Non-coding RNA profiling by high throughput sequencing
Summary
Recent work has shown that small non-coding RNAs, including miRNAs, serve an important role in controlling gene expression during development and disease. However, little detailed information exists concerning the relative expression patterns of small RNAs during development of C. elegans. Here we use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs, including miRNAs, changes dynamically during development and in the different sexes of C. elegans; approximately 16% of known miRNAs changed over 10 fold in expression during C. elegans development and about 12% of miRNAs showed major changes in expression between males and hermaphrodites of C. elegans. These results should lead to a better understanding of the expression and function of small RNAs in C. elegans development.
Examination of small RNA expression in six different developmental stages of hermaphrodites (Embryo, mid-L1, mid-L2, mid-L3, mid-L4, young adult), and young adult males (dpy-28;him-8) and spermatogenesis-defective young adult hermaphrodites (spe-9). The number of sequence reads for miRNA was assessed from the raw sequence data from Solexa sequencing using perfect sequence matching to known miRNAs (miRBase Release 11.0).
Table 2: Normalized Reads (Total number of reads that perfectly matched C. egegans genome was used for normalizing library difference. Sample1_EmbH:5742750, Sample2_mL1H:5617234, Sample3_mL2H:6047597, Sample4_mL3H:4948026, Sample5_mL4H:6072252, Sample6_yAdH:5975243, Sample7_yAdM:7602104, Sample8_yAdSPE9:5185655) header descriptions
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