Pseudogenes: Pseudo-functional or key regulators in health and disease?

Pink, Ryan C.; Wicks, Kate; Caley, Daniel P.; Punch, Emma Kathleen; Jacobs, Laura A.; Carter, David Raul Francisco

doi:10.1261/rna.2658311

Cited by 380 publications

(332 citation statements)

References 82 publications

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“…These are the "relics" of genes that have lost their coding potential due to nonsense, frameshift, and other mutations (Balakirev and Ayala 2003;Pink et al 2011). Many pseudogenes are products of tandem gene duplication or of mRNAs being carried along during retrotransposition, both of which create extra gene copies that are no longer under selective pressure.…”

Section: Pseudogenesmentioning

confidence: 99%

Long Noncoding RNAs: Past, Present, and Future

2013

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Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years as a potentially new and crucial layer of biological regulation. lncRNAs of all kinds have been implicated in a range of developmental processes and diseases, but knowledge of the mechanisms by which they act is still surprisingly limited, and claims that almost the entirety of the mammalian genome is transcribed into functional noncoding transcripts remain controversial. At the same time, a small number of well-studied lncRNAs have given us important clues about the biology of these molecules, and a few key functional and mechanistic themes have begun to emerge, although the robustness of these models and classification schemes remains to be seen. Here, we review the current state of knowledge of the lncRNA field, discussing what is known about the genomic contexts, biological functions, and mechanisms of action of lncRNAs. We also reflect on how the recent interest in lncRNAs is deeply rooted in biology's longstanding concern with the evolution and function of genomes.T HE past several years have witnessed a steep rise of interest in the study of lncRNAs. Almost on a weekly basis, it seems that a new lncRNA is found to be up-or downregulated in a particular disease, or a new class of noncoding transcripts is uncovered by a transcriptomic study, or a new article heralds a paradigm shift that lncRNAs will bring to our understanding of biology. Without a doubt, the advent of sensitive, high-throughput genomic technologies such as microarrays and next-generation sequencing (NGS) has resulted in an unprecedented ability to detect novel transcripts, the vast majority of which seem not to be derived from annotated protein-coding genes. Despite this explosion of data, however, surprisingly little is known about how lncRNAs function, how many different types of lncRNAs exist, or even whether most of them carry biological significance.In this review, we focus on recently discovered lncRNAs of .200 nt, place these new discoveries in historical context, and outline areas where additional work is needed. The review does not cover "classic" ncRNAs such as ribosomal (r) RNAs, ribozymes, transfer (t)RNAs, small nuclear (sn)RNAs, small nucleolar (sno)RNAs, and telomere-associated RNAs (TERC, TERRA); nor does it cover small ncRNAs such as microRNAs (miRNAs), endogenous small interfering (endo-si)RNAs that participate in RNA interference (RNAi), and Piwi-associated (pi)RNAs. We refer readers to the many

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Section: Pseudogenesmentioning

confidence: 99%

Long Noncoding RNAs: Past, Present, and Future

2013

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“…Recent studies have shown that processed pseudogenes function in gene regulation. 27) Therefore, we focused on the relationship of pcRNAs and pseudogenes, as described later. Figure 3 shows Venn diagrams of all RNAs, pcRNAs and pseudogenes classified by Emsembl annotation.…”

Section: Sequencing and Annotation Of Rnas From Salivary Exosomes Andmentioning

confidence: 99%

Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva

Ogawa

Tsujimoto

Yanoshita

2016

Biological & Pharmaceutical Bulletin

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Exosomes are small extracellular vesicles containing microRNAs and mRNAs that are produced by various types of cells. We previously used ultrafiltration and size-exclusion chromatography to isolate two types of human salivary exosomes (exosomes I, II) that are different in size and proteomes. We showed that salivary exosomes contain large repertoires of small RNAs. However, precise information regarding long RNAs in salivary exosomes has not been fully determined. In this study, we investigated the compositions of protein-coding RNAs (pcRNAs) and long non-protein-coding RNAs (lncRNAs) of exosome I, exosome II and whole saliva (WS) by next-generation sequencing technology. Although 11% of all RNAs were commonly detected among the three samples, the compositions of reads mapping to known RNAs were similar. The most abundant pcRNA is ribosomal RNA protein, and pcRNAs of some salivary proteins such as S100 calcium-binding protein A8 (protein S100-A8) were present in salivary exosomes. Interestingly, lncRNAs of pseudogenes (presumably, processed pseudogenes) were abundant in exosome I, exosome II and WS. Translationally controlled tumor protein gene, which plays an important role in cell proliferation, cell death and immune responses, was highly expressed as pcRNA and pseudogenes in salivary exosomes. Our results show that salivary exosomes contain various types of RNAs such as pseudogenes and small RNAs, and may mediate intercellular communication by transferring these RNAs to target cells as gene expression regulators.Key words exosome; transcriptome; human whole saliva; next-generation sequencing; non-coding RNA; pseudogene Human whole saliva (WS) contains an aqueous complex mixture of proteins, peptides, hormones, metabolites, DNAs and RNAs. WS contributes to maintain the integrity of the oral cavity through its lubricating, antibacterial, antiviral and buffering actions, and facilitates chewing and swallowing food. It plays an important role in front-line body defense. Because WS can be collected simply, cheaply and noninvasively, it has been used to monitor human health and disease. Because saliva contains ribonucleases and nucleases from various sources, which influence RNA stability, relatively few studies have analyzed human salivary RNA.1) Salivary nucleotides are protected from degradation by inclusion in extracellular vesicles such as exosomes. Recently, RNAs and DNAs in WS have been highlighted in the fields of biomarker research, disease diagnostics and forensic study. 2-4)Exosomes are small (30-100 nm) membrane vesicles of endocytic origin that are released into the extracellular environment upon fusion of multivesicular bodies with the plasma membrane. Exosomes are present in various body fluids including blood, breast milk, malignant ascites, urine, amniotic fluid and saliva. 5) Exosomes can contain the proteins and nucleic acids of their cell of origin and can transfer their contents to recipient cells at a distance. 5) Exosomes are now thought to be secreted by various cell types, and numerous comp...

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“…Interestingly, transcribed pseudogenes, including those that arose via retroposition, reportedly can be functional as RNAs or mRNAs encoding truncated proteins (Balakirev and Ayala 2003;Duret et al 2006;Frith et al 2006b;Pink et al 2011;Wen et al 2012;Sen and Ghosh 2013). For example, retropseudogene PTENP1 derived from tumor suppressor gene PTEN is transcribed.…”

Section: Competitive Rnasmentioning

confidence: 99%

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

Brosius

2014

Cold Spring Harbor Perspectives in Biology

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Pseudogenes: Pseudo-functional or key regulators in health and disease?

Cited by 380 publications

References 82 publications

Long Noncoding RNAs: Past, Present, and Future

Long Noncoding RNAs: Past, Present, and Future

Next-Generation Sequencing of Protein-Coding and Long Non-protein-Coding RNAs in Two Types of Exosomes Derived from Human Whole Saliva

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

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