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Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development
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  • 作者：Jie Lv (1)
    Hui Liu (1)
    Shihuan Yu (2)
    Hongbo Liu (1)
    Wei Cui (1)
    Yang Gao (1)
    Tao Zheng (1)
    Geng Qin (1)
    Jing Guo (1)
    Tiebo Zeng (1)
    Zhengbin Han (1)
    Yan Zhang (3)
    Qiong Wu (1)

    1. School of Life Science and Technology     ; State Key Laboratory of Urban Water Resource and Environment ; Harbin Institute of Technology ; Harbin ; 150001 ; China
    2. Department of Respiratory Medicine     ; the First Affiliated Hospital of Harbin Medical University ; Harbin ; 150001 ; Heilongjiang ; China
    3. College of Bioinformatics Science and Technology     ; Harbin Medical University ; Harbin ; 150081 ; China
  • 关键词：Long non ; coding RNAs ; Pre ; implantation embryonic development ; Mouse ; Single ; cell sequencing ; RNA sequencing
  • 刊名：Molecular Genetics and Genomics
  • 出版年：2015
  • 出版时间：April 2015
  • 年：2015
  • 卷：290
  • 期：2
  • 页码：685-697
  • 全文大小：1,147 KB
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  • 刊物类别：Biomedical and Life Sciences
  • 刊物主题：Life Sciences
    Cell Biology
    Biochemistry
    Microbial Genetics and Genomics
  • 出版者：Springer Berlin / Heidelberg
  • ISSN：1617-4623
文摘
Long intergenic non-coding RNAs (lincRNAs) as a key group of non-coding RNAs have gained substantial attention. Though lincRNAs have been systematically explored in various mouse tissues and cell lines, large-scale identification of lincRNAs in mouse pre-implantation embryonic development (PED) process has not be documented previously. Therefore, it is important to identify and characterize novel lincRNAs that may be involved in PED. In this paper, we performed transcriptome assembly based on published single-cell RNA-seq data during mouse PED and identified 4,438 putative lincRNAs. Combining these with Ensembl lincRNAs, we established a reference catalog of 5,808 transcribed lincRNAs in PED. We then systematically analyzed the lincRNAs in this reference catalog and revealed that the identified novel PED lincRNAs are generally comparable with known Ensembl lincRNAs in genomic aspects. In addition, the global expression patterns can be separated by zygote first cleavage division in clustering analysis and we further identified and analyzed differentially expressed lincRNAs involved in this process. The expression of lincRNAs involved in the process is negatively correlated with promoter methylation in trend. The identified lincRNAs involved in zygote first cleavage division could have important roles in mouse early embryonic development and need further functional studies. Altogether, a novel reference catalog of mouse PED lincRNAs is provided and characterized, which would be a valuable resource for further functional analyses and may help elucidate the pre-implantation regulatory mechanism.

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