Chromatin Accessibility of Human Mitral Valves and Functional Assessment of MVP Risk Loci

Rationale: Mitral valve prolapse (MVP) is a common valvopathy that leads to mitral insufficiency, heart failure and sudden death. Functional genomic studies in mitral valves are needed to better characterize MVP associated variants and target genes. Objective: To establish the chromatin accessibility profiles and assess functionality of variants and narrow down target genes at MVP loci. Methods and Results: We mapped the open chromatin regions in nuclei from 11 human pathogenic and 7 non-pathogenic mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq). Open chromatin peaks were globally similar between pathogenic and non-pathogenic valves. Compared to the heart tissue and cardiac fibroblasts, we found that MV-specific ATAC-Seq peaks are enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. One of the most enriched motif in MV-specific open chromatin peaks was for the nuclear factor of activated T cells (NFATC) family of transcription factors, involved in valve endocardial and interstitial cells formation. We also found that MVP-associated variants were significantly enriched (p<0.05) in mitral valve open chromatin peaks. Integration of the ATAC-Seq data with risk loci, extensive functional annotation, and gene reporter assay suggest plausible causal variants for rs2641440 at the SMG6/SRR locus and rs6723013 at the IGFBP2/IGFBP5/TNS1 locus. CRISPR-Cas9 deletion of the sequence including rs6723013 in human fibroblasts correlated with increased expression only for TNS1. 4C-Seq experiments provided evidence for several target genes, including SRR, HIC1, and DPH1 at the SMG6/SRR locus and further supported TNS1 as the most likely target gene on Chr2. Conclusions: Here we describe unprecedented genome-wide open chromatin profiles from human pathogenic and non-pathogenic MVs and report specific gene regulation profiles, compared to the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms.

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Abstract 13435: Characterization of Open Chromatin in Human Mitral Valves to Identify Regulatory Mechanisms at Mitral Valve Prolapse Genetic Loci

Circulation ◽

10.1161/circ.142.suppl_3.13435 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Sergiy Kyryachenko ◽

Adrien Georges ◽

Mengyao Yu ◽

Takiy Berrandou ◽

Tony Rubio ◽

...

Keyword(s):

Mitral Valve ◽

Mitral Valve Prolapse ◽

Target Genes ◽

Valve Disease ◽

Specific Gene ◽

Open Chromatin ◽

Mitral Insufficiency ◽

Mitral Valves ◽

Causal Variants

Introduction: Mitral valve prolapse (MVP) is a common valve disease that leads to mitral insufficiency, heart failure, and sudden death. The identification of genetic risk loci provided insight into its genetic architecture, although the causal variants and target genes need to be fully characterized. Hypothesis: Functional genomic annotation, including chromatin accessibility profiles of human mitral valves, allows the characterization of variants and target genes at MVP loci. Methods: We determined open chromatin regions using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) from surgically removed human valves and primary cultures of fibroblasts. We analyzed the spatial conformation of MVP-associated loci using circular chromatin conformation capture (4C-Seq) with candidate causal variants as viewpoints. Candidate causal variants were followed-up using reporter assays and in silico analyses. Results: We mapped the open chromatin from 11 human mitral valves and 3 primary cell cultures. We found that mitral valve-specific ATAC-Seq peaks were enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. We also found that MVP-associated variants (p<10 -5 ) observed in the MVP GWAS were significantly enriched (p<0.05) in mitral valve open chromatin regions, but not in heart tissue from ENCODE. We found that rs6723013 on Chr2 belongs to a valve-specific enhancer at the IGFBP5/TNS1 locus and is the most likely causal variant at this locus. We also identified several plausible causal SNPs and, by using 4C-Seq, potential target genes ( HIC1 and DPH1 ) at the SMG6/SRR locus. Conclusions: Here we describe unprecedented genome-wide open chromatin profiles from human mitral valves that indicate specific gene regulation profiles, compared to the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms relevant to mitral valve disease.

