Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions

Macrophages respond to inflammatory stimuli by modulating the expression of hundreds of genes in a defined temporal cascade, with diverse transcriptional and posttranscriptional mechanisms contributing to the regulatory network. We examined proinflammatory gene regulation in activated macrophages by...

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Published in:Cell Vol. 150; no. 2; p. 279
Main Authors: Bhatt, Dev M, Pandya-Jones, Amy, Tong, Ann-Jay, Barozzi, Iros, Lissner, Michelle M, Natoli, Gioacchino, Black, Douglas L, Smale, Stephen T
Format: Journal Article
Language:English
Published: United States 20.07.2012
Subjects:
Animals
Chromatin - genetics
Gene Expression Profiling
Gene Expression Regulation
Inflammation - genetics
Lipid A - immunology
Macrophages - immunology
Macrophages - metabolism
Mice
Mice, Inbred C57BL
Promoter Regions, Genetic
Receptor, Interferon alpha-beta - genetics
Receptors, Interferon - genetics
RNA Splicing
Sequence Analysis, RNA
Transcription, Genetic
ISSN:1097-4172, 1097-4172
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Summary:Macrophages respond to inflammatory stimuli by modulating the expression of hundreds of genes in a defined temporal cascade, with diverse transcriptional and posttranscriptional mechanisms contributing to the regulatory network. We examined proinflammatory gene regulation in activated macrophages by performing RNA-seq with fractionated chromatin-associated, nucleoplasmic, and cytoplasmic transcripts. This methodological approach allowed us to separate the synthesis of nascent transcripts from transcript processing and the accumulation of mature mRNAs. In addition to documenting the subcellular locations of coding and noncoding transcripts, the results provide a high-resolution view of the relationship between defined promoter and chromatin properties and the temporal regulation of diverse classes of coexpressed genes. The data also reveal a striking accumulation of full-length yet incompletely spliced transcripts in the chromatin fraction, suggesting that splicing often occurs after transcription has been completed, with transcripts retained on the chromatin until fully spliced.
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ISSN:1097-4172
1097-4172
DOI:10.1016/j.cell.2012.05.043