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      Characterization of N 6-Methyladenosine in Domesticated Yak Testes Before and After Sexual Maturity

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          Abstract

          The potential regulatory role of N 6-methyladenosine (m 6A), the most prominent mRNA modification in eukaryotes, has recently been identified in mammals, plants, and yeast. However, whether and how m 6A methylation is involved in sexual maturation in mammals remains largely unexplored. In this study, testicular tissue was obtained from yaks before and after sexual maturation, and m 6A maps were generated via preliminary experiments and methylated RNA immunoprecipitation sequencing. Only spermatogonial cells and a few primary spermatocytes were observed in the testicular tissue of yaks before sexual maturation, while spermatogenic cells at different stages of maturity could observed after sexual maturation. Experiments examining the expression of methylation-related enzymes and overall methylation levels showed that the methylation levels in yak testes increased after sexual maturation. Overall, 1,438 methylation peaks were differentially expressed before and after sexual maturation; 1,226 showed significant up-regulation and 212 showed significant down-regulation after sexual maturation. Annotation analysis showed that the differential methylation peaks were most commonly concentrated in the exon region, followed by the 3′UTR and finally the 5′UTR region. KEGG pathway analysis demonstrated that homologous recombination, the Notch signaling pathway, growth hormone synthesis, and other signaling pathways may be involved in testicular development and maturation in yaks. Levels of most m 6A modifications were positively correlated with mRNA abundance, suggesting that m 6A plays a regulatory role in mammalian sexual maturation. To our knowledge, this is the first report of an m 6A transcriptional map of the yak testes, and our study lays the foundation for elucidating the function of m 6A in the development of yak testes.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            HISAT: a fast spliced aligner with low memory requirements.

            HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.
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              MEME Suite: tools for motif discovery and searching

              The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms—MAST, FIMO and GLAM2SCAN—allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm Tomtom. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and Tomtom), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.
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                Author and article information

                Contributors
                Journal
                Front Cell Dev Biol
                Front Cell Dev Biol
                Front. Cell Dev. Biol.
                Frontiers in Cell and Developmental Biology
                Frontiers Media S.A.
                2296-634X
                11 November 2021
                2021
                : 9
                : 755670
                Affiliations
                Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
                Author notes

                Edited by: Julian Valdes, National Autonomous University of Mexico, Mexico

                Reviewed by: Yun Bai, ShanghaiTech University, China

                Diana Guallar, University of Santiago de Compostela, Spain

                *Correspondence: Ping Yan, yanping@ 123456caas.cn ; Xian Guo, guoxian@ 123456caas.cn

                This article was submitted to Developmental Epigenetics, a section of the journal Frontiers in Cell and Developmental Biology

                Article
                755670
                10.3389/fcell.2021.755670
                8632223
                34858983
                2161c01f-73c0-4f2b-9eef-51939f467543
                Copyright © 2021 Wang, Pei, Guo, Cao, Bao, Xiong, Wu, Chu, Liang, Yan and Guo.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 09 August 2021
                : 27 October 2021
                Categories
                Cell and Developmental Biology
                Original Research

                yak,before sexual maturity,after sexual maturity,n6-methyladenosine,testicular tissue

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