title: Identification of the porcine XIST gene and its differential CpG methylation status in male and female pig cells.
abstract: XIST, a long non-coding RNA, plays an important role in triggering X chromosome inactivation in eutherians, and is used extensively for qualifying stem cells and cloned embryos. However, a porcine XIST has not yet been thoroughly identified despite its biological importance in a wide variety of research fields. Here, we present a full-length porcine XIST sequence assembled using known sequences (GenBank), RNA-Seq data (NCBI SRA), and PCR/sequencing. The proposed porcine XIST gene model encodes a 25,215-bp transcript consisting of 7 exons, including two conserved and two porcine-specific repeat regions. Transcription covering the entire XIST region was observed specifically in female cells, but not in male cells. We also identified eight transcription starting sites (TSSs) and evaluated CpG methylation patterns in the upstream (+2.0 kb) and downstream (-2.0 kb) regions. Sixty-seven CG di-nucleotides identified in the target region were considered to be candidate CpG sites, and were enriched in the following two regions: -284 to +53 bp (13 sites) and +285 to +1,727 bp (54 sites) from the selected TSS. Male 5` region of XIST (64.5 sites, 96.26%) had a higher level of CpG methylation than female DNA (33.4 sites, 49.85%). Taken together, our results revealed that the porcine XIST gene is expressed exclusively in female cells, which is influenced by the lower level of CpG methylation in the putative promoter region compared with male cells. The porcine XIST presented in this study represents a useful tool for related research areas such as porcine embryology and stem cell biology.
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Jae Yeon
authors.initials: JY
authors.lastname: Hwang
authors.forename: Eun Bae
authors.initials: EB
authors.lastname: Kim
authors.forename: Hakhyun
authors.initials: H
authors.lastname: Ka
authors.forename: Chang-Kyu
authors.initials: CK
authors.lastname: Lee
mesh_terms: D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D008297:Male; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D012737:Sex Factors; D013552:Swine; D024363:Transcription Initiation Site
chemical_list: D062085:RNA, Long Noncoding
references.citation: Genomics. 2007 Oct;90(4):453-63
references.pmid: 17728098
references.citation: Trends Genet. 2006 Jan;22(1):1-5
references.pmid: 16290135
references.citation: Hum Mol Genet. 2005 Apr 1;14(7):953-65
references.pmid: 15731119
references.citation: Curr Opin Cell Biol. 2009 Jun;21(3):359-66
references.pmid: 19477626
references.citation: Nature. 1996 Jan 11;379(6561):131-7
references.pmid: 8538762
references.citation: Biol Reprod. 1999 Mar;60(3):769-75
references.pmid: 10026129
references.citation: Nature. 1961 Apr 22;190:372-3
references.pmid: 13764598
references.citation: Nature. 2012 Nov 15;491(7424):393-8
references.pmid: 23151582
references.citation: Cell. 1993 Jan 29;72(2):171-82
references.pmid: 8425217
references.citation: Science. 2010 Oct 22;330(6003):496-9
references.pmid: 20847234
references.citation: Cell. 1992 Oct 30;71(3):527-42
references.pmid: 1423611
references.citation: Cell Stem Cell. 2009 Jun 5;4(6):487-92
references.pmid: 19497275
references.citation: Cell. 1998 Sep 18;94(6):809-17
references.pmid: 9753327
references.citation: Nature. 2011 Apr 21;472(7343):370-4
references.pmid: 21471966
references.citation: Hum Mol Genet. 1993 Jun;2(6):663-72
references.pmid: 8353487
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22196-201
references.pmid: 21135235
references.citation: PLoS One. 2008 Jun 25;3(6):e2521
references.pmid: 18575625
references.citation: Anim Genet. 2006 Dec;37(6):603-4
references.pmid: 17121615
references.citation: Am J Hum Genet. 1997 Jul;61(1):5-8
references.pmid: 9245976
references.citation: Nature. 2003 Dec 18;426(6968):857-62
references.pmid: 14661031
references.citation: Nat Rev Genet. 2011 Jun;12(6):429-42
references.pmid: 21587299
references.citation: Nucleic Acids Res. 1997 Jul 1;25(13):2661-71
references.pmid: 9185579
references.citation: Nature. 1971 Mar 26;230(5291):231-2
references.pmid: 4926712
references.citation: Nat Genet. 2002 Feb;30(2):167-74
references.pmid: 11780141
references.citation: Genomics. 1998 Dec 15;54(3):379-86
references.pmid: 9878240
references.citation: PLoS One. 2013;8(1):e55345
references.pmid: 23383161
references.citation: Bioinformatics. 2010 Feb 1;26(3):401-2
references.pmid: 19965881
references.citation: Nat Rev Genet. 2011 Jul 18;12(8):542-53
references.pmid: 21765457
references.citation: Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12515-9
references.pmid: 8618932
references.citation: PLoS One. 2013;8(1):e52481
references.pmid: 23326334
references.citation: Chromosome Res. 2009;17(5):659-69
references.pmid: 19802706
references.citation: Nat Methods. 2012 Mar 04;9(4):357-9
references.pmid: 22388286
references.citation: Dev Biol. 2005 Mar 15;279(2):525-40
references.pmid: 15733677
references.citation: Mol Cell. 2000 Apr;5(4):695-705
references.pmid: 10882105
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: Cell. 1994 Apr 8;77(1):41-51
references.pmid: 8156596
references.citation: Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20621-6
references.pmid: 22065773
references.citation: Cell. 1992 Oct 30;71(3):515-26
references.pmid: 1423610
references.citation: Science. 2008 Sep 19;321(5896):1693-5
references.pmid: 18802003
references.citation: Gene. 1997 Dec 12;203(2):159-68
references.pmid: 9426246