Human library of cardiac promoters and enhancers

AbstractGenome regulatory elements play a critical role during cardiac development and maintenance of normal physiological homeostasis, and genome-wide association studies identified a large number of SNPs associated with cardiovascular diseases localized in intergenic zones. We used cap analysis of gene expression (CAGE) to identify transcription start sites (TSS) with one nucleotide resolution that effectively maps genome regulatory elements in a representative collection of human heart tissues. Here we present a comprehensive and fully annotated CAGE atlas of human promoters and enhancers from four chambers of the non-diseased human donor hearts, including both atria and ventricles. We have identified 10,528 novel regulatory elements, where 2,750 are classified as TSS and 4,258 novel enhancers, which were validated with ChIP-seq libraries and motif enrichment analysis. We found that heart-region specific expression patterns are primarily based on the alternative promoter and specific enhancer activity. Our study significantly increased evidence of the association of regulatory elements-located variants with heart morphology and pathologies. The precise location of cardiac disease-related SNPs within the regulatory regions and their correlation with a specific cell type offers a new understanding of genetic heart diseases.

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Human atlas of cardiac promoters and enhancers reveals important role of regulatory elements in heritable diseases

10.21203/rs.3.rs-37530/v1 ◽

2020 ◽

Author(s):

Ruslan Deviatiiarov ◽

Anna Gams ◽

Roman Syunyaev ◽

Tatiana Tatarinova ◽

Oleg Gusev ◽

...

Keyword(s):

Heart Diseases ◽

Association Studies ◽

Expression Patterns ◽

Critical Role ◽

Regulatory Elements ◽

Specific Cell ◽

Genome Wide Association Studies ◽

Specific Expression ◽

Enhancer Activity ◽

Human Donor

Abstract Genome regulatory elements play a critical role during cardiac development and maintenance of normal physiological homeostasis, and genome-wide association studies identified a large number of SNPs associated with cardiovascular diseases localized in intergenic zones. We used cap analysis of gene expression (CAGE) to identify transcription start sites (TSS) with one nucleotide resolution that effectively maps genome regulatory elements in a representative collection of human heart tissues. Here we present a comprehensive and fully annotated CAGE atlas of human promoters and enhancers from four chambers of the non-diseased human donor hearts, including both atria and ventricles. We have identified 10,528 novel regulatory elements, where 2,750 are classified as TSS and 4,258 novel enhancers, which were validated with ChIP-seq libraries and motif enrichment analysis. We found that heart-region specific expression patterns are primarily based on the alternative promoter and specific enhancer activity. Our study significantly increased evidence of the association of regulatory elements-located variants with heart morphology and pathologies. The precise location of cardiac disease-related SNPs within the regulatory regions and their correlation with a specific cell type offers a new understanding of genetic heart diseases.

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Genomic characterization of the adolescent idiopathic scoliosis associated transcriptome and regulome

10.1101/2020.03.02.973735 ◽

2020 ◽

Author(s):

Nadja Makki ◽

Jingjing Zhao ◽

Zhaoyang Liu ◽

Walter L. Eckalbar ◽

Aki Ushiki ◽

...

Keyword(s):

Adolescent Idiopathic Scoliosis ◽

Connective Tissue ◽

Idiopathic Scoliosis ◽

Association Studies ◽

Regulatory Elements ◽

Intervertebral Discs ◽

Genome Wide Association Studies ◽

Specific Expression ◽

Enhancer Activity ◽

Genome Wide

AbstractAdolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is the most common pediatric musculoskeletal disorder, affecting ∼3% of the population worldwide. However, its genetic bases and tissues of origin remain largely unknown. Several genome-wide association studies (GWAS) have implicated nucleotide variants in noncoding sequences that control genes with important roles in cartilage, muscle, bone, connective tissue and intervertebral discs (IVDs) as drivers of AIS susceptibility. Here, we set out to define the expression of AIS-associated genes and active regulatory elements by performing RNA-seq and ChIP-seq against H3K27ac in these tissues in mouse and human. Our study highlights genetic pathways involving AIS-associated loci that regulate chondrogenesis, IVD development and connective tissue maintenance and homeostasis. In addition, we identify thousands of putative AIS-associated regulatory elements which may orchestrate tissue-specific expression in musculoskeletal tissues of the spine. Quantification of enhancer activity of several candidate regulatory elements from our study identifies three functional enhancers carrying AIS-associated GWAS SNPs at the ADGRG6 and BNC2 loci. Our findings provide a novel genome-wide catalog of AIS-relevant genes and regulatory elements and aid in the identification of novel targets for AIS causality and treatment.

