scholarly journals A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

2021 ◽  
Author(s):  
Arushi Varshney ◽  
Yasuhiro Kyono ◽  
Venkateswaran Ramamoorthi Elangovan ◽  
Collin Wang ◽  
Michael R. Erdos ◽  
...  
Keyword(s):  
Pancreatic Islets ◽  
Transcription Initiation ◽  
Genome Wide Association Study ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Transcriptional Enhancer ◽  
Transcription Start ◽  
Enhancer Activity ◽  
Transcriptional Initiation ◽  
Human Pancreatic Islets

Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ~20% of which are islet-specific and occur mostly distal to known gene TSSs. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validated the transcriptional enhancer activity for 2,279 of 3,378 (~68%) tested islet CAGE elements (5% FDR). TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting active enhancers at GWAS loci.

scholarly journals A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

2021 ◽  
Author(s):  
Arushi Varshney ◽  
Yasuhiro Kyono ◽  
Venkateswaran Ramamoorthi Elangovan ◽  
Collin Wang ◽  
Michael R. Erdos ◽  
...  
Keyword(s):  
Pancreatic Islets ◽  
Transcription Initiation ◽  
Genome Wide Association Study ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Transcriptional Enhancer ◽  
Transcription Start ◽  
Enhancer Activity ◽  
Transcriptional Initiation ◽  
Human Pancreatic Islets

Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ~20% of which are islet-specific and occur mostly distal to known gene TSSs. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validated the transcriptional enhancer activity for 2,279 of 3,378 (~68%) tested islet CAGE elements (5% FDR). TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting active enhancers at GWAS loci.

scholarly journals A transcription start site map in human pancreatic islets reveals functional regulatory signatures

2019 ◽  
Author(s):  
Arushi Varshney ◽  
Yasuhiro Kyono ◽  
Venkateswaran Ramamoorthi Elangovan ◽  
Collin Wang ◽  
Michael R. Erdos ◽  
...  
Keyword(s):  
Pancreatic Islets ◽  
Transcription Initiation ◽  
Genome Wide Association Study ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Transcriptional Enhancer ◽  
Transcription Start ◽  
Enhancer Activity ◽  
Transcriptional Initiation ◽  
Human Pancreatic Islets

AbstractIdentifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ~20% of which are islet-specific and occur mostly distal to known gene TSSs. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validate transcriptional enhancer activity (5% FDR) for 2,279 of 3,378 (~68%) tested islet CAGE elements. TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting functional enhancers at GWAS loci.

scholarly journals A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Brynn N. Akerberg ◽  
Fei Gu ◽  
Nathan J. VanDusen ◽  
Xiaoran Zhang ◽  
Rui Dong ◽  
...  
Keyword(s):  
Heart Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Transcriptional Regulatory Network ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Mouse Heart ◽  
Transcriptional Enhancer ◽  
Enhancer Activity

Abstract Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. These maps show that TF occupancy is dynamic between developmental stages and that multiple TFs often collaboratively occupy the same chromatin region through indirect cooperativity. Multi-TF regions exhibit features of functional regulatory elements, including evolutionary conservation, chromatin accessibility, and activity in transcriptional enhancer assays. H3K27ac, a feature of many enhancers, incompletely overlaps multi-TF regions, and multi-TF regions lacking H3K27ac retain conservation and enhancer activity. TEAD1 is a core component of the cardiac transcriptional network, co-occupying cardiac regulatory regions and controlling cardiomyocyte-specific gene functions. Our study provides a resource for deciphering the cardiac transcriptional regulatory network and gaining insights into the molecular mechanisms governing heart development.

Genetic Effects on Enhancer Activity in Human Pancreatic Islets

Diabetes ◽  
2018 ◽  
Vol 67 (Supplement 1) ◽  
pp. 1706-P ◽  
Author(s):  
ARUSHI VARSHNEY ◽  
STEPHEN PARKER ◽  
Keyword(s):  
Pancreatic Islets ◽  
Genetic Effects ◽  
Enhancer Activity ◽  
Human Pancreatic Islets

scholarly journals ASC proneural transcription factors mediate the timely initiation of the neural program during neuroectodermal to neuroblast transition ensuring progeny fidelity

2021 ◽  
Author(s):  
Vasiliki Theodorou ◽  
Aikaterini Stefanaki ◽  
Minas Drakos ◽  
Dafne Triantafyllou ◽  
Christos Delidakis
Keyword(s):  
Transcription Factors ◽  
Target Genes ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cis Elements ◽  
Enhancer Activity ◽  
Timely Initiation ◽  
Chromatin Dynamics ◽  
Neural Fate ◽  
Neural Specification

