Identification of gene expression changes in rabbit uterus during embryo implantation

Genomics

Volumn 107, Issue 5, 2016, Pages 216-221

  Liu, Ji Long ^a   Zhao, Miao ^a   Peng, Ying ^a   Fu, Yong Sheng ^a  

^a SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Embryo implantation; Rabbit; RNA seq

Indexed keywords

ADULT; ANIMAL EXPERIMENT; ARTICLE; CELL ADHESION; CONTROLLED STUDY; DOWN REGULATION; FEMALE; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; NEW ZEALAND WHITE (RABBIT); NIDATION; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ANALYSIS; UPREGULATION; UTERUS; ANIMAL; BIOSYNTHESIS; ENDOMETRIUM; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HIGH THROUGHPUT SEQUENCING; METABOLISM; PROTEIN SYNTHESIS; RABBIT;

MESSENGER RNA;

ANIMALS; EMBRYO IMPLANTATION; ENDOMETRIUM; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PROTEIN BIOSYNTHESIS; RABBITS; RNA, MESSENGER; UTERUS;

EID: 84964328550     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2016.03.005     Document Type: Article

References (36)

1. Wang H., Dey S.K. Roadmap to embryo implantation: clues from mouse models. Nat. Rev. Genet. 2006, 7:185-199.
2. Lee K.Y., DeMayo F.J. Animal models of implantation. Reproduction 2004, 128:679-695.
3. Enders A.C., Schlafke S. Penetration of the uterine epithelium during implantation in the rabbit. Am. J. Anat. 1971, 132:219-230.
4. Hoffman L.H., Olson G.E., Carson D.D., Chilton B.S. Progesterone and implanting blastocysts regulate Muc1 expression in rabbit uterine epithelium. Endocrinology 1998, 139:266-271.
5. Illera M.J., Lorenzo P.L., Gui Y.T., Beyler S.A., Apparao K.B., Lessey B.A. A role for alphavbeta3 integrin during implantation in the rabbit model. Biol. Reprod. 2003, 68:766-771.
6. Das S.K., Chakraborty I., Wang J., Dey S.K., Hoffman L.H. Expression of vascular endothelial growth factor (VEGF) and VEGF-receptor messenger ribonucleic acids in the peri-implantation rabbit uterus. Biol. Reprod. 1997, 56:1390-1399.
7. Klonisch T., Wolf P., Hombach-Klonisch S., Vogt S., Kuechenhoff A., Tetens F., Fischer B. Epidermal growth factor-like ligands and erbB genes in the peri-implantation rabbit uterus and blastocyst. Biol. Reprod. 2001, 64:1835-1844.
8. Nicholls P.K., Sun Z., Heng S., Li Y., Wang J., Nie G. Embryo implantation is closely associated with dynamic expression of proprotein convertase 5/6 in the rabbit uterus. Reprod. Biol. Endocrinol. 2011, 9:43.
9. Apparao K.B., Illera M.J., Beyler S.A., Olson G.E., Osteen K.G., Corjay M.H., Boggess K., Lessey B.A. Regulated expression of osteopontin in the peri-implantation rabbit uterus. Biol. Reprod. 2003, 68:1484-1490.
10. Cha J., Sun X., Dey S.K. Mechanisms of implantation: strategies for successful pregnancy. Nat. Med. 2012, 18:1754-1767.
11. Liu J.L., Su R.W., Yang Z.M. Differential expression profiles of mRNAs, miRNAs and proteins during embryo implantation. Front. Biosci. (Schol Ed) 2011, 3:1511-1519.
12. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
13. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5:621-628.
14. Garber M., Grabherr M.G., Guttman M., Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods 2011, 8:469-477.
15. Schroeder A., Mueller O., Stocker S., Salowsky R., Leiber M., Gassmann M., Lightfoot S., Menzel W., Granzow M., Ragg T. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol. 2006, 7:3.
16. Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
17. Trapnell C., Williams B.A., Pertea G., Mortazavi A., Kwan G., van Baren M.J., Salzberg S.L., Wold B.J., Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28:511-515.
