Correction: Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

Qin, Fujun; Song, Zhenguo; Babiceanu, Mihaela; Song, Yansu; Facemire, Loryn; Singh, Ritambhara; Adli, Mazhar; Li, Hui

doi:10.1371/journal.pgen.1005161

PLoS Genet

2015

DOI: 10.1371/journal.pgen.1005161

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Correction: Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

Fujun Qin¹,

Zhenguo Song²,

Mihaela Babiceanu³

et al.

Abstract: The term FKPM (fragments per kilobase of transcript per million fragments sequenced) is incorrect throughout. The correct description should be FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped). The following references are omitted in the article: Two references are omitted from the second sentence of the second paragraph in the Introduction. The sentence should read: In recent years, several studies using the EST database and RNA-sequencing approaches have identified fusion RNAs involving nei… Show more

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Cited by 6 publications

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Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

Huminiecki

2021

Entropy

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Mendel proposed an experimentally verifiable paradigm of particle-based heredity that has been influential for over 150 years. The historical arguments have been reflected in the near past as Mendel’s concept has been diversified by new types of omics data. As an effect of the accumulation of omics data, a virtual gene concept forms, giving rise to genetical data science. The concept integrates genetical, functional, and molecular features of the Mendelian paradigm. I argue that the virtual gene concept should be deployed pragmatically. Indeed, the concept has already inspired a practical research program related to systems genetics. The program includes questions about functionality of structural and categorical gene variants, about regulation of gene expression, and about roles of epigenetic modifications. The methodology of the program includes bioinformatics, machine learning, and deep learning. Education, funding, careers, standards, benchmarks, and tools to monitor research progress should be provided to support the research program.

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Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

Huminiecki

2021

Entropy

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Landscape of Chimeric RNAs in Non-Cancerous Cells

Chen

Haddox

Tang

et al. 2021

Genes

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Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern.

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Connections between Transcription Downstream of Genes and cis-SAGe Chimeric RNA

Chwalenia

Qin

Singh

et al. 2017

Genes

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cis-Splicing between adjacent genes (cis-SAGe) is being recognized as one way to produce chimeric fusion RNAs. However, its detail mechanism is not clear. Recent study revealed induction of transcriptions downstream of genes (DoGs) under osmotic stress. Here, we investigated the influence of osmotic stress on cis-SAGe chimeric RNAs and their connection to DoGs. We found, the absence of induction of at least some cis-SAGe fusions and/or their corresponding DoGs at early time point(s). In fact, these DoGs and their cis-SAGe fusions are inversely correlated. This negative correlation was changed to positive at a later time point. These results suggest a direct competition between the two categories of transcripts when total pool of readthrough transcripts is limited at an early time point. At a later time point, DoGs and corresponding cis-SAGe fusions are both induced, indicating that total readthrough transcripts become more abundant. Finally, we observed overall enhancement of cis-SAGe chimeric RNAs in KCl-treated samples by RNA-Seq analysis.

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Correction: Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

Cited by 6 publications

References 1 publication

Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

Landscape of Chimeric RNAs in Non-Cancerous Cells

Connections between Transcription Downstream of Genes and cis-SAGe Chimeric RNA

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