Processing of Endogenous Pre-mRNAs in Association with SC-35 Domains Is Gene Specific

• Published in: The Journal of cell biology Vol. 144; no. 4; pp. 617 - 629
• Main Authors: Smith, Kelly P., Moen, Phillip T., Wydner, Karen L., Coleman, John R., Lawrence, Jeanne B.
• Format: Journal Article
• Language: English
• Published: United States Rockefeller University Press 22-02-1999; The Rockefeller University Press
• Subjects: Cell Line; Cellular biology; Complementary DNA; Dystrophin - genetics; Genes; Genomics; Humans; In Situ Hybridization, Fluorescence; Introns; Messenger RNA; Muscle fibers; Muscular system; Myosin Heavy Chains - genetics; Nuclear Proteins - metabolism; Nuclear RNA; Regular; Ribonucleic acid; Ribonucleoproteins; RNA; RNA Precursors - genetics; RNA Precursors - metabolism; RNA probes; RNA Processing, Post-Transcriptional; RNA Splicing; RNA, Messenger - genetics; RNA, Messenger - metabolism; Serine-Arginine Splicing Factors; Spliceosomes - metabolism; Splicing; Transcription, Genetic
• ISSN: 0021-9525; 1540-8140
• DOI: 10.1083/jcb.144.4.617

Analysis of six endogenous pre-mRNAs demonstrates that localization at the periphery or within splicing factor-rich (SC-35) domains is not restricted to a few unusually abundant pre-mRNAs, but is apparently a more common paradigm of many protein-coding genes. Different genes are preferentially transcribed and their RNAs processed in different compartments relative to SC-35 domains. These differences do not simply correlate with the complexity, nuclear abundance, or position within overall nuclear space. The distribution of spliceosome assembly factor SC-35 did not simply mirror the distribution of individual pre-mRNAs, but rather suggested that individual domains contain both specific pre-mRNA(s) as well as excess splicing factors. This is consistent with a multifunctional compartment, to which some gene loci and their RNAs have access and others do not. Despite similar molar abundance in muscle fiber nuclei, nascent transcript "trees" of highly complex dystrophin RNA are cotranscriptionally spliced outside of SC-35 domains, whereas posttranscriptional "tracks" of more mature myosin heavy chain transcripts overlap domains. Further analyses supported that endogenous pre-mRNAs exhibit distinct structural organization that may reflect not only the expression and complexity of the gene, but also constraints of its chromosomal context and kinetics of its RNA metabolism.