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DamID Analysis of Nuclear Organization in Caenorhabditis elegans

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The Nuclear Envelope

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1411))

Abstract

The development of genomics and next generation sequencing platforms has dramatically improved our insight into chromatin structure and organization and its fine interplay with gene expression. The nuclear envelope has emerged as a key component in nuclear organization via extensive contacts between the genome and numerous proteins at the nuclear periphery. These contacts may have profound effects on gene expression as well as cell proliferation and differentiation. Indeed, their perturbations are associated with several human pathologies known as laminopathies or nuclear envelopathies. However, due to their dynamic behavior the contacts between nuclear envelope proteins and chromatin are challenging to identify, in particular in intact tissues. Here, we propose the DamID technique as an attractive method to globally characterize chromatin organization in the popular model organism Caenorhabditis elegans. DamID is based on the in vivo expression of a chromatin-associated protein of interest fused to the Escherichia coli DNA adenine methyltransferase, which produces unique identification tags at binding site in the genome. This marking is simple, highly specific and can be mapped by sensitive enzymatic and next generation sequencing approaches.

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Acknowledgement

We gratefully acknowledge funding from the Spanish Ministry of Economy and Competitiveness (BFU2013-42709P) and the European Regional Development Fund to P.A. The Meister laboratory is funded by the Swiss National Foundation (SNF Assistant Professor grant PP00P3_133744), the Swiss Foundation for Muscle Diseases Research, and the University of Bern. G.G.-S. holds a CSIC-JAE Fellowship (JAEPre_2010_00384) and received support from EMBO (ASTF-447-2014) and EC COST Action BM1408 GENiE.

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Authors and Affiliations

  1. Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013, Seville, Spain

    Georgina Gómez-Saldivar & Peter Askjaer

  2. Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012, Bern, Switzerland

    Peter Meister

Authors
  1. Georgina Gómez-Saldivar
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  2. Peter Meister
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  3. Peter Askjaer
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Corresponding author

Correspondence to Peter Askjaer .

Editor information

Editors and Affiliations

  1. Department of Biochemistry, University of Leicester, Leicester, United Kingdom

    Sue Shackleton

  2. Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway

    Philippe Collas

  3. Wellcome Trust Centre for Cell Biol, University of Edinburgh, Edinburgh, United Kingdom

    Eric C. Schirmer

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Gómez-Saldivar, G., Meister, P., Askjaer, P. (2016). DamID Analysis of Nuclear Organization in Caenorhabditis elegans . In: Shackleton, S., Collas, P., Schirmer, E. (eds) The Nuclear Envelope. Methods in Molecular Biology, vol 1411. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3530-7_22

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  • DOI: https://doi.org/10.1007/978-1-4939-3530-7_22

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3528-4

  • Online ISBN: 978-1-4939-3530-7

  • eBook Packages: Springer Protocols

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