Molecular Genetics and Genomics

, Volume 290, Issue 2, pp 685–697 | Cite as

Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development

  • Jie Lv
  • Hui Liu
  • Shihuan Yu
  • Hongbo Liu
  • Wei Cui
  • Yang Gao
  • Tao Zheng
  • Geng Qin
  • Jing Guo
  • Tiebo Zeng
  • Zhengbin Han
  • Yan Zhang
  • Qiong Wu
Original Paper

Abstract

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.

Keywords

Long non-coding RNAs Pre-implantation embryonic development Mouse Single-cell sequencing RNA sequencing 

Supplementary material

438_2014_952_MOESM1_ESM.pdf (887 kb)
Supplementary material 1 (PDF 886 kb)
438_2014_952_MOESM2_ESM.xlsx (7.8 mb)
Supplementary material 2 (XLSX 7959 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • 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. 1.School of Life Science and Technology, State Key Laboratory of Urban Water Resource and EnvironmentHarbin Institute of TechnologyHarbinChina
  2. 2.Department of Respiratory Medicinethe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
  3. 3.College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbinChina

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