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      Profiling of open chromatin in developing pig ( Sus scrofa) muscle to identify regulatory regions

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          Abstract

          There is very little information about how the genome is regulated in domestic pigs ( Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the “Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)” to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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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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              The Sequence Alignment/Map format and SAMtools

              Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press
                2160-1836
                February 2022
                13 December 2021
                13 December 2021
                : 12
                : 2
                : jkab424
                Affiliations
                [1 ] The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh , Edinburgh EH25 9RG, UK
                [2 ] Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh , Edinburgh EH25 9RG, UK
                [3 ] Department of Animal Science, University of California Davis , Davis, CA 95616, USA
                [4 ] Department of Animal Science, Texas A&M University , College Station, TX 77843, USA
                [5 ] Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala 750 07, Sweden
                Author notes
                Corresponding authors: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK. Email: mazdak.salavati@ 123456roslin.ed.ac.uk (M.S.); emily.clark@ 123456roslin.ed.ac.uk (E.L.C.)
                Author information
                https://orcid.org/0000-0002-7349-2451
                https://orcid.org/0000-0003-1262-4585
                https://orcid.org/0000-0001-9213-1830
                https://orcid.org/0000-0002-9550-7407
                Article
                jkab424
                10.1093/g3journal/jkab424
                9210303
                34897420
                d8c51e4f-6229-4bfd-aa40-7977a401e93e
                © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 August 2021
                : 03 December 2021
                : 06 January 2022
                Page count
                Pages: 18
                Funding
                Funded by: Institute Strategic Programme (ISP18) Pump-Priming grant “Profiling Open Chromatin in Developing Pig Muscle” from Biotechnology and Biological Sciences Research Council (BBSRC);
                Funded by: Institute Strategic Programme;
                Funded by: Roslin Institute by BBSRC “Farm Animal Genomics”;
                Award ID: BBS/E/D/2021550
                Funded by: Prediction of genes and regulatory elements in farm animal genomes;
                Award ID: BBS/E/D/10002070
                Funded by: BBSRC, DOI 10.13039/501100000268;
                Award ID: BB/S02008X/1
                Funded by: University of Edinburgh Chancellors’ Fellowships;
                Funded by: Bill & Melinda Gates Foundation, DOI 10.13039/100000865;
                Funded by: UK aid from the UK Foreign, Commonwealth and Development Office;
                Award ID: OPP1127286
                Funded by: Centre for Tropical Livestock Genetics and Health (CTLGH);
                Funded by: University of Edinburgh, SRUC (Scotland’s Rural College);
                Funded by: International Livestock Research Institute, DOI 10.13039/501100014577;
                Funded by: National Agency for Research and Development (ANID)/Scholarship Program/DOCTORADO BECAS CHILE;
                Award ID: 2016—72170349
                Funded by: Bill & Melinda Gates Foundation nor the UK Government;
                Categories
                Investigation
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140
                AcademicSubjects/SCI00010
                AcademicSubjects/SCI00960

                Genetics
                atac-seq,sscrofa11.1,rna-seq,frozen tissue,muscle
                Genetics
                atac-seq, sscrofa11.1, rna-seq, frozen tissue, muscle

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