Wang et al. BMC Genomics 2011, 12:289 http://www.biomedcentral.com/1471-2164/12/289 Page 5 of 14 Figure 3 Size distribution of Chinese cabbage csRNAs and origin of RNA. (A) Size distribution of unique csRNAs of Chinese cabbage. (B) Size distribution of total csRNAs of Chinese cabbage. (C) RNA origin of csRNA population of Chinese cabbage. the 5’ and 3’ end-specific small RNAs derived from tRNAs [9] as well as some new classes of small hetero- geneous transcripts mapped to the 5’ ends of known protein-coding genes have been reported in Arabidopsis [28], Drosophila, chicken and humans [8]. Heat response of csRNAs On a subcellular level, heat stress has serious conse- quences for chloroplast activity and structure [29], for example, the loss of chloroplast Cu/Zn superoxide dis- mutase and increased damage to photosystem II [30]. In the seedlings exposed to 46°C for 1 hour (HT), csRNA abundance declined significantly compared to that of MT seedlings, accounting for approximately 25% of unique sequences and 36% of the csRNA abundance reads in the MT dataset (Figure 5). Additional File 7 lists the down-regulated csRNAs in HT seedlings (less than one-fifth), Additional File 8 shows up-regulated ones (more than 5-fold), and Additional File 9 shows the miRNA microarray analysis of the csRNAs that were remarkably changed after heat treatment. Among heat-responsive csRNAs, the rRNA-derived csRNAs (rRNA csRNAs) were the most affected. Under heat stress, the abundance of rRNA csRNAs was reduced to approximately 49%, while the number of the unique csRNAs was reduced to approximately 29% (Fig- ure 5 and Additional File 3). Specifically, the abundance of the csRNAs derived from each rRNA were drastically reduced in HT seedlings, and the rRNA-csRNAs of var- ious length were affected (Additional File 10), showing the broad sensitivity to heat stress. We chose two families of the most abundant heat- reduced rRNA csRNAs, csR-5sr-1 and csR-23sr-1, for further analyses. csR-23sr-1 and csR-5sr-1 are derived