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Genomic characterization of the adolescent idiopathic scoliosis associated transcriptome and regulome

Human Molecular Genetics ◽

10.1093/hmg/ddaa242 ◽

2020 ◽

Author(s):

Nadja Makki ◽

Jingjing Zhao ◽

Zhaoyang Liu ◽

Walter L Eckalbar ◽

Aki Ushiki ◽

...

Keyword(s):

Adolescent Idiopathic Scoliosis ◽

Connective Tissue ◽

Idiopathic Scoliosis ◽

Association Studies ◽

Regulatory Elements ◽

Intervertebral Discs ◽

Genome Wide Association Studies ◽

Specific Expression ◽

Enhancer Activity ◽

Genome Wide

Abstract Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is the most common pediatric musculoskeletal disorder, affecting ~ 3% of the population worldwide. However, its genetic bases and tissues of origin remain largely unknown. Several genome-wide association studies (GWAS) have implicated nucleotide variants in noncoding sequences that control genes with important roles in cartilage, muscle, bone, connective tissue and intervertebral discs (IVDs) as drivers of AIS susceptibility. Here, we set out to define the expression of AIS-associated genes and active regulatory elements by performing RNA-seq and ChIP-seq against H3K27ac in these tissues in mouse and human. Our study highlights genetic pathways involving AIS-associated loci that regulate chondrogenesis, IVD development and connective tissue maintenance and homeostasis. In addition, we identify thousands of putative AIS-associated regulatory elements which may orchestrate tissue-specific expression in musculoskeletal tissues of the spine. Quantification of enhancer activity of several candidate regulatory elements from our study identifies three functional enhancers carrying AIS-associated GWAS SNPs at the ADGRG6 and BNC2 loci. Our findings provide a novel genome-wide catalog of AIS-relevant genes and regulatory elements and aid in the identification of novel targets for AIS causality and treatment.

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RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes

10.1101/2021.12.16.466282 ◽

2021 ◽

Author(s):

John T Walker ◽

Diane C Saunders ◽

Vivek Rai ◽

Chunhua Dai ◽

Peter Orchard ◽

...

Keyword(s):

Type 2 Diabetes ◽

Insulin Secretion ◽

Association Studies ◽

Critical Role ◽

Regulatory Elements ◽

Genome Wide Association Studies ◽

Β Cells ◽

Β Cell ◽

Gene Regulatory

A hallmark of type 2 diabetes (T2D), a major cause of world-wide morbidity and mortality, is dysfunction of insulin-producing pancreatic islet β cells. T2D genome-wide association studies (GWAS) have identified hundreds of signals, mostly in the non-coding genome and overlapping β cell regulatory elements, but translating these into biological mechanisms has been challenging. To identify early disease-driving events, we performed single cell spatial proteomics, sorted cell transcriptomics, and assessed islet physiology on pancreatic tissue from short-duration T2D and control donors. Here, through integrative analyses of these diverse modalities, we show that multiple gene regulatory modules are associated with early-stage T2D β cell-intrinsic defects. One notable example is the transcription factor RFX6, which we show is a highly connected β cell hub gene that is reduced in T2D and governs a gene regulatory network associated with insulin secretion defects and T2D GWAS variants. We validated the critical role of RFX6 in β cells through direct perturbation in primary human islets followed by physiological and single nucleus multiome profiling, which showed reduced dynamic insulin secretion and large-scale changes in the β cell transcriptome and chromatin accessibility landscape. Understanding the molecular mechanisms of complex, systemic diseases necessitates integration of signals from multiple molecules, cells, organs, and individuals and thus we anticipate this approach will be a useful template to identify and validate key regulatory networks and master hub genes for other diseases or traits with GWAS data.

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Characterization of the human SLC30A8 promoter and intronic enhancer

Journal of Molecular Endocrinology ◽

10.1530/jme-11-0055 ◽

2011 ◽

Vol 47 (3) ◽

pp. 251-259 ◽

Cited By ~ 11

Author(s):

Lynley D Pound ◽

Suparna A Sarkar ◽

Stéphane Cauchi ◽

Yingda Wang ◽

James K Oeser ◽

...

Keyword(s):

