Table IV. Number and proportion of sRNAs in RNA silencing mutants matching PC cis-NAT transcripts and PC non-cis-NAT transcripts.
| Genotype | Total Unique sRNAsa |
sRNA Matches |
||
|---|---|---|---|---|
| PC cis-NATs (No. per Million)b | PC non-cis-NATs (No. per Million)b | Fold Differencec | ||
| dcl1-7 | 14,692 | 14 (0.408) | 467 (1.681) | 4.1 |
| dcl2-1 | 10,405 | 10 (0.411) | 340 (1.728) | 4.2 |
| dcl3-1 | 22,951 | 35 (0.652) | 714 (1.645) | 2.5 |
| dcl4-2 | 22,448 | 14 (0.267) | 587 (1.383) | 5.2 |
| rdr1-1 | 14,755 | 32 (0.928) | 529 (1.896) | 2.0 |
| rdr2-1d | 6,249 | 74 (5.065) | 841 (7.118) | 1.4 |
| rdr6-15 | 37,774 | 30 (0.340) | 934 (1.308) | 3.8 |
| Wild type | 57,966 | 75 (0.553) | 1,697 (1.548) | 2.8 |
sRNAs from RNA silencing mutants and wild-type plants were processed from sequences available from the National Center for Biotechnology Information Gene Expression Omnibus (accession no. GSE6682; Kasschau et al., 2007). bsRNAs that matched to 2,338 PC cis-NATs or 18,908 PC non-cis-NATs. Number per million, in parentheses, is the expected number of sRNAs out of 106 sRNAs that match a single cis-NAT or a single non-cis-NAT transcript. cThe frequency of sRNAs matching PC non-cis-NATs divided by the frequency of sRNAs matching PC cis-NATs. dThe number of sRNAs matching a PC transcript was higher in rdr2-1 than in other genotypes because rdr2-1 fails to produce many repeat-associated-siRNAs, leading to a high representation of sRNAs with homology to PC sequences (Kasschau et al., 2007).