Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
Institute of Education and Research, São Paulo, SP, Brazil.
Sci Rep. 2024 Aug 27;14(1):19797. doi: 10.1038/s41598-024-67975-x.
Long noncoding RNAs (lncRNAs) are versatile RNA molecules recently identified as key regulators of gene expression in response to environmental stress. Our primary focus in this study was to develop a robust computational pipeline for identifying structurally identical lncRNAs across replicates from publicly available bulk RNA-seq datasets. In order to demonstrate the effectiveness of the pipeline, we utilized the transcriptome of the thermophilic fungus Thermothelomyces thermophilus and assessed the expression pattern of lncRNAs in conjunction with Heat Shock Proteins (HSP), a well-known protein family critical for the cell's response to high temperatures. Our findings demonstrate that the identification of structurally identical transcripts among replicates in this thermophilic fungus ensures the reliability and accuracy of RNA studies, contributing to the validity of biological interpretations. Furthermore, the majority of lncRNAs exhibited a distinct expression pattern compared to HSPs. Our study contributes to advancing the understanding of the biological mechanisms comprising lncRNAs in thermophilic fungi.
长链非编码 RNA（lncRNA）是最近被鉴定为响应环境压力时基因表达关键调节因子的多功能 RNA 分子。在这项研究中，我们的主要重点是开发一种强大的计算管道，用于从公开可用的批量 RNA-seq 数据集的重复中识别结构相同的 lncRNA。为了证明该管道的有效性，我们利用嗜热真菌 Thermothelomyces thermophilus 的转录组，并评估 lncRNA 的表达模式与热休克蛋白（HSP）相结合，HSP 是一个众所周知的对细胞应对高温至关重要的蛋白质家族。我们的研究结果表明，在这种嗜热真菌中重复之间结构相同的转录本的识别确保了 RNA 研究的可靠性和准确性，有助于生物解释的有效性。此外，大多数 lncRNA 的表达模式与 HSP 明显不同。我们的研究有助于提高对嗜热真菌中 lncRNA 组成的生物学机制的理解。
