EMA2 is required for target-directed scnRNA degradation.

Piwi-associated small RNAs of the ciliated protozoan Tetrahymena uses such mechanism to induce heterochromatin formation followed by programmed DNA elimination. In this process, target-directed small RNA degradation (TDSD) of small RNAs complementary to the somatic genome enables small RNAs to specifically target the germline-limited sequences for DNA elimination. The data here indicate that the SUMO E3 ligase Ema2 is required for the accumulation of long non-coding RNAs (lncRNAs) from the somatic genome and thus for TDSD. High-throughput sequencing and analyses of small RNAs were performed as described (Mutazono et al 2019). The 2020 version of the MAC genome assembly (Sheng et al. 2020) was obtained from Tetrahymena Genome Database and fragmented into 10 kb pieces. Each 10 kb fragment that contains longer than 3 kb mappable sequence was used as a MDS tile (total 10,235 tiles). Each Type-A IES (Noto et al. 2015) was used as an IES tile (total of 4,691 tiles). Normalized numbers (RPKM [reads per kilobase of unique sequences per million]) of 26- to 32-nt small RNAs that uniquely matched one of the MDS and IES tiles were counted.