Chromatin accessibility: a window into the genome.

paper Cited Public

Authors: Tsompana, Maria; Buck, Michael J
Year: 2014
Journal: Epigenetics & chromatin
PMID: 25473421
DOI: 10.1186/1756-8935-7-33
PMCID: PMC4253006

#	Section	Preview
0	Introduction: chromatin accessibility	Eukaryotic chromatin is tightly packaged into an array of nucleosomes, each consisting of a histone…
1	Introduction: chromatin accessibility	Nucleosome eviction or destabilization at promoters and enhancers results from the binding of…
2	Introduction: chromatin accessibility	Low-throughput experiments in Drosophila using DNase I and MNase treatment, provided the first…
3	Review — Assays for genome-wide chromatin accessibility — General considerations	Chromatin accessibility approaches measure directly the effect of chromatin structure modifications…
4	Review — Assays for genome-wide chromatin accessibility — General considerations	discuss chromatin accessibility assays that directly (DNase-seq, FAIRE-seq and ATAC-seq) isolate…
5	Review — Assays for genome-wide chromatin accessibility — General considerations	of the human genome. FAIRE-seq Any cell type 100,000 to 10 million cellsPaired-end or…
6	Review — Assays for genome-wide chromatin accessibility — MNase-seq: an indirect chromatin accessibility assay	MNase is commonly reported as a single-strand-specific endo-exonuclease, although its exonuclease…
7	Review — Assays for genome-wide chromatin accessibility — MNase-seq: an indirect chromatin accessibility assay	MNase-seq thus probes chromatin accessibility indirectly by unveiling the areas of the genome…
8	Review — Assays for genome-wide chromatin accessibility — MNase-seq: an indirect chromatin accessibility assay	Important considerations in the design of MNase-seq experiments include extent of chromatin…
9	Review — Assays for genome-wide chromatin accessibility — MNase-seq: an indirect chromatin accessibility assay	However, the cause of differences in MNase-seq output across differential levels of enzymatic…
10	Review — Assays for genome-wide chromatin accessibility — MNase-seq: an indirect chromatin accessibility assay	Overall, MNase-seq is a superior method for probing genome-wide nucleosome distributions and also…
11	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — DNase-seq	Historically, open chromatin has been identified by the hypersensitivity of genomic sites to…
12	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — DNase-seq	Traditionally, identification of DHSs has been based on Southern blotting with indirect end-labeling…
13	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — DNase-seq	embedded into low-melt gel agarose plugs to prevent further shearing. Optimal digestions are…
14	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — DNase-seq	DNase-seq has been extensively used by the ENCODE consortium [26] and others to unveil cell-specific…
15	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — DNase-seq	The main controversy over DNase-seq is the ability for DNase I to introduce cleavage bias [31, 79,…
16	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — DNase-seq	Less concerning limitations of DNase-seq are that it requires many cells and involves many sample…
17	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — FAIRE-seq	One of the easiest methods for directly probing nucleosome-depleted areas of a genome is FAIRE…
18	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — FAIRE-seq	Initially demonstrated to identify accessible regulatory elements in Saccharomyces cerevisiae[90],…
19	Review — Assays for genome-wide chromatin accessibility — Direct chromatin accessibility assays — FAIRE-seq	Overall, FAIRE enriches directly for areas of active chromatin, with the added benefit that the…

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In this knowledge base

Title	Year	PMID
Integrated single-cell multiomic profiling of caudate nucleus suggests key mechanisms in alcohol use disorder.	2025	41083468

External

Title	Authors	Journal	Year	Link
An experimentally-informed polymer model reveals high resolution organization of genomic loci.	Mittal R et al.	—	2026	→
ATAC-Seq and RNA-Seq Integration Reveals Chromatin Accessibility and Transcriptional Dynamics During Fruit Color Development in Mulberry.	Zeng Y et al.	—	2026	→
