scholarly journals Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation

2019 ◽  
Author(s):  
Gregory R. Keele ◽  
Bryan C. Quach ◽  
Jennifer W. Israel ◽  
Grace A. Chappell ◽  
Lauren Lewis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Genetic Variation ◽  
Zinc Finger ◽  
Genetic Regulation ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Collaborative Cross ◽  
Mouse Population ◽  
Lung And Kidney

AbstractGene transcription profiles across tissues are largely defined by the activity of regulatory elements, most of which correspond to regions of accessible chromatin. Regulatory element activity is in turn modulated by genetic variation, resulting in variable transcription rates across individuals. The interplay of these factors, however, is poorly understood. Here we characterize expression and chromatin state dynamics across three tissues—liver, lung, and kidney—in 47 strains of the Collaborative Cross (CC) mouse population, examining the regulation of these dynamics by expression quantitative trait loci (eQTL) and chromatin QTL (cQTL). QTL whose allelic effects were consistent across tissues were detected for 1,101 genes and 133 chromatin regions. Also detected were eQTL and cQTL whose allelic effects differed across tissues, including local-eQTL for Pik3c2g detected in all three tissues but with distinct allelic effects. Leveraging overlapping measurements of gene expression and chromatin accessibility on the same mice from multiple tissues, we used mediation analysis to identify chromatin and gene expression intermediates of eQTL effects. Based on QTL and mediation analyses over multiple tissues, we propose a causal model for the distal genetic regulation of Akr1e1, a gene involved in glycogen metabolism, through the zinc finger transcription factor Zfp985 and chromatin intermediates. This analysis demonstrates the complexity of transcriptional and chromatin dynamics and their regulation over multiple tissues, as well as the value of the CC and related genetic resource populations for identifying specific regulatory mechanisms within cells and tissues.Author summaryGenetic variation can drive alterations in gene expression levels and chromatin accessibility, the latter of which defines gene regulatory elements genome-wide. The same genetic variants may associate with both molecular events, and these may be connected within the same causal path: a variant that reduces promoter region chromatin accessibility, potentially by affecting transcription factor binding, may lead to reduced expression of that gene. Moreover, these causal regulatory paths can differ between tissues depending on functions and cellular activity specific to each tissue. We identify cross-tissue and tissue-selective genetic regulators of gene expression and chromatin accessibility in liver, lung, and kidney tissues using a panel of genetically diverse inbred mouse strains. Further, we identify a number of candidate causal mediators of the genetic regulation of gene expression, including a zinc finger protein that helps silence the Akr1e1 gene. Our analyses are consistent with chromatin accessibility playing a role in the regulation of transcription. Our study demonstrates the power of genetically diverse, multi-parental mouse populations, such as the Collaborative Cross, for large-scale studies of genetic drivers of gene regulation that underlie complex phenotypes, as well as identifying causal intermediates that drive variable activity of specific genes and pathways.

scholarly journals Genetic control of pluripotency epigenome determines differentiation bias in mouse embryonic stem cells

2021 ◽  
Author(s):  
Candice Byers ◽  
Catrina Spruce ◽  
Haley J. Fortin ◽  
Anne Czechanski ◽  
Steven C. Munger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Cell Fate ◽  
Genetic Regulation ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Embryoid Bodies ◽  
Cell Fate Decisions

AbstractGenetically diverse pluripotent stem cells (PSCs) display varied, heritable responses to differentiation cues in the culture environment. By harnessing these disparities through derivation of embryonic stem cells (ESCs) from the BXD mouse genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, we demonstrate genetically determined biases in lineage commitment and identify major regulators of the pluripotency epigenome. Upon transition to formative pluripotency using epiblast-like cells (EpiLCs), B6 quickly dissolves naïve networks adopting gene expression modules indicative of neuroectoderm lineages; whereas D2 retains aspects of naïve pluripotency with little bias in differentiation. Genetic mapping identifies 6 major trans-acting loci co-regulating chromatin accessibility and gene expression in ESCs and EpiLCs, indicating a common regulatory system impacting cell state transition. These loci distally modulate occupancy of pluripotency factors, including TRIM28, P300, and POU5F1, at hundreds of regulatory elements. One trans-acting locus on Chr 12 primarily impacts chromatin accessibility in ESCs; while in EpiLCs the same locus subsequently influences gene expression, suggesting early chromatin priming. Consequently, the distal gene targets of this locus are enriched for neurogenesis genes and were more highly expressed when cells carried B6 haplotypes at this Chr 12 locus, supporting genetic regulation of biases in cell fate. Spontaneous formation of embryoid bodies validated this with B6 showing a propensity towards neuroectoderm differentiation and D2 towards definitive endoderm, confirming the fundamental importance of genetic variation influencing cell fate decisions.

