title: Cell types differ in global coordination of splicing and proportion of highly expressed genes.
abstract: Balance in the transcriptome is regulated by coordinated synthesis and degradation of RNA molecules. Here we investigated whether mammalian cell types intrinsically differ in global coordination of gene splicing and expression levels. We analyzed RNA-seq transcriptome profiles of 8 different purified mouse cell types. We found that different cell types vary in proportion of highly expressed genes and the number of alternatively spliced transcripts expressed per gene, and that the cell types that express more variants of alternatively spliced transcripts per gene are those that have higher proportion of highly expressed genes. Cell types segregated into two clusters based on high or low proportion of highly expressed genes. Biological functions involved in negative regulation of gene expression were enriched in the group of cell types with low proportion of highly expressed genes, and biological functions involved in regulation of transcription and RNA splicing were enriched in the group of cell types with high proportion of highly expressed genes. Our findings show that cell types differ in proportion of highly expressed genes and the number of alternatively spliced transcripts expressed per gene, which represent distinct properties of the transcriptome and may reflect intrinsic differences in global coordination of synthesis, splicing, and degradation of RNA molecules.
authors: Department of Neurosurgery, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
authors: Ephraim F
authors: EF
authors: Trakhtenberg
authors: Research Computing Group, Harvard Medical School, Boston, MA, USA.
authors: Nam
authors: N
authors: Pho
authors: Research Computing Group, Harvard Medical School, Boston, MA, USA.
authors: Kristina M
authors: KM
authors: Holton
authors: Research Computing Group, Harvard Medical School, Boston, MA, USA.
authors: Thomas W
authors: TW
authors: Chittenden
authors: Byers Eye Institute, Stanford University, Palo Alto, CA, USA.
authors: Jeffrey L
authors: JL
authors: Goldberg
authors: Research Computing Group, Harvard Medical School, Boston, MA, USA.
authors: Lingsheng
authors: L
authors: Dong
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D002478:Cells, Cultured; D042783:Endothelial Cells / Q000502:physiology; D005786:Gene Expression Regulation; D008822:Mice, Transgenic; D009457:Neuroglia / Q000502:physiology; D009474:Neurons / Q000502:physiology; D017423:Sequence Analysis, RNA; D059467:Transcriptome