Chromatin accessibility landscapes define stromal cell identities across tissues.	Nooranikhojasteh A et al.	—	2026	→
Deacetylase-independent HDAC1 condensation defines temozolomide response in glioblastoma.	Zhang Q et al.	—	2026	→
Euchromatin and Heterochromatin: Implications for DNA Accessibility and Transcription.	Minami K et al.	—	2026	→
Exploratory analysis of epigenetic dynamics and small extracellular vesicles in Penaeus vannamei hemocytes under inactivated Vibrio parahaemolyticus priming.	Lin YR et al.	—	2026	→
Practical NicE-seq workflow for chromatin accessibility analysis in plants.	Bader ZE et al.	—	2026	→
Single cell multiomic analysis of the impact of Delta-9-tetrahydrocannabinol on HIV infected CD4 T cells.	Ashokkumar M et al.	—	2026	→
BIT: Bayesian Identification of Transcriptional regulators from epigenomics-based query region sets.	Lu Z et al.	—	2025	→
cis- and trans-elements for the transcriptional regulation of sugar responsive genes: from current knowledge to future applications.	Cruz-López MI et al.	—	2025	→
Comprehensive guide for epigenetics and transcriptomics data quality control.	Comendul A et al.	—	2025	→
Convergent Evolution and the Epigenome.	Alvarado SG et al.	—	2025	→
Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.	Chiu HS et al.	—	2025	→
Cross-cellular analysis of chromatin accessibility markers H3K4me3 and DNase in the context of detecting cell-identity genes: An "all-or-nothing" approach.	Low BH et al.	—	2025	→
Crosstalk between metabolism and epigenetics during macrophage polarization.	Zhang K et al.	—	2025	→
Decoding the epigenetic and transcriptional basis of direct cardiac reprogramming.	Peng WG et al.	—	2025	→
Defining transcription factor nucleosome binding with Pioneer-seq.	Tsompana M et al.	—	2025	→
Differential regulation during development, aging, and disease implies heart cell specific functions of the Mediator Complex.	Kolonay DW et al.	—	2025	→
DNA intercalating drugs: Mechanisms of action in cancer treatment.	Oyeyode M et al.	—	2025	→
Dynamic chromatin accessibility landscape changes in cardiac fibrosis.	Liu ZY et al.	—	2025	→
EpiMapper: A new tool for analyzing high-throughput sequencing from CUT&Tag.	Dragland JS et al.	—	2025	→
Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea.	Locatelli NS et al.	—	2025	→
HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype.	Alfano V et al.	—	2025	→
IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder.	Li Y et al.	—	2025	→
Inferring differential protein binding from time-series chromatin accessibility data.	Mitra S et al.	—	2025	→
INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation.	Liu Y et al.	—	2025	→
Integrated single-cell multiomic profiling of caudate nucleus suggests key mechanisms in alcohol use disorder.	Green NC et al.	—	2025	→
Integrative Analysis of ATAC-Seq and RNA-Seq Identifies Key Genes Affecting Muscle Development in Ningxiang Pigs.	Tan W et al.	—	2025	→
Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.	Fan BL et al.	—	2025	→
ISDH-seq: a robust methodology for profiling and characterization of open chromatin.	Li Z et al.	—	2025	→
NuclampFISH enables cell sorting based on nuclear RNA expression for chromatin analysis.	Liu Y et al.	—	2025	→
Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites.	Wilson PD et al.	—	2025	→
Probing the effect of PEG-DNA interactions and buffer viscosity on tethered DNA in shear flow.	Zohra FT et al.	—	2025	→
Protocol for transcriptomic and epigenomic analysis of JAK inhibitor sensitivity in IFN-γ-primed human macrophages using ATAC-seq and RNA-seq.	Kwon G et al.	—	2025	→
The Converging Roles of Nucleases and Helicases in Genome Maintenance and the Aging Process.	Margariti A et al.	—	2025	→
The Link Between TGF-β Signaling and Chromatin Dynamics Takes an Unexpected Path.	Mallo M	—	2025	→
The role of DNA content in shaping chromatin architecture and gene expression.	Barragán-Rosillo AC et al.	—	2025	→
Time-course transcriptome and chromatin accessibility analyses reveal the dynamic transcriptional regulation shaping spikelet hull size.	Chen S et al.	—	2025	→
Transcriptional interferences ensure one olfactory receptor per ant neuron.	Sieriebriennikov B et al.	—	2025	→
