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      MicroRNAs in amniotic fluid and maternal blood plasma associated with sex determination and early gonad differentiation in cattle

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          Abstract

          We hypothesized that sexually dimorphic differences exist in the expression of miRNAs in amniotic fluid (AF) and maternal blood plasma (MP) in association with the process of sex determination and gonad differentiation in cattle. Amniotic fluid and MP were collected from six pregnant heifers (three carrying a single male and three a single female embryo) following slaughter on Day 39 postinsemination, coinciding with the peak of SRY expression. Samples (six AF and six MP) were profiled using an miRNA Serum/Plasma Focus PCR Panel. Differentially expressed (DE) miRNAs were identified in AF ( n = 5) and associated MP ( n = 56) of male vs. female embryos ( P < 0.05). Functional analysis showed that inflammatory and immune response were among the 13 biological processes enriched by miRNAs DE in MP in the male group (FDR < 0.05), suggesting that these sex-dependent DE miRNAs may be implicated in modulating the receptivity of the dam to a male embryo. Further, we compared the downstream targets of the sex-dependent DE miRNAs detected in MP with genes previously identified as DE in male vs. female genital ridges. The analyses revealed potential targets that might be important during this developmental stage such as SHROOM2, DDX3Y, SOX9, SRY, PPP1CB, JARID2, USP9X, KDM6A, and EIF2S3. Results from this study highlight novel aspects of sex determination and embryo–maternal communication in cattle such as the potential role of miRNAs in gonad development as well as in the modulation of the receptivity of the dam to a male embryo.

          Abstract

          Sex-dependent differentially expressed miRNAs identified in amniotic fluid and maternal plasma on Day 39 of pregnancy are associated with gonad development as well as the modulation of the receptivity of the dam to a male embryo.

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          miRBase: from microRNA sequences to function

          Abstract miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: 38 589 hairpin precursors and 48 860 mature microRNAs. We describe improvements to the database and website to provide more information about the quality of microRNA gene annotations, and the cellular functions of their products. We have collected 1493 small RNA deep sequencing datasets and mapped a total of 5.5 billion reads to microRNA sequences. The read mapping patterns provide strong support for the validity of between 20% and 65% of microRNA annotations in different well-studied animal genomes, and evidence for the removal of >200 sequences from the database. To improve the availability of microRNA functional information, we are disseminating Gene Ontology terms annotated against miRBase sequences. We have also used a text-mining approach to search for microRNA gene names in the full-text of open access articles. Over 500 000 sentences from 18 542 papers contain microRNA names. We score these sentences for functional information and link them with 12 519 microRNA entries. The sentences themselves, and word clouds built from them, provide effective summaries of the functional information about specific microRNAs. miRBase is publicly and freely available at http://mirbase.org/.
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            DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

            Abstract DIANA-TarBase v8 (http://www.microrna.gr/tarbase) is a reference database devoted to the indexing of experimentally supported microRNA (miRNA) targets. Its eighth version is the first database indexing >1 million entries, corresponding to ∼670 000 unique miRNA-target pairs. The interactions are supported by >33 experimental methodologies, applied to ∼600 cell types/tissues under ∼451 experimental conditions. It integrates information on cell-type specific miRNA–gene regulation, while hundreds of thousands of miRNA-binding locations are reported. TarBase is coming of age, with more than a decade of continuous support in the non-coding RNA field. A new module has been implemented that enables the browsing of interactions through different filtering combinations. It permits easy retrieval of positive and negative miRNA targets per species, methodology, cell type and tissue. An incorporated ranking system is utilized for the display of interactions based on the robustness of their supporting methodologies. Statistics, pie-charts and interactive bar-plots depicting the database content are available through a dedicated result page. An intuitive interface is introduced, providing a user-friendly application with flexible options to different queries.
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              microRNA functions.

              microRNAs (miRNAs) are small noncoding RNAs that play important roles in posttranscriptional gene regulation. In animal cells, miRNAs regulate their targets by translational inhibition and mRNA destabilization. Here, we review recent work in animal models that provide insight into the diverse roles of miRNAs in vivo.
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                Author and article information

                Journal
                Biol Reprod
                Biol Reprod
                biolreprod
                Biology of Reproduction
                Oxford University Press
                0006-3363
                1529-7268
                August 2021
                22 April 2021
                22 April 2021
                : 105
                : 2
                : 345-358
                Affiliations
                [1 ] Animal and Crops Sciences , School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
                [2 ] Departamento de Reproducción Animal, INIA , Madrid, Spain
                Author notes
                Correspondence: Departamento de Reproducción Animal, INIA, Madrid, Spain. E-mail: jm.sanchez@ 123456inia.es ; pat.lonergan@ 123456ucd.ie

                Grant Support. Supported by Science Foundation Ireland (13/IA/1983) and grant RTI2018–093548-BI00 from the Spanish Ministry of Science and Innovation. IG-R was supported by a predoctoral fellowship from the Spanish Ministry of Science and Innovation (BES-2016-077794), and BP was supported by a Marie Sklodowska-Curie ITN European Joint Doctorate in Biology and Technology of Reproductive Health (REP-BIOTECH 675526).

                Article
                ioab079
                10.1093/biolre/ioab079
                8335352
                33889937
                f8bf79f1-c2a6-422c-83a6-8e4b2449e6ec
                © The Author(s) 2021. Published by Oxford University Press on behalf of Society for the Study of Reproduction.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                : 8 February 2021
                : 22 March 2021
                : 12 April 2021
                Page count
                Pages: 00
                Funding
                Funded by: funder-nameMarie Sklodowska-Curie ITN European Joint Doctorate in Biology and Technology of Reproductive Health;
                Award ID: REP-BIOTECH 675526
                Funded by: funder-nameSpanish Ministry of Science and Innovation, DOI 10.13039/501100004837;
                Award ID: BES-2016-077794
                Funded by: funder-nameScience Foundation Ireland, DOI 10.13039/501100001602;
                Award ID: RTI2018–093548-BI00
                Award ID: 13/IA/1983
                Categories
                Research Article
                AcademicSubjects/MED00773
                AcademicSubjects/SCI01070

                circulating mirnas,amnion,pregnancy,cattle
                circulating mirnas, amnion, pregnancy, cattle

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