TRlnc：一个综合性的人类长非编码 RNA 转录调控信息数据库。

TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs.

机构信息

School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.

出版信息

Brief Bioinform. 2021 Mar 22;22(2):1929-1939. doi: 10.1093/bib/bbaa011.

PMID:32047897

Abstract

Long noncoding RNAs (lncRNAs) have been proven to play important roles in transcriptional processes and biological functions. With the increasing study of human diseases and biological processes, information in human H3K27ac ChIP-seq, ATAC-seq and DNase-seq datasets is accumulating rapidly, resulting in an urgent need to collect and process data to identify transcriptional regulatory regions of lncRNAs. We therefore developed a comprehensive database for human regulatory information of lncRNAs (TRlnc, http://bio.licpathway.net/TRlnc), which aimed to collect available resources of transcriptional regulatory regions of lncRNAs and to annotate and illustrate their potential roles in the regulation of lncRNAs in a cell type-specific manner. The current version of TRlnc contains 8 683 028 typical enhancers/super-enhancers and 32 348 244 chromatin accessibility regions associated with 91 906 human lncRNAs. These regions are identified from over 900 human H3K27ac ChIP-seq, ATAC-seq and DNase-seq samples. Furthermore, TRlnc provides the detailed genetic and epigenetic annotation information within transcriptional regulatory regions (promoter, enhancer/super-enhancer and chromatin accessibility regions) of lncRNAs, including common SNPs, risk SNPs, eQTLs, linkage disequilibrium SNPs, transcription factors, methylation sites, histone modifications and 3D chromatin interactions. It is anticipated that the use of TRlnc will help users to gain in-depth and useful insights into the transcriptional regulatory mechanisms of lncRNAs.

摘要

长链非编码 RNA（lncRNA）已被证明在转录过程和生物功能中发挥着重要作用。随着人类疾病和生物过程研究的不断深入，人类 H3K27ac ChIP-seq、ATAC-seq 和 DNase-seq 数据集的信息量迅速增加，因此迫切需要收集和处理数据以识别 lncRNA 的转录调控区域。为此，我们开发了一个用于人类 lncRNA 调控信息的综合数据库（TRlnc，http://bio.licpathway.net/TRlnc），旨在收集 lncRNA 转录调控区域的现有资源，并以细胞类型特异性的方式注释和说明它们在 lncRNA 调控中的潜在作用。目前的 TRlnc 版本包含 8,683,028 个典型的增强子/超级增强子和 32,348,244 个与 91,906 个人类 lncRNA 相关的染色质可及性区域。这些区域是从超过 900 个人类 H3K27ac ChIP-seq、ATAC-seq 和 DNase-seq 样本中鉴定出来的。此外，TRlnc 还提供了 lncRNA 转录调控区域（启动子、增强子/超级增强子和染色质可及性区域）内的详细遗传和表观遗传注释信息，包括常见 SNPs、风险 SNPs、eQTLs、连锁不平衡 SNPs、转录因子、甲基化位点、组蛋白修饰和 3D 染色质相互作用。预计使用 TRlnc 将有助于用户深入了解 lncRNA 的转录调控机制，并从中获得有用的信息。