{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T06:51:27Z","timestamp":1793170287076,"version":"4.5.0"},"reference-count":51,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T00:00:00Z","timestamp":1556841600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31330074"],"award-info":[{"award-number":["31330074"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"DOI":"10.3389\/fgene.2019.00409","type":"journal-article","created":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T14:11:49Z","timestamp":1556892709000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig"],"prefix":"10.3389","volume":"10","author":[{"given":"Yalan","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanmin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Ao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hua","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kui","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2019,5,3]]},"reference":[{"key":"B1","doi-asserted-by":"crossref","first-page":"947","DOI":"10.2741\/2116","article-title":"Melatonin role in the mitochondrial function.","volume":"12","author":"Acuna-Castroviejo","year":"2007","journal-title":"Front. Biosci."},{"key":"B2","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/nature12943","article-title":"The evolution of lncRNA repertoires and expression patterns in tetrapods.","volume":"505","author":"Anamaria","year":"2014","journal-title":"Nature"},{"key":"B3","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013a Python framework to work with high-throughput sequencing data.","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.1016\/j.cell.2013.02.012","article-title":"Long noncoding RNAs: cellular address codes in development and disease.","volume":"152","author":"Batista","year":"2013","journal-title":"Cell"},{"key":"B5","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1016\/j.neuron.2015.09.045","article-title":"Mechanisms of long non-coding rnas in mammalian nervous system development, plasticity, disease, and evolution.","volume":"88","author":"Briggs","year":"2015","journal-title":"Neuron"},{"key":"B6","first-page":"185","article-title":"Postnatal development of cell types in the rat pineal gland.","author":"Calvo","year":"1983","journal-title":"J. Anat."},{"key":"B7","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1385\/endo:27:2:189","article-title":"A review of the multiple actions of melatonin on the immune system.","volume":"27","author":"Carrillo-Vico","year":"2005","journal-title":"Endocrine"},{"key":"B8","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1101\/gad.234419.113","article-title":"The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration.","volume":"28","author":"Dey","year":"2014","journal-title":"Genes Dev."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-540-29805-2_4827","article-title":"Voltage-dependent calcium channels.","author":"Dolphin","year":"2007","journal-title":"Encycl. Pain"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families.","volume":"30","author":"Enright","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"B11","doi-asserted-by":"publisher","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database.","volume":"42","author":"Finn","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B12","doi-asserted-by":"publisher","first-page":"D983","DOI":"10.1093\/nar\/gks1099","article-title":"LncRNADisease: a database for long-non-coding RNA-associated diseases.","volume":"41","author":"Geng","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B13","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/j.devcel.2015.05.009","article-title":"A long non-coding RNA, LncMyoD, regulates skeletal muscle differentiation by blocking IMP2-mediated mRNA translation.","volume":"34","author":"Gong","year":"","journal-title":"Dev. Cell"},{"key":"B14","doi-asserted-by":"publisher","first-page":"D181","DOI":"10.1093\/nar\/gku1000","article-title":"lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse.","volume":"43","author":"Gong","year":"","journal-title":"Nucleic Acids Res."},{"key":"B15","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1038\/nature11622","article-title":"Analyses of pig genomes provide insight into porcine demography and evolution.","volume":"491","author":"Groenen","year":"2012","journal-title":"Nature"},{"key":"B16","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.","volume":"4","author":"Huang","year":"2008","journal-title":"Nat. Protoc."},{"key":"B17","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/ng.3192","article-title":"The landscape of long noncoding RNAs in the human transcriptome.","volume":"47","author":"Iyer","year":"2015","journal-title":"Nat. Genet."},{"key":"B18","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/j.mce.2015.01.024","article-title":"Circadian rhythms in glucose and lipid metabolism in nocturnal and diurnal mammals.","author":"Jha","year":"2015","journal-title":"Mol. Cell. Endocrinol."},{"key":"B19","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkm391","article-title":"CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.","author":"Kong","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"B20","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1016\/j.lfs.2004.03.003","article-title":"Melatonin and mitochondrial function.","volume":"75","author":"Leon","year":"2004","journal-title":"Life Sci."},{"key":"B21","first-page":"1653","article-title":"The sequence alignment\/map (SAM) format and SAMtools.","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B22","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1111\/age.12720","article-title":"LncRNAnet: a comprehensive Sus scrofa lncRNA database.","volume":"49","author":"Liang","year":"2018","journal-title":"Anim. Genet."},{"key":"B23","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/j.yfrne.2004.08.001","article-title":"Human pineal physiology and functional significance of melatonin.","volume":"25","author":"Macchi","year":"2004","journal-title":"Front. Neuroendocrinol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.tem.2007.03.001","article-title":"The mammalian pineal gland: known facts, unknown facets.","volume":"18","author":"Maronde","year":"2007","journal-title":"Trends Endocrinol. Metab."},{"key":"B25","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/s00441-002-0580-5","article-title":"The anatomy and innervation of the mammalian pineal gland.","volume":"309","author":"Moller","year":"2002","journal-title":"Cell Tissue Res."