miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

Desvignes, Thomas; Batzel, Peter; Berezikov, Eugène; Eilbeck, Karen; Eppig, Janan T.; McAndrews, Monica; Singer, Amy; Postlethwait, John H.

doi:10.1016/j.tig.2015.09.002

Cited by 165 publications

(128 citation statements)

References 114 publications

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“…The corresponding information is summarized in Table 1 for the 20 ovarian-predominant miRNAs selected. The folding information should be used with caution, as all miRNAs do not necessarily exhibit this feature42. Finally, it should be stressed that despite the overall conservation of the ovarian-predominant patterns, we observed some differences between the QPCR profiles obtained using homologous and heterologous primers.…”

Section: Discussionmentioning

confidence: 79%

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

Bouchareb

Cam

Montfort

et al. 2017

Sci Rep

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MicroRNAs (miRNAs) are small, highly conserved non-coding RNAs that play important roles in the regulation of many physiological processes. However, the role of miRNAs in vertebrate oocyte formation (i.e., oogenesis) remains poorly investigated. To gain new insights into the roles of miRNAs in oogenesis, we searched for ovarian-predominant miRNAs. Using a microarray displaying 3,800 distinct miRNAs originating from different vertebrate species, we identified 66 miRNAs that are expressed predominantly in the ovary. Of the miRNAs exhibiting the highest overabundance in the ovary, 20 were selected for further analysis. Using a combination of QPCR and in silico analyses, we identified 8 novel miRNAs that are predominantly expressed in the ovary, including 2 miRNAs (miR-4785 and miR-6352) that exhibit strict ovarian expression. Of these 8 miRNAs, 7 were previously uncharacterized in fish. The strict ovarian expression of miR-4785 and miR-6352 suggests an important role in oogenesis and/or early development, possibly involving a maternal effect. Together, these results indicate that, similar to protein-coding genes, a significant number of ovarian-predominant miRNA genes are found in fish.

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Section: Discussionmentioning

confidence: 79%

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

Bouchareb

Cam

Montfort

et al. 2017

Sci Rep

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“…In contrast, the nucleotide sequence of MiR144-5p, the mature miRNA originating from the 5’ side of the precursor hairpin, showed evolved nucleotide differences in vertebrates, including a lineage-specific one-nucleotide change (A to T) in perciformes, represented here by the three-spined stickleback and notothenioids (Near et al, 2015, 2013) (Figure 1C). MiR144-5p additionally displays a seed-shift of one nucleotide at the 5’ end in Antarctic fish, which is a change in the position of the seed region of the miRNA by one nucleotide (Figure 1C), and which can potentially have major functional repercussions (Desvignes et al, 2015). Given that the reference MiR144-5p sequences for human, spotted gar and zebrafish were obtained from tissues other than pronephric kidney (Braasch et al, 2016; Desvignes et al, 2014) and/or miRBase (Kozomara and Griffiths-Jones, 2013), we cannot, however, rule out the possibility that the most expressed MiR144-5p isomiR in some tissue other than pronephric kidney has a 5’ start similar to the one observed in human, gar and zebrafish, and that, in the pronephric-kidney specifically, the most expressed MiR144-5p isomiR has a 5’ start similar to the one observed in notothenioid fish.…”

Section: Resultsmentioning

confidence: 99%

“…Groups of sequences were then annotated against mature and hairpin sequences present in miRBase Release 21 (Kozomara and Griffiths-Jones, 2013), the extended zebrafish miRNA annotation (Desvignes et al, 2014), and the spotted gar annotation (Braasch et al, 2016). Gene nomenclature follows recent conventions (Desvignes et al, 2015), including those for zebrafish (Bradford et al, 2011). …”

Section: Methodsmentioning

confidence: 99%

“…miRNAs are small endogenous non-coding RNAs that regulate gene expression post-transcriptionally by binding to specific mRNAs and, together with the RNA-Induced Silencing Complex, either mediate transcript decay or repress transcript translation (See Carthew and Sontheimer, 2009; Christodoulou et al, 2010; Desvignes et al, 2015; Kosik, 2010 for reviews on biogenesis and function). In vertebrates, including teleost fish, several miRNAs are necessary for the formation of red blood cells and functional hemoglobin, and we refer to them here as “erythromiRs” in analogy to the well-described muscle-specific microRNAs referred to as “myomiRs” (McCarthy, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Genomic conservation of erythropoietic microRNAs (erythromiRs) in white-blooded Antarctic icefish

