Open Access Research article

Developmentally regulated expression and complex processing of barley pri-microRNAs

Katarzyna Kruszka1, Andrzej Pacak1, Aleksandra Swida-Barteczka1, Agnieszka K Stefaniak1, Elzbieta Kaja1, Izabela Sierocka1, Wojciech Karlowski2, Artur Jarmolowski1 and Zofia Szweykowska-Kulinska12*

  • * Corresponding author: Zofia Szweykowska-Kulinska zofszwey@amu.edu.pl

  • † Equal contributors

Author Affiliations

1 Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland

2 Computational Genomics Laboratory - Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland

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BMC Genomics 2013, 14:34  doi:10.1186/1471-2164-14-34

Published: 16 January 2013

Additional files

Additional file 1: Table S1:

Gene structure and composition of fully spliced and alternatively spliced variants of MIR156g and MIR1126 gene transcripts. The longest ORF detected in each variant is defined by the length of the encoding sequence, position of the ORF within the sequence, numbers of amino acids, and the lowest E-value in blastp analysis. The lengths of the spliced forms are given for the 5 and 3 RACE sequence results, and the lengths of the PCR products obtained using peripheral primers.1 Predicted sequence; e - exon; i - intron, nss - no significant similarity in blastp outcome.

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Additional file 2: Figure S1:

Growth stages studied in barley, cultivar Rolap. (A) 1-week-old plants. (B) 2-week-old plants. (C) 3-week-old plants. (D) 6-week-old plants. (E) 68-day-old plants.

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Additional file 3: Figure S2:

The purity of RNA and cDNA samples depleted of gDNA in three biological replicates. (A) RNA samples after DNase treatment. The purity of RNA samples depleted of DNA traces was controlled by PCR amplification of the barley MIR171 gene. In a positive control reaction, 1 ng of gDNA was used. (B) cDNA samples. The purity of cDNA samples containing no gDNA was controlled by PCR amplification of the barley phosphate transporter 1 (HvPht1-1) promoter fragment of 977 bp long. In a positive control reaction, 1 ng of gDNA was used. 1w: 1-week-old seedlings, 2w: 2-week-old seedlings, 3w: 3-week-old plants, 6w: 6-week-old plants, 68d: 68-day-old plants, gDNA: genomic DNA, H: no template, M: GeneRuler 100 bp Plus DNA ladder.

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Additional file 4: Table S2:

List of primers and hybridization probes used in the experiments.

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Additional file 5: Figure S3:

RT-PCR detection of MIR genes transcripts studied in two additional biological replicates (B and C). 1w: 1-week-old seedlings, 2w: 2-week-old seedlings, 3w: 3-week-old plants, 6w: 6-week-old plants, 68d: 68-day-old plants, gDNA: genomic DNA, H: no template control, M: GeneRuler 100 bp Plus or 1kb Plus DNA Ladder.

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