Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages

Alveolar macrophages function in innate and adaptive immunity, wound healing, and homeostasis in the lungs dependent on tissue-specific gene expression under epigenetic regulation. The functional diversity of tissue resident macrophages, despite their common myeloid lineage, highlights the need to study tissue-specific regulatory elements that control gene expression. Increasing evidence supports the hypothesis that subtle genetic changes alter sheep macrophage response to important production pathogens and zoonoses, for example, viruses like small ruminant lentiviruses and bacteria like Coxiella burnetii. Annotation of transcriptional regulatory elements will aid researchers in identifying genetic mutations of immunological consequence. Here we report the first genome-wide survey of regulatory elements in any sheep immune cell, utilizing alveolar macrophages. We assayed histone modifications and CTCF enrichment by chromatin immunoprecipitation with deep sequencing (ChIP-seq) in two sheep to determine cis-regulatory DNA elements and chromatin domain boundaries that control immunity-related gene expression. Histone modifications included H3K4me3 (denoting active promoters), H3K27ac (active enhancers), H3K4me1 (primed and distal enhancers), and H3K27me3 (broad silencers). In total, we identified 248,674 reproducible regulatory elements, which allowed assignment of putative biological function in macrophages to 12% of the sheep genome. Data exceeded the FAANG and ENCODE standards of 20 million and 45 million useable fragments for narrow and broad marks, respectively. Active elements showed consensus with RNA-seq data and were predictive of gene expression in alveolar macrophages from the publicly available Sheep Gene Expression Atlas. Silencer elements were not enriched for expressed genes, but rather for repressed developmental genes. CTCF enrichment enabled identification of 11,000 chromatin domains with mean size of 258 kb. To our knowledge, this is the first report to use immunoprecipitated CTCF to determine putative topological domains in sheep immune cells. Furthermore, these data will empower phenotype-associated mutation discovery since most causal variants are within regulatory elements.

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Classification of topological domains based on gene expression and regulation

Genome ◽

10.1139/gen-2013-0111 ◽

2013 ◽

Vol 56 (7) ◽

pp. 415-423 ◽

Cited By ~ 2

Author(s):

Jingjing Zhao ◽

Hongbo Shi ◽

Nadav Ahituv

Keyword(s):

Gene Expression ◽

Gene Ontology ◽

Tissue Type ◽

Specific Gene ◽

Gene Expression And Regulation ◽

Genome Chromosome ◽

Chromosome Conformation ◽

Topological Domains ◽

Tissue Specific ◽

Mouse Tissues

Tissue-specific gene expression is thought to be one of the major forces shaping mammalian gene order. A recent study that used whole-genome chromosome conformation assays has shown that the mammalian genome is divided into specific topological domains that are shared between different tissues and organisms. Here, we wanted to assess whether gene expression and regulation are involved in shaping these domains and can be used to classify them. We analyzed gene expression and regulation levels in these domains by using RNA-seq and enhancer-associated ChIP-seq datasets for 17 different mouse tissues. We found 162 domains that are active (high gene expression and regulation) in all 17 tissues. These domains are significantly shorter, contain less repeats, and have more housekeeping genes. In contrast, we found 29 domains that are inactive (low gene expression and regulation) in all analyzed tissues and are significantly longer, have more repeats, and gene deserts. Tissue-specific active domains showed some correlation with tissue-type and gene ontology. Domain temporal gene regulation and expression differences also displayed some gene ontology terms fitting their temporal function. Combined, our results provide a catalog of shared and tissue-specific topological domains and suggest that gene expression and regulation could have a role in shaping them.

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Differential evolution in 3′UTRs leads to specific gene expression in Staphylococcus

Nucleic Acids Research ◽

10.1093/nar/gkaa047 ◽

2020 ◽

Vol 48 (5) ◽

pp. 2544-2563 ◽

Cited By ~ 2

Author(s):

Pilar Menendez-Gil ◽

Carlos J Caballero ◽

Arancha Catalan-Moreno ◽

Naiara Irurzun ◽

Inigo Barrio-Hernandez ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Bacterial Species ◽

Regulatory Elements ◽

Specific Gene ◽

Species Differentiation ◽

Orthologous Genes ◽

Genome Wide ◽

Sequence Variations ◽

Species Specific

Abstract The evolution of gene expression regulation has contributed to species differentiation. The 3′ untranslated regions (3′UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3′UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3′UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3′UTR of orthologous genes and demonstrated that 3′UTR sequence variations affect protein production. This suggested that species-specific functional 3′UTRs might be specifically selected during evolution. 3′UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3′UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3′UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3′UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.

