title: Spatiotemporal-specific lncRNAs in the brain, colon, liver and lung of macaque during development.
abstract: Genome-wide expression profiling during development provides useful information to uncover the potential molecular mechanisms of development in mammals. Recent studies have revealed that a subset of lncRNAs can regulate major biological processes during development. Here, we sequenced four tissues, including brain, colon, liver and lung, using RNA-seq across three developmental stages (early, middle and late stage), and then constructed genome-wide expression profiles during macaque development. In each tissue, we identified developmental time-specific lncRNA and mRNA clusters that displayed diverse expression alteration patterns, including a gradual increase, a gradual decrease, or a reversal of expression. These lncRNAs showed more specific functional associations with their corresponding tissues relative to the developmental time-specific mRNAs. Furthermore, we identified 20 spatiotemporal-specific co-modules including 101 lncRNAs and 609 mRNAs distributed at different developmental stages in different tissues. Our findings suggested that lncRNAs could play critical roles in the development of macaques through close cooperation with mRNAs. Finally, we predicted the functions of the spatiotemporal-specific lncRNAs by their spatiotemporal cooperation with mRNAs and further validated our findings using gene knockdown data of mouse. Our study reveals the spatiotemporal characteristics of lncRNAs and provides a functional map of the spatiotemporal-specific lncRNAs during the development of macaques.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Yun
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Huang
authors.affiliation: Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Hongying
authors.initials: H
authors.lastname: Zhao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Xinrui
authors.initials: X
authors.lastname: Shi
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Shuyuan
authors.initials: S
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Xuexin
authors.initials: X
authors.lastname: Yu
authors.affiliation: Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, China.
authors.forename: Lianfeng
authors.initials: L
authors.lastname: Zhang
authors.affiliation: BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Zujing
authors.initials: Z
authors.lastname: Han
authors.affiliation: BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Longhai
authors.initials: L
authors.lastname: Luo
authors.affiliation: BGI Tech Solutions Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Qianhua
authors.initials: Q
authors.lastname: Zhu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Jiang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn and State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Cancer Institute & Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100021, China. zhangkt@cicams.ac.cn.
authors.forename: Shujun
authors.initials: S
authors.lastname: Cheng
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, 194 Xuefu Road, Harbin, 150081, China. chengshj@263.net.cn lixia@hrbmu.edu.cn.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
authors.affiliation: State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Cancer Institute & Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100021, China. zhangkt@cicams.ac.cn.
authors.forename: Kaitai
authors.initials: K
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001921:Brain / Q000196:embryology / Q000378:metabolism; D016000:Cluster Analysis; D003106:Colon / Q000196:embryology / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D008099:Liver / Q000196:embryology / Q000378:metabolism; D008168:Lung / Q000196:embryology / Q000378:metabolism; D008251:Macaca; D009928:Organ Specificity / Q000235:genetics; D038081:Organogenesis / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D013997:Time Factors
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger