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

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.

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Acknowledgments

The authors thank The Encyclopedia of DNA Elements (ENCODE) Consortium for sharing RNA-seq data. The authors also thank National Natural Science Foundation of China for funding. This work was supported by the National Natural Science Foundation of China [31171383, 31100934, 31201075, 31371478, 31371334, 61403112].

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Correspondence to Qiong Wu.

Additional information

J. Lv, H. Liu, S. Yu, H. B. Liu, W. Cui and Y. Gao have contributed equally to this work.

Communicated by S. Hohmann.

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Lv, J., Liu, H., Yu, S. et al. Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. Mol Genet Genomics 290, 685–697 (2015). https://doi.org/10.1007/s00438-014-0952-z

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Keywords

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