Chromatin Accessibility
Methods and Protocols
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Article
The killifish germline regulates longevity and somatic repair in a sex-specific manner
Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in sha** vertebrate aging remains largely unknown. In this study, ...
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Open AccessGenome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome
In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystall...
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Open AccessThe chromatin landscape of the euryarchaeon Haloferax volcanii
Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations fir...
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Open AccessCasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA map**
Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map Cas9 binding specificity...
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Protocol
Genome-Wide Map** of Active Regulatory Elements Using ATAC-seq
Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs geno...
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Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq
The ability to analyze the transcriptomic and epigenomic states of individual single cells has in recent years transformed our ability to measure and understand biological processes. Recent advancements have f...
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Protocol
Single-Molecule Map** of Chromatin Accessibility Using NOMe-seq/dSMF
The bulk of gene expression regulation in most organisms is accomplished through the action of transcription factors (TFs) on cis-regulatory elements (CREs). In eukaryotes, these CREs are generally characterized ...
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Open AccessPublisher Correction: The demographic and geographic impact of the COVID pandemic in Bulgaria and Eastern Europe in 2020
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Open AccessThe demographic and geographic impact of the COVID pandemic in Bulgaria and Eastern Europe in 2020
The COVID-19 pandemic followed a unique trajectory in Eastern Europe compared to other heavily affected regions, with most countries there only experiencing a major surge of cases and deaths towards the end of...
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Article
Open AccessThe chromatin organization of a chlorarachniophyte nucleomorph genome
Nucleomorphs are remnants of secondary endosymbiotic events between two eukaryote cells wherein the endosymbiont has retained its eukaryotic nucleus. Nucleomorphs have evolved at least twice independently, in ...
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Protocol
Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq
A hallmark feature of active cis-regulatory elements (CREs) in eukaryotes is their nucleosomal depletion and, accordingly, higher to enzymatic treatment. This property has been the basis of a number of seque...
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Open AccessIdentification and characterization of a novel Epstein-Barr Virus-encoded circular RNA from LMP-2 Gene
Epstein-Barr virus (EBV) has been recently found to generate novel circular RNAs (circRNAs) through backsplicing. However, comprehensive catalogs of EBV circRNAs in other cell lines and their functional charac...
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Open AccessTranscription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum
Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem ...
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Chromatin accessibility profiling methods
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of the eukaryotic genome. As active regulatory DNA elements are generally ‘accessible’, the genome-wide ...
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Protocol
Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq
The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Than...
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Open AccessThe changing mouse embryo transcriptome at whole tissue and single-cell resolution
During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system1. Here we systematically quantified mouse polyA-RNA from day 10.5 of embry...
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Long-range single-molecule map** of chromatin accessibility in eukaryotes
Map** open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read ...
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Article
Open AccessMitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
Pooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated...
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Open AccessResponse to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells
A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mit...
