Genetic diversity and population structure of the long-tailed goral, Naemorhedus caudatus, in South Korea.

Choi, Sung Kyoung,Chun, Suwon,An, Junghwa,Lee, Mu-Yeong,Kim, Hyeon Jeong,Min, Mi-Sook,Kwon, Soo-Wan,Choi, Tae Young,Lee, Hang,Kim, Kyung Seok Genetics Society of Japan 2015 Genes & genetic systems Vol.90 No.1

<P>The long-tailed goral, Naemorhedus caudatus, is an internationally endangered species. This species is distributed throughout Northeastern Asia including Northeastern China, the Russian Far East and the Korean peninsula. The population size of long-tailed gorals is currently decreasing in South Korea, and thus effective conservation of the animal is urgently needed. Although the evolution and phylogeny of this animal have been studied, population genetic studies are needed to design effective conservation and management strategies. To evaluate the present status of genetic diversity and genetic structure of long-tailed gorals in South Korea, we investigated genetic variability among 68 goral individuals from different regions, including 11 captive zoo animals, at 12 microsatellite loci. The level of genetic diversity was moderate in wild goral populations, but lower in the captive group. The goral population from the lower northeast region of South Korea was distinct from the upper northeast population, probably due to the natural climatic and geographic conditions. The genetic characteristics of the captive group were more similar to those of the upper northeast population than the lower northeast, confirming that the zoo animals originated in the Seorak Mountain range. Direct translocations between the upper and lower northeast populations are not currently recommended considering the natural population structure and the moderate levels of genetic diversity in the two populations. This study highlights the importance of genetic information in designing effective conservation strategies and translocations of endangered animals, including the Korean goral.</P>

Retroelements: molecular features and implications for disease.

Jung, Yi-Deun,Ahn, Kung,Kim, Yun-Ji,Bae, Jin-Han,Lee, Ja-Rang,Kim, Heui-Soo Genetics Society of Japan 2013 Genes & genetic systems Vol.88 No.1

<P>Eukaryotic genomes comprise numerous retroelements that have a major impact on the structure and regulation of gene function. Retroelements are regulated by epigenetic controls, and they generate multiple miRNAs that are involved in the induction and progression of genomic instability. Elucidation of the biological roles of retroelements deserves continuous investigation to better understand their evolutionary features and implications for disease.</P>

Identification of an evolutionarily conserved, functional noncoding element regulated by Six1 homeoprotein

Jeong, Yongsu,Oh, Sangtaek The Genetics Society of Japan 2010 Genes & genetic systems Vol.85 No.3

<P>Six1, which belongs to the <I>sine oculis</I> homeobox (<I>Six</I>) protein family, is an evolutionarily conserved transcription factor found in diverse organisms ranging from flatworms to humans. <I>Six1</I> is expressed in various tissues including the nervous system during ontogenesis and has been implicated in cell differentiation, morphogenesis, and organogenesis of the ganglia and sensory placodes. However, the molecular mechanisms by which Six1 influences these events at the transcriptional level remain largely unknown. In this study, we used ChIP-Display to discover genomic regions occupied <I>in vivo</I> by Six1 homeoprotein in the developing mouse embryo. To validate Six1 occupancy at each of Six1-bound regions, ChIP - Quantitative PCR was performed using locus-specific primers, and it showed robust enrichment of the Six1-bound sequences. To address their regulatory potential, each of the Six1-bound sequences was cloned into a reporter cassette containing beta-globin minimal promoter and <I>lacZ</I> gene and assayed for enhancer activity in transgenic mouse embryos. One of the novel sequences, which was designated Six1-bound Regulatory Element 1 (SRE1), was sufficient to activate <I>lacZ</I> reporter expression in the cranial and spinal ganglia. Comparative genomic analysis identified SRE1 sequences from a number of vertebrate phyla. Transgenic embryos carrying SRE1 sequences from human, chicken and frog showed reporter expression in a pattern similar to that of mouse SRE1, indicating their functional conservation. Through mutational analysis, we further showed that a conserved binding site matching the consensus for Six1/2/4/5 is required for the SRE1 regulatory activity. These data suggest that SRE1 is a functionally conserved transcriptional enhancer regulated by Six1.</P>

Endogenous retrovirus-related sequences provide an alternative transcript of <i>MCJ</i> genes in human tissues and cancer cells