Fusion Gene ◽

Association Studies ◽

Causal Variant ◽

Proximal Promoter ◽

Luciferase Expression ◽

Genome Wide Association Studies ◽

Promoter Regions ◽

Specific Expression ◽

Enhancer Activity ◽

Intron 2

Genome-wide association studies have shown that a polymorphic variant inSLC30A8, which encodes zinc transporter-8, is associated with altered susceptibility to type 2 diabetes (T2D). This association is consistent with the observation that glucose-stimulated insulin secretion is decreased in islets isolated fromSlc30a8knockout mice. In this study, immunohistochemical staining was first used to show thatSLC30A8is expressed specifically in pancreatic islets. Fusion gene studies were then used to examine the molecular basis for the islet-specific expression ofSLC30A8. The analysis ofSLC30A8-luciferase expression in βTC-3 cells revealed that the proximal promoter region, located between −6154 and −1, relative to the translation start site, was only active in stable but not transient transfections. VISTA analyses identified three regions in theSLC30A8promoter and a region inSLC30A8intron 2 that are conserved in the mouseSlc30a8gene. Additional fusion gene experiments demonstrated that none of theseSlc30a8promoter regions exhibited enhancer activity when ligated to a heterologous promoter whereas the conserved region inSLC30A8intron 2 conferred elevated reporter gene expression selectively in βTC-3 but not in αTC-6 cells. Finally, the functional effects of a single nucleotide polymorphism (SNP), rs62510556, in this conserved intron 2 enhancer were investigated. Gel retardation studies showed that rs62510556 affects the binding of an unknown transcription factor and fusion gene analyses showed that it modulates enhancer activity. However, genetic analyses suggest that this SNP is not a causal variant that contributes to the association betweenSLC30A8and T2D, at least in Europeans.

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Non-coding DNA in IBD: from sequence variation in DNA regulatory elements to novel therapeutic potential

Gut ◽

10.1136/gutjnl-2018-317516 ◽

2019 ◽

Vol 68 (5) ◽

pp. 928-941 ◽

Cited By ~ 5

Author(s):

Claartje Aleid Meddens ◽

Amy Catharina Johanna van der List ◽

Edward Eelco Salomon Nieuwenhuis ◽

Michal Mokry

Keyword(s):

Therapeutic Potential ◽

Association Studies ◽

Cell Types ◽

Regulatory Elements ◽

Genome Wide Association Studies ◽

Enhancer Activity ◽

Protein Coding ◽

Dna Regulatory Elements ◽

Coding Variants ◽

Novel Therapeutic

Genome-wide association studies have identified over 200 loci associated with IBD. We and others have recently shown that, in addition to variants in protein-coding genes, the majority of the associated loci are related to DNA regulatory elements (DREs). These findings add a dimension to the already complex genetic background of IBD. In this review we summarise the existing evidence on the role of DREs in IBD. We discuss how epigenetic research can be used in candidate gene approaches that take non-coding variants into account and can help to pinpoint the essential pathways and cell types in the pathogenesis of IBD. Despite the increased level of genetic complexity, these findings can contribute to novel therapeutic options that target transcription factor binding and enhancer activity. Finally, we summarise the future directions and challenges of this emerging field.

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Transcriptional Regulation of RUNX1: An Informatics Analysis

Genes ◽

10.3390/genes12081175 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1175

Author(s):

Amarni L. Thomas ◽

Judith Marsman ◽

Jisha Antony ◽

William Schierding ◽

Justin M. O’Sullivan ◽

...

Keyword(s):

Association Studies ◽

Regulatory Elements ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Runx1 Gene ◽

Gene Regulatory Elements ◽

Important Regulator ◽

Aml1 Gene ◽

Regulatory Landscape

The RUNX1/AML1 gene encodes a developmental transcription factor that is an important regulator of haematopoiesis in vertebrates. Genetic disruptions to the RUNX1 gene are frequently associated with acute myeloid leukaemia. Gene regulatory elements (REs), such as enhancers located in non-coding DNA, are likely to be important for Runx1 transcription. Non-coding elements that modulate Runx1 expression have been investigated over several decades, but how and when these REs function remains poorly understood. Here we used bioinformatic methods and functional data to characterise the regulatory landscape of vertebrate Runx1. We identified REs that are conserved between human and mouse, many of which produce enhancer RNAs in diverse tissues. Genome-wide association studies detected single nucleotide polymorphisms in REs, some of which correlate with gene expression quantitative trait loci in tissues in which the RE is active. Our analyses also suggest that REs can be variant in haematological malignancies. In summary, our analysis identifies features of the RUNX1 regulatory landscape that are likely to be important for the regulation of this gene in normal and malignant haematopoiesis.

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Genomic basis of striking fin shapes and colours in the fighting fish

Molecular Biology and Evolution ◽

10.1093/molbev/msab110 ◽

2021 ◽

Author(s):

Le Wang ◽

Fei Sun ◽

Zi Yi Wan ◽

Baoqing Ye ◽

Yanfei Wen ◽

...

Keyword(s):

Evolutionary Biology ◽

Association Studies ◽

Regulatory Element ◽

Regulatory Elements ◽

Major Effect ◽

Betta Splendens ◽

Genome Wide Association Studies ◽

Genome Wide ◽

Phenotypic Variations ◽

Genomic Basis

Abstract Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole genome sequencing, QTL mapping, genome-wide association studies and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double tail mutant was suggested to be caused by a deletion in a zic1/zic4 co-enhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.

