FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis.
FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis.
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DOI：
10.3390/ncrna8010013
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发表时间：
2022-01-28
期刊：
影响因子：
4.3
通讯作者：
Uchida S
中科院分区：
文献类型：
--
作者：
Ilieva M;Miller HE;Agarwal A;Paulus GK;Madsen JH;Bishop AJR;Kauppinen S;Uchida S
大多数长链非编码rna （lncRNAs）的表达水平低于蛋白质编码基因，它们的表达通常分别局限于特定的细胞类型、发育过程中的某些时间点以及各种应激和疾病条件。为了重新审视这个长期存在的概念，我们将重点放在成纤维细胞上，成纤维细胞是各种器官和组织中的一种常见细胞类型。利用成纤维细胞及其在纤维化过程中表达谱的变化作为模型系统，我们发现lncRNA基因的总体表达水平显著低于蛋白质编码基因。此外，我们还发现了在纤维化过程中表达上调的lncRNA基因。以真皮成纤维细胞为模型，我们进行了功能缺失实验，并表明lncRNAs LINC00622和LINC01711的敲低分别导致与细胞反应和炎症反应相关的基因表达变化。由于目前还没有专注于成纤维细胞和纤维化的lncRNA数据库，我们建立了一个web应用程序FibroDB，以进一步促进纤维化lncRNA的功能和机制研究。
Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and various stress and disease conditions, respectively. To revisit this long-held concept, we focused on fibroblasts, a common cell type in various organs and tissues. Using fibroblasts and changes in their expression profiles during fibrosis as a model system, we show that the overall expression level of lncRNA genes is significantly lower than that of protein-coding genes. Furthermore, we identified lncRNA genes whose expression is upregulated during fibrosis. Using dermal fibroblasts as a model, we performed loss-of-function experiments and show that the knockdown of the lncRNAs LINC00622 and LINC01711 result in gene expression changes associated with cellular and inflammatory responses, respectively. Since there are no lncRNA databases focused on fibroblasts and fibrosis, we built a web application, FibroDB, to further promote functional and mechanistic studies of fibrotic lncRNAs.