Exploring differentially expressed genes in the ovaries of uniparous and multiparous goats using the RNA-Seq (Quantification) method

Gene

Volumn 550, Issue 1, 2014, Pages 148-153

  Ling, Ying Hui ^a   Xiang, Hao ^a,b   Li, Yun Sheng ^a   Liu, Ya ^a   Zhang, Yun Hai ^a   Zhang, Zi Juan ^a   Ding, Jian Ping ^a   Zhang, Xiao Rong ^a  

^a ANHUI AGRICULTURAL UNIVERSITY   (China)

^b Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province   (China)

Author keywords

Differentially expressed genes; Goat; Ovary; Prolificacy; RNA Seq

Indexed keywords

RNA;

ACTIN FILAMENT; ANHUI WHITE GOAT; ANIMAL GENETICS; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DOWN REGULATION; EXTRACELLULAR MATRIX; FEMALE; FOCAL ADHESION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC SCREENING; GOAT; NONHUMAN; OVARY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; RNA SEQUENCE; UPREGULATION; ANIMAL; BIOLOGICAL MODEL; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PARITY; PREGNANCY; PROCEDURES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; VETERINARY;

CAPRA HIRCUS;

ANIMALS; FEMALE; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENE REGULATORY NETWORKS; GOATS; MODELS, GENETIC; OVARY; PARITY; PREGNANCY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION;

EID: 84906935851     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.08.008     Document Type: Article

References (42)