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Characterization of genomic regulation profiles in human mitral valve whole tissue to annotate genetic risk loci for mitral valve prolapse

10.1101/2020.06.04.20122010 ◽

2020 ◽

Author(s):

Sergiy Kyryachenko ◽

Adrien Georges ◽

Mengyao Yu ◽

Takiy E. Berrandou ◽

Patrick Bruneval ◽

...

Keyword(s):

Gene Regulation ◽

Mitral Valve ◽

High Throughput ◽

Mitral Valve Prolapse ◽

High Throughput Sequencing ◽

Target Genes ◽

Valve Disease ◽

Open Chromatin ◽

Mitral Valves ◽

Causal Variants

Rationale: Mitral valve prolapse (MVP) is a common valve disease that leads to mitral insufficiency, heart failure and sudden death. The identification of risk loci provided insight into its genetic architecture, although the causal variants and target genes need to be fully characterized. Objective: To establish the chromatin accessibility profiles and gene regulation specificities of human mitral valve and identify functional variants and target genes at MVP loci. Methods and Results: We mapped the open chromatin accessible regions in nuclei from 11 human mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq). Compared to the heart tissue and cardiac fibroblasts, we found that mitral valve-specific ATAC-Seq peaks were enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. The most enriched motif in mitral valve-specific open chromatin peaks was for the nuclear factor of activated T cells (NFATC) family of transcription factors, involved in valve endocardial and interstitial cells formation. We also found that MVP-associated variants (p < 10-5) observed in the current MVP GWAS were significantly enriched (p<0.05) in mitral valve open chromatin peaks. Integration of the ATAC-Seq data with GWAS loci, extensive functional annotation, and gene reporter assay revealed plausible causal variants at two risk loci: rs6723013 at the IGFBP5/TNS1 locus and rs2641440 at the SMG6/SRR locus. Circular chromosome conformation capture followed by high-throughput sequencing provided evidence for several target genes, including SRR, HIC1, and DPH1 at the SMG6/SRR locus and further supported TNS1 as the most likely target gene on Chr2. Conclusions: Here we describe unprecedented genome-wide open chromatin profiles from human mitral valves that indicates specific gene regulation profiles, compared to the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms relevant to mitral valve disease.

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Chromatin accessibility and regulatory vocabulary across indicine cattle tissues

Genome Biology ◽

10.1186/s13059-021-02489-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Pâmela A. Alexandre ◽

Marina Naval-Sánchez ◽

Moira Menzies ◽

Loan T. Nguyen ◽

Laercio R. Porto-Neto ◽

...

Keyword(s):

Motif Discovery ◽

Target Genes ◽

Developmental Stages ◽

Bos Taurus ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Model Organisms ◽

Open Chromatin ◽

Health And Disease ◽

Collaborative Efforts

Abstract Background Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare. Results We generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps. Conclusions Our findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.

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Ochronotic Involvement of the Aortic and Mitral Valves in a 72-Year-Old Man

Texas Heart Institute Journal ◽

10.14503/thij-14-4138 ◽

2015 ◽

Vol 42 (1) ◽

pp. 84-86 ◽

Cited By ~ 7

Author(s):

Atakan Atalay ◽

Ugur Gocen ◽

Yuksel Basturk ◽

Erkan Kozanoglu ◽

Hafize Yaliniz

Keyword(s):

Heart Disease ◽

Mitral Valve ◽

Aortic Stenosis ◽

Valve Replacement ◽

Valvular Heart Disease ◽

Metabolic Disorder ◽

Autosomal Recessive ◽

Homogentisic Acid ◽

Mitral Insufficiency ◽

Mitral Valves

Ochronosis, an autosomal recessive metabolic disorder, causes an excess of homogentisic acid that results in adverse pigmentation, calcification, and inflammation of cartilaginous and other tissues. Cardiovascular abnormalities are less frequently reported than are other manifestations. In rare cases, ochronosis can cause valvular heart disease. We report the case of a 72-year-old man with aortic stenosis and mitral insufficiency who was diagnosed with ochronosis while undergoing surgical aortic and mitral valve replacement. We discuss the history and surgical management of alkaptonuric ochronosis.

