like, rigid regime. Using polymer modeling, we investigate how these different physical states and dynamical heterogeneities may emerge from the same structural mechanisms. We found that the formation of topologically associating domains (TADs) is a key driver of chromatin motion heterogeneity. In particular, we showed that the local degree of compaction of the TAD regulates the transition from a weakly compact, fluid state of chromatin to a more compact, gel state exhibiting anomalous diffusion and coherent motion. Our work provides a comprehensive study of chromosome dynamics and a unified view of chromatin motion enabling interpretation of the wide variety of dynamical behaviors observed experimentally across different biological conditions, suggesting that the "liquid" or "solid" state of chromatin are in fact two sides of the same coin.
    DOI:  https://doi.org/10.1101/gr.275827.121
  11. Mol Cells. 2021 12 31. 44(12): 883-892
    HiCORE: Hi-C Analysis for Identification of Core Chromatin Looping Regions with Higher Resolution.
    Hongwoo Lee, Pil Joon Seo.
      Genome-wide chromosome conformation capture (3C)- based high-throughput sequencing (Hi-C) has enabled identification of genome-wide chromatin loops. Because the Hi-C map with restriction fragment resolution is intrinsically associated with sparsity and stochastic noise, Hi-C data are usually binned at particular intervals; however, the binning method has limited reliability, especially at high resolution. Here, we describe a new method called HiCORE, which provides simple pipelines and algorithms to overcome the limitations of single-layered binning and predict core chromatin regions with three-dimensional physical interactions. In this approach, multiple layers of binning with slightly shifted genome coverage are generated, and interacting bins at each layer are integrated to infer narrower regions of chromatin interactions. HiCORE predicts chromatin looping regions with higher resolution, both in human and Arabidopsis genomes, and contributes to the identification of the precise positions of potential genomic elements in an unbiased manner.
    Keywords:  3D genome; CCCTC-binding factor; CTCF; Hi-C; binning method; chromatin loop
    DOI:  https://doi.org/10.14348/molcells.2021.0014
  12. Nat Comput Sci. 2021 Apr;1(4): 253-261
    Cell type-aware analysis of RNA-seq data.
    Chong Jin, Mengjie Chen, Danyu Lin, Wei Sun.
      Most tissue samples are composed of different cell types. Differential expression analysis without accounting for cell type composition cannot separate the changes due to cell type composition or cell type-specific expression. We propose a computational framework to address these limitations: Cell Type Aware analysis of RNA-seq (CARseq). CARseq employs a negative binomial distribution that appropriately models the count data from RNA-seq experiments. Simulation studies show that CARseq has substantially higher power than a linear model-based approach and it also provides more accurate estimate of the rankings of differentially expressed genes. We have applied CARseq to compare gene expression of schizophrenia/autism subjects versus controls, and identified the cell types underlying the difference and similarities of these two neuron-developmental diseases. Our results are consistent with the results from differential expression analysis using single cell RNA-seq data.
    DOI:  https://doi.org/10.1038/s43588-021-00055-6
  13. PLoS One. 2021 ;16(12): e0261783
    Single-cell chromatin accessibility and lipid profiling reveals SCD1-dependent metabolic shift in adipocytes induced by bariatric surgery.
    Blaine Harlan, Hui Gyu Park, Roman Spektor, Bethany Cummings, J Thomas Brenna, Paul D Soloway.
      Obesity promotes type 2 diabetes and cardiometabolic pathologies. Vertical sleeve gastrectomy (VSG) is used to treat obesity resulting in long-term weight loss and health improvements that precede weight loss; however, the mechanisms underlying the immediate benefits remain incompletely understood. Because adipose plays a crucial role in energy homeostasis and utilization, we hypothesized that VSG exerts its influences, in part, by modulating adipose functional states. We applied single-cell ATAC sequencing and lipid profiling to inguinal and epididymal adipose depots from mice that received sham surgery or VSG. We observed depot-specific cellular composition and chromatin accessibility patterns that were altered by VSG. Specifically, accessibility at Scd1, a fatty acid desaturase, was substantially reduced after VSG in mature adipocytes of inguinal but not epididymal depots. This was accompanied by reduced accumulation of SCD1-produced unsaturated fatty acids. Given these findings and reports that reductions in Scd1 attenuate obesity and insulin resistance our results suggest VSG exerts its beneficial effects through an inguinal depot-specific reduction of SCD1 activity.
    DOI:  https://doi.org/10.1371/journal.pone.0261783
  14. PeerJ. 2021 ;9 e12433
    A transcription factor signature predicts the survival of patients with adrenocortical carcinoma.
    Jianyu Zhao, Bo Liu, Xiaoping Li.
       Background: Adrenocortical carcinoma (ACC) is a rare endocrine cancer that manifests as abdominal masses and excessive steroid hormone levels and is associated with poor clinical outcomes. Transcription factors (TFs) deregulation is found to be involved in adrenocortical tumorigenesis and cancer progression. This study aimed to construct a TF-based prognostic signature for the prediction of survival of ACC patients.
    Methods: The gene expression profile and clinical information for ACC patients were downloaded from The Cancer Genome Atlas (TCGA, training set) and Gene Expression Omnibus (GEO, validation set) datasets after obtained 1,639 human TFs from a previously published study. The univariate Cox regression analysis was applied to identify the survival-related TFs and the LASSO Cox regression was conducted to construct the TF signature based on these survival-associated TFs candidates. Then, multivariate analysis was used to reveal the independent prognostic factors. Furthermore, Gene Set Enrichment Analysis (GSEA) was performed to analyze the significance of the TFs constituting the prognostic signature.
    Results: LASSO Cox regression and multivariate Cox regression identified a 13-TF prognostic signature comprised of CREB3L3, NR0B1, CENPA, FOXM1, E2F2, MYBL2, HOXC11, ZIC2, ZNF282, DNMT1, TCF3, ELK4, and KLF6. The risk score based on the TF signature could classify patients into low- and high-risk groups. Kaplan-Meier analyses showed that patients in the high-risk group had significantly shorter overall survival (OS) compared to the low-risk patients. Receiver operating characteristic (ROC) curves showed that the prognostic signature predicted the OS of ACC patients with good sensitivity and specificity both in the training set (AUC > 0.9) and the validation set (AUC > 0.7). Furthermore, the TF-risk score was an independent prognostic factor.
    Conclusions: Taken together, we identified a 13-TF prognostic marker to predict OS in ACC patients.
    Keywords:  Adrenocortical carcinoma; GEO; Prognosis; TCGA; Transcription factor
    DOI:  https://doi.org/10.7717/peerj.12433
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