Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland.
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 272-8562, Japan.
Nucleic Acids Res. 2018 Jan 4;46(D1):D186-D193. doi: 10.1093/nar/gkx948.
Gene overlap plays various regulatory functions on transcriptional and post-transcriptional levels. Most current studies focus on protein-coding genes overlapping with non-protein-coding counterparts, the so called natural antisense transcripts. Considerably less is known about the role of gene overlap in the case of two protein-coding genes. Here, we provide OverGeneDB, a database of human and mouse 5' end protein-coding overlapping genes. The database contains 582 human and 113 mouse gene pairs that are transcribed using overlapping promoters in at least one analyzed library. Gene pairs were identified based on the analysis of the transcription start site (TSS) coordinates in 73 human and 10 mouse organs, tissues and cell lines. Beside TSS data, resources for 26 human lung adenocarcinoma cell lines also contain RNA-Seq and ChIP-Seq data for seven histone modifications and RNA Polymerase II activity. The collected data revealed that the overlap region is rarely conserved between the studied species and tissues. In ∼50% of the overlapping genes, transcription started explicitly in the overlap regions. In the remaining half of overlapping genes, transcription was initiated both from overlapping and non-overlapping TSSs. OverGeneDB is accessible at http://overgenedb.amu.edu.pl.
基因重叠在转录和转录后水平上发挥着各种调节功能。大多数当前的研究集中在与非蛋白编码对应物（所谓的天然反义转录本）重叠的蛋白编码基因上。关于两个蛋白编码基因的基因重叠的作用，人们知之甚少。在这里，我们提供了 OverGeneDB，这是一个人类和小鼠 5'端蛋白编码重叠基因的数据库。该数据库包含了至少在一个分析文库中使用重叠启动子转录的 582 个人类和 113 个小鼠基因对。基因对是基于对 73 个人类和 10 个小鼠器官、组织和细胞系的转录起始位点 (TSS) 坐标的分析确定的。除了 TSS 数据外，26 个人类肺腺癌细胞系的资源还包含了针对七个组蛋白修饰和 RNA 聚合酶 II 活性的 RNA-Seq 和 ChIP-Seq 数据。收集的数据表明，研究物种和组织之间重叠区域的保守性很少。在研究的重叠基因中，约有 50%的基因在重叠区域明确开始转录。在其余一半的重叠基因中，转录既从重叠的 TSS 也从非重叠的 TSS 开始。OverGeneDB 可在 http://overgenedb.amu.edu.pl 上访问。