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Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration

Scientific Reports ◽

10.1038/s41598-021-94341-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wolfgang Pita-Thomas ◽

Tassia Mangetti Gonçalves ◽

Ajeet Kumar ◽

Guoyan Zhao ◽

Valeria Cavalli

Keyword(s):

Optic Nerve ◽

Vision Loss ◽

Axon Regeneration ◽

Axon Growth ◽

Chromatin Accessibility ◽

Specific Gene ◽

Binding Motif ◽

Open Chromatin ◽

Transactivation Domain ◽

Growth Capacity

AbstractRetinal Ganglion Cells (RGCs) lose their ability to grow axons during development. Adult RGCs thus fail to regenerate their axons after injury, leading to vision loss. To uncover mechanisms that promote regeneration of RGC axons, we identified transcription factors (TF) and open chromatin regions that are enriched in rat embryonic RGCs (high axon growth capacity) compared to postnatal RGCs (low axon growth capacity). We found that developmental stage-specific gene expression changes correlated with changes in promoter chromatin accessibility. Binding motifs for TFs such as CREB, CTCF, JUN and YY1 were enriched in the regions of the chromatin that were more accessible in embryonic RGCs. Proteomic analysis of purified rat RGC nuclei confirmed the expression of TFs with potential role in axon growth such as CREB, CTCF, YY1, and JUND. The CREB/ATF binding motif was widespread at the open chromatin region of known pro-regenerative TFs, supporting a role of CREB in regulating axon regeneration. Consistently, overexpression of CREB fused to the VP64 transactivation domain in mouse RGCs promoted axon regeneration after optic nerve injury. Our study provides a map of the chromatin accessibility during RGC development and highlights that TF associated with developmental axon growth can stimulate axon regeneration in mature RGC.

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Interrogation of human hematopoiesis at single-cell and single-variant resolution

10.1101/255224 ◽

2018 ◽

Cited By ~ 6

Author(s):

Caleb A. Lareau ◽

Jacob C. Ulirsch ◽

Erik L. Bao ◽

Leif S. Ludwig ◽

Michael H. Guo ◽

...

Keyword(s):

Single Cell ◽

Target Genes ◽

Cell Types ◽

Core Gene ◽

Chromatin Accessibility ◽

Significant Heterogeneity ◽

Analytic Framework ◽

Causal Variants ◽

Using Data ◽

The Uk

AbstractIncomplete annotation of cell-to-cell state variance and widespread linkage disequilibrium in the human genome represent significant challenges to elucidating mechanisms of trait-associated genetic variation. Here, using data from the UK Biobank, we perform genetic fine-mapping for 16 blood cell traits to quantify posterior probabilities of association while allowing for multiple independent signals per region. We observe an enrichment of fine-mapped variants in accessible chromatin of lineage-committed hematopoietic progenitor cells. Further, we develop a novel analytic framework that identifies “core gene” cell type enrichments and show that this approach uniquely resolves relevant cell types within closely related populations. Applying our approach to single cell chromatin accessibility data, we discover significant heterogeneity within classically defined multipotential progenitor populations. Finally, using several lines of empirical evidence, we identify relevant cell types, predict target genes, and propose putative causal mechanisms for fine-mapped variants. In total, our study provides an analytic framework for single-variant and single-cell analyses to elucidate putative causal variants and cell types from GWAS and high-resolution epigenomic assays.

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Eda-activated RelB recruits an SWI/SNF (BAF) chromatin-remodeling complex and initiates gene transcription in skin appendage formation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1800930115 ◽

2018 ◽

Vol 115 (32) ◽

pp. 8173-8178 ◽

Cited By ~ 2

Author(s):

Jian Sima ◽

Zhijiang Yan ◽

Yaohui Chen ◽

Elin Lehrmann ◽

Yongqing Zhang ◽

...