Enhancer Landscapes Reveal Transcription Factor Network Dependencies in Chronic Lymphocytic Leukemia

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 436-436 ◽  
Author(s):  
Christopher J. Ott ◽  
Alexander J. Federation ◽  
Siddha Kasar ◽  
Josephine L. Klitgaard ◽  
Stacey M. Fernandes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Chronic Lymphocytic Leukemia ◽  
Genome Sequencing ◽  
Chromatin Structure ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Lymphocytic Leukemia ◽  
Protein Coding ◽  
Transcription Factor Network

Abstract Genome sequencing efforts of chronic lymphocytic leukemia have revealed mutations that disrupt protein-coding elements of the genome (Puente et al, 2011; Wang et al, 2011; Landau et al, 2013). Recently, comprehensive whole-genome sequencing efforts have begun to reveal the genetic aberrations that occur outside of protein-coding exons, many that may perturb gene regulatory sites (Puente et al, 2015). These include enhancer elements that make physical contact with gene promoters to regulate gene expression in a cell-type specific manner. While mutations certainly promote CLL leukemogenesis, epigenomic alterations may also play an important role in facilitating disease progression and maintenance by inducing the gene expression aberrations that have long been observed in CLL. Epigenomic alterations include chromatin structure changes that facilitate altered transcription and chromatin factor recruitment to regulatory elements. While comprehensive genome-wide DNA methylation studies have been performed on human cancers and normal cell counterparts including CLL, other comprehensive studies of cancer epigenomes have been lacking. We have completed an analysis of chromatin structures in a cohort of primary chronic lymphocytic leukemia (CLL) samples with comparisons to normal CD19+ B lymphocytes (n = 18 CLL samples, n = 5 normal B lymphocyte samples). We used chromatin accessibility assays (ATAC-seq) and genome-wide enhancer mapping (H3K27ac ChIP-seq) to comprehensively define the transcriptionally active chromatin landscape of CLL. We have discovered greater than 15,000 novel regulatory elements when compared to previously annotated regulatory elements. Moreover, sites within the loci of several hundred genes were found to have large regions of gained chromatin accessibility and H3K27 acetylation, revealing the appearance of aberrant enhancer activity. These gained enhancer elements correspond with increased gene expression and are found at gene loci such as LEF1, PLCG1, CTLA4, and ITGB1. We have also systematically identified the super-enhancers of CLL - large complex regulatory regions that possess unique tissue-specific regulatory capabilities. Many of these super-enhancers are found in normal B lymphocytes, yet the super-enhancer at the ITGB1 and LEF1 loci are CLL-specific and may be considered to facilitate leukemia-specific expression. We have found CLL-specific enhancers are also significantly associated with annotated CLL risk variants, and have identified enhancer-associated SNPs found within CLL-risk loci predicted to disrupt transcription factor binding sites. These include SNPs at the IRF8 and LEF1 locithat lead to the creation and destruction of SMAD4 and RXRA binding sites, respectively. Additionally, we have analyzed whole-genome sequencing data from a subset of our sample cohort. Mutational hotspots in the CXCR4 and BACH2 promoters occur within open, acetylated regions. Moreover, we discover recurrent mutations in enhancers of the ETS1 and ST6GAL1 locus that have not been previously annotated. Using a transcription factor network modeling approach, we used these global chromatin structure characteristics to determine networks that are highly active in CLL. We find that transcription factors such as NFATc1, E2F5, and NR3C2 are among the most interconnected transcription factors of the CLL genome, and their connectivity is significantly higher in CLL cells compared to normal B cells. In contrast, network profiling of CLL cells predicts loss of MXI1 connectivity, a negative regulator of the MYC oncogene. By treating cells with specific pharmacological inhibitors of NFAT family members including cyclosporin and FK506, we are able to reduce NFAT-mediated network connectivity, resulting in a selective loss of NFAT-bound enhancers. This leads to CLL cell death in vitro of both cell lines and primary CLL patient samples. Our results reveal the unique chromatin structure landscape of CLL for the first time, and identify the CLL-specific enhancer elements that confer the transcriptional dysregulation that has long been observed in this disease. Use of these chromatin structure analyses and enhancer landscapes has allowed us to construct the intrinsic transcription factor network of CLL, and determine a particular dependency on NFAT signaling for cell survival. Disclosures No relevant conflicts of interest to declare.

