Published microarray data shows that a majority of the genes predicted to be regulated by a slicing mechanism are expressed dur ing seed development however this does not preclude the non www.selleckchem.com/products/SB-203580.html overlapping expression of miRNA and target in the same cell types. In addition we found four sliced targets in our dataset that were pre dicted to be regulated through a translational repression mechanism only. Our observations suggest that there are inadequacies in the algorithms currently used to predict miRNA targets, hence experi mental verification is required to confirm these predic tions in planta. miRNA regulation during Inhibitors,Modulators,Libraries seed development The early development of the grain is controlled by a complex interaction of signalling and gene regulation networks to allow the proper expansion and specialisa tion of the different tissues that will constitute the ma ture grain.

Based on our combined analysis of smRNA and degradome Inhibitors,Modulators,Libraries data we identified 96 genes likely to be miRNA regulated during Inhibitors,Modulators,Libraries the first 15 DPA of seed development. Using annotated sequences from barley, wheat, rice and Arabidopsis, we found significant homology to an annotated gene for 77 of the miRNA target genes. Based on sequence homology these genes are predicted to encode a wide range of protein func tions, including transcription factors, kinases, oxidore ductases, hydrolases, transferases, receptors and transporters. We performed an ontol ogy analysis of these targets and compared it to a set of over 8000 ESTs previously detected in the seed and annotated by Sreenivasulu et al.

Enrich ment of GO terms was declared statistically significant if they met the criteria of P 0. 01 using a hypergeo metric one tailed test with correction for multiple test ing. This analysis shows that in the barley grain, miRNAs target a significantly higher percentage of genes annotated in the hormone signalling pathways, RNA cellular processes and energy mobilization Inhibitors,Modulators,Libraries categories. Using our data, the variation of mature miRNA abun dance was compared to that of the cognate degradation products across the three stages of grain development. The detection of mRNA cleavage products indicates that the expression domains of the miRNA and target gene are at least partially overlapping. The more the miRNA and its target are expressed, the more degradation pro ducts should be generated.

The following paragraphs highlight what we think are the more interesting data based on the function of the targets. Since it is impos sible to distinguish which one of the miRNAs are present and functional in the same tissue as the tar get, all miRNAs with zero offset to the cleavage site were Inhibitors,Modulators,Libraries considered. The number of distinct Ponatinib 284028-89-3 miRNAs and the sum of their reads for each library is summarised in Table 5. As noted above, related miRNAs tend to have similar expression profiles and thus the sum of their reads is a good indication of their individual expression patterns.