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Tissue-specific nuclei purification from animal models for genome-wide expression and chromatin profiling.

ABSTRACT: Here we describe a method for purifying nuclei from specific tissues of animal models that allows simultaneous analysis of both expression and chromatin profiles. The method is based on in vivo labeling of the nuclear envelope and subsequent affinity purification. We describe the use of the method to isolate nuclei from muscle. We determined genes preferentially expressed in muscle cells of adult C. elegans by analyzing RNA from total and affinity-puridied muscle nuclei using microarrays. We also determined the nucleosome occupancy in these nuclei by micrococcal nuclease mapping and paired-end sequencing.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Jorja Henikoff

PROVIDER: E-GEOD-31602 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Steiner Florian A FA Talbert Paul B PB Kasinathan Sivakanthan S Deal Roger B RB Henikoff Steven S

Genome research 20120104 4

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 ...[more]

PMID: 22219512

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