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Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets

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CpG Islands

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1766))

Abstract

The regulatory mechanisms that ensure an accurate control of gene transcription are central to cellular function, development and disease. Such mechanisms rely largely on noncoding regulatory sequences that allow the establishment and maintenance of cell identity and tissue-specific cellular functions.

The study of chromatin structure and nucleosome positioning allowed revealing transcription factor accessible genomic sites with regulatory potential, facilitating the comprehension of tissue-specific cis-regulatory networks. Recently a new technique coupled with high-throughput sequencing named Assay for Transposase Accessible Chromatin (ATAC-seq) emerged as an efficient method to chart open chromatin genome wide. The application of such technique to different cell types allowed unmasking tissue-specific regulatory elements and characterizing cis-regulatory networks. Herein we describe the implementation of the ATAC-seq method to human pancreatic islets, a tissue playing a central role in the control of glucose metabolism.

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Acknowledgment

This work was supported by a grant from the Spanish Ministry of Economy and Competiveness (BFU2014-58150-R), the Spanish Diabetes Society and Fundació La Marató de TV3. LP is a recipient of a Ramon y Cajal contract from the Spanish Ministry of Economy and Competitiveness (RYC 2013-12864). Helena Raurell-Vila and Mireia Ramos-Rodríguez contributed equally to this work.

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Author notes

  1. Helena Raurell-Vila and Mireia Ramos-Rodríguez contributed equally to this work.

Authors and Affiliations

  1. Program of Predictive and Personalized Medicine of Cancer (PMPPC), Endocrine Regulatory Genomics Laboratory, Department of Endocrinology and Nutrition, Germans Trias i Pujol University Hospital and Research Institute, Badalona, Spain

    Lorenzo Pasquali

  2. Josep Carreras Leukaemia Research Institute, Badalona, Spain

    Lorenzo Pasquali

  3. CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain

    Lorenzo Pasquali

Authors
  1. Helena Raurell-Vila
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  2. Mireia Ramos-Rodríguez
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  3. Lorenzo Pasquali
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Corresponding author

Correspondence to Lorenzo Pasquali .

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Editors and Affiliations

  1. Josep Carreras Leukaemia, Research Institute, Badalona, Barcelona, Spain

    Tanya Vavouri

  2. IGTP, IMPPC, Badalona, Barcelona, Spain

    Miguel A. Peinado

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Raurell-Vila, H., Ramos-Rodríguez, M., Pasquali, L. (2018). Assay for Transposase Accessible Chromatin (ATAC-Seq) to Chart the Open Chromatin Landscape of Human Pancreatic Islets. In: Vavouri, T., Peinado, M. (eds) CpG Islands. Methods in Molecular Biology, vol 1766. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7768-0_11

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  • DOI: https://doi.org/10.1007/978-1-4939-7768-0_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7767-3

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