Background: ASC/ASCL proneural transcription factors are oncogenic and exhibit impressive reprogramming and pioneer activities. In both Drosophila and mammals, these factors are central in the early specification of the neural fate, where they act in opposition to Notch signalling. However, the role of ASC on the chromatin during CNS neural stem cells birth remains elusive. Results: We investigated the chromatin changes accompanying neural commitment using an integrative genetics and genomics methodology. We found that ASC factors bind equally strongly to two distinct classes of cis-regulatory elements: open regions remodeled earlier during maternal to zygotic transition by Zelda and Zelda-independent, less accessible regions. Both classes cis-elements exhibit enhanced chromatin accessibility during neural specification and correlate with transcriptional regulation of genes involved in many biological processes necessary for neuroblast function. We identified an ASC-Notch regulated TF network that most likely act as the prime regulators of neuroblast function. Using a cohort of ASC target genes, we report that ASC null neuroblasts are defectively specified, remaining initially stalled, lacking expression of many proneural targets and unable to divide. When they eventually start proliferating, they produce compromised progeny. Generation of lacZ reporter lines driven by proneural-bound elements display enhancer activity within neuroblasts and proneural dependency. Therefore, the partial neuroblast identity seen in the absence of ASC genes is driven by other, proneural-independent, cis-elements. Neuroblast impairment and the late differentiation defects of ASC mutants are corrected by ectodermal induction of individual ASC genes but not by individual members of the TF network downstream of ASC. However, in wild type embryos induction of individual members of this network induces CNS hyperplasia, suggesting that they synergize with the activating function of ASC to establish the chromatin dynamics that promote neural specification. Conclusion: ASC factors bind a large number of enhancers to orchestrate the timely activation of the neural chromatin program during neuroectodermal to neuroblast transition. This early chromatin remodeling is crucial for both neuroblast homeostasis as well as future progeny fidelity.

scholarly journals Systematic dissection of genomic features determining transcription factor binding and enhancer function

2017 ◽  
Vol 114 (7) ◽  
pp. E1291-E1300 ◽  
Author(s):  
Sharon R. Grossman ◽  
Xiaolan Zhang ◽  
Li Wang ◽  
Jesse Engreitz ◽  
Alexandre Melnikov ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Binding Assays ◽  
Genomic Locus ◽  
Enhancer Activity ◽  
Genomic Features ◽  
Motif Site ◽  
Reporter Assays ◽  
Enhancer Function

Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function—including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis. We show that distinct sets of features govern PPARγ binding vs. enhancer activity. PPARγ binding is largely governed by the affinity of the specific motif site and higher-order features of the larger genomic locus, such as chromatin accessibility. In contrast, the enhancer activity of PPARγ binding sites depends on varying contributions from dozens of TFs in the immediate vicinity, including interactions between combinations of these TFs. Different pairs of motifs follow different interaction rules, including subadditive, additive, and superadditive interactions among specific classes of TFs, with both spatially constrained and flexible grammars. Our results provide a paradigm for the systematic characterization of the genomic features underlying regulatory elements, applicable to the design of synthetic regulatory elements or the interpretation of human genetic variation.

scholarly journals Pancreatic islet chromatin accessibility and conformation defines distal enhancer networks of type 2 diabetes risk

2018 ◽  
Author(s):  
William W Greenwald ◽  
Joshua Chiou ◽  
Jian Yan ◽  
Yunjiang Qiu ◽  
Ning Dai ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Pancreatic Islets ◽  
Regulatory Networks ◽  
Complex Disease ◽  
Protein Transport ◽  
Target Genes ◽  
Regulatory Elements ◽  
Distal Enhancer ◽  
Enhancer Activity

AbstractThe gene targets of enhancer activity in pancreatic islets are largely unknown, impeding discovery of islet regulatory networks involved in type 2 diabetes (T2D) risk. We mapped chromatin state, accessibility and conformation using ChIP-seq, ATAC-seq and Hi-C in human pancreatic islets, which we integrated with T2D genetic fine-mapping and islet expression QTL data. Active islet regulatory elements preferentially interacted with other active elements, often at distances over 1MB, and we identified target genes for thousands of distal islet enhancers. A third of T2D risk signals mapped in islet enhancers, and target genes regulated by these signals were specifically involved in processes related to protein transport and secretion. Among implicated target genes of T2D islet enhancer signals with no prior known role in islet function, we demonstrated that reduced IGF2BP2 activity in mouse islets leads to impaired glucose-stimulated insulin secretion. These results link distal islet enhancer regulation of protein secretion and transport to genetic risk of T2D, and highlight the utility of high-throughput chromatin conformation maps to uncover the gene regulatory networks of complex disease.

