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      A microRNA cluster in the Fragile‐X region expressed during spermatogenesis targets FMR1

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          Abstract

          Testis‐expressed X‐linked genes typically evolve rapidly. Here, we report on a testis‐expressed X‐linked micro RNA (mi RNA) cluster that despite rapid alterations in sequence has retained its position in the Fragile‐X region of the X chromosome in placental mammals. Surprisingly, the mi RNAs encoded by this cluster ( Fx‐mir ) have a predilection for targeting the immediately adjacent gene, Fmr1, an unexpected finding given that mi RNAs usually act in trans, not in cis. Robust repression of Fmr1 is conferred by combinations of Fx‐mir mi RNAs induced in Sertoli cells ( SCs) during postnatal development when they terminate proliferation. Physiological significance is suggested by the finding that FMRP, the protein product of Fmr1, is downregulated when Fx‐mir mi RNAs are induced, and that FMRP loss causes SC hyperproliferation and spermatogenic defects. Fx‐mir mi RNAs not only regulate the expression of FMRP, but also regulate the expression of eIF4E and CYFIP1, which together with FMRP form a translational regulatory complex. Our results support a model in which Fx‐mir family members act cooperatively to regulate the translation of batteries of mRNAs in a developmentally regulated manner in SCs.

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          Most cited references72

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          Gene silencing by microRNAs: contributions of translational repression and mRNA decay.

          Despite their widespread roles as regulators of gene expression, important questions remain about target regulation by microRNAs. Animal microRNAs were originally thought to repress target translation, with little or no influence on mRNA abundance, whereas the reverse was thought to be true in plants. Now, however, it is clear that microRNAs can induce mRNA degradation in animals and, conversely, translational repression in plants. Recent studies have made important advances in elucidating the relative contributions of these two different modes of target regulation by microRNAs. They have also shed light on the specific mechanisms of target silencing, which, although it differs fundamentally between plants and animals, shares some common features between the two kingdoms.
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            Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

            mirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score. The algorithm trains a regression model on sequence and contextual features extracted from miRanda-predicted target sites. In a large-scale evaluation, miRanda-mirSVR is competitive with other target prediction methods in identifying target genes and predicting the extent of their downregulation at the mRNA or protein levels. Importantly, the method identifies a significant number of experimentally determined non-canonical and non-conserved sites.
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              The evolution of gene expression levels in mammalian organs.

              Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals.
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                Author and article information

                Contributors
                mfwilkinson@ucsd.edu
                Journal
                EMBO Rep
                EMBO Rep
                10.1002/(ISSN)1469-3178
                EMBR
                embor
                EMBO Reports
                John Wiley and Sons Inc. (Hoboken )
                1469-221X
                1469-3178
                20 December 2018
                February 2019
                20 December 2018
                : 20
                : 2 ( doiID: 10.1002/embr.v20.2 )
                : e46566
                Affiliations
                [ 1 ] Department of Obstetrics, Gynecology, and Reproductive Sciences University of California, San Diego La Jolla CA USA
                [ 2 ] Chemical Neurobiology Laboratory Center for Genomic Medicine Boston MA USA
                [ 3 ] Departments of Neurology and Psychiatry Massachusetts General Hospital Boston MA USA
                [ 4 ] Department of Biological Sciences Dartmouth College Hanover NH USA
                [ 5 ] Center for Reproductive Medicine and Andrology University of Münster Münster Germany
                [ 6 ] Division of Biological Sciences University of California, San Diego La Jolla CA USA
                [ 7 ] Institute of Genomic Medicine University of California, San Diego La Jolla CA USA
                Author notes
                [*] [* ]Corresponding author. Tel: +1 858 8224819; Fax: +1 858 5348329; E‐mail: mfwilkinson@ 123456ucsd.edu
                [†]

                These authors contributed equally to this work

                Author information
                http://orcid.org/0000-0002-8567-7795
                http://orcid.org/0000-0002-6416-3058
                Article
                EMBR201846566
                10.15252/embr.201846566
                6362356
                30573526
                a0322b1f-fc13-4077-8a4f-23c560b438b5
                © 2018 The Authors. Published under the terms of the CC BY NC ND 4.0 license

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 11 June 2018
                : 12 November 2018
                : 21 November 2018
                Page count
                Figures: 10, Tables: 0, Pages: 17, Words: 13789
                Funding
                Funded by: UCSD Interfaces Scholar Program
                Funded by: NASA‐Ames
                Funded by: HHS | NIH | National Institute of General Medical Sciences (NIGMS)
                Award ID: R01 GM119128
                Award ID: T32 HD007203
                Award ID: F32 GM113487
                Award ID: F30 HD089579
                Funded by: Lalor Foundation
                Funded by: German Research Foundation
                Award ID: 1547
                Funded by: FRAXA Research Foundation
                Funded by: Harvard Stem Cell Institute
                Categories
                Article
                Articles
                Custom metadata
                2.0
                embr201846566
                February 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.5.8 mode:remove_FC converted:05.02.2019

                Molecular biology
                evolution,fmr1,microrna,testis,translation,development & differentiation,molecular biology of disease,rna biology

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