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PMID: 20627084 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

A simple method for gene expression and chromatin profiling of individual cell types within a tissue.

Developmental cell ·Vol. 18 ·No. 6 ·2010-06-15 ·Pages 1030-40

Deal RB, Henikoff S

Abstract

Understanding the production and function of specialized cells during development requires the isolation of individual cell types for analysis, but this is currently a major technical challenge. Here we describe a method for cell type-specific RNA and chromatin profiling that circumvents many of the limitations of current methods for cell isolation. We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. We identified hundreds of genes that are preferentially expressed in each cell type and show that genes with the largest expression differences between hair and non-hair cells also show differences between cell types in the trimethylation of histone H3 at lysines 4 and 27. This method should be applicable to any organism that is amenable to transformation.

MeSH Terms
Arabidopsis/growth & development Arabidopsis Proteins/genetics Biotin/chemistry Cell Differentiation/genetics Chromatin/genetics Gene Expression Profiling/methods Gene Expression Regulation, Developmental/genetics Gene Expression Regulation, Plant/physiology Histones/genetics,metabolism Lysine/metabolism Methylation Models, Genetic Molecular Biology/methods Nuclear Proteins/genetics,metabolism Plant Epidermis/growth & development Plant Roots/growth & development RNA/genetics Staining and Labeling/methods
Chemicals
Arabidopsis Proteins Chromatin Histones Nuclear Proteins RNA Biotin Lysine
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Deal Roger B
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Henikoff Steven
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Article Info
Journal
Developmental cell
Abbr.
Dev Cell
ISSN
1878-1551
DOI
10.1016/j.devcel.2010.05.013
Published
2010-06-15
Pages
1030-40
Language
English
Region
United States
NLM ID
101120028
PMCID
PMC2905389
Subset
IM
Grants
Howard Hughes Medical Institute · United States
Databases
GEO
GSE19654
Corrections
ErratumIn
-
External Links
PubMed source DOI: 10.1016/j.devcel.2010.05.013 PMC Full Text View journal details
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