UCSC Genomic Database Research Articles

Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures.

Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC), which serve as slow-wave electrical pacemakers for gastrointestinal (GI) smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome) based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies.

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome

BackgroundTransposable elements (TEs) comprise ~10% of the chicken (Gallus gallus) genome. The content of TEs is much lower than that of mammalian genomes, where TEs comprise around half of the genome. Endogenous retroviruses are responsible for ~1.3% of the chicken genome. Among them is Gallus gallus endogenous retrovirus 10 (GGERV10), one of the youngest endogenous retrovirus families, which emerged in the chicken genome around 3 million years ago.ResultsWe identified a total of 593 GGERV10 elements in the chicken reference genome using UCSC genome database and RepeatMasker. While most of the elements were truncated, 49 GGERV10 elements were full-length retaining 5′ and 3′ LTRs. We examined in detail their structural features, chromosomal distribution, genomic environment, and phylogenetic relationships. We compared LTR sequence among five different GGERV10 subfamilies and found sequence variations among the LTRs. Using a traditional PCR assay, we examined a polymorphism rate of the 49 full-length GGERV10 elements in three different chicken populations of the Korean domestic chicken, Leghorn, and Araucana. The result found a breed-specific GGERV10B insertion locus in the Korean domestic chicken, which could be used as a Korean domestic chicken-specific marker.ConclusionsGGERV10 family is the youngest ERV family and thus might have contributed to recent genomic variations in different chicken populations. The result of this study showed that one of GGERV10 elements integrated into the chicken genome after the divergence of Korean domestic chicken from other closely related chicken populations, suggesting that GGERV10 could be served as a molecular marker for chicken breed identification.

Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome.

Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA) transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72); Retroposed Pseudogenes V5 (processed only), and Yale Pseudo60 (processed and unprocessed, Ensembl 60); two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation.

Analysis of L1-chimeric transcripts derived from bidirectional promoter of human-specific L1

LINE-1s (L1s) have contributed to gene structure variation and they can affect the expression of nearby genes in the human genome. Here, we collected 35 human-specific L1s that may play a role as alternative promoters. In addition, we identified 54 L1-chimeric transcripts generated from these L1s using bioinformatics’ tools and carried out reverse transcription-PCR to analyze their expressional pattern in 20 human normal tissues and 9 human cancer tissues. Consequently, 30 L1-chimeric transcripts were experimentally confirmed. Most L1-chimeric transcripts were broadly expressed. Interestingly, we found that EST CD709363 derived from C14orf37 gene was expressed in trachea only among normal tissues, but it was expressed in several cancer tissues including brain, lung, skin, and esophagus. We also newly identified three alternative transcripts, which were not in the UCSC genome database. One alternative transcript was derived from RABGAP1L gene and the other two transcripts were from CAMK4 gene. In addition, we analyzed putative transcription binding sites within the four L1s located in the promoter region. These had several transcription factor binding sites related to promoters. Our results show that human-specific L1s could contribute to human transcriptome diversity and transcriptional gene expression in different types of human tissues.

Applying the Complexity of Networks to Mine Disease Risk Genes

Rheumatoid arthritis (RA) is a complex disease determined by multilocus genetic factors. Although genome-wide association studies have been proven to be a powerful approach to identify risk loci, the molecular regulatory mechanisms of RA are still not clearly understood. It is therefore important to consider the interplay between genetic factors and biological networks in elucidating the mechanisms of RA pathogenesis. Here, we applied the complexity of Protein-Protein Interaction (PPI) network to identify disease risk genes. First, we assigned risk SNPs to genes from UCSC genome database and mapped these genes to PPI networks. With the aid in PPI networks, gene modules were extracted and risk feature genes were identified. As a result, risk feature genes, such as CD40, PKCA, were identified as significant risk gene sets associated with RA.

