ATAC-STARR-seq v2

2021 ◽  
Author(s):  
Tyler Hansen ◽  
Emily Hodges
Keyword(s):  
Regulatory Region ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
High Signal ◽  
Regulatory Pathways ◽  
Information Accessibility ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Accessible Chromatin

Massively parallel reporter assays test the capacity of putative cis-regulatory elements (CREs) to drive transcription on a genome-wide scale. In nearly all cases, chromatin accessibility is necessary to drive activity, so most CREs are inactive due to chromatin context rather than intrinsic DNA sequence properties. Here, we combined assay for transposase-accessible chromatin (ATAC-seq) with self-transcribing active regulatory region sequencing (STARR-seq) to selectively assay the regulatory potential of nucleosome-free DNA genome-wide. Our approach enabled high-resolution testing of ~50 million unique DNA fragments tiling ~101,000 accessible chromatin regions in human lymphoblastoid cells. To illustrate the application of our approach, we show that 30% of all accessible regions contain an activator, a silencer or both. Benchmarking against standard ATAC-seq, our approach faithfully captures chromatin accessibility and transcription factor (TF) footprints with high signal-to-noise. Integrating three layers of genomic information (accessibility, TF occupancy, and activity) provided by ATAC-STARR-seq, we stratified active and silent CREs by the presence of several TF footprints and show that CREs with specific TF combinations are associated with distinct gene regulatory pathways. Altogether, these data highlight the power of ATAC-STARR-seq to comprehensively investigate the regulatory landscape of the human genome from a single DNA source.

scholarly journals Integrative analysis of epigenetics data identifies gene-specific regulatory elements

2019 ◽  
Author(s):  
Florian Schmidt ◽  
Alexander Marx ◽  
Marie Hebel ◽  
Martin Wegner ◽  
Nina Baumgarten ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Genome Wide ◽  
A Genome ◽  
Gene Level ◽  
Regulatory Landscape ◽  
Regulatory Sites ◽  
Validation Experiments

AbstractUnderstanding the complexity of transcriptional regulation is a major goal of computational biology. Because experimental linkage of regulatory sites to genes is challenging, computational methods considering epigenomics data have been proposed to create tissue-specific regulatory maps. However, we showed that these approaches are not well suited to account for the variations of the regulatory landscape between cell-types. To overcome these drawbacks, we developed a new method called STITCHIT, that identifies and links putative regulatory sites to genes. Within STITCHIT, we consider the chromatin accessibility signal of all samples jointly to identify regions exhibiting a signal variation related to the expression of a distinct gene. STITCHIToutperforms previous approaches in various validation experiments and was used with a genome-wide CRISPR-Cas9 screen to prioritize novel doxorubicin-resistance genes and their associated non-coding regulatory regions. We believe that our work paves the way for a more refined understanding of transcriptional regulation at the gene-level.

Cis-regulatory elements and human evolution

2014 ◽  
Author(s):  
Adam Siepel ◽  
Leonardo Arbiza
Keyword(s):  
Transcriptional Regulation ◽  
Human Evolution ◽  
Large Scale ◽  
Regulatory Elements ◽  
Data Sets ◽  
Regulatory Evolution ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Human Polymorphism

Modification of gene regulation has long been considered an important force in human evolution, particularly through changes to cis-regulatory elements (CREs) that function in transcriptional regulation. For decades, however, the study of cis-regulatory evolution was severely limited by the available data. New data sets describing the locations of CREs and genetic variation within and between species have now made it possible to study CRE evolution much more directly on a genome-wide scale. Here, we review recent research on the evolution of CREs in humans based on large-scale genomic data sets. We consider inferences based on primate divergence,human polymorphism, and combinations of divergence and polymorphism. We then consider "new frontiers" in this field stemming from recent research on transcriptional regulation.

scholarly journals Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale

2011 ◽  
Vol 6 (1) ◽  
pp. 15 ◽  
Author(s):  
Evgeny Shmelkov ◽  
Zuojian Tang ◽  
Iannis Aifantis ◽  
Alexander Statnikov
Keyword(s):  
Regulatory Pathways ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
A Genome ◽  
Wide Scale

scholarly journals Chromatin accessibility analysis uncovers regulatory element landscape in prostate cancer progression

2020 ◽  
Author(s):  
Joonas Uusi-Mäkelä ◽  
Ebrahim Afyounian ◽  
Francesco Tabaro ◽  
Tomi Häkkinen ◽  
Alessandro Lussana ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Progression ◽  
Regulatory Element ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Prostate Cancer Progression ◽  
Accessibility Analysis ◽  
A Genome