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Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0022 ◽

2013 ◽

Vol 368 (1632) ◽

pp. 20130022 ◽

Cited By ~ 13

Author(s):

Noboru Jo Sakabe ◽

Marcelo A. Nobrega

Keyword(s):

Gene Expression ◽

Target Genes ◽

Expression Patterns ◽

Dna Interaction ◽

Regulatory Elements ◽

Specific Gene ◽

Genome Wide ◽

Identify Transcription Factor ◽

Specific Proteins ◽

Species Specific

The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis -regulatory elements) in entire genomes. Comparing protein–DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis -regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein–DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression.

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Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

10.1101/2020.06.16.155481 ◽

2020 ◽

Author(s):

Maud Fagny ◽

Marieke Lydia Kuijjer ◽

Maike Stam ◽

Johann Joets ◽

Olivier Turc ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Binding Sites ◽

Regulatory Network ◽

Tissue Specificity ◽

Target Genes ◽

Specific Gene ◽

Tissue Specific ◽

Genome Wide ◽

Gene Regulatory

AbstractEnhancers are important regulators of gene expression during numerous crucial processes including tissue differentiation across development. In plants, their recent molecular characterization revealed their capacity to activate the expression of several target genes through the binding of transcription factors. Nevertheless, identifying these target genes at a genome-wide level remains a challenge, in particular in species with large genomes, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to regulatory network is still poorly understood in plants. In this study, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage and husks (bracts) at flowering. Using a systems biology approach, we integrate genomic, epigenomic and transcriptomic data to model the regulatory relationship between transcription factors and their potential target genes. We identify regulatory modules specific to husk and V2-IST, and show that they are involved in distinct functions related to the biology of each tissue. We evidence enhancers exhibiting binding sites for two distinct transcription factor families (DOF and AP2/ERF) that drive the tissue-specificity of gene expression in seedling immature leaf and husk. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposon Mutator and MITE Pif/Harbinger) have shaped the regulatory network in each tissue, and that MITEs have provided new transcription factor binding sites that are involved in husk tissue-specificity.SignificanceEnhancers play a major role in regulating tissue-specific gene expression in higher eukaryotes, including angiosperms. While molecular characterization of enhancers has improved over the past years, identifying their target genes at the genome-wide scale remains challenging. Here, we integrate genomic, epigenomic and transcriptomic data to decipher the tissue-specific gene regulatory network controlled by enhancers at two different stages of maize leaf development. Using a systems biology approach, we identify transcription factor families regulating gene tissue-specific expression in husk and seedling leaves, and characterize the enhancers likely to be involved. We show that a large part of maize enhancers is derived from transposable elements, which can provide novel transcription factor binding sites crucial to the regulation of tissue-specific biological functions.

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SNPnotes: high-throughput tissue-specific functional annotation of single nucleotide variants

F1000Research ◽

10.12688/f1000research.20415.1 ◽

2019 ◽

Vol 8 ◽

pp. 1784

Author(s):

Shraddha Pai ◽

Michael J. Apostolides ◽

Andrew Jung ◽

Matthew A. Moss

Keyword(s):

Gene Expression ◽

Gene Mapping ◽

High Throughput ◽

Regulatory Elements ◽

Specific Gene ◽

Tissue Specific ◽

Functional Variants ◽

Genome Regulation ◽

Organ Systems ◽

Variant Gene

A key challenge in the application of whole-genome sequencing (WGS) for clinical diagnostic and research is the high-throughput prioritization of functional variants in the non-coding genome. This challenge is compounded by context-specific genetic modulation of gene expression, and variant-gene mapping depends on the tissues and organ systems affected in a given disease; for instance, a disease affecting the gastrointestinal system would use maps specific to genome regulation in gut-related tissues. While there are large-scale atlases of genome regulation, such as GTEx and NIH Roadmap Epigenomics, the clinical genetics community lacks publicly-available stand-alone software for high-throughput annotation of custom variant data with user-defined tissue-specific epigenetic maps and clinical genetic databases, to prioritize variants for a specific biomedical application. In this work, we provide a simple software pipeline, called SNPnotes, which takes as input variant calls for a patient and prioritizes those using information on clinical relevance from ClinVar, tissue-specific gene regulation from GTEx and disease associations from the NHGRI-EBI GWAS catalogue. This pipeline was developed as part of SVAI Research's "Undiagnosed-1" event for collaborative patient diagnosis. We applied this pipeline to WGS-based variant calls for an individual with a history of gastrointestinal symptoms, using 12 gut-specific eQTL maps and GWAS associations for metabolic diseases, for variant-gene mapping. Out of 6,248,584 SNPs, the pipeline identified 151 high-priority variants, overlapping 129 genes. These top SNPs all have known clinical pathogenicity, modulate gene expression in gut tissues and have genetic associations with metabolic disorders, and serve as starting points for hypotheses about mechanisms driving clinical symptoms. Simple software changes can be made to customize the pipeline for other tissue-specific applications. Future extensions could integrate maps of tissue-specific regulatory elements, higher-order chromatin loops, and mutations affecting splice variants.

