Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus

Journal of Biotechnology

Volumn 165, Issue 1, 2013, Pages 37-44

  Jakhesara, Subhash J ^a   Koringa, Prakash G ^a   Joshi, Chaitanya G ^a  

^a Chhattisgarh Kamdhenu Vishwa Vidyalaya   (India)

Author keywords

Gene ontology; GS FLX titanium; Horn cancer; Reactome pathways; RNA Seq

Indexed keywords

DIFFERENTIAL EXPRESSIONS; DIFFERENTIALLY EXPRESSED GENE; EPITHELIAL CELLS; GENE ONTOLOGY; HIGH THROUGHPUT; HORN CANCER; REACTOME PATHWAYS; RNA-SEQ;

DISEASES; GENES; LOSSES; RNA; TISSUE;

POLYMERASE CHAIN REACTION;

MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; BOS INDICUS; CATTLE DISEASE; EXON; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENE MAPPING; GENETIC ANALYSIS; HORN CANCER; MILK PRODUCTION; NEOPLASM; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE;

ANIMALS; CATTLE; EXONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HORNS; MOLECULAR SEQUENCE ANNOTATION; NEOPLASMS;

BOS; BOS INDICUS;

EID: 84875784285     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2013.02.015     Document Type: Article

References (44)

1. An J., Wan H., Zhou X., Hu D.N., Wang L., Hao L., Yan D., Shi F., Zhou Z., Wang J., Hu S., Yu J., Qu J. A comparative transcriptomic analysis of uveal melanoma and normal uveal melanocyte. PLoS One 2011, 6:e16516.
2. Bauersachs S., Wolf E. Transcriptome analyses of bovine, porcine and equine endometrium during the pre-implantation phase. Animal Reproduction Science 2012, 134:84-94.
3. Burggraaf H. Kanker aan de basis van de hoorns bij zebus. Tijdschr Diergeneeskd 1935, 62:1121-1136.
4. Chattopadhyay S.K., Jandrotia V.S., Ramkumar Iyer P.K.R. Horn cancer in sheep. Indian Veterinary Journal 1982, 59:319-320.
5. Coma S., Amin D.N., Shimizu A., Lasorella A., Iavarone A., Klagsbrun M. Id2 promotes tumor cell migration and invasion through transcriptional repression of semaphorin 3F. Cancer Research 2010, 70:3823-3832.
6. Crivelini M.M., Felipini R.C., Miyahara G.I., de Sousa S.C. Expression of odontogenic ameloblast-associated protein, amelotin, ameloblastin, and amelogenin in odontogenic tumors: immunohistochemical analysis and pathogenetic considerations. Journal of Oral Pathology and Medicine 2012, 41:272-280.
7. D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Methods in Molecular Biology 2011, 694:49-61.
8. Damodaran S., Sundararaj A., Ramakrishnan R. Horn cancer in bulls. Indian Veterinary Journal 1979, 56:248-249.
9. Damon M., Wyszynska-Koko J., Vincent A., Herault F., Lebret B. Comparison of muscle transcriptome between pigs with divergent meat quality phenotypes identifies genes related to muscle metabolism and structure. PLoS One 2012, 7:e33763.
10. Dreszer T.R., Karolchik D., Zweig A.S., Hinrichs A.S., Raney B.J., Kuhn R.M., Meyer L.R., Wong M., Sloan C.A., Rosenbloom K.R., Roe G., Rhead B., Pohl A., Malladi V.S., Li C.H., Learned K., Kirkup V., Hsu F., Harte R.A., Guruvadoo L., Goldman M., Giardine B.M., Fujita P.A., Diekhans M., Cline M.S., Clawson H., Barber G.P., Haussler D., James Kent W. The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Research 2012, 40:D918-D923.
11. Eswaran J., Cyanam D., Mudvari P., Reddy S.D., Pakala S.B., Nair S.S., Florea L., Fuqua S.A., Godbole S., Kumar R. Transcriptomic landscape of breast cancers through mRNA sequencing. Science Report 2012, 2:264.
12. Fu T.Y., Chang C.C., Lin C.T., Lai C.H., Peng S.Y., Ko Y.J., Tang P.C. Let-7b-mediated suppression of basigin expression and metastasis in mouse melanoma cells. Experimental Cell Research 2011, 317:445-451.
13. Gasse B., Silvent J., Sire J.Y. Evolutionary analysis suggests that AMTN is enamel-specific and a candidate for AI. Journal of dental research 2012, 91:1085-1089.
14. Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N., Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 2011, 29:644-652.
15. Gupta R.K., Sadana J.R., Kuchroo V.K., Kalra D.S. Horn cancer in an intact bull. Veterinary Record 1980, 107:312.
16. Guttman M., Garber M., Levin J.Z., Donaghey J., Robinson J., Adiconis X., Fan L., Koziol M.J., Gnirke A., Nusbaum C., Rinn J.L., Lander E.S., Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology 2010, 28:503-510.
17. Kent W.J. BLAT - the BLAST-like alignment tool. Genome Research 2002, 12:656-664.
18. Kulkarni H.V. Carcinoma of horn in bovines of old Baroda State. Indian Veterinary Journal 1953, 29:415-421.
