Chapter title |
Enhancer RNAs
|
---|---|
Chapter number | 1 |
Book title |
Enhancer RNAs
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-4035-6_1 |
Pubmed ID | |
Book ISBNs |
978-1-4939-4033-2, 978-1-4939-4035-6
|
Authors |
Conrad, Thomas, Ørom, Ulf Andersson, Thomas Conrad, Ulf Andersson Ørom Ph.D., Ulf Andersson Ørom |
Editors |
Ulf Andersson Ørom |
Abstract |
In eukaryotic cells, the synthesis, processing, and functions of RNA molecules are confined to distinct subcellular compartments. Biochemical fractionation of cells prior to RNA isolation thus enables the analysis of distinct steps in the lifetime of individual RNA molecules that would be masked in bulk RNA preparations from whole cells. Here, we describe a simple two-step differential centrifugation protocol for the isolation of cytoplasmic, nucleoplasmic, and chromatin-associated RNA that can be used in downstream applications such as qPCR or deep sequencing. We discuss various aspects of this fractionation protocol, which can be readily applied to many mammalian cell types. For the study of long noncoding RNAs and enhancer RNAs in regulation of transcription especially the preparation of chromatin-associated RNA can contribute significantly to further developments. |
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