FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis

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...

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Bibliographic Details
Published in:Non-coding RNA 2022-01, Vol.8 (1), p.13
Main Authors: Ilieva, Mirolyuba, Miller, Henry E, Agarwal, Arav, Paulus, Gabriela K, Madsen, Jens Hedelund, Bishop, Alexander J R, Kauppinen, Sakari, Uchida, Shizuka
Format: Article
Language:English
Subjects:
Blood clots
Datasets
Extracellular matrix
fibroblast
Fibroblasts
Fibrosis
Gene expression
Inflammation
lncRNA
Lungs
Non-coding RNA
Proteins
Pulmonary arteries
Pulmonary fibrosis
Pulmonary hypertension
RNA-seq
Severe acute respiratory syndrome coronavirus 2
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Summary: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 and 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.
ISSN:2311-553X
2311-553X
DOI:10.3390/ncrna8010013