Joomyeong Kim

Summary

Affiliation: Louisiana State University
Country: USA

Publications

  1. pmc Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1
    Jeong Do Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Nucleic Acids Res 35:3442-52. 2007
  2. ncbi request reprint In vivo YY1 knockdown effects on genomic imprinting
    Joomyeong Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Hum Mol Genet 17:391-401. 2008
  3. pmc AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2
    Hana Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Nucleic Acids Res 37:2940-50. 2009
  4. pmc Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites
    Keunsoo Kang
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Nucleic Acids Res 37:2003-13. 2009
  5. pmc Aebp2 as an epigenetic regulator for neural crest cells
    Hana Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
    PLoS ONE 6:e25174. 2011
  6. pmc Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain
    Michelle M Thiaville
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
    PLoS ONE 8:e75417. 2013
  7. pmc Recruitment and biological consequences of histone modification of H3K27me3 and H3K9me3
    Joomyeong Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    ILAR J 53:232-9. 2012
  8. pmc Imprinting control region (ICR) of the Peg3 domain
    Joomyeong Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Hum Mol Genet 21:2677-87. 2012
  9. pmc YY1's role in DNA methylation of Peg3 and Xist
    Jeong Do Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Nucleic Acids Res 37:5656-64. 2009
  10. pmc Two evolutionarily conserved sequence elements for Peg3/Usp29 transcription
    Jeong Do Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    BMC Mol Biol 9:108. 2008

Collaborators

Detail Information

Publications36

  1. pmc Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1
    Jeong 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...
  2. ncbi request reprint In vivo YY1 knockdown effects on genomic imprinting
    Joomyeong 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...
  3. pmc AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2
    Hana 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...
  4. pmc Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites
    Keunsoo 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...
  5. pmc Aebp2 as an epigenetic regulator for neural crest cells
    Hana 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...
  6. pmc Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain
    Michelle M Thiaville
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
    PLoS ONE 8:e75417. 2013
    ....
  7. pmc Recruitment and biological consequences of histone modification of H3K27me3 and H3K9me3
    Joomyeong Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    ILAR J 53:232-9. 2012
    ....
  8. pmc Imprinting control region (ICR) of the Peg3 domain
    Joomyeong 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...
  9. pmc YY1's role in DNA methylation of Peg3 and Xist
    Jeong 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...
  10. pmc Two evolutionarily conserved sequence elements for Peg3/Usp29 transcription
    Jeong 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...
  11. ncbi request reprint Multiple YY1 and CTCF binding sites in imprinting control regions
    Joomyeong 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...
  12. ncbi request reprint Genomic organization and imprinting of the Peg3 domain in bovine
    Joomyeong 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...
  13. pmc Identification of clustered YY1 binding sites in imprinting control regions
    Jeong 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...
  14. pmc YY1 as a controlling factor for the Peg3 and Gnas imprinted domains
    Jeong 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...
  15. pmc DNA methylation analysis of the mammalian PEG3 imprinted domain
    Jennifer 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...
  16. pmc Retrotransposons as a major source of epigenetic variations in the mammalian genome
    Muhammad B Ekram
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
    Epigenetics 7:370-82. 2012
    ....
  17. pmc YY1's longer DNA-binding motifs
    Jeong 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...
  18. ncbi request reprint Rapid evolution of a recently retroposed transcription factor YY2 in mammalian genomes
    Chunqing Luo
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Genomics 87:348-55. 2006
    ....
  19. pmc Rex1/Zfp42 as an epigenetic regulator for genomic imprinting
    Jeong 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...
  20. ncbi request reprint Allele-specific deposition of macroH2A1 in imprinting control regions
    Jung 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...
  21. pmc MacroH2A1 knockdown effects on the Peg3 imprinted domain
    Jung 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)...
  22. pmc DNA-binding motif and target genes of the imprinted transcription factor PEG3
    Michelle 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...
  23. ncbi request reprint An improved cloning strategy for chromatin-immunoprecipitation-derived DNA fragments
    Jennifer 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
  24. pmc YY1's DNA-binding motifs in mammalian olfactory receptor genes
    Christopher 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...
  25. pmc YY1 is autoregulated through its own DNA-binding sites
    Jeong 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...
  26. ncbi request reprint APeg3: regulation of Peg3 through an evolutionarily conserved ncRNA
    Wesley D Frey
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Gene 540:251-7. 2014
    ..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. ..
  27. pmc Identification of an antisense transcript to ZIM2 in the primate lineage
    Jennifer 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...
  28. pmc Imprinting of an evolutionarily conserved antisense transcript gene APeg3
    Jung Ha Choo
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
    Gene 409:28-33. 2008
    ....
  29. pmc Peg3 mutational effects on reproduction and placenta-specific gene families
    Joomyeong Kim
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
    PLoS ONE 8:e83359. 2013
    ....
  30. pmc Sexual differences of imprinted genes' expression levels
    Mohammad Faisal
    Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
    Gene 533:434-8. 2014
    ....
  31. pmc Oncogenic potential of yin yang 1 mediated through control of imprinted genes
    Michelle M Thiaville
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
    Crit Rev Oncog 16:199-209. 2011
    ....
  32. ncbi request reprint High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS): Genome-Wide DNA Methylation Analysis of IAP LTR Retrotransposon
    Muhammad B Ekram
    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
    PLoS ONE 9:e101683. 2014
    ..Overall, these data demonstrate the efficiency and robustness of the new technique, HT-TREBS, and also provide new insights regarding the genome-wide DNA methylation patterns of the IAP LTR repeat elements. ..
  33. ncbi request reprint Position-based clustering of microarray expression data
    Christopher 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...
  34. pmc A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors
    Stuart 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...
  35. ncbi request reprint Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2
    Joomyeong 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...
  36. ncbi request reprint Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3
    Joomyeong 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 Grants8

  1. Imprinting studies of a paternally expressed Usp29 gene
    Joomyeong Kim; Fiscal Year: 2010
    ..The current proposal is aiming to characterize regulatory mechanisms of genomic imprinting. ..
  2. Imprinting studies of a paternally expressed Usp29 gene
    Joomyeong Kim; Fiscal Year: 2004
    ..These studies will provide new clues to imprinting-related phenotypes linked to this domain in human and mouse. ..
  3. Imprinting studies of a paternally expressed Usp29 gene
    Joomyeong Kim; Fiscal Year: 2005
    ..These studies will provide new clues to imprinting-related phenotypes linked to this domain in human and mouse. ..
  4. Imprinting studies of a paternally expressed Usp29 gene
    Joomyeong Kim; Fiscal Year: 2004
    ..These studies will provide new clues to imprinting-related phenotypes linked to this domain in human and mouse. ..
  5. Imprinting studies of a paternally expressed Usp29 gene
    Joomyeong Kim; Fiscal Year: 2006
    ..These studies will provide new clues to imprinting-related phenotypes linked to this domain in human and mouse. ..
  6. Imprinting studies of a paternally expressed Usp29 gene
    Joomyeong Kim; Fiscal Year: 2007
    ..These studies will provide new clues to imprinting-related phenotypes linked to this domain in human and mouse. ..
  7. Imprinting studies of a paternally expressed Usp29 gene
    Joomyeong Kim; Fiscal Year: 2009
    ..These studies will provide new clues to imprinting-related phenotypes linked to this domain in human and mouse. ..