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A modified pod specific promoter for high level heterologous expression of genes in legumes

Legume Research - An International Journal ◽

10.18805/lr-4073 ◽

2019 ◽

Author(s):

Aravind Kumar Konda ◽

Pallavi Singh ◽

Khela Ram Soren ◽

Narendra Pratap Singh

Keyword(s):

Gene Expression ◽

Regulatory Elements ◽

Specific Gene ◽

Specific Expression ◽

Tissue Specific ◽

Cis Acting ◽

Inducible Promoters ◽

Expression Of Genes ◽

Enhanced Expression ◽

High Level

Promoters are cis-acting regulatory elements that are usually present upstream to the coding sequences and determine the gene expression. Deployment of tissue specific and inducible promoters are constantly increasing for development of successful and stable multiple transgenic plants. To this end, as a strategy for enhanced expression of cis or transgenes, promoter engineering of the native msg promoter from soya bean has been carried out for executing pod specific expression of genes. Cis regulatory elements such as 5’UTR and poly (A) tract have been incorporated for imparting mRNA stability and translational enhancement to generate the modified 1.285 Kb pod specific promoter. Further to attain transcriptional enhancement the modified promoter has been cloned to generate Bi-directional Duplex Promoters (BDDP). The engineered msg promoter gene constructs can be deployed for high level tissue specific gene expression of cis/trans genes along with chosen terminator in chickpea. soybean and other legumes as well.

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Epigenetics of Cellular Memory: Insights from the Chromatin Accessibility Landscape of the Mitotic Genome

Blood ◽

10.1182/blood.v124.21.4342.4342 ◽

2014 ◽

Vol 124 (21) ◽

pp. 4342-4342

Author(s):

Chris C.S. Hsiung ◽

Christapher Morrissey ◽

Maheshi Udugama ◽

Christopher Frank ◽

Cheryl A. Keller ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Transcription Factors ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Dnase I ◽

Specific Gene ◽

Tissue Specific ◽

Dnase I Sensitivity ◽

Mitotic Chromatin

Abstract Normal development requires the coordination of cell cycle progression and gene expression to produce physiologically appropriate cell numbers of various lineages. The concomitant dysregulation of these two cellular programs is central to many malignant and non-malignant hematologic diseases, yet researchers still lack clear, general principles of how intrinsic properties of cell division could influence transcriptional regulation. Mitosis is a unique phase of the cell cycle that dramatically disrupts transcription: chromosomes condense to form microscopically recognizable structures, the nucleus is disassembled, RNA synthesis ceases, and the transcription machinery and many transcription factors are evicted from mitotic chromatin. How cells “remember” tissue-specific transcriptional programs through mitotic divisions remains largely unknown. Some transcription factors, including the erythroid master regulator, GATA1, and certain chromatin features are known to remain associated with DNA during mitosis. These molecular entities have been proposed to serve as mitotic “bookmarks” -- molecules that store gene regulatory information at individual loci through mitosis. However, we have limited knowledge of the composition, mechanism and function of mitotic bookmarks. In this context, chromatin structure deserves special consideration, as chromosome condensation during mitosis could potentially hinder transcription factor binding. To obtain the first genome-wide view of chromatin accessibility during mitosis, we mapped the DNase I sensitivity of the interphase versus mitotic genome in two maturation stages in a murine erythroblast cell line, G1E. Despite microscopic condensation of chromosomes during mitosis, we found that DNase I sensitivity is extensively preserved throughout the mappable genome, indicating that mitotic chromatin is not as condensed as commonly presumed. Individual genes and cis-regulatory elements can maintain all, part of, or none of its interphase accessibility during mitosis, demonstrating that accessibility of mitotic chromatin is locally specified. Promoters generally maintain accessibility during mitosis; moreover, promoters with the highest degree of accessibility preservation in mitosis in G1E cells tend to also be accessible across many murine tissues in interphase. In contrast to promoters, we found that enhancer accessibility is preferentially lost during mitosis, raising the possibility that memory of enhancer regulation may be altered during mitosis. Since enhancers play crucial roles in specifying tissue-specific gene expression patterns, we propose that this phase of the cell cycle may be especially susceptible to resetting of transcriptional programs. This hypothesis is supported by our preliminary results that revealed aberrant RNA polymerase II re-engagement with the genome and transcript production in early G1. Thus, mitosis could be a source of gene expression heterogeneity, with potential implications for cell fate transitions in proliferative cells, such as during stem cell lineage commitment, experimental reprogramming, and tumorigenesis. Disclosures No relevant conflicts of interest to declare.

