title: DamID Analysis of Nuclear Organization in Caenorhabditis elegans.
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.
authors.affiliation: Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013, Seville, Spain.
authors.forename: Georgina
authors.initials: G
authors.lastname: Gómez-Saldivar
authors.affiliation: Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012, Bern, Switzerland.
authors.forename: Peter
authors.initials: P
authors.lastname: Meister
authors.affiliation: Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, 41013, Seville, Spain. pask@upo.es.
authors.forename: Peter
authors.initials: P
authors.lastname: Askjaer
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans; D002467:Cell Nucleus / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D015870:Gene Expression; D005822:Genetic Vectors / Q000235:genetics; D015698:Genomic Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008780:Methyltransferases / Q000235:genetics* / Q000378:metabolism; D009687:Nuclear Proteins / Q000378:metabolism; D011993:Recombinant Fusion Proteins
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D011993:Recombinant Fusion Proteins; D008780:Methyltransferases; C022556:mRNA (2'-O-methyladenosine-N6-)-methyltransferase
keywords: Caenorhabditis elegans; Chromatin; DamID; Laminopathies; Nuclear envelope; Nuclear lamina; Nuclear organization