Transcriptome analysis reveals lncRNA‐mediated complex regulatory network response to DNA damage in the liver tissue of Rattus norvegicus

Abstract

DNA is prone to damages, which would result in genetic disorders and enhance risk of tumorigenesis. Hence, understanding the molecular mechanisms of DNA damage and repair will provide deep insights into tumorigenesis, carcinogenesis as well as the corresponding treatments. Aiming at investigating potential long noncoding RNAs (lncRNAs) response against DNA damage, we performed a comprehensive transcriptomic analysis based on RNA sequencing data of the liver tissue from Rattus norvegicus, in which DNA damage was induced using aflatoxin B1, ifosfamide and Nnitrosodimethylamine. Through our analyses, numerous novel lncRNAs are identified for the first time, and differential network analysis discloses lncRNA-mediated regulatory networks related to DNA-damage response. The result shows that these DNA-damage-inducing chemicals might disrupt many lncRNA-mediated interactions involved in diverse biological processes and pathways, for example, immune function and cell adhesion. In contrast, the host might also activate a few RNA interactions in response to DNA damage, involving response to drug and regulation of cell cycle.

Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma

“…Despite the function of majority of lncRNAs are unknown so far, their important roles in diverse biological processes has already been demonstrated, particularly close correlations to diseases. In the present study, we detected at least one order of magnitude lncRNAs larger than those identified in our previous studies about lncRNAs [ 38 , 42 , 43 ]. One of reason is the strategy of RNA sequencing in our previous studies is to capture the RNAs with polyA tail (mRNAs), which could only identify around half of lncRNAs.…”

“…Subsequent network analysis based on PCC method displayed that GUSBP2 might target on KLRK1, whose expression was also already found to be up-regulated after desensitization treatment. Notably, the cutoff of correlation value was not set to traditional threshold (0.9 ~ 0.95) since the correlation between those transcripts in this study is not as strong as our previous lncRNA studies [ 38 , 43 ]. One of possible reason is that the desensitization treatment might not make a big change of RNAs in peripheral blood of these asthmatics, which further led to weak correlations among those RNAs.…”

“… Stéphane Kerbrat et al [ 29 ]; Nicholas Goplen et al [ 42 ] TRIO significantly enriched in the process of positive regulation of apoptosis – Others WWP2 detected to be differentially expressed from HBEC (human bronchial epithelial cells) ALI cultures stimulated with IL-6/sIL-6R compared to non-stimulated control. Zala Jevnikar et al [ 43 ] VPS37A GPR160 VWA5A SPDYE6 …”

Transcriptome analysis of peripheral whole blood reveals key lncRNAs implicated in childhood asthma

“…Despite the function of majority of lncRNAs are unknown so far, their important roles in diverse biological processes has already been demonstrated, particularly close correlations to diseases. In the present study, we detected at least one order of magnitude lncRNAs larger than those identified in our previous studies about lncRNAs [43][44][45]. One of reason is the strategy of RNA sequencing in our previous studies is to capture the RNAs with polyA tail (mRNAs), which could only identify around half of lncRNAs.…”

“…Notably, the cutoff of correlation value was not set to traditional threshold (0.9~0.95) since the correlation between those transcripts in this study is not as strong as our previous lncRNA studies [44,45]. One of possible reason is that the desensitization treatment might not make a big change of RNAs in peripheral blood of these asthmatics, which further led to weak correlations among those RNAs.…”