cDNA Cloning, Bioinformatic and Tissue-specific Expression Analysis of Porcine JARID1C Gene

Lu Yi; Zhenhua Hao; Tongtong Yang; Shaobing Wang; Baosong Xing; Yinxue Xu

doi:10.1016/S1673-8527(07)60124-6

Volume 34 Issue 12

Dec. 2007

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Article Navigation > Journal of Genetics and Genomics > 2007 > 34(12): 1088-1096

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cDNA Cloning, Bioinformatic and Tissue-specific Expression Analysis of Porcine JARID1C Gene

doi: 10.1016/S1673-8527(07)60124-6

College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China

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Corresponding author: E-mail address: xuyinxue@yahoo.com (Yinxue Xu)
Received Date: 2007-03-30
Rev Recd Date: 2007-06-15

Available Online: 2007-12-31

Publish Date: 2007-12-20

Abstract

Abstract

Jumonji, AT-rich interactive domain 1C (JARID1C) protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiation, and development. In humans, this gene plays a vital role in normal brain development and function. Using an in silico approach in combination with 5′ rapid amplification of cDNA ends (5′ RACE), the full-length cDNA of JARID1C (GenBank accession No. EF139241) from porcine ovary, which contains 5,908 bp nucleotides, with an open reading frame (ORF) of 4,548 bp, has been cloned. The putative porcine JARID1C protein, which is located in the nucleus, encodes 1,516 amino acids with a molecular weight of 170 kDa and a pI of 5.44. Bioinformatic prediction indicates that the protein contains several conserved domains: a JmjN domain, an ARID domain, a JmjC domain, a C5HC2 zinc finger domain, and a PHD zinc finger domain. Similarity comparisons for nucleic and amino acid sequences reveal that the porcine JARID1C protein shares a high identity with its dog, mouse, rat, and human counterparts. The phylogenetic tree of the JARID1 subfamily proteins has been constructed to reveal the evolutionary relationship of various species. Real-time PCR analysis shows that theJARID1C gene is expressed in various tissues, but at different levels. The expression levels of this gene are higher in the brain and gonad than in other tissues, suggesting that the JARID1C protein plays a role in porcine brain and gonad functions.
- pig,
- JARID1C gene,
- cDNA cloning,
- bioinformatic analysis,
- gene expression

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References(25)

References

[1]	Herrscher, RF, Kaplan, et al. The immunoglobulin heavy-chain matrix associating regions are bound by Bright: a B cell-specific transactivator that describes a new DNA-binding protein family Genes Dev, 9 (1999),pp. 3067-3082
[2]	Gregory, SL, Kortschak, et al. Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA binding proteins Mol Cell Biol, 16 (1996),pp. 792-799
[3]	Kim, S, Zhang, et al. Structure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition J Biol Chem, 279 (2004),pp. 16670-16676
[4]	Wilsker, D, Probst, et al. Nomenclature of the ARID family of DNA-binding proteins Genomics, 86 (2005),pp. 242-251
[5]	Wilsker, D, Patsialou, et al. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development Cell Growth Differ, 13 (2002),pp. 95-106
[6]	Jensen, LR, Amende, et al. Am J Hum Genet, 76 (2005),pp. 227-236
[7]	Iwase, S, Lan, et al. The X-Linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases Cell, 128 (2007),pp. 1077-1088
[8]	Agulnik, AI, Mitchell, et al. A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human Hum Mol Genet, 3 (1994),pp. 879-884
[9]	Sheardown, S, Norris, et al. Hum Mol Genet, 5 (1996),pp. 1355-1360
[10]	Xu, J, Burgoyne, et al. Sex differences in sex chromosomes gene expression in mouse brain Hum Mol Genet, 11 (2002),pp. 1409-1419
[11]	Bulimo, WD, Miskin, et al. An ARID family protein binds to the African swine fever virus encoded ubiquitin conjugating enzyme UBCv1 FEBS Lett, 471 (2000),pp. 17-22
[12]	Sambrook, J, Russell, et al.
[13]	Gasteiger, E, Gattiker, et al. ExPasy: the proteomics server for in-depth protein knowledge and analysis Nucleic Acids Res, 31 (2003),pp. 3784-3788
[14]	Bendtsen, JD, Nielsen, et al. Improved prediction of signal peptides: SignalP 3.0 J Mol Biol, 340 (2004),pp. 783-795
[15]	Gasteiger, E, Hoogland, et al.
[16]	Moller, S, Croning, et al. Evaluation of methods for the prediction of membrane spanning regions Bioinformatics, 17 (2001),pp. 646-653
[17]	Nakai, K, Horton, et al. PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization Trends Biochem Sci, 24 (1999),pp. 34-35
[18]	Marchler-Bauer, A, Bryant, et al. CD-Search: protein domain annotations on the fly Nucleic Acids Res, 32 (2004),pp. 327-331
[19]	Tan, XJ, Huang, et al. Acta Genet Sin, 33 (2006),pp. 294-303
[20]	Zhang, HL, Deng, et al. Acta Genet Sin, 30 (2003),pp. 317-320
[21]	Yin, Chen, Zhao, et al. Am J Respir Crit Care Med, 164 (2001),pp. 1059-1066
[22]	Wang, JF, Lin, et al. Acta Genet Sin, 29 (2002),pp. 1012-1016
[23]	Kortschak, RD, Tucker, et al. ARID proteins come in from the desert Trends Biochem Sci, 25 (2000),pp. 294-299
[24]	Clissold, PM, Ponting, et al. JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta Trends Biochem Sci, 26 (2001),pp. 7-9
[25]	Pascual, J, Martinez-Yamout, et al. Structure of the PHD zinc finger from human williams-beuren syndrome transcription factor J Mol Biol, 304 (2000),pp. 723-729