Sin, Ho-Su,Huh, Jae-Won,Kim, Dae-Soo,Kim, Tae-Hong,Ha, Hong-Seok,Kim, Woo-Yeon,Park, Hee-Kyung,Kim, Cheol-Min,Kim, Heui-Soo The Genetics Society of Japan 2006 Genes & genetic systems Vol.81 No.5

<P>The <I>MCJ</I> gene is a member of the <I>DNAJ</I> family, and its transcriptional event is controlled by methylation of the CpG island. In our study, we found LTR33 and LTR7 elements provided an alternative transcript within the <I>MCJ</I> gene. To detect different expression patterns between the originally reported <I>MCJ</I> transcript and the LTR-related transcript, we performed a RT-PCR approach using various human tissues and cancer cells. The original <I>MCJ</I> transcript was detected in human tissues and cancer cells, whereas the LTR-related transcript was only revealed in some cancer cells (HCT106, MCF-3, TE-1, Hela, and CCHM). We also performed a PCR analysis to compare the insertion lineage of the LTR elements with the genomic DNAs of primates, indicating that those LTR33 and LTR7 elements of HERV-H have been integrated into the primate genome at different times. Taken together, we suggest that HERV-related elements trigger transcriptome diversification during primate evolution.</P>

Evolutionary characterization of a highly repetitive sequence identified from the false killer whale (<i>Pseudorca crassidens</i>)

Kim, Dae-Won,Kang, Aram,Choi, Sang-Haeng,Kim, Zang Geun,Kim, Woo-Jin,Kim, Hyung-Cheol,Park, Hong-Seog The Genetics Society of Japan 2009 Genes & genetic systems Vol.84 No.2

<P>We report here that a novel 1,869 bp repetitive sequence identified from the false killer whale (<I>Pseudorca crassidens</I>) could be a new molecular phylogenetic marker in cetaceans. Results of PCR amplification and southern blot hybridization using 16 species’ genomic DNAs from five different families revealed that the repetitive sequence is highly conserved within all Delphinidae species. Notably, specific primers designed for this repetitive sequence effectively amplified the targeted repetitive units, which were critically dependent upon the genetic phylogenies in the members of the Delphinidae cetaceans. Therefore, the novel sequences can be used as a useful phylogenetic marker for understanding the molecular evolutional studies in members of the Delphinidae family of cetaceans.</P>

Four different ways of alternative transcripts generation mechanism in <i>ADRA1A</i> gene

Huh, Jae-Won,Kim, Young-Hyun,Lee, Sang-Rae,Kim, Dae-Soo,Park, Sang-Je,Kim, Hyoungwoo,Kim, Ji-Su,Song, Bong-Seok,Kim, Heui-Soo,Chang, Kyu-Tae The Genetics Society of Japan 2010 Genes & genetic systems Vol.85 No.1

<P>The <I>ADRA1A</I> (Alpha-1-adrenergic receptor) gene is one of the members of G protein-coupled receptor superfamily. Alternative splicing of this gene was known to generate four transcript variants which code four isoforms with various C-terminal regions. In this study, we conducted expression analysis and evolutionary characterization of alternative transcripts of the <I>ADRA1A</I> gene. In total, 10 alternative transcripts were identified using experimental approaches and <I>in silico</I> analysis. Among them, 6 alternative transcripts (T1, T2, T3, T4, T4-1, and T8) were validated by RT-PCR approaches and sequencing procedures. From the alternative splicing analysis, it could be assumed that there were three different alternative transcripts generation mechanisms and unknown mechanism. First one is the integration event of three different TEs (<I>AluSc</I>, L1MC5, and MIR3) as seen on the last exons of T3, T4, T4-1, T5, T6, and T7 transcripts. The second mechanism is a differential promoter usage on T8. The third one is a substitution event of the 3’ splicing site during the primate evolution on T3. The last one is an unknown mechanism which was identified in the T4-1 transcript. Therefore, alternative transcripts of human <I>ADRA1A</I> gene occurred by four different ways, such as integration of TEs, differential promoter usage, substitution of splicing sites, and unknown mechanism.</P>

Functional characterization of pectin methylesterase inhibitor (<i>PMEI</i>) in wheat

Hong, Min Jeong,Kim, Dae Yeon,Lee, Tong Geon,Jeon, Woong Bae,Seo, Yong Weon The Genetics Society of Japan 2010 Genes & genetic systems Vol.85 No.2

