RNA-sequencing reveals genome-wide long non-coding RNAs profiling associated with early development of diabetic nephropathy

Oncotarget
Wanxin TangXiaoke Ma

Abstract

Diabetic nephropathy (DN) seriously threatens the lives of patients, and the mechanism of DN remains largely unknown because of the complex regulation between long non-coding RNA (lncRNA) and protein-coding genes. In early development of diabetic nephropathy (DN), pathogenesis remains largely unknown. We used RNA-sequencing to profile protein-coding and lncRNA gene transcriptome of mouse kidney proximal tubular cells during early stage of DN at various time points. Over 7000 protein-coding and lncRNA genes were differentially expressed, and most of them were time-specific. Nearly 40% of lncRNA genes overlapped with functional element signals using CHIP-Seq data from ENCODE database. Disease progression was characterized by lncRNA expression patterns, rather than protein-coding genes, indicating that the lncRNA genes are potential biomarkers for DN. For gene ontologies related to kidney, enrichment was observed in protein-coding genes co-expressed with neighboring lncRNA genes. Based on protein-coding and lncRNA gene profiles, clustering analysis reveals dynamic expression patterns for kidney, suggesting that they are highly correlated during disease progression. To evaluate translation of mouse model to human conditions, we exp...Continue Reading

Citations

Nov 21, 2018·Scandinavian Cardiovascular Journal : SCJ·Yongheng ChenJianming Li
Jul 7, 2019·International Journal of Molecular Sciences·Michael IgnarskiRoman-Ulrich Müller
Nov 30, 2018·Diabetes & Vascular Disease Research : Official Journal of the International Society of Diabetes and Vascular Disease·Tarun PantAnuradha Dhanasekaran
Sep 27, 2018·Kidney Research and Clinical Practice·Mitsuo Kato

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Datasets Mentioned

BETA
GSE95367

Methods Mentioned

BETA
RNA-Seq
ChIP-Seq
urine collections
enzyme-linked immunosorbent assay
flow cytometry
PCR

Software Mentioned

TOMTOM
WGCNA
NONCODE
BLAST
edgeR
Tophat
Refseq
Cufflinks

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