},{"key":"B26","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1111\/j.1471-4159.2007.04605.x","article-title":"NeuroD1: developmental expression and regulated genes in the rodent pineal gland.","volume":"102","author":"Munoz","year":"2007","journal-title":"J. Neurochem."},{"key":"B27","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1126\/science.aan4187","article-title":"Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9.","volume":"357","author":"Niu","year":"2017","journal-title":"Science"},{"key":"B28","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1101\/gr.133009.111","article-title":"Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.","volume":"22","author":"Pauli","year":"2012","journal-title":"Genome Res."},{"key":"B29","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1007\/s10142-011-0221-8","article-title":"Melatonin as a central molecule connecting neural development and calcium signaling.","volume":"11","author":"Poloni","year":"2011","journal-title":"Funct. Integrat. Genomics"},{"key":"B30","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/nbt.2490","article-title":"Pig genomics for biomedicine.","volume":"31","author":"Prather","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"D168","DOI":"10.1093\/nar\/gku988","article-title":"lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.","volume":"43","author":"Quek","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1111\/j.1471-4159.2006.03773.x","article-title":"Expression of the Otx2 homeobox gene in the developing mammalian brain: embryonic and adult expression in the pineal gland.","volume":"97","author":"Rath","year":"2006","journal-title":"J. Neurochem."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1007\/s11064-012-0906-y","article-title":"Homeobox genes in the rodent pineal gland: roles in development and phenotype maintenance.","volume":"38","author":"Rath","year":"2013","journal-title":"Neurochem. Res."},{"key":"B34","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1007\/bf01923947","article-title":"The melatonin rhythm: both a clock and a calendar.","volume":"49","author":"Reiter","year":"1993","journal-title":"Experientia"},{"key":"B35","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a bioconductor package for differential expression analysis of digital gene expression data.","volume":"26","author":"Robinson","year":"2009","journal-title":"Bioinformatics"},{"key":"B36","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/B978-0-12-416021-7.00005-5","article-title":"The pineal gland from development to function.","volume":"106","author":"Sap\u00e8de","year":"2013","journal-title":"Curr. Top. Dev. Biol."},{"key":"B37","doi-asserted-by":"crossref","first-page":"11608","DOI":"10.1016\/S0021-9258(18)67286-2","article-title":"Essential role of calcium influx in the adrenergic regulation of cAMP and cGMP in rat pinealocytes.","volume":"261","author":"Sugden","year":"1986","journal-title":"J. Biol. Chem."},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt646","article-title":"Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.","volume":"41","author":"Sun","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1038\/srep43166","article-title":"Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa.","volume":"7","author":"Tang","year":"2017","journal-title":"Sci. Rep."},{"key":"B40","doi-asserted-by":"publisher","first-page":"1535","DOI":"10.1038\/nprot.2009.177","article-title":"Network visualization and analysis of gene expression data using biolayout express(3D).","volume":"4","author":"Theocharidis","year":"2009","journal-title":"Nat. Protoc."},{"key":"B41","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq.","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"B42","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat. Protoc."},{"key":"B43","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1002\/mc.22274","article-title":"Melatonin modulated autophagy and Nrf2 signaling pathways in mice with colitis-associated colon carcinogenesis.","volume":"55","author":"Trivedi","year":"2016","journal-title":"Mol. Carcinog."},{"key":"B44","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information.","volume":"43","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B45","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/nature25739","article-title":"A molecular atlas of cell types and zonation in the brain vasculature.","volume":"554","author":"Vanlandewijck","year":"2018","journal-title":"Nature"},{"key":"B46","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1093\/nar\/gku1060","article-title":"An update on LNCipedia: a database for annotated human lncRNA sequences.","volume":"43","author":"Volders","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B47","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.cub.2013.11.045","article-title":"Transcription in pronuclei and one- to four-cell embryos drives early development in a nematode.","volume":"24","author":"Wang","year":"2014","journal-title":"Curr. Biol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1038\/nature12364","article-title":"Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.","volume":"500","author":"Xue","year":"2013","journal-title":"Nature"},{"key":"B49","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1007\/s00429-014-0740-x","article-title":"The Lhx9 homeobox gene controls pineal gland development and prevents postnatal hydrocephalus.","volume":"220","author":"Yamazaki","year":"2015","journal-title":"Brain Struct. Funct."},{"key":"B50","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1016\/j.cell.2018.03.005","article-title":"A Huntingtin knockin pig model recapitulates features of selective neurodegeneration in huntington\u2019s disease.","volume":"173","author":"Yan","year":"2018","journal-title":"Cell"},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1155\/2017\/6152582","article-title":"Systematic identification and molecular characteristics of long noncoding rnas in pig tissues.","volume":"2017","author":"Yang","year":"2017","journal-title":"Biomed. Res. Int."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2019.00409\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,17]],"date-time":"2022-09-17T10:18:29Z","timestamp":1663409909000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2019.00409\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,3]]},"references-count":51,"alternative-id":["10.3389\/fgene.2019.00409"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2019.00409","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,3]]},"article-number":"409"}}