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© The Rockefeller University Press, 0021-9525/1999//617 $5.00
The Journal of Cell Biology, Volume 144, Number 4, , 1999 617-629

Regular Articles

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



Kelly P. Smith*, Phillip T. Moen, Jr.*, Karen L. Wydner*, John R. Coleman{ddagger}, and Jeanne B. Lawrence*

* Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; and {ddagger} Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912

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.

Key Words: cultured cells • cell nucleus • RNA splicing • muscle • fluorescence in situ hybridization

Abbreviations used in this paper: DME-low, low-glucose DME; LBR, lamin B receptor; LMNA, lamin A/C; LMNB1, lamin B1; MyHC, myosin heavy chain; snRNP, small nuclear ribonucleoprotein; polII, RNA polymerase II.

This publication was made possible by grants from the National Institutes of Health (NIH) (GM 49254) and the Muscular Dystrophy Association (MDA) to J.B. Lawrence. K.L. Wydner was supported by a postdoctoral fellowship from the NIH. P.T. Moen was a fellow of the MDA. The comments of this manuscript are solely the responsibility of the authors and do not necessarily represent the official views of the NIH or MDA.

K.P. Smith and P.T. Moen contributed equally to this work.

P.T. Moen's current address is NEN Life Science Products, 549 Albany St., Boston, MA 02118.

K.L.Wydner's current address is Department of Diagnostic Genetics, Robert Wood Johnson Medical School, NE Robert Wood Johnson Place, New Brunswick, NJ 08901.


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