Transient alterations in nucleosome distribution and sensitivity to nuclease define the THP-1 monocyte-to-macrophage transition.	Benoit JM et al.	—	2025	→
A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.	Li Z et al.	—	2024	→
Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets.	Lu Z et al.	—	2024	→
Century-old chromatin architecture revealed in formalin-fixed vertebrates.	Hahn EE et al.	—	2024	→
Chromatin accessibility mediated transcriptome changes contribute to flavor substance alterations and jasmonic acid hyperaccumulation during oolong tea withering process.	Kong W et al.	—	2024	→
Chromatin accessibility profiling reveals that human fibroblasts respond to mechanical stimulation in a cell-specific manner.	Logan NJ et al.	—	2024	→
Chromatin remodeling in tissue stem cell fate determination.	Li X et al.	—	2024	→
Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription.	Altıntaş UB et al.	—	2024	→
Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements.	Silver BD et al.	—	2024	→
Differential chromatin accessibility and Gene Expression Associated with Backfat Deposition in pigs.	Zhang Z et al.	—	2024	→
Dissecting the Immune System through Gene Regulation.	Yoshida H	—	2024	→
Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development.	Wang Y et al.	—	2024	→
Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.	Sunitha Kumary VUN et al.	—	2024	→
Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injury.	Long H et al.	—	2024	→
Eomes-dependent mitochondrial regulation promotes survival of pathogenic CD4+ T cells during inflammation.	Joulia E et al.	—	2024	→
Epigenetic Effects of Resveratrol on Oncogenic Signaling in Breast Cancer.	Kurzava Kendall L et al.	—	2024	→
Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.	Hu G et al.	—	2024	→
Experimental evidence for cancer resistance in a bat species.	Hua R et al.	—	2024	→
Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility and regulatory DNA elements under drought stress in rice cultivars.	Rajkumar MS et al.	—	2024	→
How chromatin senses plant hormones.	Shao Z et al.	—	2024	→
Increased DNA damage in full-grown oocytes is correlated with diminished autophagy activation.	Sun F et al.	—	2024	→
Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa.	Li M et al.	—	2024	→
NFIC mediates m6A mRNA methylation to orchestrate transcriptional and post-transcriptional regulation to represses malignant phenotype of non-small cell lung cancer cells.	Shi K et al.	—	2024	→
OliTag-seq enhances in cellulo detection of CRISPR-Cas9 off-targets.	Yang ZX et al.	—	2024	→
scACT: Accurate Cross-modality Translation via Cycle-consistent Training from Unpaired Single-cell Data.	Xu S et al.	—	2024	→
Self-assembling viral histones are evolutionary intermediates between archaeal and eukaryotic nucleosomes.	Irwin NAT et al.	—	2024	→
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue.	Farzad N et al.	—	2024	→
The importance of DNA sequence for nucleosome positioning in transcriptional regulation.	Sahrhage M et al.	—	2024	→
The importance of functional genomics studies in precision rheumatology.	Piedade AP et al.	—	2024	→
The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9.	Klein DC et al.	—	2024	→
Transcriptional landscape and dynamics involved in sugar and acid accumulation during apple fruit development.	Li B et al.	—	2024	→
Transcriptomic Approaches to Cardiomyocyte-Biomaterial Interactions: A Review.	Wen Y et al.	—	2024	→
Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.	Wirthlin ME et al.	—	2024	→
WRN loss accelerates abnormal adipocyte metabolism in Werner syndrome.	Tian Y et al.	—	2024	→
Aneuploidy effects on human gene expression across three cell types.	Liu S et al.	—	2023	→
Application of ATAC-seq in tumor-specific T cell exhaustion.	Chen C et al.	—	2023	→
BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes.	Weng Z et al.	—	2023	→
C/EBPα Confers Dependence to Fatty Acid Anabolic Pathways and Vulnerability to Lipid Oxidative Stress-Induced Ferroptosis in FLT3-Mutant Leukemia.	Sabatier M et al.	—	2023	→
Cellcano: supervised cell type identification for single cell ATAC-seq data.	Ma W et al.	—	2023	→
Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling.	Sandoval L et al.	—	2023	→
Characterization of the angiotensin-converting enzyme 2 (ACE2), the main receptor for the SARS-CoV-2 virus.	Jami G et al.	—	2023	→
Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development.	Huang Y et al.	—	2023	→
cisDynet: An integrated platform for modeling gene-regulatory dynamics and networks.	Zhu T et al.	—	2023	→
Comparative valuation of the chlorpyrifos, acetamiprid, and lambda-cyhalothrin toxicity and their hematological and histopathological consequences in pigeons.	Noreen S et al.	—	2023	→
C<sub>4</sub> gene induction during de-etiolation evolved through changes in cis to allow integration with ancestral C<sub>3</sub> gene regulatory networks.	Singh P et al.	—	2023	→
Dose rate dependent reduction in chromatin accessibility at transcriptional start sites long time after exposure to gamma radiation.	Dahl H et al.	—	2023	→
Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis.	Cheng J et al.	—	2023	→
Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in <i>Aegilops tauschii</i>.	Kong C et al.	—	2023	→
Factors and Methods for the Detection of Gene Expression Regulation.	Wang M et al.	—	2023	→
Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq.	Zhang A et al.	—	2023	→
High-capacity sample multiplexing for single cell chromatin accessibility profiling.	Booth GT et al.	—	2023	→
Innate Immune Memory in Macrophages.	Maheshwari A	—	2023	→
Integration of ATAC-Seq and RNA-Seq reveals FOSL2 drives human liver progenitor-like cell aging by regulating inflammatory factors.	Ding M et al.	—	2023	→
Integration of RNA-seq and ATAC-seq analyzes the effect of low dose neutron-γ radiation on gene expression of lymphocytes from oilfield logging workers.	Li W et al.	—	2023	→
Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells.	Senapati P et al.	—	2023	→
Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA.	Lainscsek X et al.	—	2023	→
Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique.	Nowling RJ et al.	—	2023	→
Prevention, Diagnosis and Eradication of Mycoplasma Contamination in Cell Culture.	Huang X et al.	—	2023	→
Profiling Chromatin Accessibility Responses in Goat Bronchial Epithelial Cells Infected with <i>Pasteurella multocida</i>.	Chen Q et al.	—	2023	→
Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches.	Chomthong M et al.	—	2023	→
RefTM: reference-guided topic modeling of single-cell chromatin accessibility data.	Zhang Z et al.	—	2023	→
Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2.	Suresh V et al.	—	2023	→
The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure.	Kraus L et al.	—	2023	→
Transcriptional responses of cancer cells to heat shock-inducing stimuli involve amplification of robust HSF1 binding.	Dastidar SG et al.	—	2023	→
Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells.	Chin HG et al.	—	2023	→
When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development.	Kretschmer M et al.	—	2023	→
Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation.	Huang N et al.	—	2022	→
A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells.	Li S et al.	—	2022	→
A Multigraph-Based Representation of Hi-C Data.	Makai D et al.	—	2022	→
A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses.	Coda DM et al.	—	2022	→
CharID: a two-step model for universal prediction of interactions between chromatin accessible regions.	Shen Y et al.	—	2022	→
Chromatin Dynamics in Digestive System Cancer: Commander and Regulator.	Li Z et al.	—	2022	→
Computational modeling of chromatin accessibility identified important epigenomic regulators.	Zhao Y et al.	—	2022	→
Confined migration induces heterochromatin formation and alters chromatin accessibility.	Hsia CR et al.	—	2022	→
Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins.	Nanduri R et al.	—	2022	→
Epigenetics of wheat-rust interaction: an update.	Shilpa et al.	—	2022	→
Epigenomic dynamics of early Xenopus Embryos.	Zhou JJ et al.	—	2022	→
Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes.	Schächner C et al.	—	2022	→
Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud.	Koyano-Nakagawa N et al.	—	2022	→
Fragile sites, chromosomal lesions, tandem repeats, and disease.	Mirceta M et al.	—	2022	→
Mapping open chromatin by ATAC-seq in bread wheat.	Wang X et al.	—	2022	→
MEPP: more transparent motif enrichment by profiling positional correlations.	Delos Santos NP et al.	—	2022	→
