Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam, India.
Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam, India.
BMC Genomics. 2021 May 10;22(1):336. doi: 10.1186/s12864-021-07615-0.
Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules.
In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them.
With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.
随着新的基因调控模式不断被发现，我们对基因组调控的理解也在不断发展，哺乳动物基因组的转录组研究揭示了在表达的转录本中存在相当数量的非编码 RNA 分子。其中一种非编码 RNA 分子是长非编码 RNA（lncRNA）。然而，lncRNA 在基因调控中的功能还不是很清楚；此外，在不同物种中找到保守的 lncRNA 是一项具有挑战性的任务。因此，我们提出了一种新的方法来识别保守的 lncRNA 并对这些分子进行功能注释。
在这项研究中，我们利用现有的成肌转录组数据，在小鼠和人类中鉴定了保守的 lncRNA。我们鉴定了在肌肉发育早期和晚期表达差异的 lncRNA。在培养的小鼠肌肉 C2C12 细胞中，通过实验证实了这些 lncRNA 的差异表达。我们利用基因组的三维结构，鉴定了这些 lncRNA 的拓扑相关结构域。此外，我们还将这些跨 lncRNA 在成肌过程中的功能注释与基因在结构域中的表达相关联。通过这种方法，我们鉴定了在人类和小鼠的成肌过程中保守的 lncRNA 并对其进行了功能注释。
通过这种新方法，我们鉴定了人类和小鼠成肌过程中的保守 lncRNA 并对其进行了功能注释。该方法鉴定了大量参与成肌的 lncRNA。需要进一步研究以探讨为什么在人类和小鼠中 lncRNA 序列不同，但它们却保守。我们的方法可用于鉴定不同物种中保守的新 lncRNA 并对其进行功能注释。
