Yoonsoo Hahn

Mit1/Lb9 and Copg2, new members of mouse imprinted genes closely linked to Peg1/Mest.

Two mouse genes, Mit1/Lb9 and Copg2, linked to Peg1/Mest on mouse chromosome 6, were identified to be imprinted maternally and paternally, respectively. Mit1/Lb9 encoding untranslated transcripts resides within the intron 20 of Copg2. The gene is maternally imprinted in adult mouse brain, partially imprinted in other tissues. Copg2 consists of 24 exons within the >40 kb genomic region, being expressed ubiquitously in mouse tissues with a partial imprinting pattern in embryos, neonates, and adult brain in contrast to maternally imprinted human COPG2. In addition, we identified an antisense transcript of Copg2, Copg2AS, which overlaps 3′‐UTRs of Copg2 and Peg1/Mest. The Copg2AS transcript is maternally imprinted in embryos, neonates, and adult tissues.

Duplication of genes encoding non-clathrin coat protein γ-COP in vertebrate, insect and plant evolution.

Coatomer is a major component of COPI vesicles and consists of seven subunits. The γ‐COP subunit of the coatomer is believed to mediate the binding to the cytoplasmic dilysine motifs of membrane proteins. We characterized cDNAs for Copg genes encoding γ‐COP from mouse, zebrafish, Drosophila melanogaster and Bombyx mori. Two copies of Copg genes are present in vertebrates and in B. mori. Phylogenetic analysis revealed that two paralogous genes had been derived from a single ancestral gene by duplication independently in vertebrates and in B. mori. Mouse Copg1 showed ubiquitous expression with the highest level in testis. Zebrafish copg2 was biallelically expressed in hybrid larvae in contrast to its mammalian ortholog expressed in a parent‐of‐origin‐specific manner. A phylogenetic analysis with partial plant cDNA sequences suggested that copg gene was also duplicated in the grass family (Poaceae).

Structural analysis of phylogenetically conserved J domain protein gene

Novel cDNAs encoding evolutionarily conserved J Domain Proteins (JDPs) were investigated from Drosophila and mouse. Each of the full coding sequences potentially encodes a conserved J domain, but lacks additional characteristic structures present in DnaJ family proteins. The expression was restricted to head in Drosophila. However, ubiquitous expression was observed in mice with the highest level in kidney.

Genomic structure and expression of murine poly(A) binding protein II gene

The genomic structure and expression of the murine poly(A) binding protein II (mPABII) gene were analyzed by using genomic DNA and cDNA clones. The expression level of the mPABII gene varied among tissues. Besides two transcripts detected in all tissues, an additional transcript was detected in testis. The mPAB gene has pseudogenes or related genes in its genome.

Characterization of JDP genes, an evolutionarily conserved J domain-only protein family, from human and moths.

We characterized evolutionarily conserved J domain containing protein (JDP) genes from human, Bombyx mori, and Manduca sexta. Each of the JDP proteins contains a J domain at its N-terminus and a highly conserved C-terminal domain. Southern blot analysis revealed that the human JDP1 gene is present as a single copy in the human genome. Expression was higher in brain, heart, and testis than in kidney or stomach. Human JDP1 was mapped in silico to chromosome 10q21.1, which exhibits a conserved synteny with the central region of mouse chromosome 10. Drosophila jdp is located at 99F4-99F11 on the right arm of the third chromosome.

Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment

A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated tidal flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; tidal flat-naphthalene (TF-N), tidal flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (tidal flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits –– its notable PAH degradation capability in seasonally cold tidal flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.

SiNG-PCRseq: Accurate inter-sequence quantification achieved by spiking-in a neighbor genome for competitive PCR amplicon sequencing.

Despite the recent technological advances in DNA quantitation by sequencing, accurate delineation of the quantitative relationship among different DNA sequences is yet to be elaborated due to difficulties in correcting the sequence-specific quantitation biases. We here developed a novel DNA quantitation method via spiking-in a neighbor genome for competitive PCR amplicon sequencing (SiNG-PCRseq). This method utilizes genome-wide chemically equivalent but easily discriminable homologous sequences with a known copy arrangement in the neighbor genome. By comparing the amounts of selected human DNA sequences simultaneously to those of matched sequences in the orangutan genome, we could accurately draw the quantitative relationships for those sequences in the human genome (root-mean-square deviations <0.05). Technical replications of cDNA quantitation performed using different reagents at different time points also resulted in excellent correlations (R2 > 0.95). The cDNA quantitation using SiNG-PCRseq was highly concordant with the RNA-seq-derived version in inter-sample comparisons (R2 = 0.88), but relatively discordant in inter-sequence quantitation (R2 < 0.44), indicating considerable level of sequence-dependent quantitative biases in RNA-seq. Considering the measurement structure explicitly relating the amount of different sequences within a sample, SiNG-PCRseq will facilitate sharing and comparing the quantitation data generated under different spatio-temporal settings.

Increment of efficiency in the identification of noble genes by colony hybridization assay

For the rapid identification of noble genes in a specific tissue by computer analysis from the cDNA sequences determined by single‐pass cDNA sequencing, clone redundancy was one of the major obstacles. To facilitate the efficiency in identification of noble genes, it was necessary to reduce the number of clones to be sequenced by eliminating the redundant clones for a rapid analysis. In order to increase the probability of isolating noble sequences from the cDNA clones of human fetal liver tissue origin, colony hybridization assay was adopted and redundant clones were efficiently removed. Four cDNA clones highly redundant in the human fetal liver cDNA libraries including α‐globin, γ‐globin, serum albumin and H19 RNA sequences were selected as the probes. Two hundreds and sixty two cDNA clones were randomly selected and tested with the probes for hybridization properties. The identity of each cDNA clone giving positive or negative signals in the hybridization assay was determined by DNA homology search with the nucleic acid databases. Among the 76 clones giving positive signals, 57 clones (75%) were found to be identical to the probe sequences and could be eliminated by colony hybridization assay before neucleotide sequencing.

Loss of gene function and evolution of human phenotypes.

Humans have acquired many distinct evolutionary traits after the human-chimpanzee divergence. These phenotypes have resulted from genetic changes that occurred in the human genome and were retained by natural selection. Comparative primate genome analyses reveal that loss-of-function mutations are common in the human genome. Some of these gene inactivation events were revealed to be associated with the emergence of advantageous phenotypes and were therefore positively selected and fixed in modern humans (the “less-ismore” hypothesis). Representative cases of human gene inactivation and their functional implications are presented in this review. Functional studies of additional inactive genes will provide insight into the molecular mechanisms underlying acquisition of various human-specific traits. [BMB Reports 2015; 48(7): 373-379]

Normalization of human RNA-seq experiments using chimpanzee RNA as a spike-in standard.

Normalization of human RNA-seq experiments employing chimpanzee RNA as a spike-in standard is reported. Human and chimpanzee RNAs exhibit single nucleotide variations (SNVs) in average 210-bp intervals. Spike-in chimpanzee RNA would behave the same as the human counterparts during the whole NGS procedures owing to the high sequence similarity. After discrimination of species origins of the NGS reads based on SNVs, the chimpanzee reads were used to read-by-read normalize biases and variations of human reads. By this approach, as many as 10,119 transcripts were simultaneously normalized for the entire NGS procedures leading to accurate and reproducible quantification of differential gene expression. In addition, incomparable data sets from different in-process degradations or from different library preparation methods were made well comparable by the normalization. Based on these results, we expect that the normalization approaches using near neighbor genomes as internal standards could be employed as a standard protocol, which will improve both accuracy and comparability of NGS results across different sample batches, laboratories and NGS platforms.