Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic.
Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 32300, Pilsen, Czech Republic.
BMC Genomics. 2024 Jun 28;25(1):649. doi: 10.1186/s12864-024-10558-x.
Despite the fact that introns mean an energy and time burden for eukaryotic cells, they play an irreplaceable role in the diversification and regulation of protein production. As a common feature of eukaryotic genomes, it has been reported that in protein-coding genes, the longest intron is usually one of the first introns. The goal of our work was to find a possible difference in the biological function of genes that fulfill this common feature compared to genes that do not. Data on the lengths of all introns in genes were extracted from the genomes of six vertebrates (human, mouse, koala, chicken, zebrafish and fugu) and two other model organisms (nematode worm and arabidopsis). We showed that more than 40% of protein-coding genes have the relative position of the longest intron located in the second or third tertile of all introns. Genes divided according to the relative position of the longest intron were found to be significantly increased in different KEGG pathways. Genes with the longest intron in the first tertile predominate in a range of pathways for amino acid and lipid metabolism, various signaling, cell junctions or ABC transporters. Genes with the longest intron in the second or third tertile show increased representation in pathways associated with the formation and function of the spliceosome and ribosomes. In the two groups of genes defined in this way, we further demonstrated the difference in the length of the longest introns and the distribution of their absolute positions. We also pointed out other characteristics, namely the positive correlation between the length of the longest intron and the sum of the lengths of all other introns in the gene and the preservation of the exact same absolute and relative position of the longest intron between orthologous genes.
尽管内含子对真核细胞意味着能量和时间的负担，但它们在蛋白质生产的多样化和调控中起着不可替代的作用。作为真核基因组的一个共同特征，据报道，在蛋白质编码基因中，最长的内含子通常是第一个内含子之一。我们工作的目标是找到满足这一共同特征的基因与不满足这一特征的基因在生物学功能上可能存在的差异。从六种脊椎动物（人类、小鼠、树袋熊、鸡、斑马鱼和河豚）和另外两种模式生物（线虫和拟南芥）的基因组中提取了所有基因的内含子长度数据。我们表明，超过 40%的蛋白质编码基因的最长内含子的相对位置位于所有内含子的第二或第三四分位数内。根据最长内含子的相对位置划分的基因在不同的 KEGG 途径中显著增加。具有第一四分位最长内含子的基因在氨基酸和脂质代谢、各种信号转导、细胞连接或 ABC 转运体等多种途径中占主导地位。具有第二或第三四分位最长内含子的基因在与剪接体和核糖体形成和功能相关的途径中表现出增加的代表性。在以这种方式定义的两组基因中，我们进一步证明了最长内含子的长度差异及其绝对位置的分布差异。我们还指出了其他特征，即最长内含子的长度与基因中所有其他内含子长度之和之间的正相关，以及同源基因中最长内含子的绝对和相对位置的精确保存。
