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Additional file 5: Summary of the unique tags of the repeated associate sRNAs matched on the genomes (the used number was above 19000).
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Another fraction was derived from highly repeated elements named repeat-associated small RNAs.
This analysis showed that most of these piwi-RNAs (piRNAs) correspond to repeat associated small interfering RNA (rasiRNA [3], [7]).
Eukaryotic chromosomes end with telomeres, which in most organisms are composed of tandem DNA repeats associated with telomeric proteins.
Motivated by the impact of gene regulatory alterations on carcinogenesis, we studied repeat-associated gene expression changes.
Nuclear export of GGGGCC repeat RNA is likely to be a key step leading to repeat associated non-ATG translation in the cytoplasm.
Similarly, 59% of RNAP V-dependent clusters were repeat-associated while 41% (904 out of 2,201) of these clusters were not associated with repetitive sequences.
In contrast to conserved and known miRNAs, 190 silkworm-specific miRNA genes were located in predicted transposable elements, and were repeat-associated.
Among the clusters generating small RNAs at a level greater than 100 RP59% 59% of clusters were repeat-associated while 41% (4,740 out of 11,667) were not associated with known repeats (Table S4 ).
Then, the sequences were matched against the genome to discover the repeat associate sRNAs and to observe the expression of sRNAs and known miRNAs using the miRBase.
By applying a method that is independent of alignment to the genome assembly, we found that satellite repeats associate with distinct H3 tail modifications, such as H3K9me2 and H3K9me3 for short repeats and H3K9me1 for 359 bp repeats.
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