scholarly journals Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs

2020 ◽  
Author(s):  
Swann Floc’hlay ◽  
Emily Wong ◽  
Bingqing Zhao ◽  
Rebecca R. Viales ◽  
Morgane Thomas-Chollier ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Transcription Factors ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cis Acting ◽  
Dna Mutations ◽  
Allele Specific ◽  
Regulatory Dna ◽  
The Impact

AbstractPrecise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequence, and chromatin. How DNA mutations affecting any one of these regulatory ‘layers’ is buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eight Drosophila crosses, at three embryonic stages, yielding a comprehensive dataset of 240 samples spanning multiple regulatory layers. Genetic variation in cis-regulatory elements is common, highly heritable, and surprisingly consistent in its effects across embryonic stages. Much of this variation does not propagate to gene expression. When it does, it acts through H3K4me3 or alternatively through chromatin accessibility and H3K27ac. The magnitude and evolutionary impact of mutations is influenced by a genes’ regulatory complexity (i.e. enhancer number), with transcription factors being most robust to cis-acting, and most influenced by trans-acting, variation. Overall, the impact of genetic variation on regulatory phenotypes appears context-dependent even within the constraints of embryogenesis.

scholarly journals FGF signalling regulates enhancer activation during ear progenitor induction

2019 ◽  
Author(s):  
Monica Tambalo ◽  
Maryam Anwar ◽  
Mohi Ahmed ◽  
Andrea Streit
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
De Novo ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Fibroblast Growth ◽  
Active Chromatin ◽  
Histone Acetyl Transferase ◽  
Fgf Signalling ◽  
Genomic Regions

ABSTRACTThe fibroblast growth factor pathway is essential for inner ear induction in many vertebrates, however how it regulates the chromatin landscape to coordinate the activation of otic genes remains unclear. Here we show that FGF exposure of sensory progenitors leads to rapid deposition of active chromatin marks H3K27ac near hundreds of FGF-responsive, otic-epibranchial progenitor (OEP) genes, while H3K27ac is depleted in the vicinity of non-otic genes. Genomic regions that gain H3K27ac act as cis-regulatory elements controlling OEP gene expression in time and space and define a unique transcription factor signature likely to control their activity. Finally, we provide evidence that in response to FGF signalling the transcription factor dimer AP1 recruits the histone acetyl transferase p300 to OEP enhancers and that de novo acetylation is required for subsequent expression of OEP genes. Thus, during ear induction FGF signalling modifies the chromatin landscape to promote enhancer activation and chromatin accessibility.

scholarly journals Profiling of chromatin accessibility across Aspergillus species and identification of transcription factor binding sites in the Aspergillus genome using filamentous fungi ATAC-seq

2019 ◽  
Author(s):  
Lianggang Huang ◽  
Xuejie Li ◽  
Liangbo Dong ◽  
Bin Wang ◽  
Li Pan
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Filamentous Fungi ◽  
Binding Sites ◽  
Regulatory Elements ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Factor Binding ◽  
Tn5 Transposase

AbstractTo identify cis-regulatory elements (CREs) and motifs of TF binding is an important step in understanding the regulatory functions of TF binding and gene expression. The lack of experimentally determined and computationally inferred data means that the genome-wide CREs and TF binding sites (TFBs) in filamentous fungi remain unknown. ATAC-seq is a technique that provides a high-resolution measurement of chromatin accessibility to Tn5 transposase integration. In filamentous fungi, the existence of cell walls and the difficulty in purifying nuclei have prevented the routine application of this technique. Herein, we modified the ATAC-seq protocol in filamentous fungi to identify and map open chromatin and TF-binding sites on a genome-scale. We applied the assay for ATAC-seq among different Aspergillus species, during different culture conditions, and among TF-deficient strains to delineate open chromatin regions and TFBs across each genome. The syntenic orthologues regions and differential changes regions of chromatin accessibility were responsible for functional conservative regulatory elements and differential gene expression in the Aspergillus genome respectively. Importantly, 17 and 15 novel transcription factor binding motifs that were enriched in the genomic footprints identified from ATAC-seq data of A. niger, were verified in vivo by our artificial synthetic minimal promoter system, respectively. Furthermore, we first confirmed the strand-specific patterns of Tn5 transposase around the binding sites of known TFs by comparing ATAC-seq data of TF-deficient strains with the data from a wild-type strain.