Proximal and Distal Regions of Pathogenic Th17 Related Chromatin Loci Are Sequentially Accessible During Pathogenicity of Th17.	Hu L et al.	—	2022	→
Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5.	Collins JM et al.	—	2022	→
SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs.	Cao L et al.	—	2022	→
SMOC: a smart model for open chromatin region prediction in rice genomes.	Guo W et al.	—	2022	→
Tethered MNase Structure Probing as Versatile Technique for Analyzing RNPs Using Tagging Cassettes for Homologous Recombination in Saccharomyces cerevisiae.	Teubl F et al.	—	2022	→
The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.	McKay LGA et al.	—	2022	→
The landscape of accessible chromatin in quiescent cardiac fibroblasts and cardiac fibroblasts activated after myocardial infarction.	Li C et al.	—	2022	→
Thermodynamics-based modeling reveals regulatory effects of indirect transcription factor-DNA binding.	Bhogale S et al.	—	2022	→
Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures.	Oberhofer A et al.	—	2022	→
Transcriptomic and chromatin accessibility dynamics of porcine alveolar macrophages in exposure to fumonisin B1.	Jin J et al.	—	2022	→
Translator: A <i>Trans</i>fer <i>L</i>earning Approach to Facilitate Single-Cell <i>AT</i>AC-Seq Data Analysis fr<i>o</i>m <i>R</i>eference Dataset.	Xu S et al.	—	2022	→
Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin.	Marr LT et al.	—	2022	→
Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.	Kanapeckaitė A et al.	—	2021	→
CD4+ T cells from children with active juvenile idiopathic arthritis show altered chromatin features associated with transcriptional abnormalities.	Tarbell E et al.	—	2021	→
CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes.	Shen Y et al.	—	2021	→
Chromatin accessibility and regulatory vocabulary across indicine cattle tissues.	Alexandre PA et al.	—	2021	→
Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors.	Ding P et al.	—	2021	→
Chromatin accessibility profiling provides insights into larval cuticle color and adult longevity in butterflies.	Wan WT et al.	—	2021	→
Chromatin Dynamics and Gene Expression Response to Heat Exposure in Field-Conditioned versus Laboratory-Cultured <i>Nematostella vectensis</i>.	Weizman E et al.	—	2021	→
Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay.	Tachiwana H et al.	—	2021	→
cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data	Karakaslar EO et al.	—	2021	—
Circular dichroism spectroscopy of DNA duplexes at near-biological concentrations.	Vanloon J et al.	—	2021	→
Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq.	Cao X et al.	—	2021	→
Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle.	Nair VD et al.	—	2021	→
Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid.	Lewis EMA et al.	—	2021	→
Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus<sup>1</sup>.	Beacon TH et al.	—	2021	→
Evidence of widespread, independent sequence signature for transcription factor cobinding.	Zhou M et al.	—	2021	→
Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome.	Farley EJ et al.	—	2021	→
Insights into epigenetic patterns in mammalian early embryos.	Xu R et al.	—	2021	→
Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model.	Jiang JC et al.	—	2021	→
Local states of chromatin compaction at transcription start sites control transcription levels.	Ishihara S et al.	—	2021	→
Molecular and computational approaches to map regulatory elements in 3D chromatin structure.	Lee BH et al.	—	2021	→
Multi-omic analysis suggests tumor suppressor genes evolved specific promoter features to optimize cancer resistance.	Huang D et al.	—	2021	→
Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology.	Fort RS et al.	—	2021	→
Panobinostat Effectively Increases Histone Acetylation and Alters Chromatin Accessibility Landscape in Canine Embryonic Fibroblasts but Does Not Enhance Cellular Reprogramming.	Moshref M et al.	—	2021	→
PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map.	Nowling RJ et al.	—	2021	→
Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks.	Diedrich JD et al.	—	2021	→
RA3 is a reference-guided approach for epigenetic characterization of single cells.	Chen S et al.	—	2021	→
Regulatory association of long noncoding RNAs and chromatin accessibility facilitates erythroid differentiation.	Ren Y et al.	—	2021	→
