Research Topics
Genomes and Genes
| Joomyeong KimSummaryAffiliation: Louisiana State University Country: USA Publications
Research Grants
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Detail Information
Publications
Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1Jeong Do Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Nucleic Acids Res 35:3442-52. 2007..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...
In vivo YY1 knockdown effects on genomic imprintingJoomyeong Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Hum Mol Genet 17:391-401. 2008..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...- Imprinting control region (ICR) of the Peg3 domainJoomyeong Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Hum Mol Genet 21:2677-87. 2012..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... - Two evolutionarily conserved sequence elements for Peg3/Usp29 transcriptionJeong Do Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
BMC Mol Biol 9:108. 2008..This CpG island is a likely ICR (Imprinting Control Region) that controls transcription of the 500-kb genomic region of the Peg3 imprinted domain... - Multiple YY1 and CTCF binding sites in imprinting control regionsJoomyeong Kim
Department of Biological Sciences Louisiana State University, Baton Rouge, Louisiana, USA
Epigenetics 3:115-8. 2008..This idea remains to be tested in the near future, but it is one of the most likely explanations for all those unusual features that are associated with the functionally critical regions (ICRs) of genomic imprinting... - YY1's role in DNA methylation of Peg3 and XistJeong Do Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Nucleic Acids Res 37:5656-64. 2009..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... - Genomic organization and imprinting of the Peg3 domain in bovineJoomyeong Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Genomics 90:85-92. 2007..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... - Identification of clustered YY1 binding sites in imprinting control regionsJeong Do Kim
Department of Biological Sciences, Center for BioModular Multi Scale Systems, Louisiana State University, Baton Rouge, Louisiana 70803, USA
Genome Res 16:901-11. 2006..Overall, our identification of three additional clustered YY1 binding sites in imprinted domains suggests a significant role for YY1 in mammalian genomic imprinting... - YY1 as a controlling factor for the Peg3 and Gnas imprinted domainsJeong Do Kim
Department of Biological Sciences, Center for BioModular Multi Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
Genomics 89:262-9. 2007..YY1 knockdown also resulted in changes in the expression levels of Xist and Snrpn. These results support the idea that YY1 plays a major role, as a trans factor, in the control of these imprinted domains... - DNA methylation analysis of the mammalian PEG3 imprinted domainJennifer M Huang
Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, USA
Gene 442:18-25. 2009..Overall, this study shows that the PEG3 imprinted domain of humans, cows, and mice contains differing numbers of DMRs, but the PEG3-CpG island is the only DMR that is conserved among these three species... - Retrotransposons as a major source of epigenetic variations in the mammalian genomeMuhammad B Ekram
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
Epigenetics 7:370-82. 2012.... - YY1's longer DNA-binding motifsJeong Do Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Genomics 93:152-8. 2009..Also, this shortening suggests that the DNA recognition by YY1 is mediated through the concerted, but not modular, contribution by its four zinc finger units... - Rex1/Zfp42 as an epigenetic regulator for genomic imprintingJeong Do Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Hum Mol Genet 20:1353-62. 2011..Overall, the functional connection of Rex1 to genomic imprinting represents another case where newly made genes have co-evolved with lineage-specific phenomena... - Rapid evolution of a recently retroposed transcription factor YY2 in mammalian genomesChunqing Luo
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Genomics 87:348-55. 2006.... - Aebp2 as an epigenetic regulator for neural crest cellsHana Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
PLoS ONE 6:e25174. 2011..Taken together, these results suggest that Aebp2 may regulate the migration and development of the neural crest cells through the PRC2-mediated epigenetic mechanism... - MacroH2A1 knockdown effects on the Peg3 imprinted domainJung Ha Choo
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
BMC Genomics 8:479. 2007..MacroH2A1 is a histone variant that is closely associated with the repressed regions of chromosomes. A recent study revealed that this histone variant is highly enriched in the inactive alleles of Imprinting Control Regions (ICRs)... - Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sitesKeunsoo Kang
