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Results: 5

1.
Figure 5.

Figure 5. From: Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation.

Nuclear RNA quality control discards incompletely or aberrantly spliced forms of MATa1 that result in aberrant a1 isoforms. (A) Model of degradation of unspliced, partially spliced and mis-spliced forms of MATa1 by Rnt1p, Rat1p and the nuclear exosome. (B) Diagram of the different isoforms of a1 encoded by the different unspliced, partially spliced and mis-spliced forms of MATa1.

Defne E. Egecioglu, et al. Nucleic Acids Res. 2012 February;40(4):1787-1796.
2.
Figure 4.

Figure 4. From: Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation.

Analysis of exon2 skipping for the DYN2, SUS1 and YOS1 genes in the rat1-1 and rrp6Δ strains. All panels show RT–PCR products obtained using a Cy3-labeled exon1 primer and an unlabeled exon3-primer specific for the corresponding genes in the strains grown at the indicated temperatures. The exon2-skipped products (shown on the bottom panels) were detected on the same gels as the spliced and unspliced species but that portion of the gel was scanned separately to increase the signal to noise ratio. No other species were detected in the portions of the gel that are not shown.

Defne E. Egecioglu, et al. Nucleic Acids Res. 2012 February;40(4):1787-1796.
3.
Figure 2.

Figure 2. From: Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation.

Northern blot analysis of MATa1 expression in rnt1Δ and exonuclease mutant strains. The isozymes of the Glyceraldehyde 3 Phosphate Dehydrogenase enzyme (G3PDH, or GAPDH) were used as a loading control. (A) The membrane was hybridized with a riboprobe covering most of the MATa1 sequence (3 exons and 2 introns) prior to GAPDH hybridization. (B) The membrane was hybridized with an intron2-specific oligonucleotide probe (Supplementary Table S1).

Defne E. Egecioglu, et al. Nucleic Acids Res. 2012 February;40(4):1787-1796.
4.
Figure 3.

Figure 3. From: Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation.

RT–PCR and primer extension analysis of MATa1 expression in rnt1Δ and ribonuclease mutant strains. (A) RT–PCR analysis. All panels show RT–PCR products obtained using a Cy3-labeled exon1 primer and an unlabeled exon3-primer specific for MATa1 in the corresponding strains grown at the indicated temperatures. The exon2-skipped products (shown on the bottom panels) were detected on the same gel as the spliced and unspliced species but that portion of the gel was scanned separately to increase the signal to noise ratio. No other species were detected in the portions of the gel that are not shown. (B) Primer extension analysis of MATa1 in the corresponding strains using an oligonucleotide hybridizing to exon3. (C) Primer extension analysis of MATa1 in the corresponding strains using an oligonucleotide hybridizing to intron2.

Defne E. Egecioglu, et al. Nucleic Acids Res. 2012 February;40(4):1787-1796.
5.
Figure 1.

Figure 1. From: Quality control of MATa1 splicing and exon skipping by nuclear RNA degradation.

Architecture of the MAT locus, analysis of MATa1 expression in Rnt1p mutant strains and cleavage by Rnt1p. (A) Schematic representation of gene structures at the MATa and MATalpha loci. (B) Northern blot analysis of MATa1 expression in wild-type and rnt1Δ strains in the SK1 background. 2N indicate diploid cells. (C) In vitro cleavage of a model MATa1 substrate by recombinant Rnt1p. Shown is a primer extension analysis of RNAs incubated in buffer or with recombinant Rnt1p. A sequencing ladder was obtained using the same oligonucleotide. 1 and 2 indicate the location of the major cleavage products. No other cleavage products were observed in the central portion of the gel which is not shown. (D) Predicted Rnt1p stem–loop structure. Shown are the locations of the cleavage sites mapped in vitro (panel C) or in vivo (panel E). (E) RT–PCR analysis of Rnt1p cleavage intermediates. RNAs presenting a 5′-phosphate group from the corresponding strains were ligated to an adaptor RNA, amplified using a MATa1-specific reverse primer and an adaptor forward primer, and fractionated on an acrylamide gel.

Defne E. Egecioglu, et al. Nucleic Acids Res. 2012 February;40(4):1787-1796.

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