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration.	Cao Y et al.	—	2021	→
Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders.	Kouakou MR et al.	—	2021	→
The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs.	Yue J et al.	—	2021	→
The native cistrome and sequence motif families of the maize ear.	Savadel SD et al.	—	2021	→
Are Parallel Proliferation Pathways Redundant?	Nussinov R et al.	—	2020	→
ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq.	Lu RJ et al.	—	2020	→
ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation.	Reske JJ et al.	—	2020	→
CATA: a comprehensive chromatin accessibility database for cancer.	Zhou J et al.	—	2020	→
Chromatin accessibility dynamics of Chlamydia-infected epithelial cells.	Hayward RJ et al.	—	2020	→
Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress.	Murai J et al.	—	2020	→
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data.	Ramirez RN et al.	—	2020	→
Enhancer-Driven Gene Expression (EDGE) enables the generation of cell type specific tools for the analysis of neural circuits.	Blankvoort S et al.	—	2020	→
Eosinophil diversity in asthma.	Van Hulst G et al.	—	2020	→
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis.	Yan F et al.	—	2020	→
Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq.	Zhao X et al.	—	2020	→
Genomic methods in profiling DNA accessibility and factor localization.	Klein DC et al.	—	2020	→
Genomic resources for dissecting the role of non-protein coding variation in gene-environment interactions.	Levings D et al.	—	2020	→
HiCoP, a simple and robust method for detecting interactions of regulatory regions.	Zhang Y et al.	—	2020	→
Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.	Chen D et al.	—	2020	→
LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells.	Cebrià-Costa JP et al.	—	2020	→
MEDEA: analysis of transcription factor binding motifs in accessible chromatin.	Mariani L et al.	—	2020	→
Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes.	Levitsky VG et al.	—	2020	→
Predicting transcription factor binding in single cells through deep learning.	Fu L et al.	—	2020	→
Quantification of the effect of site-specific histone acetylation on chromatin transcription rate.	Wakamori M et al.	—	2020	→
Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging.	Liu L et al.	—	2020	→
Single-cell multiomics: technologies and data analysis methods.	Lee J et al.	—	2020	→
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.	Hu-Lieskovan S et al.	—	2020	→
Specification of the First Mammalian Cell Lineages In Vivo and In Vitro.	White MD et al.	—	2020	→
Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues.	Chin HG et al.	—	2020	→
Agent-Based Modelling to Delineate Spatiotemporal Control Mechanisms of the Stem Cell Niche.	Mines R et al.	—	2019	→
A practical guide for DNase-seq data analysis: from data management to common applications.	Liu Y et al.	—	2019	→
B4GALT1 Is a New Candidate to Maintain the Stemness of Lung Cancer Stem Cells.	De Vitis C et al.	—	2019	→
Biochemical analysis of nucleosome targeting by Tn5 transposase.	Sato S et al.	—	2019	→
Chromatin condensation fluctuations rather than steady-state predict chromatin accessibility.	Audugé N et al.	—	2019	→
Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis.	Weizman EN et al.	—	2019	→
Classifying cells with Scasat, a single-cell ATAC-seq analysis tool.	Baker SM et al.	—	2019	→
Computational Biology Solutions to Identify Enhancers-target Gene Pairs.	Hariprakash JM et al.	—	2019	→
CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases.	Singh DD et al.	—	2019	→
Defining TP53 pioneering capabilities with competitive nucleosome binding assays.	Yu X et al.	—	2019	→
Determination of Chromatin Accessibility in <i>Drosophila</i> MidgutEnterocytes by <i>in situ</i> 5mC Labeling.	Bitman-Lotan E et al.	—	2019	→
Differential viral accessibility (DIVA) identifies alterations in chromatin architecture through large-scale mapping of lentiviral integration sites.	Timms RT et al.	—	2019	→
Epigenetic regulation of renal development.	El-Dahr SS et al.	—	2019	→
FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation.	Lee K et al.	—	2019	→
Genome-wide identification of enhancer elements in the placenta.	Abdulghani M et al.	—	2019	→
Genomic insights into chromatin reprogramming to totipotency in embryos.	Ladstätter S et al.	—	2019	→
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.	Tarbell ED et al.	—	2019	→
Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines.	Jiang JC et al.	—	2019	→
Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation.	Michael DG et al.	—	2019	→
Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint.	Bosire R et al.	—	2019	→
MeCP2 inhibits cell functionality through FoxO3a and autophagy in endothelial progenitor cells.	Zha S et al.	—	2019	→
Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo.	Liu G et al.	—	2019	→
Multi-study inference of regulatory networks for more accurate models of gene regulation.	Castro DM et al.	—	2019	→
Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression.	Sasse SK et al.	—	2019	→
Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.	Kanada R et al.	—	2019	→
Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways.	Zhao Y et al.	—	2019	→
SCALE method for single-cell ATAC-seq analysis via latent feature extraction.	Xiong L et al.	—	2019	→
Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem.	Frerichs A et al.	—	2019	→
The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia.	Weizman E et al.	—	2019	→
Advances of DNase-seq for mapping active gene regulatory elements across the genome in animals.	Chen A et al.	—	2018	→
Analysis of rat cardiac myocytes and fibroblasts identifies combinatorial enhancer organization and transcription factor families.	Golan-Lagziel T et al.	—	2018	→
An optimized FAIRE procedure for low cell numbers in yeast.	Segorbe D et al.	—	2018	→
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.	Ou J et al.	—	2018	→
CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo.	Aughey GN et al.	—	2018	→
Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio).	Uusi-Mäkelä MIE et al.	—	2018	→
Computational Methods for Assessing Chromatin Hierarchy.	Chang P et al.	—	2018	→
Developmental Chromatin Restriction of Pro-Growth Gene Networks Acts as an Epigenetic Barrier to Axon Regeneration in Cortical Neurons.	Venkatesh I et al.	—	2018	→
Epigenetic Applications in Adverse Outcome Pathways and Environmental Risk Evaluation.	Angrish MM et al.	—	2018	→
Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment.	Xu Q et al.	—	2018	→
Human Papillomavirus Replication Regulation by Acetylation of a Conserved Lysine in the E2 Protein.	Thomas Y et al.	—	2018	→
Identification of cis-regulatory elements by chromatin structure.	Lu Z et al.	—	2018	→
Integrating ChIP-seq with other functional genomics data.	Jiang S et al.	—	2018	→
Interferon regulatory factor 1 and a variant of heterogeneous nuclear ribonucleoprotein L coordinately silence the gene for adhesion protein CEACAM1.	Dery KJ et al.	—	2018	→
Investigating Nucleosome Accessibility for MNase, Fe<sup>II</sup> Peplomycin, and Duocarmycin B<sub>2</sub> by Using Capillary Electrophoresis.	Zou T et al.	—	2018	→
MeCP2-mediated epigenetic regulation in senescent endothelial progenitor cells.	Wang C et al.	—	2018	→
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution.	Roscito JG et al.	—	2018	→
Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome.	Zhao H et al.	—	2018	→
Quantitative imaging of chromatin decompaction in living cells.	Dultz E et al.	—	2018	→
Regulatory chromatin landscape in <i>Arabidopsis thaliana</i> roots uncovered by coupling INTACT and ATAC-seq.	Tannenbaum M et al.	—	2018	→
Single-Cell (Multi)omics Technologies.	Chappell L et al.	—	2018	→
Single Copy Transgene Integration in a Transcriptionally Active Site for Recombinant Protein Synthesis.	O'Brien SA et al.	—	2018	→
Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns.	Javasky E et al.	—	2018	→
The Identification and Interpretation of <i>cis</i>-Regulatory Noncoding Mutations in Cancer.	Patel MB et al.	—	2018	→
Translating GWAS in rheumatic disease: approaches to establishing mechanism and function for genetic associations with ankylosing spondylitis.	Osgood JA et al.	—	2018	→
Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle.	Luo H et al.	—	2017	→
Chromatin accessibility dynamics reveal novel functional enhancers in <i>C. elegans</i>.	Daugherty AC et al.	—	2017	→
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings.	Sauerwald N et al.	—	2017	→