19. Lassmann T., Hayashizaki Y., Daub C.O. SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 2011, 27:130-131.
20. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
21. Liu Z., Sun C., Zhang Y., Ji Z., Yang G. Phosphatidylinositol 3-kinase-C2beta inhibits cisplatin-mediated apoptosis via the Akt pathway in oesophageal squamous cell carcinoma. Journal of International Medical Research 2011, 39:1319-1332.
22. Maffucci T., Cooke F.T., Foster F.M., Traer C.J., Fry M.J., Falasca M. Class II phosphoinositide 3-kinase defines a novel signaling pathway in cell migration. Journal of Cell Biology 2005, 169:789-799.
23. Mamo S., Rizos D., Lonergan P. Transcriptomic changes in the bovine conceptus between the blastocyst stage and initiation of implantation. Animal Reproduction Science 2012, 134:56-63.
24. Mobasheri M.B., Jahanzad I., Mohagheghi M.A., Aarabi M., Farzan S., Modarressi M.H. Expression of two testis-specific genes, TSGA10 and SYCP3, in different cancers regarding to their pathological features. Cancer Detection and Prevention 2007, 31:296-302.
25. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods 2008, 5:621-628.
26. O'Prey J., Wilkinson S., Ryan K.M. Tumor antigen LRRC15 impedes adenoviral infection: implications for virus-based cancer therapy. Journal of Virology 2008, 82:5933-5939.
27. Oberley L.W., Buettner G.R. Role of superoxide dismutase in cancer: a review. Cancer Research 1979, 39:1141-1149.
28. Rezende A.M.L., Naves P.T. Horn core cancer in a zebu cow, imported to Brazil. Pesq. Agropec. Bras., Série Veterinária 1975, 10:41-44.
29. Roberts A., Pimentel H., Trapnell C., Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011, 27:2325-2329.
30. Sacomoto G.A., Kielbassa J., Chikhi R., Uricaru R., Antoniou P., Sagot M.F., Peterlongo P., Lacroix V. KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics 2012, 13(Suppl. 6):S5.
31. Sasaki Y., Sugisaka J., Maruyama R., Tamura M., Suzuki H., Idogawa M., Shinomura Y., Tokino T. CLCA2, a target of the p53 family, negatively regulates cancer cell migration and invasion. Cancer Biology and Therapy 2012, 13.
32. Schmidt V.A., Chiariello C.S., Capilla E., Miller F., Bahou W.F. Development of hepatocellular carcinoma in Iqgap2-deficient mice is IQGAP1 dependent. Molecular and Cellular Biology 2008, 28:1489-1502.
33. Schulz M.H., Zerbino D.R., Vingron M., Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012, 28:1086-1092.
34. Thorvaldsdottir H., Robinson J.T., Mesirov J.P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 2012, 10.1093/bib/bbs017.
35. 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. Nature Biotechnology 2010, 28:511-515.
36. Tripathi A.K., Koringa P.G., Jakhesara S.J., Ahir V.B., Ramani U.V., Bhatt V.D., Sajnani M.R., Patel D.A., Joshi A.J., Shanmuga S.J., Rank D.N., Joshi C.G. A preliminary sketch of horn cancer transcriptome in Indian zebu cattle. Gene 2012, 493:124-131.
37. Untergasser A., Cutcutache I., Koressaar T., Ye J., Faircloth B.C., Remm M., Rozen S.G. Primer3 - new capabilities and interfaces. Nucleic Acids Research 2012, 40:e115.
38. White C.D., Brown M.D., Sacks D.B. IQGAPs in cancer: a family of scaffold proteins underlying tumorigenesis. FEBS Letters 2009, 583:1817-1824.
39. Wu T.D., Watanabe C.K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875.
40. Xie Y., Yan J., Cutz J.C., Rybak A.P., He L., Wei F., Kapoor A., Schmidt V.A., Tao L., Tang D. IQGAP2, A candidate tumour suppressor of prostate tumorigenesis. Biochimica et Biophysica Acta 2012, 1822:875-884.
41. Ye J., Coulouris G., Zaretskaya I., Cutcutache I., Rozen S., Madden T.L. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 2012, 13:134.
42. Zeeberg B.R., Qin H., Narasimhan S., Sunshine M., Cao H., Kane D.W., Reimers M., Stephens R.M., Bryant D., Burt S.K., Elnekave E., Hari D.M., Wynn T.A., Cunningham-Rundles C., Stewart D.M., Nelson D., Weinstein J.N. High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 2005, 6:168.
43. Zhao G., Chen J., Deng Y., Gao F., Zhu J., Feng Z., Lv X., Zhao Z. Identification of NDRG1-regulated genes associated with invasive potential in cervical and ovarian cancer cells. Biochemical and Biophysical Research Communications 2011, 408:154-159.
44. Zubaidy A.J. Horn cancer in cattle in Iraq. Veterinary Pathology 1976, 13:435-454.