Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235, India.
Planta. 2021 Sep 14;254(4):72. doi: 10.1007/s00425-021-03689-y.
We have predicted miRNAs, their targets and lncRNAs from the genome of Brassica oleracea along with their functional annotation. Selected miRNAs and their targets are experimentally validated. Roles of these non-coding RNAs in post-transcriptional gene regulation are also deciphered. Cauliflower (Brassica oleracea var. Botrytis) is an important vegetable crop for its dietary and medicinal values with rich source of vitamins, dietary fibers, flavonoids and antioxidants. MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs), which regulate gene expression by inhibiting translation or by degrading messenger RNAs (mRNAs). On the other hand, long non-coding RNAs (lncRNAs) are responsible for the up regulation and the down regulation of transcription. Although the genome of cauliflower is reported, yet the roles of these ncRNAs in post-transcriptional gene regulation (PTGR) remain elusive. In this study, we have computationally predicted 355 miRNAs, of which 280 miRNAs are novel compared to miRBase 22.1. All the predicted miRNAs belong to 121 different families. We have also identified 934 targets of 125 miRNAs along with their functional annotation. These targets are further classified into biological processes, molecular functions and cellular components. Moreover, we have predicted 634 lncRNAs, of which 61 are targeted by 30 novel miRNAs. Randomly chosen 10 miRNAs and 10 lncRNAs are experimentally validated. Five miRNA targets including squamosa promoter-binding-like protein 9, homeobox-leucine zipper protein HDG12-like, NAC domain-containing protein 100, CUP-SHAPED COTYLEDON 1 and kinesin-like protein NACK2 of four miRNAs including bol-miR156a, bol-miR162a, bol-miR164d and bol-miR2673 are also experimentally validated. We have built network models of interactions between miRNAs and their target mRNAs, as well as between miRNAs and lncRNAs. Our findings enhance the knowledge of non-coding genome of cauliflower and their roles in PTGR, and might play important roles in improving agronomic traits of this economically important crop.
我们从甘蓝基因组中预测了 miRNA、它们的靶基因和 lncRNA，并对其功能进行了注释。我们还对选定的 miRNA 和它们的靶基因进行了实验验证。此外，我们还解析了这些非编码 RNA 在转录后基因调控中的作用。花椰菜（甘蓝 var. Botrytis）是一种重要的蔬菜作物，具有丰富的维生素、膳食纤维、类黄酮和抗氧化剂，具有食用和药用价值。microRNAs（miRNAs）是一类小的非编码 RNA（ncRNA），通过抑制翻译或降解信使 RNA（mRNA）来调节基因表达。另一方面，长非编码 RNA（lncRNA）负责转录的上调和下调。尽管已经报道了花椰菜的基因组，但这些 ncRNA 在转录后基因调控（PTGR）中的作用仍不清楚。在这项研究中，我们通过计算预测了 355 个 miRNA，其中 280 个 miRNA 是与 miRBase 22.1 相比的新 miRNA。所有预测的 miRNA 都属于 121 个不同的家族。我们还鉴定了 125 个 miRNA 的 934 个靶基因，并对其功能进行了注释。这些靶基因进一步分为生物过程、分子功能和细胞成分。此外，我们还预测了 634 个 lncRNA，其中 61 个被 30 个新 miRNA 靶向。随机选择的 10 个 miRNA 和 10 个 lncRNA 进行了实验验证。包括 squamosa promoter-binding-like protein 9、homeobox-leucine zipper protein HDG12-like、NAC domain-containing protein 100、CUP-SHAPED COTYLEDON 1 和 kinesin-like protein NACK2 在内的五个 miRNA 靶基因，包括 bol-miR156a、bol-miR162a、bol-miR164d 和 bol-miR2673 在内的四个 miRNA 的实验验证也得到了证实。我们还构建了 miRNA 和它们的靶基因 mRNA 之间以及 miRNA 和 lncRNA 之间相互作用的网络模型。我们的研究结果提高了对花椰菜非编码基因组及其在 PTGR 中作用的认识，可能对提高这种经济重要作物的农艺性状发挥重要作用。
