Biomedical subjects

Yong-Chul Jung

Publications and source records attributed to Yong-Chul Jung.

3 recordsLinked to original sources

PubMed2006

A large quantity of novel human antisense transcripts detected by LongSAGE.

MOTIVATION: Taking advantage of the high sensitivity and specificity of LongSAGE tag for transcript detection and genome mapping, we analyzed the 632 813 unique human LongSAGE tags deposited in public databases to identify novel human antisense transcripts. RESULTS: Our study identified 45 321 tags that match the antisense strand of 9804 known mRNA sequences, 6606 of which contain antisense ESTs and 3198 are mapped only by SAGE tags. Quantitative analysis showed that the detected antisense transcripts are present at levels lower than their counterpart sense transcripts. Experimental results confirmed the presence of antisense transcripts detected by the antisense tags. We also constructed an antisense tag database that can be used to identify the antisense SAGE tags originated from the antisense strand of known mRNA sequences included in the RefSeq database. CONCLUSIONS: Our study highlights the benefits of exploring SAGE data for comprehensive identification of human antisense transcripts and demonstrates the prevalence of antisense transcripts in the human genome.

Base Sequence↗

PubMed2005

Annotating nonspecific SAGE tags with microarray data.

SAGE (serial analysis of gene expression) detects transcripts by extracting short tags from the transcripts. Because of the limited length, many SAGE tags are shared by transcripts from different genes. Relying on sequence information in the general gene expression database has limited power to solve this problem due to the highly heterogeneous nature of the deposited sequences. Considering that the complexity of gene expression at a single tissue level should be much simpler than that in the general expression database, we reasoned that by restricting gene expression to tissue level, the accuracy of gene annotation for the nonspecific SAGE tags should be significantly improved. To test the idea, we developed a tissue-specific SAGE annotation database based on microarray data (). This database contains microarray expression information represented as UniGene clusters for 73 normal human tissues and 18 cancer tissues and cell lines. The nonspecific SAGE tag is first matched to the database by the same tissue type used by both SAGE and microarray analysis; then the multiple UniGene clusters assigned to the nonspecific SAGE tag are searched in the database under the matched tissue type. The UniGene cluster presented solely or at higher expression levels in the database is annotated to represent the specific gene for the nonspecific SAGE tags. The accuracy of gene annotation by this database was largely confirmed by experimental data. Our study shows that microarray data provide a useful source for annotating the nonspecific SAGE tags.

Cell Line↗

PubMed2004

Mutants of Agrobacterium tumefaciens virG gene that activate transcription of vir promoter in Escherichia coli.

The virA and virG two-component regulatory system is essential for transcriptional activation of virulence (vir) genes in Agrobacterium tumefaciens in the presence of inducer molecules. The VirA/VirG mediated vir gene transcription depends on a specific interaction between the C-terminal domain of the alpha subunit (RpoA) of A. tumefaciens RNA polymerase (RNAP) and N-terminal domain of the VirG. However, such interaction does not occur between RNAP of E. coli and the VirG, thus vir gene activation in E. coli requires the presence of rpoA gene from A. tumefaciens. In this report, we describe VirG mutants that are capable of activating the expression of vir genes in E. coli in the absence of A. tumefaciens RpoA. The selected 45 VirG mutants exhibited a common amino acid substitution at position 56 and additional one or more substitutions at different positions; thus the amino acid at position 56 is likely to play a key role in the interaction with the RpoA of E. coli. Furthermore, two virG mutants, with amino acid substitutions of G56V/V7I/I106N and G56V/I77V, respectively, are capable of activating vir genes in E. coli in response to inducer acetosyringone in a virA-dependent manner, demonstrating that the interaction site between VirG and RpoA is separable from that of VirG and VirA. Therefore, it is possible to establish inducer-mediated vir gene expression in heterologous hosts using virG mutants that are capable of interacting with the RpoA of the respective bacterial hosts while retaining the ability to interact with the sensor VirA.

Acetophenones↗