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PARP1–RNA interaction analysis: PARP1 regulates the expression of extracellular matrix‐related genes in HK‐2 renal proximal tubular epithelial cells
Author(s) -
Ke Jing,
Liu Feng,
Tu Yafang,
Cai Zhitao,
Luo Yu,
Wu Xiongfei
Publication year - 2021
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1002/1873-3468.14065
Subject(s) - gene knockdown , parp1 , rna , biology , intron , transcriptome , gene , microbiology and biotechnology , gene expression , messenger rna , polymerase , poly adp ribose polymerase , genetics
Recent studies suggest that Poly(ADP‐ribose) polymerase 1 (PARP1) acts as an RNA‐binding protein in a majority of renal diseases with tubular cell injury. However, detailed knowledge of RNA targets and the RNA‐binding regions for PARP1 is unknown. Herein, mapping of iRIP‐seq reads in HK‐2 renal tubular epithelial cells showed a biased distribution at coding sequence (CDS) and intron regions that is specific to these cells. A total of 1708 differentially expressed genes were identified after PARP1 knockdown using RNA‐seq. Furthermore, transcriptome analysis also showed that selective variable splicing was globally regulated by PARP1 in HK‐2 cells. By comparison of PARP1 RNA‐seq and iRIP‐seq data, we found 68 overlapping genes that are enriched in ‘extracellular matrix’ pathway. Follow‐up identification of their interactions may contribute vital insights into the regulatory role of PARP1 as an RNA‐binding protein in HK‐2 cells.