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Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice transcriptome [RNA-seq]

ABSTRACT: Purpose: To reveal the cystogenesis regulatory mechanism by miRNA and miRNA targeted genes in ADPKD mouse models. Method (mRNA-seq): In order to construct cDNA libraries with the TruSeq RNA library kit, 1ug of total RNA was used. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100nt paired-end sequencing by Illumina HiSeq2000. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer. The transcript counts in isoform level and gene level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks. Method (common): Both miRNA-seq and RNA-seq were carried out using the kidney tissues from two mouse models at postnatal day 1, 3 and 7 in triplicate samples. Total RNA was isolated using TRIzol method according to manufacturer’s protocol (Invitrogen Life Technologies). Result: UIn RNA-seq analysis, total 3,040 transcripts in Pkd1f/f:HoxB7-cre mice and 2,470 transcripts in Pkd2f/f:HoxB7-cre mice were differentially expressed at indicated time points (FDR<0.05). In addition, we also identified 1,297 common transcripts in both mouse models. In miRNA analysis, total 243 of miRNAs were identified as differentially expressed genes while 130 miRNAs were common in both mouse models. Among common miRNAs, total 13 miRNAs including 11 upregulated and 2 downregulated miRNAs were selected based on comparison of expression patterns at each time point. Conclusion: Our study described the parallel integrated analysis of miRNA-seq and RNA-seq data and validated the expression, direct interaction and cystogenesis-related functions of key miRNAs and mRNA targets.

ORGANISM(S): Mus musculus

PROVIDER: GSE86507 | GEO | 2018/01/26

REPOSITORIES: GEO

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Project description:Schmitz2014 - RNA triplex formation The model is parameterized using the parameters for gene CCDC3 from Supplementary Table S1. The two miRNAs which form the triplex together with CCDC3 are miR-551b and miR-138. This model is described in the article: Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK. Nucleic Acids Res. 2014 Jul; 42(12): 7539-7552 Abstract: MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs of miRNAs can repress the translation of a target mRNA in a cooperative manner, which leads to an enhanced effectiveness and specificity in target repression. However, it remains unclear which miRNA pairs can synergize and which genes are target of cooperative miRNA regulation. In this paper, we present a computational workflow for the prediction and analysis of cooperating miRNAs and their mutual target genes, which we refer to as RNA triplexes. The workflow integrates methods of miRNA target prediction; triplex structure analysis; molecular dynamics simulations and mathematical modeling for a reliable prediction of functional RNA triplexes and target repression efficiency. In a case study we analyzed the human genome and identified several thousand targets of cooperative gene regulation. Our results suggest that miRNA cooperativity is a frequent mechanism for an enhanced target repression by pairs of miRNAs facilitating distinctive and fine-tuned target gene expression patterns. Human RNA triplexes predicted and characterized in this study are organized in a web resource at www.sbi.uni-rostock.de/triplexrna/. This model is hosted on BioModels Database and identified by: BIOMD0000000530. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice transcriptome [RNA-seq]

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