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Differential pre-mRNA Splicing Alters the Transcript Diversity of Helitrons Between the Maize Inbred Lines.

Lynch BT, Patrick TL, Moreno JJ, Siebert AE, Klusman KM, Shodja DN, Hannah LC, Lal SK - G3 (Bethesda) (2015)

Bottom Line: The comparison of Helitron sequences identified unique polymorphisms in inbred B73, which potentially give rise to the alternatively spliced sites utilized by transcript isoforms.Some alterations in splicing, however, do not have obvious explanations.These observations not only add another level to the creation of transcript diversity by Helitrons among inbred lines but also provide novel insights into the cis-acting elements governing splice-site selection during pre-mRNA processing.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Oakland University, Rochester, Minnesota 48309-4401.

No MeSH data available.


Expression analysis of Helitrons in different maize inbred lines. (A−C) Reverse-transcription polymerase chain reaction products extracted from roots (top) and shoots (bottom) of various inbred lines using primers specific for Helitrons, Hel1-331, Hel1-332, and Hel1-333, respectively. These Helitron-specific primers were based on the inbred B73 sequence described previously (Barbaglia et al. 2012). The inbred lines are shown at top of the panel. Molecular weight markers in kilobases are displayed on the left of each panel.
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fig1: Expression analysis of Helitrons in different maize inbred lines. (A−C) Reverse-transcription polymerase chain reaction products extracted from roots (top) and shoots (bottom) of various inbred lines using primers specific for Helitrons, Hel1-331, Hel1-332, and Hel1-333, respectively. These Helitron-specific primers were based on the inbred B73 sequence described previously (Barbaglia et al. 2012). The inbred lines are shown at top of the panel. Molecular weight markers in kilobases are displayed on the left of each panel.

Mentions: We recently reported the expression analysis of several Helitrons in maize inbred line B73 (Barbaglia et al. 2012). The elements analyzed were selected initially from expressed sequence tag evidence of captured gene transcription. Our data indicated that these Helitrons produced multiple transcripts via differential selection of splice sites during pre-mRNA processing and read-through transcription. Because alternative splicing and Helitrons are both viewed as potentially important forces in the processes of evolution, we examined the expression of Helitrons Hel1-331, Hel1-332, and Hel1-333 in different maize inbred lines. Total RNA from etiolated root and shoot tissues from inbred lines B73, CML277, CML322, HP301, Ki11, Mo17, Ms71, OH43, OH7B, and Tzi8 was subjected to RT-PCR analysis using the same primers for each Helitron reported previously in B73 (Barbaglia et al. 2012). The resultant amplified products were resolved on an agarose gel and stained with ethidium bromide. As displayed in Figure 1, the profile of RT-PCR products for each Helitron in the other inbreds dramatically differed from B73. For example, several RT-PCR products from both roots (Figure 1A) and shoots (Figure 1B) were derived from Helitron Hel1-331 in inbred B73. In contrast, only a single product of approximately 1.0kb was amplified from roots in inbred lines CML277, CML322, HP301, OH7B, and Tzi8 and shoots in inbred lines CML322, HP301, Ki11, Mo17, Ms71, OH43, OH7B, and Tzi8 (Figure 1, A and B).


Differential pre-mRNA Splicing Alters the Transcript Diversity of Helitrons Between the Maize Inbred Lines.

Lynch BT, Patrick TL, Moreno JJ, Siebert AE, Klusman KM, Shodja DN, Hannah LC, Lal SK - G3 (Bethesda) (2015)

Expression analysis of Helitrons in different maize inbred lines. (A−C) Reverse-transcription polymerase chain reaction products extracted from roots (top) and shoots (bottom) of various inbred lines using primers specific for Helitrons, Hel1-331, Hel1-332, and Hel1-333, respectively. These Helitron-specific primers were based on the inbred B73 sequence described previously (Barbaglia et al. 2012). The inbred lines are shown at top of the panel. Molecular weight markers in kilobases are displayed on the left of each panel.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528327&req=5

fig1: Expression analysis of Helitrons in different maize inbred lines. (A−C) Reverse-transcription polymerase chain reaction products extracted from roots (top) and shoots (bottom) of various inbred lines using primers specific for Helitrons, Hel1-331, Hel1-332, and Hel1-333, respectively. These Helitron-specific primers were based on the inbred B73 sequence described previously (Barbaglia et al. 2012). The inbred lines are shown at top of the panel. Molecular weight markers in kilobases are displayed on the left of each panel.
Mentions: We recently reported the expression analysis of several Helitrons in maize inbred line B73 (Barbaglia et al. 2012). The elements analyzed were selected initially from expressed sequence tag evidence of captured gene transcription. Our data indicated that these Helitrons produced multiple transcripts via differential selection of splice sites during pre-mRNA processing and read-through transcription. Because alternative splicing and Helitrons are both viewed as potentially important forces in the processes of evolution, we examined the expression of Helitrons Hel1-331, Hel1-332, and Hel1-333 in different maize inbred lines. Total RNA from etiolated root and shoot tissues from inbred lines B73, CML277, CML322, HP301, Ki11, Mo17, Ms71, OH43, OH7B, and Tzi8 was subjected to RT-PCR analysis using the same primers for each Helitron reported previously in B73 (Barbaglia et al. 2012). The resultant amplified products were resolved on an agarose gel and stained with ethidium bromide. As displayed in Figure 1, the profile of RT-PCR products for each Helitron in the other inbreds dramatically differed from B73. For example, several RT-PCR products from both roots (Figure 1A) and shoots (Figure 1B) were derived from Helitron Hel1-331 in inbred B73. In contrast, only a single product of approximately 1.0kb was amplified from roots in inbred lines CML277, CML322, HP301, OH7B, and Tzi8 and shoots in inbred lines CML322, HP301, Ki11, Mo17, Ms71, OH43, OH7B, and Tzi8 (Figure 1, A and B).

Bottom Line: The comparison of Helitron sequences identified unique polymorphisms in inbred B73, which potentially give rise to the alternatively spliced sites utilized by transcript isoforms.Some alterations in splicing, however, do not have obvious explanations.These observations not only add another level to the creation of transcript diversity by Helitrons among inbred lines but also provide novel insights into the cis-acting elements governing splice-site selection during pre-mRNA processing.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Oakland University, Rochester, Minnesota 48309-4401.

No MeSH data available.