AbstractAberrant oncogene functions and structural variation alter the chromatin structure in cancer cells. While gene regulation by chromatin states has been studied extensively, chromatin accessibility and its relevance in aberrant gene expression during prostate cancer progression is not well understood. Here, we report a genome-wide chromatin accessibility analysis of clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC) and castration-resistant prostate cancer (CRPC) and integrative analysis with transcriptome, methylome, and proteome profiles of the same samples to uncover disease-relevant regulatory elements and their association to altered gene expression during prostate cancer progression. While promoter accessibility is consistent during disease initiation and progression, at distal sites chromatin accessibility is variable enabling transcription factors (TFs) binding patterns that are differently activated in different patients and disease stages. We identify consistent progression-related chromatin alterations during the progression to CRPC. By studying the TF binding patterns, we demonstrate the activation and suppression of androgen receptor-driven regulatory programs during PC progression and identify complementary TF regulatory modules characterized by e.g. MYC and glucocorticoid receptor. By correlation analysis we assign at least one putative regulatory region for 62% of genes and 85% of proteins differentially expressed during prostate cancer progression. Taken together, our analysis of the chromatin landscape in PC identifies putative regulatory elements for the majority of cancer-associated genes and characterizes their impact on the cancer phenotype.

scholarly journals Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 186
Author(s):  
Elise J. Farley ◽  
Heather Eggleston ◽  
Michelle M. Riehle
Keyword(s):  
Regulatory Elements ◽  
Protein Coding ◽  
Apicomplexan Parasites ◽  
Susceptibility To Infection ◽  
Genome Wide ◽  
A Genome ◽  
Gene And Protein Expression ◽  
Wide Scale ◽  
Differential Gene ◽  
Analytical Approaches

The portion of the mosquito genome that does not code for proteins contains regulatory elements that likely underlie variation for important phenotypes including resistance and susceptibility to infection with arboviruses and Apicomplexan parasites. Filtering the non-coding genome to uncover these functional elements is an expanding area of research, though identification of non-coding regulatory elements is challenging due to the lack of an amino acid-like code for the non-coding genome and a lack of sequence conservation across species. This review focuses on three types of non-coding regulatory elements: (1) microRNAs (miRNAs), (2) long non-coding RNAs (lncRNAs), and (3) enhancers, and summarizes current advances in technical and analytical approaches for measurement of each of these elements on a genome-wide scale. The review also summarizes and highlights novel findings following application of these techniques in mosquito-borne disease research. Looking beyond the protein-coding genome is essential for understanding the complexities that underlie differential gene expression in response to arboviral or parasite infection in mosquito disease vectors. A comprehensive understanding of the regulation of gene and protein expression will inform transgenic and other vector control methods rooted in naturally segregating genetic variation.

scholarly journals Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies

2017 ◽  
Author(s):  
Dinesh Manandhar ◽  
Lingyun Song ◽  
Ami Kabadi ◽  
Jennifer Kwon ◽  
Lee Edsall ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Remodeling ◽  
Global Gene Expression ◽  
Chromatin Accessibility ◽  
Marker Genes ◽  
Target Cells ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Quantitative Analyses

Our current understanding of cellular transdifferentiation systems is limited. It is oftentimes unknown, at a genome-wide scale, how much transdifferentiated cells differ quantitatively from both the starting cells and the target cells. Focusing on transdifferentiation of primary human skin fibroblasts by forced expression of myogenic transcription factor MyoD, we performed quantitative analyses of gene expression and chromatin accessibility profiles of transdifferentiated cells compared to fibroblasts and myoblasts. In this system, we find that while many of the early muscle marker genes are reprogrammed, global gene expression and accessibility changes are still incomplete when compared to myoblasts. In addition, we find evidence of epigenetic memory in the transdifferentiated cells, with reminiscent features of fibroblasts being visible both in chromatin accessibility and gene expression. Quantitative analyses revealed a continuum of changes in chromatin accessibility induced by MyoD, and a strong correlation between chromatin-remodeling deficiencies and incomplete gene expression reprogramming. Classification analyses identified genetic and epigenetic features that distinguish reprogrammed from non-reprogrammed sites, and suggested ways to potentially improve transdifferentiation efficiency. Our approach for combining gene expression, DNA accessibility, and protein-DNA binding data to quantify and characterize the efficiency of cellular transdifferentiation on a genome-wide scale can be applied to any transdifferentiation system.

Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors

2021 ◽  
Author(s):  
Shelsa S. Marcel ◽  
Austin L. Quimby ◽  
Melodie P. Noel ◽  
Oscar C. Jaimes ◽  
Marjan Mehrab-Mohseni ◽  
...  
Keyword(s):  
Human Tumor ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Primary Tumors ◽  
Genome Wide ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Cellular Components ◽  
Accessible Chromatin

Chromatin accessibility states that influence gene expression and other nuclear processes can be altered in disease. The constellation of transcription factors and chromatin regulatory complexes in cells results in characteristic patterns of chromatin accessibility. The study of these patterns in tissues has been limited because existing chromatin accessibility assays are ineffective for archival formalin-fixed, paraffin-embedded (FFPE) tissues. We have developed a method to efficiently extract intact chromatin from archival tissue via enhanced cavitation with a nanodroplet reagent consisting of a lipid shell with a liquid perfluorocarbon core. Inclusion of nanodroplets during the extraction of chromatin from FFPE tissues enhances the recovery of intact accessible and nucleosome-bound chromatin. We show that the addition of nanodroplets to the chromatin accessibility assay formaldehyde-assisted isolation of regulatory elements (FAIRE), does not affect the accessible chromatin signal. Applying the technique to FFPE human tumor xenografts, we identified tumor-relevant regions of accessible chromatin shared with those identified in primary tumors. Further, we deconvoluted non-tumor signal to identify cellular components of the tumor microenvironment. Incorporation of this method of enhanced cavitation into FAIRE offers the potential for extending chromatin accessibility to clinical diagnosis and personalized medicine, while also enabling the exploration of gene regulatory mechanisms in archival samples.

scholarly journals Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development

2021 ◽  
Author(s):  
Andrew Clugston ◽  
Andrew Bodnar ◽  
Débora Malta Cerqueira ◽  
Yu Leng Phua ◽  
Alyssa Lawler ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Kidney Development ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Microrna Expression ◽  
Genome Wide ◽  
Extracellular Matrix Interactions ◽  
Genomic Regions ◽  
Nephron Progenitor ◽  
Accessible Chromatin

AbstractMammalian nephrons originate from a population of nephron progenitor cells (NPCs), and it is known that NPCs’ transcriptomes change throughout nephrogenesis during healthy kidney development. To characterize chromatin accessibility and microRNA (miRNA) expression throughout this process, we collected NPCs from mouse kidneys at embryonic day 14.5 (E14.5) and postnatal day zero (P0) and assayed cells for transposase-accessible chromatin and small RNA expression. We observe 46,374 genomic regions of accessible chromatin, with 2,103 showing significant changes in accessibility between E14.5 and P0. In addition, we detect 1,104 known microRNAs, with 114 showing significant changes in expression. Genome-wide, changes in DNA accessibility and microRNA expression highlight biological processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways such as Notch. Furthermore, our data identify novel candidate cis-regulatory elements for Eya1 and Pax8, both genes with a role in NPC differentiation; we also associate expression-changing microRNAs, including let-7-5p, miR-125b-5p, miR-181a-2-3p, and miR-9-3p, with candidate cis-regulatory elements. Overall, our data characterize NPCs during kidney development and point out new candidate regulatory elements for genes and microRNA with key roles in nephrogenesis.

scholarly journals Chromatin accessibility dynamics of myogenesis at single cell resolution

2017 ◽  
Author(s):  
Hannah A. Pliner ◽  
Jonathan Packer ◽  
José L. McFaline-Figueroa ◽  
Darren A. Cusanovich ◽  
Riza Daza ◽  
...  
Keyword(s):  
Single Cell ◽  
Chromatin Remodeling ◽  
Target Genes ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
New Approach ◽  
Genome Wide ◽  
A Genome ◽  
Histone Modifying Enzymes ◽  
Dna Regulatory Elements

AbstractOver a million DNA regulatory elements have been cataloged in the human genome, but linking these elements to the genes that they regulate remains challenging. We introduce Cicero, a statistical method that connects regulatory elements to target genes using single cell chromatin accessibility data. We apply Cicero to investigate how thousands of dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of co-accessible regulatory elements linked by Cicero meet criteria of “chromatin hubs”, in that they are physically proximal, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of gene expression. Pseudotemporal analysis revealed a subset of elements bound by MYOD in myoblasts that exhibit early opening, potentially serving as the initial sites of recruitment of chromatin remodeling and histone-modifying enzymes. The methodological framework described here constitutes a powerful new approach for elucidating the architecture, grammar and mechanisms of cis-regulation on a genome-wide basis.

scholarly journals A genome-wide map of regulatory elements in zebrafish

Lab Animal ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 17-17
Author(s):  
Alexandra Le Bras
Keyword(s):  
Regulatory Elements ◽  
Genome Wide ◽  
A Genome
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