TY - JOUR
T1 - FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis
AU - Ilieva, Mirolyuba Simeonova
AU - Miller, Henry E.
AU - Agarwal, Arav
AU - Paulus, Gabriela K.
AU - Madsen, Jens Hedelund
AU - Bishop, Alexander J. R.
AU - Kauppinen, Sakari
AU - Uchida, Shizuka
PY - 2022/1/28
Y1 - 2022/1/28
N2 - 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.
AB - 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.
KW - Fibroblast
KW - Fibrosis
KW - Gene expression
KW - LncRNA
KW - RNA-seq
UR - http://www.scopus.com/inward/record.url?scp=85123714341&partnerID=8YFLogxK
U2 - 10.3390/ncrna8010013
DO - 10.3390/ncrna8010013
M3 - Journal article
SN - 2311-553X
VL - 8
JO - Non-coding RNA
JF - Non-coding RNA
IS - 1
M1 - 13
ER -