Vaz Candida, Ahmad Hafiz M, Bharti Richa, Pandey Priyatama, Kumar Lalit, Kulshreshtha Ritu, Bhattacharya Alok
School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
BMC Res Notes. 2013 Sep 28;6:390. doi: 10.1186/1756-0500-6-390.
MicroRNAs (miRNAs) have been recognized as one of the key regulatory non-coding RNAs that are involved in a number of basic cellular processes. miRNA expression profiling helps to identify miRNAs that could serve as biomarkers. Next generation sequencing (NGS) platforms provide the most effective way of miRNA profiling, particularly as expression of different isoforms of miRNA (IsomiRs) can be estimated by NGS. Therefore, it is now possible to discern the overall complexity of miRNA populations that participate in gene regulatory networks. It is thus important to consider different isoforms of miRNA as part of total profiling in order to understand all aspects of the biology of miRNAs.
Here next generation sequencing data of small RNAs derived from normal peripheral blood mononuclear cells (PBMC) and Chronic myeloid leukemia (CML) patients has been used to generate miRNA profiles using a computation pipeline which can identify isomiRs that are natural variants of mature miRNAs. IsomiR profiles have been generated for all the 5p and 3p miRNAs (previously known as major mature miRNA and minor or miRNA*) and the data has been presented as a composite total miRNA transcriptome. The results indicated that the most abundant isomiR sequence of about 68% miRNAs, did not match the reference miRNA sequence as entered in the miRBase and that there is a definite pattern in relative concentration of different isomiRs derived from same precursors. Finally, a total of 17 potential novel miRNA sequences were identified suggesting that there are still some new miRNAs yet to be discovered.
Inclusion of different isoforms provides a detailed miRnome of a cell type or tissues. Availability of miRnome will be useful for finding biomarkers of different cell types and disease states. Our results also indicate that the relative expression levels of different isoforms of a miRNA are likely to be dynamic and may change with respect to changes in the cell or differentiation status.
微小RNA（miRNA）已被公认为是参与多种基本细胞过程的关键调控非编码RNA之一。miRNA表达谱有助于识别可作为生物标志物的miRNA。新一代测序（NGS）平台提供了最有效的miRNA谱分析方法，特别是因为NGS可以估计miRNA不同异构体（异源miRNA）的表达。因此，现在有可能辨别参与基因调控网络的miRNA群体的整体复杂性。因此，将不同的miRNA异构体作为总谱分析的一部分来考虑，对于理解miRNA生物学的各个方面很重要。
在这里，来自正常外周血单个核细胞（PBMC）和慢性粒细胞白血病（CML）患者的小RNA的新一代测序数据已被用于使用计算管道生成miRNA谱，该管道可以识别作为成熟miRNA天然变体的异源miRNA。已针对所有5p和3p miRNA（以前称为主要成熟miRNA和次要或miRNA*）生成了异源miRNA谱，并且数据已呈现为复合总miRNA转录组。结果表明，约68%的miRNA最丰富的异源miRNA序列与miRBase中输入的参考miRNA序列不匹配，并且来自相同前体的不同异源miRNA的相对浓度存在确定的模式。最后，共鉴定出17个潜在的新型miRNA序列，表明仍有一些新的miRNA有待发现。
纳入不同的异构体可提供细胞类型或组织的详细miRNA组。miRNA组的可用性将有助于寻找不同细胞类型和疾病状态的生物标志物。我们的结果还表明，miRNA不同异构体的相对表达水平可能是动态的，并且可能随细胞或分化状态的变化而变化。