18. Cunningham F., Amode M.R., Barrell D., Beal K., Billis K., Brent S., Carvalho-Silva D., Clapham P., Coates G., Fitzgerald S., Gil L., Giron C.G., Gordon L., Hourlier T., Hunt S.E., Janacek S.H., Johnson N., Juettemann T., Kahari A.K., Keenan S., Martin F.J., Maurel T., McLaren W., Murphy D.N., Nag R., Overduin B., Parker A., Patricio M., Perry E., Pignatelli M., Riat H.S., Sheppard D., Taylor K., Thormann A., Vullo A., Wilder S.P., Zadissa A., Aken B.L., Birney E., Harrow J., Kinsella R., Muffato M., Ruffier M., Searle S.M., Spudich G., Trevanion S.J., Yates A., Zerbino D.R., Flicek P. Ensembl 2015. Nucleic Acids Res. 2015, 43:D662-D669.
19. Huang D.W., Sherman B.T., Tan Q., Kir J., Liu D., Bryant D., Guo Y., Stephens R., Baseler M.W., Lane H.C., Lempicki R.A. DAVID bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007, 35:W169-W175.
20. Szklarczyk D., Franceschini A., Wyder S., Forslund K., Heller D., Huerta-Cepas J., Simonovic M., Roth A., Santos A., Tsafou K.P., Kuhn M., Bork P., Jensen L.J., von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015, 43:D447-D452.
21. Assenov Y., Ramirez F., Schelhorn S.E., Lengauer T., Albrecht M. Computing topological parameters of biological networks. Bioinformatics 2008, 24:282-284.
22. Ma X.H., Hu S.J., Ni H., Zhao Y.C., Tian Z., Liu J.L., Ren G., Liang X.H., Yu H., Wan P., Yang Z.M. Serial analysis of gene expression in mouse uterus at the implantation site. J. Biol. Chem. 2006, 281:9351-9360.
23. Chen Y., Ni H., Ma X.H., Hu S.J., Luan L.M., Ren G., Zhao Y.C., Li S.J., Diao H.L., Xu X., Zhao Z.A., Yang Z.M. Global analysis of differential luminal epithelial gene expression at mouse implantation sites. J. Mol. Endocrinol. 2006, 37:147-161.
24. Yoon S.J., Choi D.H., Lee W.S., Cha K.Y., Kim S.N., Lee K.A. A molecular basis for embryo apposition at the luminal epithelium. Mol. Cell. Endocrinol. 2004, 219:95-104.
25. Kolodziejczyk A.A., Kim J.K., Svensson V., Marioni J.C., Teichmann S.A. The technology and biology of single-cell RNA sequencing. Mol. Cell 2015, 58:610-620.
26. Saliba A.E., Westermann A.J., Gorski S.A., Vogel J. Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res. 2014, 42:8845-8860.
27. Heino J. The collagen family members as cell adhesion proteins. BioEssays 2007, 29:1001-1010.
28. Ricard-Blum S. The collagen family. Cold Spring Harb. Perspect. Biol. 2011, 3:a004978.
29. Hurst P.R., Gibbs R.D., Clark D.E., Myers D.B. Temporal changes to uterine collagen types I, III and V in relation to early pregnancy in the rat. Reprod. Fertil. Dev. 1994, 6:669-677.
30. Blankenship T.N., Given R.L. Loss of laminin and type IV collagen in uterine luminal epithelial basement membranes during blastocyst implantation in the mouse. Anat. Rec. 1995, 243:27-36.
31. Mulholland J., Aplin J.D., Ayad S., Hong L., Glasser S.R. Loss of collagen type VI from rat endometrial stroma during decidualization. Biol. Reprod. 1992, 46:1136-1143.
32. Fata J.E., Ho A.T., Leco K.J., Moorehead R.A., Khokha R. Cellular turnover and extracellular matrix remodeling in female reproductive tissues: functions of metalloproteinases and their inhibitors. Cell. Mol. Life Sci. 2000, 57:77-95.
33. Daikoku T., Matsumoto H., Gupta R.A., Das S.K., Gassmann M., DuBois R.N., Dey S.K. Expression of hypoxia-inducible factors in the peri-implantation mouse uterus is regulated in a cell-specific and ovarian steroid hormone-dependent manner. Evidence for differential function of HIFs during early pregnancy. J. Biol. Chem. 2003, 278:7683-7691.
34. Kazi A.A., Jones J.M., Koos R.D. Chromatin immunoprecipitation analysis of gene expression in the rat uterus in vivo: estrogen-induced recruitment of both estrogen receptor alpha and hypoxia-inducible factor 1 to the vascular endothelial growth factor promoter. Mol. Endocrinol. 2005, 19:2006-2019.
35. Kirkland J.L., Murthy L., Stancel G.M. Progesterone inhibits the estrogen-induced expression of c-fos messenger ribonucleic acid in the uterus. Endocrinology 1992, 130:3223-3230.
36. Bhurke A.S., Bagchi I.C., Bagchi M.K. Progesterone-regulated endometrial factors controlling implantation. Am. J. Reprod. Immunol. 2016, 75:237-245.