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Nucleic Acids Res 37:2003-13. 2009..Individual ChIP experiments confirmed the in vivo binding of the YY1 and CTCF proteins to most of these newly discovered binding sites, demonstrating the feasibility and usefulness of ECMFinder... - AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2Hana Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Nucleic Acids Res 37:2940-50. 2009..In fact, many of these loci are co-occupied by the two proteins, AEBP2 and SUZ12. This suggests that AEBP2 is most likely a targeting protein for the mammalian PRC2 complex... - DNA-binding motif and target genes of the imprinted transcription factor PEG3Michelle M Thiaville
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Gene 512:314-20. 2013..Overall, these results confirm PEG3 as a DNA-binding protein controlling specific target genes that are involved in distinct cellular functions... - An improved cloning strategy for chromatin-immunoprecipitation-derived DNA fragmentsJennifer M Huang
Department of Biological Sciences, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
Anal Biochem 356:145-7. 2006 - Allele-specific deposition of macroH2A1 in imprinting control regionsJung Ha Choo
Department of Biological Sciences, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
Hum Mol Genet 15:717-24. 2006..Overall, our results indicate that besides DNA methylation macroH2A1 is another epigenetic component in the chromatin of ICRs displaying differential association with two parental alleles... - YY1 is autoregulated through its own DNA-binding sitesJeong Do Kim
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
BMC Mol Biol 10:85. 2009..As a general transcription factor, the proper levels of YY1 protein need to be maintained for the normal function of cells and organisms. However, the mechanism for the YY1 homeostasis is currently unknown... - YY1's DNA-binding motifs in mammalian olfactory receptor genesChristopher D Faulk
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
BMC Genomics 10:576. 2009..The statistical significance of this observation was further analyzed... - Imprinting of an evolutionarily conserved antisense transcript gene APeg3Jung Ha Choo
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
Gene 409:28-33. 2008.... - Identification of an antisense transcript to ZIM2 in the primate lineageJennifer M Huang
Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
Gene 445:1-6. 2009..Overall, this study reports the presence of a previously unreported primate-specific antisense transcript in the PEG3 imprinted domain, suggesting that the formation of this transcript may coincide with the loss of the OLFR cluster... - Oncogenic potential of yin yang 1 mediated through control of imprinted genesMichelle M Thiaville
Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
Crit Rev Oncog 16:199-209. 2011.... - Position-based clustering of microarray expression dataChristopher Faulk
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
CSH Protoc 2009:pdb.prot5280. 2009..Overall, this method is useful in detecting regional regulatory changes. It should allow for greater use of the large quantity of previously overlooked microarray data... - Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2Joomyeong Kim
Genome Biology Division, Biology and Biotechnology Research Program, L 441, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94551, USA
Genomics 84:47-58. 2004..These observations are striking in light of the structural and functional conservation that typifies other imprinted domains and suggest that the PEG3/ZIM2 imprinted domain may have evolved in an unusual lineage-specific pattern... - A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressorsStuart Huntley
Genome Biology, Lawrence Livermore National Laboratory, CA 94550, USA
Genome Res 16:669-77. 2006..To facilitate further study, we have developed a Web-based public resource with access to gene models, sequences, and other data, including visualization tools to provide genomic context and interaction with other public data sets... - Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3Joomyeong Kim
Genomics Division, Biology and Biotechnology Research Program, L 441, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94551, USA
Hum Mol Genet 12:233-45. 2003..The current study is the first report demonstrating the involvement of YY1 in methylation-sensitive insulator activity and suggests a potential role of this highly conserved protein in mammalian genomic imprinting...
Research Grants
- Imprinting studies of a paternally expressed Usp29 geneJoomyeong Kim; Fiscal Year: 2010..The current proposal is aiming to characterize regulatory mechanisms of genomic imprinting. ..
- Imprinting studies of a paternally expressed Usp29 geneJoomyeong Kim; Fiscal Year: 2009..These studies will provide new clues to imprinting-related phenotypes linked to this domain in human and mouse. ..