Mouse genome annotation by the RefSeq project

McGarvey, Kelly M.; Goldfarb, Tamara; Cox, Eric; Farrell, Catherine; Gupta, Tripti; Joardar, Vinita; Kodali, Vamsi K.; Murphy, Michael R.; O’Leary, Nuala; Pujar, Shashikant; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D.; Webb, David; Wright, Mathew W.; Murphy, Terence; Pruitt, Kim D.

doi:10.1007/s00335-015-9585-8

Cited by 19 publications

(17 citation statements)

References 26 publications

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“…All mRNA and sequence data used in this study were acquired from the NCBI Reference Sequence Database (RefSeq) collection release 69 58 . A data set was prepared by extracting all mRNAs of Nfkbid , which amounted to sequences of 68 mammalian species.…”

Section: Methodsmentioning

confidence: 99%

Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation

et al. 2018

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The RNA-binding proteins Roquin-1 and Roquin-2 redundantly control gene expression and cell-fate decisions. Here, we show that Roquin not only interacts with stem–loop structures, but also with a linear sequence element present in about half of its targets. Comprehensive analysis of a minimal response element of the Nfkbid 3′-UTR shows that six stem–loop structures cooperate to exert robust and profound post-transcriptional regulation. Only binding of multiple Roquin proteins to several stem–loops exerts full repression, which redundantly involved deadenylation and decapping, but also translational inhibition. Globally, most Roquin targets are regulated by mRNA decay, whereas a small subset, including the Nfat5 mRNA, with more binding sites in their 3′-UTRs, are also subject to translational inhibition. These findings provide insights into how the robustness and magnitude of Roquin-mediated regulation is encoded in complex cis-elements.

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Section: Methodsmentioning

confidence: 99%

Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation

et al. 2018

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“…The list of miRNAs and their associated target mRNAs were then subjected to core functional analysis in IPA ® that uses ~1.5 million microRNA targeting interactions from sources including miRecords, TarBase, TargetScan, Ingenuity Expert findings and Ingenuity ExpertAssist findings to identify the miRNA-mRNA target relationships. Specifically, TargetScanMouse 6.2 [ 64 ], which was integrated with the latest versions of miRBase [ 65 ] and RefSeq [ 66 , 67 ] databases, was used to identify mRNA targets. The stringency level for miRNA-mRNA interactions was set at “High (predicted)” or “Experimentally Observed”.…”

Section: Methodsmentioning

confidence: 99%

Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice

et al. 2016

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Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology. We found a total of 53 differentially expressed miRNAs in the retina and no differences in miRNA expression in the sclera of C57BL/6J mice after 10 days of visual form deprivation, which induced -6.93 ± 2.44 D (p < 0.000001, n = 12) of myopia. We also identified their putative mRNA targets among mRNAs found to be differentially expressed in myopic retina and potential signaling pathways involved in the development of form-deprivation myopia using miRNA-mRNA interaction network analysis. Analysis of myopia-associated signaling pathways revealed that myopic response to visual form deprivation in the retina is regulated by a small number of highly integrated signaling pathways. Our findings highlighted that changes in microRNA expression are involved in the regulation of refractive eye development and predicted how they may be involved in the development of myopia by regulating retinal gene expression.

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“…Improvements in input reagent quality in turn add significant quality and reproducibility to the resultant genome annotation. This type of manual curation has historically been focused on human and mouse because of their unique biomedical importance ( 6 ). More recently these curation efforts have given greater attention to Rattus norvegicus , Danio rerio , Bos taurus , and Gallus gallus .…”

Section: Introductionmentioning

confidence: 99%

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

O’Leary¹,

Wright²,

Brister³

et al. 2015

Nucleic Acids Res

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5,193

4,246

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The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

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Mouse genome annotation by the RefSeq project

Cited by 19 publications

References 26 publications

Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation

Roquin targets mRNAs in a 3′-UTR-specific manner by different modes of regulation

Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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