Keyword(s):

Chromatin Remodeling ◽

Gene Transcription ◽

Target Genes ◽

Specific Gene ◽

Open Chromatin ◽

Transcription Profiling ◽

Baf Complex ◽

Skin Appendage ◽

Chromatin Remodeling Complex ◽

Appendage Formation

Ectodysplasin A (Eda) signaling activates NF-κB during skin appendage formation, but how Eda controls specific gene transcription remains unclear. Here, we find that Eda triggers the formation of an NF-κB–associated SWI/SNF (BAF) complex in which p50/RelB recruits a linker protein, Tfg, that interacts with BAF45d in the BAF complex. We further reveal that Tfg is initially induced by Eda-mediated RelB activation and then bridges RelB and BAF for subsequent gene regulation. The BAF component BAF250a is particularly up-regulated in skin appendages, and epidermal knockout of BAF250a impairs skin appendage development, resulting in phenotypes similar to those of Eda-deficient mouse models. Transcription profiling identifies several target genes regulated by Eda, RelB, and BAF. Notably, RelB and the BAF complex are indispensable for transcription of Eda target genes, and both BAF complex and Eda signaling are required to open chromatin of Eda targets. Our studies thus suggest that Eda initiates a signaling cascade and recruits a BAF complex to specific gene loci to facilitate transcription during organogenesis.

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Concentration dependent chromatin states induced by the bicoid morphogen gradient

eLife ◽

10.7554/elife.28275 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 35

Author(s):

Colleen E Hannon ◽

Shelby A Blythe ◽

Eric F Wieschaus

Keyword(s):

Large Scale ◽

Common Property ◽

Target Genes ◽

Positional Information ◽

Chromatin Accessibility ◽

Chromatin State ◽

Open Chromatin ◽

Genome Wide ◽

High Concentrations

In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset of its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations. This may be a common property of developmental transcription factors that must gain early access to their target enhancers while the chromatin state of the genome is being remodeled during large-scale transitions in the gene regulatory landscape.

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Accurate transcription start sites enable mining for the cis-regulatory determinants of tissue specific gene expression

10.1101/2020.09.01.278424 ◽

2020 ◽

Author(s):

Mitra Ansariola ◽

Valerie N. Fraser ◽

Sergei A. Filichkin ◽

Maria G. Ivanchenko ◽

Zachary A. Bright ◽

...

Keyword(s):

Gene Expression ◽

Binding Sites ◽

Chromatin Accessibility ◽

Specific Gene ◽

Open Chromatin ◽

Transcription Start ◽

Tissue Specific ◽

Transcription Start Sites ◽

Tissue Specific Gene ◽

Specific Gene Expression

AbstractAcross tissues, gene expression is regulated by a combination of determinants, including the binding of transcription factors (TFs), along with other aspects of cellular state. Recent studies emphasize the importance of both genetic and epigenetic states – TF binding sites and binding site chromatin accessibility have emerged as potentially causal determinants of tissue specificity. To investigate the relative contributions of these determinants, we constructed three genome-scale datasets for both root and shoot tissues of the same Arabidopsis thaliana plants: TSS-seq data to identify Transcription Start Sites, OC-seq data to identify regions of Open Chromatin, and RNA-seq data to assess gene expression levels. For genes that are differentially expressed between root and shoot, we constructed a machine learning model predicting tissue of expression from chromatin accessibility and TF binding information upstream of TSS locations. The resulting model was highly accurate (over 90% auROC and auPRC), and our analysis of model contributions (feature weights) strongly suggests that patterns of TF binding sites within ∼500 nt TSS-proximal regions are predominant explainers of tissue of expression in most cases. Thus, in plants, cis-regulatory control of tissue-specific gene expression appears to be primarily determined by TSS-proximal sequences, and rarely by distal enhancer-like accessible chromatin regions. This study highlights the exciting future possibility of a native TF site-based design process for the tissue-specific targeting of plant gene promoters.

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Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient

10.1101/133348 ◽

2017 ◽

Cited By ~ 3

Author(s):

Colleen E. Hannon ◽

Shelby A. Blythe ◽

Eric F. Wieschaus

Keyword(s):

Target Genes ◽

Positional Information ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Genome Wide ◽

Low Concentrations ◽

High Concentrations ◽

Accessible Chromatin ◽

Anterior Posterior

ABSTRACTIn Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations.

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