Computational inference of gene regulatory networks: Approaches, limitations and opportunities.	Banf M et al.	—	2017	→
Contribution of Neuroepigenetics to Huntington's Disease.	Francelle L et al.	—	2017	→
dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization.	Zhang Y et al.	—	2017	→
Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome.	Wang Y et al.	—	2017	→
Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein.	Urban J et al.	—	2017	→
Epigenetic Landscape during Coronavirus Infection.	Schäfer A et al.	—	2017	→
High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss.	Siersbæk M et al.	—	2017	→
I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples.	Ahmed Z et al.	—	2017	→
Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts.	Pascual-Garcia P et al.	—	2017	→
NicE-seq: high resolution open chromatin profiling.	Ponnaluri VKC et al.	—	2017	→
Nucleosome Positioning Assay.	Zhao Z et al.	—	2017	→
Polymorphisms in sex steroid receptors: From gene sequence to behavior.	Maney DL	—	2017	→
Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data.	Jung S et al.	—	2017	→
Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes.	Shen JJ et al.	—	2017	→
Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints.	Schwessinger R et al.	—	2017	→
STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species.	Lai X et al.	—	2017	→
Towards genome-wide prediction and characterization of enhancers in plants.	Marand AP et al.	—	2017	→
Understanding nucleosome dynamics and their links to gene expression and DNA replication.	Lai WKM et al.	—	2017	→
Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.	Deschamps S et al.	—	2016	→
ChIP bias as a function of cross-linking time.	Baranello L et al.	—	2016	→
Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases.	Murakawa Y et al.	—	2016	→
Epigenetic Changes During Food-Specific Immunotherapy.	Bunning BJ et al.	—	2016	→
Genetics of congenital heart disease: the contribution of the noncoding regulatory genome.	Postma AV et al.	—	2016	→
Genetics of movement disorders in the next-generation sequencing era.	Olgiati S et al.	—	2016	→
Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes.	Baek S et al.	—	2016	→
Genome-wide epigenomic profiling for biomarker discovery.	Dirks RA et al.	—	2016	→
High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility.	Pattenden SG et al.	—	2016	→
Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis.	Gallagher JP et al.	—	2016	→
Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes.	Ackermann AM et al.	—	2016	→
Molecular Actions of Glucocorticoids in Cartilage and Bone During Health, Disease, and Steroid Therapy.	Hartmann K et al.	—	2016	→
Occupancy of RNA Polymerase II Phosphorylated on Serine 5 (RNAP S5P) and RNAP S2P on Varicella-Zoster Virus Genes 9, 51, and 66 Is Independent of Transcript Abundance and Polymerase Location within the Gene.	Henderson HH et al.	—	2016	→
Open chromatin reveals the functional maize genome.	Rodgers-Melnick E et al.	—	2016	→
Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers.	Sun J et al.	—	2016	→
Persistent Chromatin Modifications Induced by High Fat Diet.	Leung A et al.	—	2016	→
Protein Palmitoylation Regulates Neural Stem Cell Differentiation by Modulation of EID1 Activity.	Chen X et al.	—	2016	→
Self-renewal of tumor cells: epigenetic determinants of the cancer stem cell phenotype.	Ravasio R et al.	—	2016	→
The Functionality and Evolution of Eukaryotic Transcriptional Enhancers.	Buffry AD et al.	—	2016	→
An increased expression of PI-PLCβ1 is associated with myeloid differentiation and a longer response to azacitidine in myelodysplastic syndromes.	Cocco L et al.	—	2015	→
Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins.	David Y et al.	—	2015	→
Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators.	Sun J et al.	—	2015	→
Do changes in the BDNF promoter methylation indicate the risk of alcohol relapse?	Heberlein A et al.	—	2015	→
Histone profiles in cancer.	Riedel SS et al.	—	2015	→
Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana.	Cumbie JS et al.	—	2015	→
On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions.	Madrigal P	—	2015	→
Regulation of catalase expression in healthy and cancerous cells.	Glorieux C et al.	—	2015	→
Three-dimensional regulation of transcription.	Cao J et al.	—	2015	→