NDLI: Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Steiner, Florian A. Talbert, Paul B. Kasinathan, Sivakanthan Deal, Roger B. Henikoff, Steven
Description	Country affiliation: United States Author Affiliation: Steiner FA ( Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.)
Abstract	An understanding of developmental processes requires knowledge of transcriptional and epigenetic landscapes at the level of tissues and ultimately individual cells. However, obtaining tissue- or cell-type-specific expression and chromatin profiles for animals has been challenging. Here we describe a method for purifying nuclei from specific cell types of animal models that allows simultaneous determination of both expression and chromatin profiles. The method is based on in vivo biotin-labeling of the nuclear envelope and subsequent affinity purification of nuclei. We describe the use of the method to isolate nuclei from muscle of adult Caenorhabditis elegans and from mesoderm of Drosophila melanogaster embryos. As a case study, we determined expression and nucleosome occupancy profiles for affinity-purified nuclei from C. elegans muscle. We identified hundreds of genes that are specifically expressed in muscle tissues and found that these genes are depleted of nucleosomes at promoters and gene bodies in muscle relative to other tissues. This method should be universally applicable to all model systems that allow transgenesis and will make it possible to determine epigenetic and expression profiles of different tissues and cell types.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
DOI	10.1101/gr.131748.111
Journal	Genome Research
Issue Number	4
Volume Number	22
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2012-04-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Cell Nucleus Genetics Gene Expression Profiling Gene Expression Regulation, Developmental Genome Animals Animals, Genetically Modified Caenorhabditis Elegans Growth & Development Metabolism Chromatin Drosophila Proteins Drosophila Melanogaster Embryology Embryo, Nonmammalian Cytology Helminth Proteins Luminescent Proteins Mesoderm Microscopy, Fluorescence Muscle Development Muscles Nucleosomes Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling.

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