Extrachromosomal circular DNA produces regulatory small RNAs involved in zygotic genome remodeling

Extrachromosomal circular DNA (eccDNA) is widely distributed in eukaryotes.ParameciumeccDNA is generated through random concatenation of short, transposon-derived sequences that are excised from the germline genomeand transcribed to generateregulatory small RNA.These small RNAs help to eliminate a bulk of transposon remnants from the zygotic somatic genome through a positive feedback loop mechanism. Here we present evidence that Paramecium eccDNA transcription depends oneukaryotic DNA-dependent RNA polymerase III (RNAP III) and knockdown of RNAP III subunit RPC2 results in specific loss of small RNA deriving from eccDNAand an incomplete elimination of transposable elements from the genome.We identified thousands of unique eccDNA sequences, each falling within the size range of 100 -600 bp. Furthermore, our research indicates that transcription start sites are distributed across the entire eccDNA sequences. This suggests that factors other than conserved sequence elements play a role in recruiting RNAP III to these unconventional DNA templates.

染色体外环状DNA（Extrachromosomal circular DNA，eccDNA）广泛分布于真核生物中。草履虫的eccDNA通过从生殖系基因组中剪切获得的短转座子衍生序列的随机串联生成，并经转录产生调控小RNA。这类调控小RNA可通过正反馈环路机制，从合子体细胞基因组中清除大量转座子残留序列。本研究提供证据表明，草履虫eccDNA的转录依赖于真核生物依赖DNA的RNA聚合酶III（DNA-dependent RNA polymerase III，RNAP III）；敲降RNAP III的亚基RPC2会特异性丢失源自eccDNA的小RNA，并导致基因组中转座因子的清除不完全。本研究共鉴定到数千条独特的eccDNA序列，其长度均处于100~600 bp的范围内。此外，本研究发现转录起始位点遍布整条eccDNA序列。这提示，除保守序列元件外，其他因子也参与将RNAP III招募至这些非典型DNA模板中。