Dataset Information

Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs.

ABSTRACT: Measuring the essentiality of genes is critically important in biology and medicine. Here we proposed a computational method, GIC (Gene Importance Calculator), which can efficiently predict the essentiality of both protein-coding genes and long noncoding RNAs (lncRNAs) based on only sequence information. For identifying the essentiality of protein-coding genes, GIC outperformed well-established computational scores. In an independent mouse lncRNA dataset, GIC also achieved an exciting performance (AUC = 0.918). In contrast, the traditional computational methods are not applicable to lncRNAs. Moreover, we explored several potential applications of GIC score. Firstly, we revealed a correlation between gene GIC score and research hotspots of genes. Moreover, GIC score can be used to evaluate whether a gene in mouse is representative for its homolog in human by dissecting its cross-species difference. This is critical for basic medicine because many basic medical studies are performed in animal models. Finally, we showed that GIC score can be used to identify candidate genes from a transcriptomics study. GIC is freely available at http://www.cuilab.cn/gic/.

SUBMITTER: Zeng P

PROVIDER: S-EPMC6189311 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs.

Zeng Pan P Chen Ji J Meng Yuhong Y Zhou Yuan Y Yang Jichun J Cui Qinghua Q

Frontiers in genetics 20181009

Measuring the essentiality of genes is critically important in biology and medicine. Here we proposed a computational method, GIC (Gene Importance Calculator), which can efficiently predict the essentiality of both protein-coding genes and long noncoding RNAs (lncRNAs) based on only sequence information. For identifying the essentiality of protein-coding genes, GIC outperformed well-established computational scores. In an independent mouse lncRNA dataset, GIC also achieved an exciting performanc ...[more]

PMID: 30356729

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Project description:Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. In addition, recent studies have shown that functional ncRNAs can also be derived from gene 3' untranslated regions (3'UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated noncoding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions rather than in the UTRs. We show that these decRNAs are "carved out" of the mRNA through the action of RNase E and that they are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest that mRNA protein-coding regions may harbor a large set of potentially functional small RNAs.IMPORTANCE Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are "carved out" from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.

Project description:BackgroundLong non-coding RNAs (lncRNAs) are increasingly recognized as regulators of tissue-specific cellular functions and have been shown to regulate transcriptional and translational processes, acting as signals, decoys, guides, and scaffolds. It has been suggested that some lncRNAs act in cis to regulate the expression of neighboring protein-coding genes (PCGs) in a mechanism that fine-tunes gene expression. Gut microbiome is increasingly recognized as a regulator of development, inflammation, host metabolic processes, and xenobiotic metabolism. However, there is little known regarding whether the gut microbiome modulates lncRNA gene expression in various host metabolic organs. The goals of this study were to 1) characterize the tissue-specific expression of lncRNAs and 2) identify and annotate lncRNAs differentially regulated in the absence of gut microbiome.ResultsTotal RNA was isolated from various tissues (liver, duodenum, jejunum, ileum, colon, brown adipose tissue, white adipose tissue, and skeletal muscle) from adult male conventional and germ-free mice (n = 3 per group). RNA-Seq was conducted and reads were mapped to the mouse reference genome (mm10) using HISAT. Transcript abundance and differential expression was determined with Cufflinks using the reference databases NONCODE 2016 for lncRNAs and UCSC mm10 for PCGs. Although the constitutive expression of lncRNAs was ubiquitous within the enterohepatic (liver and intestine) and the peripheral metabolic tissues (fat and muscle) in conventional mice, differential expression of lncRNAs by lack of gut microbiota was highly tissue specific. Interestingly, the majority of gut microbiota-regulated lncRNAs were in jejunum. Most lncRNAs were co-regulated with neighboring PCGs. STRING analysis showed that differentially expressed PCGs in proximity to lncRNAs form tissue-specific networks, suggesting that lncRNAs may interact with gut microbiota/microbial metabolites to regulate tissue-specific functions.ConclusionsThis study is among the first to demonstrate that gut microbiota critically regulates the expression of lncRNAs not only locally in intestine but also remotely in other metabolic organs, suggesting that common transcriptional machinery may be shared to transcribe lncRNA-PCG pairs, and lncRNAs may interact with PCGs to regulate tissue-specific pathways.

Dataset Information

Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs.

Publications

Defining Essentiality Score of Protein-Coding Genes and Long Noncoding RNAs.

Similar Datasets

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