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mtDNA eQTLs and the m1A 16S rRNA modification explain mtDNA tissue-specific gene expression pattern in humans

10.1101/495838 ◽

2018 ◽

Author(s):

Tal Cohen ◽

Chen Mordechai ◽

Alal Eran ◽

Dan Mishmar

Keyword(s):

Gene Expression ◽

Mitochondrial Dna ◽

16S Rrna ◽

Gene Expression Pattern ◽

Regulatory Elements ◽

Specific Gene ◽

Dependent Manner ◽

Rna Seq ◽

Genome Wide ◽

The Impact

Expression quantitative trait loci (eQTLs) are instrumental in genome-wide identification of regulatory elements, yet were overlooked in the mitochondrial DNA (mtDNA). By analyzing 5079 RNA-seq samples from 23 tissues we identified association of ancient mtDNA SNPs (haplogroups T2, L2, J2 and V) and recurrent SNPs (mtDNA positions 263, 750, 1438 and 10398) with tissue-dependent mtDNA gene-expression. Since the recurrent SNPs independently occurred in different mtDNA genetic backgrounds, they constitute the best candidates to be causal eQTLs. Secondly, the discovery of mtDNA eQTLs in both coding and non-coding mtDNA regions, propose the identification of novel mtDNA regulatory elements. Third, we identified association between low m1A 947 MT-RNR2 (16S) rRNA modification levels and altered mtDNA gene-expression in twelve tissues. Such association disappeared in skin which was exposed to sun, as compared to sun-unexposed skin from the same individuals, thus supporting the impact of UV on mtDNA gene expression. Taken together, our findings reveal that both mtDNA SNPs and mt-rRNA modification affect mtDNA gene expression in a tissue-dependent manner.

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KDM6A knockout in human iPSCs alters the genome-wide histone methylation profile at active and poised enhancers, activating expression of ectoderm gene expression pathways

10.1101/2021.03.09.434633 ◽

2021 ◽

Author(s):

Shailendra S. Maurya ◽

Wei Yang ◽

Qiang Zhang ◽

Petra Erdmann-Gilmore ◽

Amelia Bystry ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Histone Modification ◽

Histone Modifications ◽

Embryonic Stem ◽

Specific Gene ◽

Regulatory Domains ◽

Genome Wide ◽

Human Ipscs ◽

Expression Pathways

AbstractKDM6A is a histone demethylase, known to remove methyl moieties at the lysine residues of histone 3-labeled (H3K27me3) poised enhancers and bivalent promoters, which regulates gene expression during the differentiation of embryonic stem cells and tissue-specific development. However, while tissue- and disease-specific analyses have been performed, little is known about the location and consequences on gene expression of these regulatory regions in human pluripotent cells. Poised enhancers and bivalent promoters function in a coordinated fashion during development, which requires timely and efficient histone modifications. Identification of KDM6A-specific gene-regulatory domains is important for understanding the developmental mechanisms controlled by these histone modifications in pluripotency. In this study, we compared genome-wide histone modification and gene expression differences in isogenic wild type and cas9-mediated KDM6A knockout human induced pluripotent stem cells (hiPSC) lines. Here, we report that the absence of KDM6A does not alter the pluripotent phenotype but does substantially alter the histone modification profile at poised and active enhancers, resulting in decreased expression of associated COMPASS complex genes KMT2C and KMT2D and subsequently increasing the expression of gene pathways involved in ectoderm differentiation.

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Tissue-specific 5-hydroxymethylcytosine landscape of the human genome

10.21203/rs.3.rs-39144/v1 ◽

2020 ◽

Author(s):

Bo He ◽

Chao Zhang ◽

Xiaoxue Zhang ◽

Yu Fan ◽

Hu Zeng ◽

...

Keyword(s):

Gene Expression ◽

Human Genome ◽

Genome Wide Association Study ◽

Regulatory Element ◽

Regulatory Elements ◽

Specific Gene ◽

Epigenetic Mark ◽

Human Tissues ◽

Tissue Specific ◽

Regulatory Functions

Abstract 5-Hydroxymethylcytosine (5hmC) is an important epigenetic mark that regulates gene expression. Charting the landscape of 5hmC in human tissues is fundamental to understand its regulatory functions. Here, we systematically profiled the whole-genome 5hmC landscape at single-base resolution for 19 types of human tissues. We found that 5hmC preferentially decorates gene bodies and outperforms gene body 5mC in reflecting gene expression. Approximately one-third of 5hmC peaks are tissue-specific differentially hydroxymethylated regions (tsDhMRs), which are deposited in regulatory elements that regulate the expression of nearby tissue-specific functional genes. In addition, tsDhMRs are enriched with tissue-specific transcription-factor-binding sites and may rewire tissue-specific gene expression networks. Moreover, tsDhMRs are associated with SNPs identified by genome-wide association study (GWAS), linked to tissue-specific phenotypes and diseases. Collectively, our results show the tissue-specific 5hmC landscape of the human genome and demonstrate that 5hmC serves as a fundamental regulatory element affecting tissue-specific development and diseases.

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