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

Smith KP, Moen PT, Wydner KL, Coleman JR, Lawrence JB - J. Cell Biol. (1999)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.

ABSTRACT
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.

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Related in: MedlinePlus

Structure of the dystrophin RNA track.  (A) Map of relative positions of dystrophin  probes. All distances are approximations due to  the lack of a detailed map of the entire dystrophin gene locus. The dystrophin gene is represented by equally spaced hash marks that represent exons. The variability of intron sizes is not  represented here. Positions of the two genomic  and two cDNA probes relative to the dystrophin  gene and mRNA are shown. (B–D) 5′ cDNA sequences overlap more 3′ sequences. 5′ cDNA  signal (B, red) runs into and overlaps the mid  cDNA signal (C, green) as seen in the combined  photo (D), indicating that 5′ sequences are transcribed first and carried along as midgene exons  are transcribed. (E–G) RNA sequences seen  with 5′ intron sequences do not overlap more 3′  intron sequences. 5′ genomic sequences (E, red)  do not overlap midgene genomic sequences (F,  green) as shown in the combined photo (G).  Both probes are almost entirely intron sequences. Only minute amounts of 5′ sequences  can be seen overlapping the midgene RNA signal. Separation suggests that the intron sequences are cleaved out of the transcribing  RNA. (H) Model of cotranscriptional processing  of dystrophin RNA. As RNA is transcribed  along the gene, introns are spliced out, whereas  the spliced exons move down the gene. So the intron foci would appear spatially separate and the  5′ and midgene exon tracks would overlap.
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Figure 5: Structure of the dystrophin RNA track. (A) Map of relative positions of dystrophin probes. All distances are approximations due to the lack of a detailed map of the entire dystrophin gene locus. The dystrophin gene is represented by equally spaced hash marks that represent exons. The variability of intron sizes is not represented here. Positions of the two genomic and two cDNA probes relative to the dystrophin gene and mRNA are shown. (B–D) 5′ cDNA sequences overlap more 3′ sequences. 5′ cDNA signal (B, red) runs into and overlaps the mid cDNA signal (C, green) as seen in the combined photo (D), indicating that 5′ sequences are transcribed first and carried along as midgene exons are transcribed. (E–G) RNA sequences seen with 5′ intron sequences do not overlap more 3′ intron sequences. 5′ genomic sequences (E, red) do not overlap midgene genomic sequences (F, green) as shown in the combined photo (G). Both probes are almost entirely intron sequences. Only minute amounts of 5′ sequences can be seen overlapping the midgene RNA signal. Separation suggests that the intron sequences are cleaved out of the transcribing RNA. (H) Model of cotranscriptional processing of dystrophin RNA. As RNA is transcribed along the gene, introns are spliced out, whereas the spliced exons move down the gene. So the intron foci would appear spatially separate and the 5′ and midgene exon tracks would overlap.

Mentions: The approximate positions of the dystrophin probes are presented in Fig. 5 A. The designations and probe descriptions are as follows: (a) mid-genomic, a probe specific for the portion of the dystrophin gene surrounding exon 44, (15lDMD), obtained from C.T. Caskey (Baylor College of Medicine, Houston, TX). It contains a 16-kb insert corresponding to a portions of intron 43, exon 44 (147 bp), and intron 44. This probe is >99% intron sequences. (b) 5′ Genomic, dystrophin clone 24A2, contains a 10-kb genomic sequence from the 5′ region of the gene. (c) 5′ cDNA, DMD13 (exons 1–11, ∼1.67 kb). (d) mid-cDNA, DMD10 (exons 17–27, ∼2.8 kb), the 5′ genomic and cDNA probes were provided by L. Kunkel (Harvard School of Medicine, Boston, MA).


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

Smith KP, Moen PT, Wydner KL, Coleman JR, Lawrence JB - J. Cell Biol. (1999)

Structure of the dystrophin RNA track.  (A) Map of relative positions of dystrophin  probes. All distances are approximations due to  the lack of a detailed map of the entire dystrophin gene locus. The dystrophin gene is represented by equally spaced hash marks that represent exons. The variability of intron sizes is not  represented here. Positions of the two genomic  and two cDNA probes relative to the dystrophin  gene and mRNA are shown. (B–D) 5′ cDNA sequences overlap more 3′ sequences. 5′ cDNA  signal (B, red) runs into and overlaps the mid  cDNA signal (C, green) as seen in the combined  photo (D), indicating that 5′ sequences are transcribed first and carried along as midgene exons  are transcribed. (E–G) RNA sequences seen  with 5′ intron sequences do not overlap more 3′  intron sequences. 5′ genomic sequences (E, red)  do not overlap midgene genomic sequences (F,  green) as shown in the combined photo (G).  Both probes are almost entirely intron sequences. Only minute amounts of 5′ sequences  can be seen overlapping the midgene RNA signal. Separation suggests that the intron sequences are cleaved out of the transcribing  RNA. (H) Model of cotranscriptional processing  of dystrophin RNA. As RNA is transcribed  along the gene, introns are spliced out, whereas  the spliced exons move down the gene. So the intron foci would appear spatially separate and the  5′ and midgene exon tracks would overlap.
© Copyright Policy
Related In: Results  -  Collection

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Figure 5: Structure of the dystrophin RNA track. (A) Map of relative positions of dystrophin probes. All distances are approximations due to the lack of a detailed map of the entire dystrophin gene locus. The dystrophin gene is represented by equally spaced hash marks that represent exons. The variability of intron sizes is not represented here. Positions of the two genomic and two cDNA probes relative to the dystrophin gene and mRNA are shown. (B–D) 5′ cDNA sequences overlap more 3′ sequences. 5′ cDNA signal (B, red) runs into and overlaps the mid cDNA signal (C, green) as seen in the combined photo (D), indicating that 5′ sequences are transcribed first and carried along as midgene exons are transcribed. (E–G) RNA sequences seen with 5′ intron sequences do not overlap more 3′ intron sequences. 5′ genomic sequences (E, red) do not overlap midgene genomic sequences (F, green) as shown in the combined photo (G). Both probes are almost entirely intron sequences. Only minute amounts of 5′ sequences can be seen overlapping the midgene RNA signal. Separation suggests that the intron sequences are cleaved out of the transcribing RNA. (H) Model of cotranscriptional processing of dystrophin RNA. As RNA is transcribed along the gene, introns are spliced out, whereas the spliced exons move down the gene. So the intron foci would appear spatially separate and the 5′ and midgene exon tracks would overlap.
Mentions: The approximate positions of the dystrophin probes are presented in Fig. 5 A. The designations and probe descriptions are as follows: (a) mid-genomic, a probe specific for the portion of the dystrophin gene surrounding exon 44, (15lDMD), obtained from C.T. Caskey (Baylor College of Medicine, Houston, TX). It contains a 16-kb insert corresponding to a portions of intron 43, exon 44 (147 bp), and intron 44. This probe is >99% intron sequences. (b) 5′ Genomic, dystrophin clone 24A2, contains a 10-kb genomic sequence from the 5′ region of the gene. (c) 5′ cDNA, DMD13 (exons 1–11, ∼1.67 kb). (d) mid-cDNA, DMD10 (exons 17–27, ∼2.8 kb), the 5′ genomic and cDNA probes were provided by L. Kunkel (Harvard School of Medicine, Boston, MA).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus