Chitkara Pragya, Singh Ajeet, Gangwar Rashmi, Bhardwaj Rohan, Zahra Shafaque, Arora Simran, Hamid Fiza, Arya Ajay, Sahu Namrata, Chakraborty Srija, Ramesh Madhulika, Kumar Shailesh
Bioinformatics Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
Baylor College of Medicine, Houston, TX, USA.
BMC Plant Biol. 2024 Dec 4;24(1):1162. doi: 10.1186/s12870-024-05900-0.
Fusion transcripts (FTs), generated by the fusion of genes at the DNA level or RNA-level splicing events significantly contribute to transcriptome diversity. FTs are usually considered unique features of neoplasia and serve as biomarkers and therapeutic targets for multiple cancers. The latest findings show the presence of FTs in normal human physiology. Several discrete reports mentioned the presence of fusion transcripts in planta, has important roles in stress responses, morphological alterations, or traits (e.g. seed size, etc.).
In this study, we identified 169,197 fusion transcripts in 2795 transcriptome datasets of Arabidopsis thaliana, Cicer arietinum, and Oryza sativa by using a combination of tools, and confirmed the translational activity of 150 fusion transcripts through proteomic datasets. Analysis of the FT junction sequences and their association with epigenetic factors, as revealed by ChIP-Seq datasets, demonstrated an organised process of fusion formation at the DNA level. We investigated the possible impact of three-dimensional chromatin conformation on intra-chromosomal fusion events by leveraging the Hi-C datasets with the incidence of fusion transcripts. We further utilised the long-read RNA-Seq datasets to validate the most reoccurring fusion transcripts in each plant species followed by further authentication through RT-PCR and Sanger sequencing.
Our findings suggest that a significant portion of fusion events may be attributed to alternative splicing during transcription, accounting for numerous fusion events without a proportional increase in the number of RNA pairs. Even non-nuclear DNA transcripts from mitochondria and chloroplasts can participate in intra- and inter-chromosomal fusion formation. Genes in close spatial proximity are more prone to undergoing fusion formation, especially in intra-chromosomal FTs. Most of the fusion transcripts may not undergo translation and serve as long non-coding RNAs. The low validation rate of FTs in plants indicated that the fusion transcripts are expressed at very low levels, like in the case of humans. FTs often originate from parental genes involved in essential biological processes, suggesting their relevance across diverse tissues and stress conditions. This study presents a comprehensive repository of fusion transcripts, offering valuable insights into their roles in vital physiological processes and stress responses.
融合转录本（FTs）由DNA水平的基因融合或RNA水平的剪接事件产生，对转录组多样性有显著贡献。FTs通常被认为是肿瘤形成的独特特征，并作为多种癌症的生物标志物和治疗靶点。最新研究结果表明FTs存在于正常人体生理过程中。一些独立报告提到植物中存在融合转录本，其在应激反应、形态改变或性状（如种子大小等）中发挥重要作用。
在本研究中，我们通过组合多种工具，在拟南芥、鹰嘴豆和水稻的2795个转录组数据集中鉴定出169,197个融合转录本，并通过蛋白质组数据集证实了150个融合转录本的翻译活性。对FT连接序列及其与表观遗传因子的关联进行分析（如ChIP-Seq数据集所示），证明了DNA水平上融合形成的有序过程。我们利用Hi-C数据集结合融合转录本的发生率，研究三维染色质构象对染色体内融合事件的可能影响。我们进一步利用长读长RNA-Seq数据集验证每种植物中最常出现的融合转录本，随后通过RT-PCR和Sanger测序进行进一步验证。
我们的研究结果表明，很大一部分融合事件可能归因于转录过程中的可变剪接，这导致了大量融合事件，而RNA对的数量没有相应增加。甚至线粒体和叶绿体的非核DNA转录本也能参与染色体内和染色体间的融合形成。空间距离较近的基因更容易发生融合形成，尤其是在染色体内FTs中。大多数融合转录本可能不进行翻译，而是作为长链非编码RNA。植物中FTs的验证率较低，表明融合转录本的表达水平很低，与人类情况类似。FTs通常源自参与基本生物学过程的亲本基因，表明它们在不同组织和应激条件下都具有相关性。本研究提供了一个融合转录本的综合库，为其在重要生理过程和应激反应中的作用提供了有价值的见解。