scholarly journals MARGE: Mutation Analysis for Regulatory Genomic Elements

2018 ◽  
Author(s):  
Verena M. Link ◽  
Casey E. Romanoski ◽  
Dirk Metzler ◽  
Christopher K. Glass
Keyword(s):  
Transcription Factor ◽  
Genetic Variation ◽  
Transcription Factors ◽  
Regulatory Elements ◽  
Peritoneal Macrophages ◽  
Chromatin Accessibility ◽  
Natural Genetic Variation ◽  
Binding Data ◽  
Great Utility ◽  
Collaborative Interactions

AbstractCell-specific patterns of gene expression are determined by combinatorial actions of sequence-specific transcription factors at cis-regulatory elements. Studies indicate that relatively simple combinations of lineage-determining transcription factors (LDTFs) play dominant roles in the selection of enhancers that establish cell identities and functions. LDTFs require collaborative interactions with additional transcription factors to mediate enhancer function, but the identities of these factors are often unknown. We have shown that natural genetic variation between individuals has great utility for discovering collaborative transcription factors. Here, we introduce MARGE (Mutation Analysis of Regulatory Genomic Elements), the first publicly available suite of software tools that integrates genome-wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. MARGE is optimized to work with chromatin accessibility assays (such as ATAC-seq or DNase I hypersensitivity), as well as transcription factor binding data collected by ChlP-seq. Herein, we provide investigators with rationale for each step in the MARGE pipeline and key differences for analysis of datasets with different experimental designs. We demonstrate the utility of MARGE using mouse peritoneal macrophages, liver cells, and human lymphoblastoid cells. MARGE provides a powerful tool to identify combinations of cell type-specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.

scholarly journals Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karolina Stępniak ◽  
Magdalena A. Machnicka ◽  
Jakub Mieczkowski ◽  
Anna Macioszek ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Molecular Mechanisms ◽  
Genome Mapping ◽  
Malignant Gliomas ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Multiple Tumor ◽  
Genes Encoding ◽  
Methylation Patterns

AbstractChromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

scholarly journals Leveraging epigenetics to enhance the efficacy of immunotherapy

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Jonathan D. Licht ◽  
Richard L. Bennett
Keyword(s):  
Gene Expression ◽  
Clinical Trials ◽  
Antigen Presentation ◽  
Tumor Cells ◽  
Immune Evasion ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Epigenetic Modifications ◽  
Main Body ◽  
Epigenetic Mechanisms

Abstract Background Epigenetic mechanisms regulate chromatin accessibility patterns that govern interaction of transcription machinery with genes and their cis-regulatory elements. Mutations that affect epigenetic mechanisms are common in cancer. Because epigenetic modifications are reversible many anticancer strategies targeting these mechanisms are currently under development and in clinical trials. Main body Here we review evidence suggesting that epigenetic therapeutics can deactivate immunosuppressive gene expression or reprogram tumor cells to activate antigen presentation mechanisms. In addition, the dysregulation of epigenetic mechanisms commonly observed in cancer may alter the immunogenicity of tumor cells and effectiveness of immunotherapies. Conclusions Therapeutics targeting epigenetic mechanisms may be helpful to counter immune evasion and improve the effectiveness of immunotherapies.

scholarly journals The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
José L Ruiz ◽  
Lisa C Ranford-Cartwright ◽  
Elena Gómez-Díaz
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Anopheles Gambiae ◽  
Mosquito Control ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Malaria Vectors ◽  
Specific Gene ◽  
Mosquito Vector ◽  
Human Malaria

Abstract Anopheles gambiae mosquitoes are primary human malaria vectors, but we know very little about their mechanisms of transcriptional regulation. We profiled chromatin accessibility by the assay for transposase-accessible chromatin by sequencing (ATAC-seq) in laboratory-reared A. gambiae mosquitoes experimentally infected with the human malaria parasite Plasmodium falciparum. By integrating ATAC-seq, RNA-seq and ChIP-seq data, we showed a positive correlation between accessibility at promoters and introns, gene expression and active histone marks. By comparing expression and chromatin structure patterns in different tissues, we were able to infer cis-regulatory elements controlling tissue-specific gene expression and to predict the in vivo binding sites of relevant transcription factors. The ATAC-seq assay also allowed the precise mapping of active regulatory regions, including novel transcription start sites and enhancers that were annotated to mosquito immune-related genes. Not only is this study important for advancing our understanding of mechanisms of transcriptional regulation in the mosquito vector of human malaria, but the information we produced also has great potential for developing new mosquito-control and anti-malaria strategies.

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