Genomes and Genes
Affiliation: Louisiana State University
- Kim J, Faulk C, Kim J. Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1. Nucleic Acids Res. 2007;35:3442-52 pubmed..Overall, the conservation of YY2 and REX1 in all placental mammals predicts that each duplicate has co-evolved with some unique features of eutherian mammals. ..
- Kim J, Kim J. In vivo YY1 knockdown effects on genomic imprinting. Hum Mol Genet. 2008;17:391-401 pubmed..In sum, these results demonstrate that YY1 indeed functions as a trans factor for transcriptional regulation and DNA methylation of these imprinted domains in vivo. ..
- Perera B, Kim J. Next-generation sequencing-based 5' rapid amplification of cDNA ends for alternative promoters. Anal Biochem. 2016;494:82-4 pubmed publisher..This protocol has successfully identified several alternative promoters for an imprinted gene, PEG3. Overall, this NGS-based 5'RACE protocol is a sensitive and reliable method for detecting low-abundant transcripts and promoters. ..
- Faulk C, Kim J. YY1's DNA-binding motifs in mammalian olfactory receptor genes. BMC Genomics. 2009;10:576 pubmed publisher..YY1, or YY1-related transcription factors, may help regulate olfactory receptor genes. Furthermore, the protein-coding regions of vertebrate genes can contain cis-regulatory elements for transcription factor binding as well as codons. ..
- Kim J, Hinz A, Bergmann A, Huang J, Ovcharenko I, Stubbs L, et al. Identification of clustered YY1 binding sites in imprinting control regions. Genome Res. 2006;16:901-11 pubmed..Overall, our identification of three additional clustered YY1 binding sites in imprinted domains suggests a significant role for YY1 in mammalian genomic imprinting. ..
- Kim J, Bergmann A, Choo J, Stubbs L. Genomic organization and imprinting of the Peg3 domain in bovine. Genomics. 2007;90:85-92 pubmed..The imprinting of Mim1 and Usp29 along with Peg3 is the most evolutionarily selected feature in this imprinted domain, suggesting significant function of these three genes, either as protein-coding or as untranslated transcript genes. ..
- Kim J, Yu S, Choo J, Kim J. Two evolutionarily conserved sequence elements for Peg3/Usp29 transcription. BMC Mol Biol. 2008;9:108 pubmed publisher..CSE2 (YY1 binding sites) functions as an activator for Peg3 transcription, while CSE1 acts as a repressor for the transcription of both Peg3 and Usp29. ..
- Kim J, Kang K, Kim J. YY1's role in DNA methylation of Peg3 and Xist. Nucleic Acids Res. 2009;37:5656-64 pubmed publisher..Overall, the current study suggests that YY1 likely plays a role in the de novo DNA methylation of the DMRs of Peg3 and Xist during oogenesis and also in the maintenance of unmethylation status of these DMRs during spermatogenesis. ..
- Kim J, Ekram M, Kim H, Faisal M, Frey W, Huang J, et al. Imprinting control region (ICR) of the Peg3 domain. Hum Mol Genet. 2012;21:2677-87 pubmed publisher..Taken together, deletion of the Peg3-DMR caused global changes in the imprinting and transcription of the Peg3 domain, confirming that the Peg3-DMR is an ICR for this imprinted domain. ..
- Frey W, Kim J. APeg3: regulation of Peg3 through an evolutionarily conserved ncRNA. Gene. 2014;540:251-7 pubmed publisher..The observed down-regulation by APeg3 is also somewhat orientation-independent. Overall, these results suggest that APeg3 has evolved as a ncRNA gene and controls the function of its sense gene Peg3 within specific neuronal cells. ..
- Kim H, Ekram M, Bakshi A, Kim J. AEBP2 as a transcriptional activator and its role in cell migration. Genomics. 2015;105:108-15 pubmed publisher..These results suggest that the two protein isoforms of AEBP2 may have opposite functions for the PcG target genes, and may play significant roles in cell migration during development. ..
- He H, Ye A, Perera B, Kim J. YY1's role in the Peg3 imprinted domain. Sci Rep. 2017;7:6427 pubmed publisher..Overall, the results indicated that YY1 is mainly involved in controlling the transcriptional levels, but not the DNA methylation, of the Peg3 domain. ..