scholarly journals Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Luisa Nardini ◽  
Inge Holm ◽  
Adrien Pain ◽  
Emmanuel Bischoff ◽  
Daryl M. Gohl ◽  
...  
Keyword(s):  
Gene Expression ◽  
Malaria Vector ◽  
Functional Activity ◽  
Regulatory Elements ◽  
Transmission Efficiency ◽  
Luciferase Reporter ◽  
Anopheles Coluzzii ◽  
Transcriptional Enhancer ◽  
Enhancer Activity ◽  
Enhancer Sequences

Abstract Enhancers are cis-regulatory elements that control most of the developmental and spatial gene expression in eukaryotes. Genetic variation of enhancer sequences is known to influence phenotypes, but the effect of enhancer variation upon enhancer functional activity and downstream phenotypes has barely been examined in any species. In the African malaria vector, Anopheles coluzzii, we identified candidate enhancers in the proximity of genes relevant for immunity, insecticide resistance, and development. The candidate enhancers were functionally validated using luciferase reporter assays, and their activity was found to be essentially independent of their physical orientation, a typical property of enhancers. All of the enhancers segregated genetically polymorphic alleles, which displayed significantly different levels of functional activity. Deletion mutagenesis and functional testing revealed a fine structure of positive and negative regulatory elements that modulate activity of the enhancer core. Enhancer polymorphisms segregate in wild A. coluzzii populations in West Africa. Thus, enhancer variants that modify target gene expression leading to likely phenotypic consequences are frequent in nature. These results demonstrate the existence of naturally polymorphic A. coluzzii enhancers, which may help explain important differences between individuals or populations for malaria transmission efficiency and vector adaptation to the environment.

scholarly journals Recent advances in high-throughput approaches to dissect enhancer function

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 939 ◽  
Author(s):  
David Santiago-Algarra ◽  
Lan T.M. Dao ◽  
Lydie Pradel ◽  
Alexandre España ◽  
Salvatore Spicuglia
Keyword(s):  
High Throughput ◽  
Regulatory Elements ◽  
Genetic Alterations ◽  
Regulatory Sequences ◽  
Transcription Start ◽  
Enhancer Activity ◽  
Recent Advances ◽  
Reporter Assays ◽  
Enhancer Function ◽  
Higher Eukaryotes

The regulation of gene transcription in higher eukaryotes is accomplished through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. It is now well acknowledged that enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Many strategies have been developed to identify and characterize enhancers. Here, we discuss recent advances in high-throughput approaches to assess enhancer activity, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies. We highlight how these approaches contribute toward a better understanding of enhancer function, eventually leading to the discovery of new types of regulatory sequences, and how the alteration of enhancers can affect transcriptional regulation.

scholarly journals A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

2016 ◽  
Author(s):  
Fumitaka Inoue ◽  
Martin Kircher ◽  
Beth Martin ◽  
Gregory M. Cooper ◽  
Daniela M. Witten ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Sequence Information ◽  
Regulatory Sequences ◽  
Enhancer Activity ◽  
Functional Activities ◽  
Reporter Assays ◽  
Bona Fide ◽  
Massively Parallel Reporter Assay

AbstractCandidate enhancers can be identified on the basis of chromatin modifications, the binding of chromatin modifiers and transcription factors and cofactors, or chromatin accessibility. However, validating such candidates as bona fide enhancers requires functional characterization, typically achieved through reporter assays that test whether a sequence can drive expression of a transcriptional reporter via a minimal promoter. A longstanding concern is that reporter assays are mainly implemented on episomes, which are thought to lack physiological chromatin. However, the magnitude and determinants of differences incis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this question in a systematic manner, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2,236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated with different subsets of ENCODE annotations. The results of chromosomally-based reporter assays are also more reproducible and more strongly predictable by both ENCODE annotations and sequence-based models. With a linear model that combines chromatin annotations and sequence information, we achieve a Pearson’s R2of 0.347 for predicting the results of chromosomally integrated reporter assays. This level of prediction is better than with either chromatin annotations or sequence information alone and also outperforms predictive models of episomal assays. Our results have broad implications for howcis-regulatory elements are identified, prioritized and functionally validated.

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