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Novel mechanism of conjoined gene formation in the human genome.
Kim, Ryong Nam,Kim, Aeri,Choi, Sang-Haeng,Kim, Dae-Soo,Nam, Seong-Hyeuk,Kim, Dae-Won,Kim, Dong-Wook,Kang, Aram,Kim, Min-Young,Park, Kun-Hyang,Yoon, Byoung-Ha,Lee, Kang Seon,Park, Hong-Seog Springer 2012 Functional & integrative genomics Vol.12 No.1
<P>Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.</P>
Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing
Kim, Ryong Nam,Kim, Dae-Soo,Choi, Sang-Haeng,Yoon, Byoung-Ha,Kang, Aram,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Jong-Joo,Ha, Ji-Hong,Toyoda, Atsushi,Fujiyama, Asao,Kim, Aeri,Kim, Min-Young,Park, Kun-Hyan Oxford University Press 2012 DNA research Vol.19 No.3
<P>Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the <I>TCOF1</I> locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.</P>
Major chimpanzee-specific structural changes in sperm development-associated genes
Kim, Ryong Nam,Kim, Dae-Won,Choi, Sang-Haeng,Chae, Sung-Hwa,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Aeri,Kang, Aram,Park, Kun-Hyang,Lee, Yong Seok,Hirai, Momoki,Suzuki, Yutaka,Sugano, Sumio,Hashimoto, Ka Springer-Verlag 2011 Functional & integrative genomics Vol.11 No.3
Woon Kim, Yea,Kim, Seoyeon,Geun Kim, Chul,Kim, AeRi Oxford University Press 2011 Nucleic acids research Vol.39 No.16
<P>GATA-1 and NF-E2 are erythroid specific activators that bind to the β-globin locus. To explore the roles of these activators in transcription of the human fetal stage specific γ-globin genes, we reduced GATA-1 and p45/NF-E2 using shRNA in erythroid K562 cells. GATA-1 or p45/NF-E2 knockdown inhibited the transcription of the γ-globin genes, hypersensitive site (HS) formation in the LCR and chromatin loop formation of the β-globin locus, but histone acetylation across the locus was decreased only in the case of GATA-1 knockdown. In p45/NF-E2 knockdown cells, GATA-1 binding was maintained at the LCR HSs and γ-globin promoter, but NF-E2 binding at the LCR HSs was reduced by GATA-1 knockdown regardless of the amount of p45/NF-E2 in K562 cells. These results indicate that histone acetylation is dependent on GATA-1 binding, but the binding of GATA-1 is not sufficient for the γ-globin transcription, HS formation and chromatin loop formation and NF-E2 is required. This idea is supported by the distinctive binding pattern of CBP and Brg1 in the β-globin locus. Furthermore GATA-1-dependent loop formation between HS5 and 3′HS1 suggests correlation between histone modifications and chromatin looping.</P>
Danzmann, Roy,Kim, Dae-Won,Choi, Sang-Haeng,Kim, Ryong Nam,Kim, Sun-Hong,Paik, Sang-Gi,Nam, Seong-Hyeuk,Kim, Dong-Wook,Kim, Aeri,Kang, Aram,Park, Hong-Seog Canadian Science Publishing 2010 Genome Vol.53 No.9
<P> The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMBR1 locus could shed new light on the evolution of limb development. We sequenced two false killer whale BAC clones, corresponding to 156 kb and 144 kb, respectively, harboring the tightly linked RNF32, LMBR1, and NOM1 genes. Our annotation of the false killer whale LMBR1 gene showed that it consists of 17 exons (1473 bp), in contrast to 18 exons (1596 bp) in human, and it displays 93.1% and 95.6% nucleotide and amino acid sequence similarity, respectively, compared with the human gene. In particular, we discovered that exon 10, deleted in the false killer whale LMBR1 gene, is present only in primates, and this fact strongly implies that exon 10 might be crucial in determining primate-specific limb development. ZRS and TFBS sequences have been well conserved across 11 species, suggesting that these regions could be involved in an important function of limb development and limb patterning. The neighboring gene RNF32 showed several lineage-conserved exons, such as exons 2 through 9 conserved in eutherian mammals, exons 3 through 9 conserved in mammals, and exons 5 through 9 conserved in vertebrates. The other neighboring gene, NOM1, had undergone a substitution (ATG→GTA) at the start codon, giving rise to a 36 bp shorter N-terminal sequence compared with the human sequence. Our comparative analysis of the false killer whale LMBR1 genomic locus provides important clues regarding the genetic regions that may play crucial roles in limb development and patterning. </P>
Expression of hMLH1, hMSH2 and hMSH6 in small intestinal carcinomas.
Gu, Mi Jin,Bae, Young Kyung,Kim, Aeri,Hong, Seung-Mo,Yu, Eunsil,Kim, Jihun,Jang, Kee-Taek,Chang, Hee-Kyung,Jung, Eun Sun,Bae, Han-Ik,Yoon, Ghil Suk,Kim, Joon Mee,Kim, Jung Yeon,Kim, Gwang Il,Oh, Young G. Thieme 2012 Hepato-gastroenterology Vol.59 No.119
<P>Although primary small intestinal carcinoma (SIC) is morphologically similar to colorectal carcinoma and shares many of the genetic changes of carcinogenesis, little is known about the role of defective mismatch repair (MMR) genes involved in the SIC. The aim of this study is to investigate the role of defective MMR genes and correlation between clinicopathological factors and loss of MMR protein in SIC.</P>