Analysis and Screening of Reproductive Long Non-coding RNAs Through Genome-Wide Analyses of Goat Endometrium During the Pre-attachment Phase

Overview

Journal Front Genet

Date 2020 Nov 16

PMID 33193661

Citations 10

Authors

Linjun Hong

Qun Hu

Xupeng Zang

Yanshe Xie

Chen Zhou

Xian Zou

Yaokun Li

Ming Deng

Yongqing Guo

Guangbin Liu

Dewu Liu

Affiliations

Soon will be listed here.

Abstract

Reproduction in goat is highly impeded by implantation failure. Of concern, the underlying mechanism leading to embryo implantation remains unclear. In this study, deep sequencing was employed through strand-specific Ribo-Zero RNA-Seq to characterize transcriptome changes in the endometrium during the maternal recognition of pregnancy. A total of 996 differential transcripts (115 lncRNAs and 881 mRNAs) existing between the pregnant and non-pregnant endometrium were revealed through bioinformatics analysis. The screening was performed on lncRNAs (XR_001918173.1, LNC_002760, and LNC_000599) and LNC_009053, to determine their potential role in regulating the synthesis of retinol and endometrium remolding through the proteasome pathway, respectively. The hypothesis of whether certain lncRNAs, namely, LNC_007223, LNC_005256, and LNC_010092 could play important roles in embryo implantation was tested. These novel findings are of paramount relevance to further elucidate the molecular mechanisms of embryo implantation and uncover new targets to improve goat reproduction.

Citing Articles

Comprehensive characterization of lncRNA N-methyladenosine modification dynamics throughout bovine skeletal muscle development.

Mao C, You W, Yang Y, Cheng H, Hu X, Lan X J Anim Sci Biotechnol. 2025; 16(1):36.

PMID: 40045371 PMC: 11884139. DOI: 10.1186/s40104-025-01164-2.

Comprehensive analysis of lncRNAs modified by m6A methylation in sheep skin.

Meng J, Li J, Zhao Y Anim Biosci. 2024; 37(11):1887-1990.

PMID: 38754841 PMC: 11541038. DOI: 10.5713/ab.24.0039.

Transcriptomic Analysis of the Developing Testis and Spermatogenesis in Qianbei Ma Goats.

Zou Y, Chen X, Tian X, Guo W, Ruan Y, Tang W Genes (Basel). 2023; 14(7).

PMID: 37510239 PMC: 10379175. DOI: 10.3390/genes14071334.

Uterus proliferative period ceRNA network of Yunshang black goat reveals candidate genes on different kidding number trait.

Du X, Liu Y, He X, Tao L, Fang M, Chu M Front Endocrinol (Lausanne). 2023; 14:1165409.

PMID: 37251683 PMC: 10213787. DOI: 10.3389/fendo.2023.1165409.

Analyses of lncRNAs, circRNAs, and the Interactions between ncRNAs and mRNAs in Goat Submandibular Glands Reveal Their Potential Function in Immune Regulation.

Wang A, Wang J, Mao M, Zhao X, Li Q, Xuan R Genes (Basel). 2023; 14(1).

PMID: 36672927 PMC: 9859278. DOI: 10.3390/genes14010187.

References

Carson D, Bagchi I, Dey S, Enders A, Fazleabas A, Lessey B . Embryo implantation. Dev Biol. 2000; 223(2):217-37. DOI: 10.1006/dbio.2000.9767. View

Ocon-Grove O, Cooke F, Alvarez I, Johnson S, Ott T, Ealy A . Ovine endometrial expression of fibroblast growth factor (FGF) 2 and conceptus expression of FGF receptors during early pregnancy. Domest Anim Endocrinol. 2007; 34(2):135-45. DOI: 10.1016/j.domaniend.2006.12.002. View

Robinson M, McCarthy D, Smyth G . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139-40. PMC: 2796818. DOI: 10.1093/bioinformatics/btp616. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Bateman A, Birney E, Durbin R, Eddy S, Howe K, Sonnhammer E . The Pfam protein families database. Nucleic Acids Res. 1999; 28(1):263-6. PMC: 102420. DOI: 10.1093/nar/28.1.263. View

Li S . Expression of Concern: The functional role of long non-coding RNAs and epigenetics. Biol Proced Online. 2016; 18:12. PMC: 4901470. DOI: 10.1186/s12575-016-0042-1. View

Pan Q, Luo X, Toloubeydokhti T, Chegini N . The expression profile of micro-RNA in endometrium and endometriosis and the influence of ovarian steroids on their expression. Mol Hum Reprod. 2007; 13(11):797-806. DOI: 10.1093/molehr/gam063. View

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M . KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2007; 36(Database issue):D480-4. PMC: 2238879. DOI: 10.1093/nar/gkm882. View

Blomhoff R, Blomhoff H . Overview of retinoid metabolism and function. J Neurobiol. 2006; 66(7):606-30. DOI: 10.1002/neu.20242. View

10.

Kang Y, Yang D, Kong L, Hou M, Meng Y, Wei L . CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 2017; 45(W1):W12-W16. PMC: 5793834. DOI: 10.1093/nar/gkx428. View

11.

Sigurgeirsson B, Amark H, Jemt A, Ujvari D, Westgren M, Lundeberg J . Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle. Biol Reprod. 2017; 96(1):24-33. DOI: 10.1095/biolreprod.116.142547. View

12.

Plewka P, Thompson A, Szymanski M, Nuc P, Knop K, Rasinska A . A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis. RNA Biol. 2018; 15(6):726-738. PMC: 6152437. DOI: 10.1080/15476286.2018.1445404. View

13.

Bazer F . Pregnancy recognition signaling mechanisms in ruminants and pigs. J Anim Sci Biotechnol. 2013; 4(1):23. PMC: 3710217. DOI: 10.1186/2049-1891-4-23. View

14.

Afonso S, Romagnano L, Babiarz B . The expression and function of cystatin C and cathepsin B and cathepsin L during mouse embryo implantation and placentation. Development. 1997; 124(17):3415-25. DOI: 10.1242/dev.124.17.3415. View

15.

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

16.

Liu Y, Qi B, Xie J, Wu X, Ling Y, Cao X . Filtered reproductive long non-coding RNAs by genome-wide analyses of goat ovary at different estrus periods. BMC Genomics. 2018; 19(1):866. PMC: 6278114. DOI: 10.1186/s12864-018-5268-7. View

17.

Xia H, Jin X, Song P, Cui Y, Liu C, Ma X . Temporal and spatial regulation of miR-320 in the uterus during embryo implantation in the rat. Int J Mol Sci. 2010; 11(2):719-730. PMC: 2852863. DOI: 10.3390/ijms11020719. View

18.

Cao J . The functional role of long non-coding RNAs and epigenetics. Biol Proced Online. 2014; 16:11. PMC: 4177375. DOI: 10.1186/1480-9222-16-11. View

19.

Wango E, Wooding F, HEAP R . The role of trophoblast binucleate cells in implantation in the goat: a quantitative study. Placenta. 1990; 11(5):381-94. DOI: 10.1016/s0143-4004(05)80214-0. View

20.

Sha A, Liu J, Jiang X, Ren J, Ma C, Lei W . Genome-wide identification of micro-ribonucleic acids associated with human endometrial receptivity in natural and stimulated cycles by deep sequencing. Fertil Steril. 2011; 96(1):150-155.e5. DOI: 10.1016/j.fertnstert.2011.04.072. View