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Assessing the 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data

100%

Szymanski M., Karlowski W.

2016

vol. 63

issue 4

841-844

In eukaryotes, ribosomal 5S rRNAs are products of multigene families organized within clusters of tandemly repeated units. Accumulation of genomic data obtained from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a large number of variants, often incompatible with folding into a correct secondary structure. Here, we present results of an analysis of a large set of short RNA sequences generated by the next generation sequencing techniques, to address the problem of heterogeneity of the 5S rRNA transcripts in Arabidopsis and identification of potentially functional rRNA-derived fragments.

Developmental changes in barley microRNA expression profiles coupled with miRNA target analysis

61%

Pacak A., Kruszka K., Swida-Barteczka A., Nuc P., Karlowski W., Jarmolowski A., Szweykowska-Kulinska Z.

2016

vol. 63

issue 4

799-809

MicroRNAs are 19- to 24-nt-long single-stranded RNAs that are crucial regulators of gene expression which control plant development and response to environmental cues. We have analyzed microtranscriptomes of five barley developmental stages. Generally, during the barley development, miR168-3p and miR1432-5p levels increase while the 5'U-miR156-5p level decreases (with exception for the 2-week-old barley). We have identified two miR156-5p izomiRs (called 5'U-miR156-5p [20 nt] and 5'UU-miR156-5p [21 nt]), which were expressed differently during barley development. The 5' U-miR156-5p level decreased in 3-week-, 6-week-, and 68-day-old barley, when compared to the 1-week-old plants. Meanwhile, the 5' UU-miR156-5p level increased significantly in the 68-day-old barley plants. Moreover, only the 5' U-miR156 isomiR recognizes and guides unique transcription factor mRNAs from the Squamosa Promoter Binding Protein-Like (SPL) family. We identified many non-canonical microRNAs with changed expression levels during the barley development. Here, we present the profiles of microRNA expression characteristics for particular barley developmental stages. These analyses are accompanied by the experimental degradome analysis of miRNA targets.

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2 Acta Biochimica Polonica

2 2016

2 Karlowski W.

1 Jarmolowski A.

1 Kruszka K.

1 Nuc P.

1 Pacak A.

1 Swida-Barteczka A.

1 Szweykowska-Kulinska Z.

1 Szymanski M.

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Assessing the 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data

Developmental changes in barley microRNA expression profiles coupled with miRNA target analysis