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Methods Mol Biol
2021 Jan 01;2219:253-265. doi: 10.1007/978-1-0716-0974-3_16.
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ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos.
Magri MS
,
Voronov D
,
Ranđelović J
,
Cuomo C
,
Gómez-Skarmeta JL
,
Arnone MI
.
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Cis-regulatory elements (CREs) and transcription factors (TFs) associated with them determine temporal and spatial domains of gene expression. Therefore, identification of these CREs and TFs is crucial to elucidating transcriptional programs across taxa. With chromatin accessibility facilitating transcription factor access to DNA, the identification of regions of open chromatin sheds light both on the function of the regulatory elements and their evolution, thus allowing the recognition of potential CREs. Buenrostro and colleagues have developed a novel method for exploring chromatin accessibility: assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), which can be used for the purpose of identifying putative CREs. This method was shown to have considerable advantages when compared to traditional methods such as sequence conservation analyses or functional assays. Here we present the adaptation of the ATAC-seq method to echinoderm species and discuss how it can be used for CRE discovery.
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