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Upregulation of c-MYC in cis through a Large Chromatin Loop Linked to a Cancer Risk-Associated Single-Nucleotide Polymorphism in Colorectal Cancer Cells

Molecular and Cellular Biology ◽

10.1128/mcb.01384-09 ◽

2010 ◽

Vol 30 (6) ◽

pp. 1411-1420 ◽

Cited By ~ 177

Author(s):

Jason B. Wright ◽

Seth J. Brown ◽

Michael D. Cole

Keyword(s):

Cancer Risk ◽

Cancer Cells ◽

Association Studies ◽

Beta Catenin ◽

Genome Wide Association Studies ◽

Chromatin Loop ◽

Nucleotide Polymorphisms ◽

Distal Enhancer ◽

Enhancer Activity ◽

Single Nucleotide

ABSTRACT Genome-wide association studies have mapped many single-nucleotide polymorphisms (SNPs) that are linked to cancer risk, but the mechanism by which most SNPs promote cancer remains undefined. The rs6983267 SNP at 8q24 has been associated with many cancers, yet the SNP falls 335 kb from the nearest gene, c-MYC. We show that the beta-catenin-TCF4 transcription factor complex binds preferentially to the cancer risk-associated rs6983267(G) allele in colon cancer cells. We also show that the rs6983267 SNP has enhancer-related histone marks and can form a 335-kb chromatin loop to interact with the c-MYC promoter. Finally, we show that the SNP has no effect on the efficiency of chromatin looping to the c-MYC promoter but that the cancer risk-associated SNP enhances the expression of the linked c-MYC allele. Thus, cancer risk is a direct consequence of elevated c-MYC expression from increased distal enhancer activity and not from reorganization/creation of the large chromatin loop. The findings of these studies support a mechanism for intergenic SNPs that can promote cancer through the regulation of distal genes by utilizing preexisting large chromatin loops.

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Conserved and distinct roles of kreisler in regulation of the paralogous Hoxa3 and Hoxb3 genes

Development ◽

10.1242/dev.126.4.759 ◽

1999 ◽

Vol 126 (4) ◽

pp. 759-769 ◽

Cited By ~ 3

Author(s):

M. Manzanares ◽

S. Cordes ◽

L. Ariza-McNaughton ◽

V. Sadl ◽

K. Maruthainar ◽

...

Keyword(s):

Binding Sites ◽

Hox Genes ◽

Expression Patterns ◽

Regulatory Elements ◽

Enhancer Activity ◽

Anteroposterior Patterning ◽

Endogenous Gene ◽

Transgenic Embryos ◽

The Individual ◽

Segmental Expression

During anteroposterior patterning of the developing hindbrain, the anterior expression of 3′ Hox genes maps to distinct rhombomeric boundaries and, in many cases, is upregulated in specific segments. Paralogous genes frequently have similar anterior boundaries of expression but it is not known if these are controlled by common mechanisms. The expression of the paralogous Hoxa3 and Hoxb3 genes extends from the posterior spinal cord up to the rhombomere (r) 4/5 boundary and both genes are upregulated specifically in r5. However, in this study, we have found that Hoxa3 expression is also upregulated in r6, showing that there are differences in segmental expression between paralogues. We have used transgenic analysis to investigate the mechanisms underlying the pattern of segmental expression of Hoxa3. We found that the intergenic region between Hoxa3 and Hoxa4 contains several enhancers, which summed together mediate a pattern of expression closely resembling that of the endogenous Hoxa3 gene. One enhancer specifically directs expression in r5 and r6, in a manner that reflects the upregulation of the endogenous gene in these segments. Deletion analysis localized this activity to a 600 bp fragment that was found to contain a single high-affinity binding site for the Maf bZIP protein Krml1, encoded by the kreisler gene. This site is necessary for enhancer activity and when multimerized it is sufficient to direct a kreisler-like pattern in transgenic embryos. Furthermore the r5/r6 enhancer activity is dependent upon endogenous kreisler and is activated by ectopic kreisler expression. This demonstrates that Hoxa3, along with its paralog Hoxb3, is a direct target of kreisler in the mouse hindbrain. Comparisons between the Krml1-binding sites in the Hoxa3 and Hoxb3 enhancers reveal that there are differences in both the number of binding sites and way that kreisler activity is integrated and restricted by these two control regions. Analysis of the individual sites revealed that they have different requirements for mediating r5/r6 and dorsal roof plate expression. Therefore, the restriction of Hoxb3 to r5 and Hoxa3 to r5 and r6, together with expression patterns of Hoxb3 in other vertebrate species suggests that these regulatory elements have a common origin but have later diverged during vertebrate evolution.

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