<P>Pectin, one of the main components of plant cell wall, is deesterified by the pectin methylesterase (PME). PME activity is regulated by inhibitor proteins known as the pectin methylesterase inhibitor (PMEI), which plays a key role in wounding, osmotic stress, senescence and seed development. However, the role of PMEI in many plant species still remains to be elucidated, especially in wheat. To facilitate the expression analysis of the <I>TaPMEI</I> gene, RT-PCR was performed using leaf, stem and root tissues that were treated with exogeneous application of phytohormones and abiotic stresses. High transcription was detected in salicylic acid (SA) and hydrogen peroxide treatments. To elucidate the subcellular localization of the TaPMEI protein, the <I>TaPMEI</I>:<I>GFP</I> fusion construct was transformed into onion epidermal cells by particle bombardment. The fluorescence signal was exclusively detected in the cell wall. Using an enzyme assay, we confirmed that PME was completely inhibited by TaPMEI. These results indicated that TaPMEI was involved in inhibition of pectin methylesterification and may play a role in the plant defense mechanism <I>via</I> cell wall fortification.</P>

Genome-wide SNP-based linkage analysis for ADNSHL families identifies novel susceptibility loci with positive evidence for linkage

Park, Mi-Hyun,Park, Hong-Joon,Kim, Kwang-Joong,Woo, Hae-Mi,Kim, Hyung-Jin,Lee, Jong-Young,Park, Hyun-Young,Koo, Soo Kyung The Genetics Society of Japan 2011 Genes & genetic systems Vol.86 No.2

<P>The linkage search for susceptibility loci using SNP markers in hereditary hearing loss has proven challenging due to genetic heterogeneity. We conducted a genome-wide linkage analysis using high-density SNP markers in two Korean families (families coded SD-J and SR-167) with autosomal dominant non-syndromic hearing loss (ADNSHL). Evidence was found of linkage at 8q24.13~q24.3 and 10p11.21~q22.2 (LOD 3.01) in the SD-J family. In the case of family SR-167, which had the most affected members, the parametric LOD score was low owing to the lack of power for linkage analysis. However, using non-parametric linkage analysis, it was possible to obtain significant evidence for linkage at 10q22.1~q23.31 (LOD 1.79; NPL 6.47, <I>P</I> < 0.00001). There is an overlapping region with a significant LOD score between the SD-J and SR-167 families, which encompasses 4 cM at 10q22.1~22.2. Interestingly, the characteristics of hearing loss in both families were similar, and the haplotype within overlapping region was shared in the affected individuals of the two families. We performed direct sequencing of the candidate genes that are thought to be causing the condition, but no disease-causing mutations were identified.</P>

Molecular Phylogenetic Analysis of the Human Endogenous Retrovirus E (HERV-E) Family in Human Tissues and Human Cancers

Yi, Joo-Mi,Kim, Heui-Soo The Genetics Society of Japan 2007 Genes & genetic systems Vol.82 No.1

<P>The human genome is estimated to contain up to 50 copies of full-length and truncated members of HERV-E family. They are thought to be involved in human gene transcription. Here we examine the expression pattern and phylogenetic relationships of the HERV-E in diverse human tissues and cancer cells using RT-PCR amplification and bioinformatic tools. The <I>env</I> gene was expressed in many human tissues (brain, prostate, testis, kidney, placenta, spleen, thymus and uterus) but not in heart, liver, lung and skeletal muscle, importantly, HERV-E expression was detected in all cancer cell lines examined (RT4, PFSK-1, BT-474, HCT-116, TE-1, UO-31, Jurkat, HepG2, A549, MCF7, OVCAR-3, MIA-PaCa-2, PC3, LOX-IMVI, AZ521, 2F7, U-937 and C-33A), suggesting that HERV-E family are expressed corresponding to the transcriptional program of human tissues and human cancer cells. Phylogenetic analysis of HERV-E <I>env</I> family from human tissues, cancer cells and our previous data identify two groups (I and II) through evolutionary divergence. Taken together, HERV-E family expression in human tissues and human cancer cells exhibited close relationships of the <I>env</I> gene sequences across human chromosomes. These active HERV-E elements deserve further investigation as potential pathogenic factors in human diseases such as cancers.</P>

Identification of gamma ray irradiation-induced mutations in membrane transport genes in a rice population by TILLING

Hwang, Jung Eun,Jang, Duk-Soo,Lee, Kyung Jun,Ahn, Joon-Woo,Kim, Sang Hoon,Kang, Si-Yong,Kim, Dong Sub,Kim, Jin-Baek The Genetics Society of Japan 2016 Genes & genetic systems Vol.91 No.5