Agarwal Suyash, Nagpure N S, Srivastava Prachi, Kumar Ravindra, Pandey Manmohan, Srivastava Shreya, Jena J K, Das P, Kushwaha Basdeo
Division of Molecular Biology and Biotechnology, ICAR- National Bureau of Fish Genetic Resources, Canal Ring Road, Lucknow, Uttar Pradesh, 226 002, India.
AMITY University Uttar Pradesh, Lucknow Campus, Lucknow, Uttar Pradesh, 226 028, India.
Appl Biochem Biotechnol. 2017 Jul;182(3):956-966. doi: 10.1007/s12010-016-2373-4. Epub 2016 Dec 21.
MicroRNAs are small non-coding RNAs which play significant role in RNA interference. The present work deals with mining of the conserved miRNA and their target genes from the contigs, ESTs, and BAC end sequences of commercially important catfish, Clarias batrachus, from India. A total of 138, 1 and 1 conserved pre-miRNA sequences, were mined from the contigs, ESTs, and BAC end sequences, respectively. The analysis of families of the conserved pre-miRNA revealed conservation of the fish-specific family mir-430 and other important families, such as mir-455, let-7, mir-133, and mir-137. The mir-455 is involved in hypoxia signaling, let-7 family represents potential anti-tumor molecules involved in human cancer therapy, whereas mir-133 and mir-137 have high therapeutic potentials. Using an alternate computational in silico approach, mining of mature miRNAs resulted in identification of 210 mature miRNAs from contigs, 1 from EST, and 2 each from forward as well as reverse BAC end sequences. Target prediction of these putative miRNAs resulted in the identification of 66,758 and 18,747 target genes in C. batrachus and Danio rerio, respectively. Functional annotation of these miRNAs indicated their involvement in diverse biological functions. The findings of the present study can serve as a valuable resource for further functional genomics studies in C. batrachus.
微小RNA是一类小的非编码RNA，在RNA干扰中发挥着重要作用。目前的工作是从印度具有商业重要性的鲶鱼（印度胡子鲶）的重叠群、EST序列和BAC末端序列中挖掘保守的微小RNA及其靶基因。分别从重叠群、EST序列和BAC末端序列中挖掘出了总共138个、1个和1个保守的前体微小RNA序列。对保守前体微小RNA家族的分析揭示了鱼类特异性家族mir-430以及其他重要家族（如mir-455、let-7、mir-133和mir-137）的保守性。mir-455参与缺氧信号传导，let-7家族代表参与人类癌症治疗的潜在抗肿瘤分子，而mir-133和mir-137具有很高的治疗潜力。使用另一种计算机模拟方法，对成熟微小RNA的挖掘从重叠群中鉴定出210个成熟微小RNA，从EST中鉴定出1个，从正向和反向BAC末端序列中各鉴定出2个。对这些假定微小RNA的靶标预测分别在印度胡子鲶和斑马鱼中鉴定出66758个和18747个靶基因。这些微小RNA的功能注释表明它们参与了多种生物学功能。本研究的结果可为印度胡子鲶进一步的功能基因组学研究提供有价值的资源。
