Abstract: Statistics of piRNA
Piwi-interacting RNA (piRNA) form RNA-protein complexes through
interactions with piwi proteins in animal cells. These piRNA
complexes have been linked to both epigenetic and
post-transcriptional gene silencing of retrotransposons and other
genetic elements in germ line cells, particularly those in
spermatogenesis. Among small non-coding RNA molecules,
Piwi-interacting RNA (piRNA) is much more than small interacting RNAs
(siRNAs) and mircoRNAs (miRNAs).
Biogenesis
Figure 1. Biogenesis of piwiRNA (Nat Rev Mol Cell Biol. 2011 Apr;12(4):246-58)
Statistics of
piRNAs
piRNAs are longer and lack of sequence conservation, differing from
microRNA (miRNA) in size (21-23 nt mostly). The dataset for
statistics of piRNAs was downloaded from piRNABank
(http://pirnabank.ibab.ac.in/index.shtml).
A total of 667,944 piRNA
records share 23,439 unique
sequences from hsa-piR-000001 to hsa-piR-023449 in human. The most
human piRNAs are 26-32 nt (Figure
2).
Figure 2. Length distribution of human piRNAs.
Of 23,439 unqiue piRNA sequences, 19,260 sequences (82%) own one
copy, and the other 4,179 sequences can be located in different
region of human genome sequences. As the list below showed, a lot of
piRNA might be multiply aligned into different regions.
sequence
seq_len num of copies
1 UGUAAUCCCAGCACUUUGGGAGGCCGAGG 29 92138
2 CCUCCCAAAGUGCUGGGAUUACAGGCGUGAG 31 89266
3 UGUUAGCCAGGAUGGUCUCGAUCUCCUGA 29 38272
4 UAGUCCCAGCUACUUGGGAGGCUGAGGCA 29 27727
5 GGCUGGUCUCGAACUCCUGACCUCAGGU 28 23808
6 UGCCUGUAAUCCCAGCACUUUGGGAGGCCG 30 23336
7 UGCCUGUAAUCCCAGCACUUUGGGAGGCC 29 20784
8 UGCCUGUAAUCCCAGCUACUCAGGAGGCUG 30 18885
9 AGUAGAGACAGGGUUUCACCAUGUUGGCCA 30 18813
10 GAGUUUGAGACCAGCCUGGCCAACAUGGU 29 18746
11 CUGCAUAGUAUUCCAUGGUGUAUAUGUGC 29 17221
12 CACUUUGGGAGGCCGAGGCGGGUGGAUC 28 15868
13 UGAACCUGGGAGGCGGAGGUUGCAGUGAGC 30 13156
14 UGGUCUCGAACUCCUGACCUCAGGUGAUCCA 31 12150
15 UACUCAGGAGGCUGAGGCAGGAGAAUGGC 29 10609
16 UGAGAACACAUGGACACAGGAAGGGGAA 28 8977
17 UGGUCUCGAACUCCUGACCUCAGGUGAUCU 30 6228
18 UGGGAGGCGGAGGUUGCAGUGAGCCGAGA 29 5886
19 UGGUCUCGAACUCCUGACCUCAGGUGAUCC 30 5061
20 UACAGCACACUGAUGGGUCUUGACUC 26
4983
Reference
1. PIWI-interacting small RNAs: the vanguard of genome defence. Nat
Rev Mol Cell Biol. 2011 Apr;12(4):246-58. doi: 10.1038/nrm3089.
2. "piRNABank: a web resource on classified and clustered
Piwi-interacting RNAs". Nucleic Acids Research 2008 January; 36
(Database issue): D173–D177.
Writing date: 2014.11.10, 2015.02.17
