Processing of endogenous pre-mRNAs in association with SC-35 domains is gene specific

Journal of Cell Biology

Volumn 144, Issue 4, 1999, Pages 617-629

  Smith, Kelly P ^a   Moen Jr , Phillip T ^a,c   Wydner, Karen L ^a,d   Coleman, John R ^b   Lawrence, Jeanne B ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b BROWN UNIVERSITY   (United States)

^c NEN Life Science Products   (United States)

^d ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

Cell nucleus; Cultured cells; Fluorescence in situ hybridization; Muscle; RNA splicing

Indexed keywords

DYSTROPHIN; MESSENGER RNA PRECURSOR; MYOSIN HEAVY CHAIN;

ARTICLE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; PRIORITY JOURNAL; RNA ANALYSIS; RNA METABOLISM; RNA PROCESSING; SPLICEOSOME;

CELL LINE; DYSTROPHIN; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MYOSIN HEAVY CHAINS; NUCLEAR PROTEINS; RIBONUCLEOPROTEINS; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA SPLICING; RNA, MESSENGER; SPLICEOSOMES; TRANSCRIPTION, GENETIC;

EID: 0033593806     PISSN: 00219525     EISSN: None     Source Type: Journal    
DOI: 10.1083/jcb.144.4.617     Document Type: Article

References (49)

