title: 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.
authors.affiliation: School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Lv
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.forename: Shihuan
authors.initials: S
authors.lastname: Yu
authors.forename: Hongbo
authors.initials: H
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Cui
authors.forename: Yang
authors.initials: Y
authors.lastname: Gao
authors.forename: Tao
authors.initials: T
authors.lastname: Zheng
authors.forename: Geng
authors.initials: G
authors.lastname: Qin
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.forename: Tiebo
authors.initials: T
authors.lastname: Zeng
authors.forename: Zhengbin
authors.initials: Z
authors.lastname: Han
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wu
mesh_terms: D000818:Animals; D047108:Embryonic Development / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D051379:Mice; D062085:RNA, Long Noncoding / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D015053:Zygote / Q000502:physiology
chemical_list: D062085:RNA, Long Noncoding