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ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos.

Marta S Magri1, Danila Voronov2, Jovana Ranđelović2

  • 1Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide, Sevilla, Spain.

Methods in Molecular Biology (Clifton, N.J.)
|October 19, 2020
PubMed
Summary
This summary is machine-generated.

Identifying cis-regulatory elements (CREs) is key to understanding gene expression. The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) method is adapted for echinoderms to discover these crucial regulatory elements.

Keywords:
ATAC-seqCis-regulatory elementDevelopmentEchinodermEvolution

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Area of Science:

  • Genomics
  • Developmental Biology
  • Evolutionary Biology

Background:

  • Cis-regulatory elements (CREs) and transcription factors (TFs) control gene expression patterns.
  • Understanding CREs and TFs is vital for deciphering transcriptional programs across diverse species.
  • Chromatin accessibility is essential for TF binding and regulatory element function.

Purpose of the Study:

  • To adapt the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) for use in echinoderm species.
  • To leverage ATAC-seq for the discovery of novel CREs in echinoderms.
  • To highlight the advantages of ATAC-seq over traditional methods for CRE identification.

Main Methods:

  • Adaptation of the ATAC-seq protocol for echinoderm samples.
  • High-throughput sequencing to profile chromatin accessibility.
  • Bioinformatic analysis to identify potential CREs from sequencing data.

Main Results:

  • Successful implementation of ATAC-seq in echinoderm species.
  • Identification of regions with open chromatin, indicative of potential CREs.
  • Demonstration of ATAC-seq's utility for CRE discovery in a non-model organism group.

Conclusions:

  • ATAC-seq is a powerful and adaptable method for identifying CREs in echinoderms.
  • This approach facilitates the study of gene regulation and evolution in these marine invertebrates.
  • The adapted ATAC-seq method offers significant advantages for regulatory element discovery.