1. Blencowe, B.J., J.A. Nickerson, R. Issner, S. Penman, and P.A. Sharp. 1994. Association of nuclear matrix antigens with exon-containing splicing complexes. J. Cell Biol. 127:593-607.
2. Blobel, G. 1985. Gene gating: a hypothesis. Proc. Natl. Acad. Sci. USA. 82: 8527-8529.
3. Bregman, D.B., L. Du, S. van der Zee, and S.L. Warren. 1995. Transcription-dependent redistribution of the large subunit of RNA polymerase II to discrete nuclear domains. J. Cell Biol. 129:287-298.
4. Carter, K.C., K.L. Taneja, and J.B. Lawrence. 1991. Discrete nuclear domains of poly(A). RNA and their relationship to the functional organization of the nucleus. J. Cell Biol. 115:1191-1202.
5. Carter, K.C., D. Bowman, W. Carrington, K. Fogarty, J.A. McNeil, F.S. Fay, and J.B. Lawrence. 1993. A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus. Science. 259:1330-1335.
6. Chelly, J., D. Montarras, C. Pinset, Y. Berwald-Netter, and J.C. Kaplan. 1990. Quantitative estimation of minor mRNAs by cDNA polymerase chain reaction: application to dystrophin mRNA in cultured myogenic and brain cells. Eur. J. Biochem. 187:691-698.
7. Clemson, C.M., and J.B. Lawrence. 1996. Multifunctional compartments in the nucleus: insights from DNA and RNA localization. J. Cell. Biochem. 62: 181-190.
8. Clemson, C.M., J.A. McNeil, H.F. Willard, and J.B. Lawrence. 1996. XIST RNA paints the inactive X chromosome at interphase: evidence for a structural association. J. Cell Biol. 132:259-275.
9. Comings, D. 1968. The rationale for an ordered arrangement of chromatin in the interphase nucleus. Am. J. Hum. Genet. 20:440-457.
10. Fakan, S., and E. Puvion. 1980. The ultrastructural visualization of nuclear and extranucleolar RNA synthesis and distribution. Int. Rev. Cytol. 65:255-299.
11. Fu, X.-D., and T. Maniatis. 1990. Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature. 343:437-444.
12. Gee, S., S.W. Krauss, E. Miller, K. Aoyagi, J. Arenas, and J.G. Conboy. 1997. Cloning of mDEAH9, a putative RNA helicase and mammalian homologue of Saccharomyces cerevisiae splicing factor Prp 43. Proc. Natl. Acad. Sci. USA. 94:11803-11807.
13. Ginsberg, D., G. Vairo, T. Chittenden, Z.X. Xiao, G. Xu, K.L. Wydner, J.A. DeCaprio, J.B. Lawrence, and D.M. Livingston. 1994. E2F-4, a new member of the E2F transcription factor family, interacts with p107. Genes Dev. 8:2665-2679.
14. Hochstrasser, M., D. Mathoy, Y. Gruenbaum, H. Saumweber, and J.W. Sedat. 1986. Spatial organization of chromosomes in the salivary gland nuclei of Drosophila melanogaster. J. Cell Biol. 102:112-123.
15. Hoffman, E.H., A.P. Monaco, C.A. Feener, and L.M. Kunkel. 1987. Conservation of the Duchenne muscular dystrophy gene in mice and humans. Science. 238:347-350.
16. Huang, S., and D.L. Spector. 1991. Nascent pre-mRNA transcripts are associated with nuclear regions enriched in splicing factors. Genes Dev. 5:2288-2302.
17. Huang, S., and D.L. Spector. 1996. Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J. Cell Biol. 133:719-732.
18. Hughes, S.M., M. Cho, I. Karsch-Mizrachi, M. Travis, L. Silberstein, L.A. Leinwand, and H. Blau. 1993. Three slow myosin heavy chains sequentially expressed in developing mammalian skeletal muscle. Dev. Biol. 158:183-199.
19. Jackson, D.A., A.B. Hassan, R.J. Errington, and P.R. Cook. 1993. Visualization of focal sites of transcription within human nuclei. EMBO (Eur. Mol. Biol. Organ.) J. 12:1059-1065.
20. Johnson, C.V., R.H. Singer, and J.B. Lawrence. 1991. Fluorescent detection of nuclear RNA and DNA: implication for genome organization. Methods Cell Biol. 35:73-99.
21. Lawrence, J.B., C.A. Villnave, and R.H. Singer. 1988. Sensitive high-resolution chromatin and chromosome mapping in situ: presence and orientation of two closely integrated copies of EBV in a lymphoma line. Cell. 52:51-61.
22. Lawrence, J.B., K. Taneja, and R.H. Singer. 1989. Temporal resolution and sequential expression of muscle-specific genes revealed by in situ hybridization. Dev. Biol. 133:235-246.
23. Lawrence, J.B., R.H. Singer, and J.A. McNeil. 1990. Interphase and metaphase resolution of different distances within the human dystrophin gene. Science. 249:928-932.
24. Lawrence, J.B., K.C. Carter, and Y. Xing. 1993. Probing functional organization within the nucleus: is genome structure integrated with RNA metabolism? Cold Spring Harbor Symp. Quam Biol. 58:807-818.