1. Anderson L.L., Ford J.J., Klindt J., et al. Growth hormone and prolactin secretion in hypophysial stalk-transected pigs as affected by growth hormone and prolactin-releasing and inhibiting factors. Proc. Soc. Exp. Biol. Med. 1991, 196:194-202.
2. Ashburner M., Ball C.A., Blake J.A., et al. Gene ontology: tool for the unification of biology. Nat. Genet. 2000, 25:25-29.
3. Benjamini Y., Drai D., Elmer G., et al. Controlling the false discovery rate in behavior genetics research. Behav. Brain Res. 2001, 125:279-284.
4. Bosman F.T., Stamenkovic I. Functional structure and composition of the extracellular matrix. J. Pathol. 2003, 200(4):423-428.
5. Cawthon R.M., O'Connell P., Buchberg A.M., et al. Identification and characterization of transcripts from the neurofibromatosis 1 region: the sequence and genomic structure of EVI2 and mapping of other transcripts. Genomics 1990, 7(4):555-565.
6. Chang B.L., Zheng S.L., Isaacs S.D., et al. Evaluation of SRD5A2 sequence variants in susceptibility to hereditary and sporadic prostate cancer. Prostate 2003, 56(1):37-44.
7. Chen S., Cheng G.L., Zhu D.J., et al. Determination on the body properties and meat performance of Anhui white goat. Anim. Husb. Feed Sci. 2009, 30(4):150-152.
8. Davis G.H., Galloway S.M., Ross I.K., et al. DNA tests in prolific sheep from eight countries provide new evidence on origin of the Booroola (FecB) mutation. Biol. Reprod. 2002, 66(6):1869-1874.
9. Galloway S.M., McNatty K.P., Cambridge L.M., et al. Mutations in an oocyte-derived growth factor gene (BMP15) cause increased ovulation rate and infertility in a dosage-sensitive manner. Nat. Genet. 2000, 25(3):279-283.
10. Ganss B., Kim R.H., Sodek J. Bone sialoprotein. Crit. Rev. Oral Biol. Med. 1999, 10(1):79-98.
11. Geier C., Gehmlich K., Ehler E., et al. Beyond the sarcomere: CSRP3 mutations cause hypertrophic cardiomyopathy. Hum. Mol. Genet. 2008, 17(18):2753-2765.
12. Gunawan A., Sahadevan S., Neuhoff C., et al. RNA deep sequencing reveals novel candidate genes and polymorphisms in boar testis and liver tissues with divergent androstenone levels. PLos One 2013, 8(5):e63259.
13. Habas R., He X. Activation of Rho and Rac by Wnt/frizzled signaling. Methods Enzymol. 2006, 406:500-511.
14. Hackett N.R., Butler M.W., Shaykhiev R., et al. RNA-Seq quantification of the human small airway epithelium transcriptome. BMC Genomics 2012, 13:82.
15. Hanrahan J.P., Gregan S.M., Mulsant P., et al. Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both increased ovulation rate and sterility in Cambridge and Belclare sheep (Ovis aries). Biol. Reprod. 2004, 70:900-909.
16. Huang W., Khatib H. Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics 2010, 11:711.
17. Ishida-Takagishi M., Enomoto A., Asai N., et al. The Dishevelled-associating protein Daple controls the non-canonical Wnt/Rac pathway and cell motility. Nat. Commun. 2012, 3:859.
18. Ishihara T., Ikeda K., Sato S. Differential expression of Eya1 and Eya2 during chick. Gene Expr. Patterns 2008, 8(5):357-367.
19. Issop L., Rone M.B., Papadopoulos V. Organelle plasticity and interactions in cholesterol transport and steroid biosynthesis. Mol. Cell. Endocrinol. 2013, 371(1-2):34-46.
20. Jack L.J., Mather I.H. Cloning and analysis of cDNA encoding bovine butyrophilin, an apical glycoprotein expressed in mammary tissue and secreted in association with the milk-fat globule membrane during lactation. J. Biol. Chem. 1990, 265(24):14481-14486.
21. Kanehisa M., Araki M., Goto S., et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36(Suppl. 1):D480-D484.
22. Kerpedjiev P., Frellsen J., Lindgreen S., et al. Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC Bioinforma. 2014, 15:100.
23. Kisseleva T., Bhattacharya S., Braunstein J., et al. Signaling through the JAK/STAT pathway, recent advances and future challenges. Gene 2002, 285(1-2):1-24.
24. Knoll R., Hoshijima M., Hoffman H.M., et al. The cardiac mechanical stretch sensor machinery involves a Z disc complex that is defective in a subset of human dilated cardiomyopathy. Cell 2002, 111:943-955.
25. Koji S., You Q.S., John J.E. Does bone morphogenetic protein 6 (BMP-6) affect female fertility in the mouse?. Biol. Reprod. 2010, 83(6):997-1004.
26. Larkin M.K., Holder K., Yost C., et al. Expression of constitutively active Notch arrests follicle cells at a precursor stage during Drosophila oogenesis and disrupts the anterior-posterior axis of the oocyte. Development 1996, 122(11):3639-3650.
27. Lee S.H., Dominguez R. Regulation of actin cytoskeleton dynamics in cells. Mol. Cells 2010, 29:311-325.
28. Li R.Q., Yu C., Li Y.R., et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967.
29. Lindgreen S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 2012, 5:337.
30. Lopez-Schier H., St Johnston D. Delta signaling from the germ line controls the proliferation and differentiation of the somatic follicle cells during Drosophila oogenesis. Genes Dev. 2001, 15(11):1393-1405.
31. Mortazavi A., Williams B.A., McCue K., et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 2008, 5(7):621-628.
32. Seo Y.K., Zhu B., Jeon T.I., et al. Regulation of steroid 5-alpha reductase type 2 (Srd5a2) by sterol regulatory element binding proteins and statin. Exp. Cell Res. 2009, 315(18):3133-3139.
33. Shi Y.G., Massagué J. Mechanisms of TGF-β signaling from cell membrane to the nucleus. Cell 2003, 113(6):685-700.
34. Steinheuer R., Drögemüller C., Hamann H., et al. Possible uses of genetic markers for improving fertility and health in swine production. Dtsch. Tierarztl. Wochenschr. 2003, 110(6):255-265.
35. Sun W., Chang H., Musa H.H., et al. Study on relationship between microsatellite polymorphism and producing ability on litter size trait of Hu sheep in China. Afr. J. Biotechnol. 2010, 9(50):8704-8711.
36. Tadjuidje E., Hegde R.S. The Eyes Absent proteins in development and disease. Cell. Mol. Life Sci. 2013, 70(11):1897-1913.
37. Toosi B.M., Seekallu S.V., Rawlings N.C. Effects of the rate and duration of physiological increases in serum FSH concentrations on emergence of follicular waves in cyclic ewes. Biol. Reprod. 2010, 83(4):648-655.
38. Xiao Y., Yang F.Q., Li S.P., et al. Furanodiene induces G2/M cell cycle arrest and apoptosis through MAPK signaling and mitochondria-caspase pathway in human hepatocellular carcinoma cells. Cancer Biol. Ther. 2007, 6(7):1044-1050.
39. Xu X.W., Qiu H.F., Du Z.Q., et al. Porcine CSRP3: polymorphism and association analyses with meat quality traits and comparative analyses with CSRP1 and CSRP2. Mol. Biol. Rep. 2010, 37(1):451-459.
40. Ye J., Fang L., Zheng H.K., et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34(Suppl. 2):W293-W297.
41. Zhang X.J., Hao L.L., Meng L.J., et al. Digital gene expression tag profiling analysis of the gene expression patterns regulating the early stage of mouse spermatogenesis. PLos One 2013, 8(3):e58680.
42. Zhou X., Su Z. EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species. BMC Genomics 2007, 8:246.