title: Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos.
abstract: Human and mouse orthologs are expected to have similar biological functions; however, many discrepancies have also been reported. We systematically compared human and mouse orthologs in terms of alternative splicing patterns and expression profiles. Human-mouse orthologs are divergent in alternative splicing, as human orthologs could generally encode more isoforms than their mouse orthologs. In early embryos, exon skipping is far more common with human orthologs, whereas constitutive exons are more prevalent with mouse orthologs. This may correlate with divergence in expression of splicing regulators. Orthologous expression similarities are different in distinct embryonic stages, with the highest in morula. Expression differences for orthologous transcription factor genes could play an important role in orthologous expression discordance. We further detected largely orthologous divergence in differential expression between distinct embryonic stages. Collectively, our study uncovers significant orthologous divergence from multiple aspects, which may result in functional differences and dynamics between human-mouse orthologs during embryonic development.
authors.affiliation: The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.|Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, 201203, China.
authors.forename: Geng
authors.initials: G
authors.lastname: Chen
authors.affiliation: The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
authors.forename: Jiwei
authors.initials: J
authors.lastname: Chen
authors.affiliation: The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Yang
authors.affiliation: The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
authors.forename: Long
authors.initials: L
authors.lastname: Chen
authors.affiliation: The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
authors.forename: Xiongfei
authors.initials: X
authors.lastname: Qu
authors.affiliation: The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
authors.forename: Caiping
authors.initials: C
authors.lastname: Shi
authors.affiliation: National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
authors.forename: Baitang
authors.initials: B
authors.lastname: Ning
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, 201203, China.|National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.affiliation: National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.affiliation: Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China. yongxiangzhao@126.com.
authors.forename: Yongxiang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China. zhangmeixia@medmail.com.cn.
authors.forename: Meixia
authors.initials: M
authors.lastname: Zhang
authors.affiliation: The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China. tlshi@bio.ecnu.edu.cn.
authors.forename: Tieliu
authors.initials: T
authors.lastname: Shi
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D047108:Embryonic Development / Q000235:genetics*; D005091:Exons; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D051379:Mice; D020033:Protein Isoforms / Q000235:genetics; D017423:Sequence Analysis, RNA; D059010:Single-Cell Analysis; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D020033:Protein Isoforms; D014157:Transcription Factors
keywords: RNA-seq; alternative splicing; early embryo; gene expression; ortholog