25. Leinwand, L.A., L. Saez, E. McNalley, and B. Nadal-Ginard. 1983. Isolation and characterization of human myosin heavy chain genes. Proc. Natl. Acad. Sci. USA. 80:3716-3720.
26. Lin, F., and H.J. Worman. 1993. Structural organization of the human gene encoding nuclear lamin A and nuclear lamin C. J. Biol. Chem. 268:16321-16326.
27. Lin, F., and H.J. Worman. 1995. Structural organization of the human gene (LMNB1) encoding nuclear lamin B1. Genomics. 27:230-236.
28. Manuelidis, L. 1484. Active nucleolus organizers are precisely positioned in adult central nervous system cells but not in neuroectodermal tumor cells. J. Neuropath. Exp. Neuro. 43:225-241.
29. Marshall, W.F., A. Straight, J.F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A.W. Murray, D.A. Agard, and J.W. Sedat. 1997. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7:930-939.
30. Moen, P.T., Jr., K.P. Smith, and J.B. Lawrence. 1995. Compartmentalization of specific pre-mRNA metabolism: an emerging view. Human Mulec. Genet. 4:1779-1789.
31. Nyman, U., H. Hallman, G. Hadlaczky, I. Pettersson, G. Sharp, and N.R. Ringertz. 1986. Intranuclear localization of snRNP antigens. J. Cell Biol. 102:137-144.
32. Sacz, L.J., K.M. Gianola, E.M. McNally, R. Feghali, R. Eddy, T.B. Shows, and L.A. Leinwand. 1987. Human cardiac myosin heavy chain genes and their linkage in the genome. Nucleic Acids Res. 15:5443-5459.
33. Sardet, C., M. Vidal, D. Cobrinik, T. Geng, C. Onufryk, A. Chen, and R.A. Weinberg. 1995. E2F-4 and E2F-5, two members of the E2F family, are expressed in the early phases of the cell cycle. Proc. Natl. Acad. Sci. USA. 92: 2403-2407.
34. Scheer, U., M. Thiry, and G. Goessens. 1943. Structure, function and assembly of the nucleolus. Trends Cell Biol. 3:237-241.
35. Schul, W., R. van Driel, and L. de Jong. 1998. A subset of poly(A) polymerase is concentrated at sites of RNA synthesis and is associated with domains enriched in splicing factors and poly(A) RNA. Exp. Cell Res. 238:1-12.
36. Schuler, E., F. Lin, and H.J. Worman. 1994. Characterization of the human gene encoding LBR, an integral protein of the nuclear envelope inner membrane. J. Biol. Chem. 269:11312-11317.
37. Spector, D.L., X.-D. Fu, and T. Maniatis. 1991. Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO (Eur. Mol. Biol. Organ.) J. 10:3467-3481.
38. Tennyson, C.N., H.J. Klamut, and R.G. Worton. 1995. The human dystrophin gene requires to hours to be transcribed and is cotranscriptionally spliced. Nature Genetics. 9:184-190.
39. Tennyson, C.N., O. Shi, and R.G. Worton. 1996. Stability of the human dystrophin transcript in muscle. Nucleic Acids Res. 24:3059-3064.
40. Trask, B., D. Pinkel, and G. Van den Engh. 1989. The proximity of DNA sequences in interphase cell nuclei is correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs. Genomics. 5:710-717.
41. Visa, N., F. Puvion-Dutilleul, F. Harper, J.-P. Bachellerie, and F. Puvion. 1993. Intranuclear distribution of poly(A) RNA determined by electron microscope in situ hybridization. Exp. Cell Res. 208:19-34.
42. Wang, J., L. Cao, Y. Wang, and T. Pederson. 1991. Localization of pre-messenger RNA at discrete nuclear sites. Proc. Natl. Acad. Sci. USA. 88:7391-7395.
43. Wansink, D.G., W. Schul, I. van der Kraan, B. van Steensel, R. van Driel, and L. de Jong. 1993. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerasc II in domains scattered throughout the nucleus. J. Cell Biol. 122:283-293.
44. Webster, C., G.K. Pavlath, D.R. Parks, F.S. Walsh, and H.M. Blau. 1988. Isolation of human myoblasts with the fluorescence-activated cell sorter. Exp. Cell Res. 174:252-265.
45. Wu, J.Y., and T. Maniatis. 1993. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell. 75:1061-1070.
46. Xing, Y., C.V. Johnson, P.R. Dobner, and J.B. Lawrence. 1993. Higher level organization of individual gene transcription and RNA splicing. Science. 259: 1326-1330.
47. Xing, Y., C.V. Johnson, P.T. Moen, J.A. McNeil, and J.B. Lawrence. 1995. Non-random gene organization: structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 131:1635-1647.
48. Yamauchi-Takihara, K., M.J. Sole, J. Liew, D. Ing, and C.-C. Liew. 1989. Characterization of human cardiac myosin heavy chain genes. Proc. Natl. Acad. Sci. USA. 86:3504-3508.
49. Zachar, Z., J. Kramer, I.P. Mims, and P.M. Bingham. 1993. Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans. J. Cell Biol. 121:729-742.