2016

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White-blooded Antarctic crocodile icefish are the only vertebrates known to lack functional hemoglobin genes and red blood cells throughout their lives. We do not yet know, however, whether extinction of hemoglobin genes preceded loss of red blood cells or vice versa, nor whether erythropoiesis regulators disappeared along with hemoglobin genes in this erythrocyte-null clade. Several microRNAs, which we here call erythromiRs, are expressed primarily in developing red blood cells in zebrafish, mouse, and humans. Abrogating some erythromiRs, like Mir144 and Mir451a, leads to profound anemia, demonstrating a functional role in erythropoiesis. Here, we tested two not mutually exclusive hypotheses: 1) that the loss of one or more erythromiR genes extinguished the erythropoietic program of icefish and/or led to the loss of globin gene expression through pseudogenization; and 2) that some erythromiR genes were secondarily lost after the loss of functional hemoglobin and red blood cells in icefish. We explored smallRNA transcriptomes generated from the hematopoietic kidney marrow of four Antarctic notothenioids: two red-blooded species (bullhead notothen Notothenia coriiceps and emerald notothen Trematomus bernacchii) and two white-blooded icefish (blackfin icefish Chaenocephalus aceratus and hooknose icefish Chionodraco hamatus). The N. coriiceps genome assembly anchored analyses. Results showed that, like the two red-blooded species, the blackfin icefish genome possessed and the marrow expressed all known erythromiRs. This result indicates that loss of hemoglobin and red blood cells in icefish was not caused by loss of known erythromiR genes. Furthermore, expression of only one erythromiR, mir96, appears to have been lost after the loss of red blood cells and hemoglobin – expression was not detected in the erythropoietic organ of hooknose icefish but was present in blackfin icefish. All other erythromiRs investigated, including mir144 and mir451a, were expressed by all four species and thus are present in the genomes of at least the two white-blooded icefish. Our results rule out the hypothesis that genomic loss of any known erythromiRs extinguished erythropoiesis in icefish, and suggest that after the loss of red blood cells, few erythromiRs experienced secondary loss. Results suggest that functions independent of erythropoiesis maintained erythromiRs, thereby highlighting the evolutionary resilience of miRNA genes in vertebrate genomes.

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“…Previously these have been referred to as miR-142 (dominant) and miR-142* (from opposite arm); however, this has shifted to naming each strand for the arm from which it originated: for example: miR-142-3p (from the 3' arm) and miR-142-5p (from the 5' arm) [35,[39][40][41][42].…”

Section: Nomenclaturementioning

confidence: 99%

Evaluating cellular microRNA expression in human papillomavirus associated head and neck squamous cell carcinoma

Emmett¹

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Squamous cell carcinoma of mucosal head and neck sites (HNSCC) is the sixth most common cause of cancer world-wide, and is associated with a significant morbidity and mortality despite advances in therapeutic options over the past decades. HNSCC includes tumours of the oral cavity, oropharynx, larynx and hypopharynx. While there has been a decline in tumours occurring as a result of exposure to the traditional risk factors of tobacco smoking and alcohol consumption, a significant increase has been observed in the number of tumours attributed to the Human Papillomavirus (HPV). This has primarily been associated with causation of tumours in the oropharynx, however, a smaller number of tumours at other subsites are also likely to be related to the virus. Although HPV-related tumours tend to have an improved prognosis and a better response to chemo-and radiotherapy, the pathobiology underlying these differences is not yet fully understood.MiRNAs are short, non-coding single strands of RNA which regulate gene expression at the posttranscriptional level. They have been identified to be dysregulated and function as tumour suppressor or oncogenes in a number of human cancers, including head and neck cancers. MiRNAs have also been associated with prognostication including associations with recurrence of disease and diseasefree survival. As they are readily available across a range of body tissues including solid tissue, saliva, and plasma, these biomarkers have potential utility in relation to screening for disease diagnosis, recurrence or progression. Although there is an established difference between HPV-positive and negative tumours in the oropharynx clinically, the majority of studies investigating miRNA expression in HNSCC have not taken this factor into account. In the small number of studies which have examined the effect of HPV on miRNA expression in HNSCC, there is a lack of consistency in the results described.This thesis aimed to assess the difference in miRNA expression between HPV-positive and negative tumours, through use of miRNA microarray followed by validation with real-time PCR using TaqMan assays combined with a sensitive detection method (Fluidigm HD) in a larger cohort of patients. It also investigated differences in miRNA expression in association with lifestyle factors, demographics and clinical outcomes. A set of seven miRNAs was identified to be differentially expressed between HPV-positive and negative tumours in the oropharynx. No difference in miRNA expression was observed between the two tumour cohorts at other subsites in the head and neck.Differences in miRNA expression were also observed with lifestyle factors such as smoking status and alcohol consumption. Recurrence of the primary tumour and overall disease-free survival were further associated with altered miRNA expression. The findings outlined in this thesis add to the present literature regarding differences in miRNA expression between HPV-positive and negative iii tumours in the oropharynx, and provide a basis for further...

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miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

Cited by 165 publications

References 114 publications

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

Genome-wide identification of novel ovarian-predominant miRNAs: new insights from the medaka (Oryzias latipes)

Genomic conservation of erythropoietic microRNAs (erythromiRs) in white-blooded Antarctic icefish

Evaluating cellular microRNA expression in human papillomavirus associated head and neck squamous cell carcinoma

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