Rice Papers

Genome Res. 2009 Aug

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice 锛圥DF)

genome research 杩戝嚑骞村彂浜嗕笉灏戠瘒鍏充簬small RNA锛圡iRNA锛夌殑鏂囩珷锛屾柊鐨勫皬RNA锛屼互鍙婂湪鍩哄洜缁勫唴鐨勫垎甯� 瑙勫緥鎴栬�呭仛绉嶉棿绉嶅唴姣旇緝鐮旂┒锛岄兘鑴变笉寮�涓板瘜鐨勫熀鍥犵粍瀛︾煡璇嗭紝瀵规按绋诲皬RNA浠庡垵鏈熷埌瀵瑰悇涓粍缁囧悇涓椂鏈熷缓搴撳垎鏋愶紝杩欏凡缁忔槸绗琋绡囦簡锛岄鐩鐨勬槸鑺辨湡鐨勫皬RNA锛岋紙鍏跺疄鍟ラ兘鍋氫簡锛夛紝siRNA鏃╂湡涔熸湁浜哄仛杩囩皣鐘跺垎甯冪殑鐮旂┒锛屼絾鏄偅鏃跺�欏鏁翠釜small RNA鐨勪簡瑙ｈ繕娌￠偅涔堜赴瀵屽锛岀幇鍦ㄥ洖杩囧ご鏉ュ啀鍒嗘瀽涓�鐣紝閰嶄笂婕備寒鐨勫浘鐗囷紝鍙堟槸涓�绡囧ソ鏂囥��

涓轰簡鐮旂┒姘寸ɑ鍙戣偛杩囩▼涓璼mall RNA鐨勮皟鑺備綔鐢紝瀵规垚鐔熷彾鐗囷紝鏍癸紝鑼庡拰鑺眘mall RNA鍋�454娴嬪簭鍒嗘瀽锛堟湁閽辨湁鎶�鏈晩锛侊級锛宑luster澶氱敱涓ょsmall RNA缁勬垚24-nt RNA鍜�21锛峮tRNA锛屽畠浠殑鍒嗗竷鍜岃〃杈炬ā寮忛兘涓嶄竴鏍枫��24锛峮tRNA瀵岄泦鍦ㄥ熀鍥犵粍鐨勯噸澶嶅尯鍩熷苟涓斿湪鍥涚缁勭粐閮借〃杈句絾鏄尯鍒笉澶э紝鏂囩珷缁欑殑缁撹鏄�24锛峮t RNA瀵归噸澶嶅尯鍏冧欢鐨勬矇榛樿捣鐫�housekeeping 聽鐪嬪鍔熻兘锛岃��21nt RNA缁勬垚铏藉皯锛屼笖鍦ㄥ熀鍥犵粍鍒嗗竷涓婇潪闅忔満锛� 鍗磋兘琚垎鎴�31 superclusters,锛坢iRNA鏋滅劧灏忛褰撳锛夛紝杩欑被閲嶅鍜宻mall RNA鐨勫舰鎴愮浉鍏筹紝骞朵笖浼樺厛鍦ㄨ姳鏈熻〃杈撅紝鍏朵腑杩樺寘鎷竴閮ㄥ垎閫�鍖栫殑22nt RNA锛岀爺绌惰繕鍙戠幇涓�绫绘柊鍨媘iRNA鍙兘浠嬪cleavage of the cluster motif銆傘�傘��

To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from mature leaves and developing roots, shoots, and inflorescences. Using a spatial clustering algorithm, we identified 36,780 genomic groups of small RNAs. Most consisted of 24-nt RNAs that are expressed in all four tissues and enriched in repeat regions of the genome; 1029 clusters were composed primarily of 21-nt small RNAs and, strikingly, 831 of these contained phased RNAs and were preferentially expressed in developing inflorescences. Thirty-eight of the 24-mer clusters were also phased and preferentially expressed in inflorescences. The phased 21-mer clusters derive from nonprotein coding, nonrepeat regions of the genome and are grouped together into superclusters containing 10鈥�46 clusters. The majority of these 21-mer clusters (705/831) are flanked by a degenerate 22-nt motif that is offset by 12 nt from the main phase of the cluster. Small RNAs complementary to these flanking 22-nt motifs define a new miRNA family, which is conserved in maize and expressed in developing reproductive tissues in both plants. These results suggest that the biogenesis of phased inflorescence RNAs resembles that of tasiRNAs and raise the possibility that these novel small RNAs function in early reproductive development in rice and other monocots.