An in silicoanalysis of dynamic changes in microRNA expression profiles in stepwise development of nasopharyngeal carcinoma

BackgroundMicroRNAs (miRNAs) are small non-coding RNAs that participate in the spatiotemporal regulation of messenger RNA (mRNA) and protein synthesis. Recent studies have shown that some miRNAs are involved in the progression of nasopharyngeal carcinoma (NPC). However, the aberrant miRNAs implicated in different clinical stages of NPC remain unknown and their functions have not been systematically studied.MethodsIn this study, miRNA microarray assay was performed on biopsies from different clinical stages of NPC. TargetScan was used to predict the target genes of the miRNAs. The target gene list was narrowed down by searching the data from the UniGene database to identify the nasopharyngeal-specific genes. The data reduction strategy was used to overlay with nasopharyngeal-specifically expressed miRNA target genes and complementary DNA (cDNA) expression data. The selected target genes were analyzed in the Gene Ontology (GO) biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway. The microRNA-Gene-Network was build based on the interactions of miRNAs and target genes. miRNA promoters were analyzed for the transcription factor (TF) binding sites. UCSC Genome database was used to construct the TF-miRNAs interaction networks.ResultsForty-eight miRNAs with significant change were obtained by Multi-Class Dif. The most enriched GO terms in the predicted target genes of miRNA were cell proliferation, cell migration and cell matrix adhesion. KEGG analysis showed that target genes were significantly involved in adherens junction, cell adhesion molecules, p53 signalling pathway et al. Comprehensive analysis of the coordinate expression of miRNAs and mRNAs reveals that miR-29a/c, miR-34b, miR-34c-3p, miR-34c-5p, miR-429, miR-203, miR-222, miR-1/206, miR-141, miR-18a/b, miR-544, miR-205 and miR-149 may play important roles on the development of NPC. We proposed an integrative strategy for identifying the miRNA-mRNA regulatory modules and TF-miRNA regulatory networks. TF including ETS2, MYB, Sp1, KLF6, NFE2, PCBP1 and TMEM54 exert regulatory functions on the miRNA expression.ConclusionsThis study provides perspective on the microRNA expression during the development of NPC. It revealed the global trends in miRNA interactome in NPC. It concluded that miRNAs might play important regulatory roles through the target genes and transcription factors in the stepwise development of NPC.

Genetic variants of 6q25 and breast cancer susceptibility: a two-stage fine mapping study in a Chinese population

A recent genome-wide association study identified a novel single nucleotide polymorphism (SNP), rs2046210, in the 6q25 region as a breast cancer susceptibility locus in Chinese and subsequently replicated in a multicenter study. Further fine-mapping of this region may help identify the potential causative SNPs of breast cancer. We employed a block-based fine mapping analysis to investigate the tagging SNPs in a 41 kb block with the marker-SNP rs2046210 in the 6q25 region, and also extended our study by including two potentially functional SNPs (rs2234693 and rs1801132) within the ESR1 gene by a two-stage case-control study with 1,792 breast cancer cases and 1,867 controls (878 cases and 900 controls in the testing set and 914 cases and 967 controls in the validation set). Significant associations with breast cancer risk were observed for rs1038304, rs6929137, rs2046210, and rs10484919 in the 41 kb block of the 6q25 region in the testing set after controlling multiple testing. Together with the validation set samples, these four SNPs were all significantly associated with increased risk of breast cancer (additive OR from 1.25 to 1.34, additive P from 4.84 × 10(-6) to 7.17 × 10(-9)). After conditional regression and linkage disequilibrium analyses, rs6929137 and rs10484919 tend to be susceptible markers of breast cancer in this region and both of them were located at sites of histone modification according to the UCSC (http://genome.ucsc.edu/) genome database. Our results support that the 6q25 region is an important susceptibility region for breast cancer in Chinese women, and rs6929137 and rs10484919 are causative or marker SNPs for this region.

Genome Wide DNA Methylation Profiling In Patients with Multiple Myeloma.

AbstractAbstract 3622 Introduction:Epigenetic factors such as DNA methylation have been shown to play a crucial role in the pathogenesis and progression of multiple myeloma (MM), yet studies of DNA methylation in MM are still limited. Therefore, in order to better understand the role of DNA methylation and identify specific genes that may be affected by differential methylation in MM patients, we conducted genome-wide DNA methylation profiling in cd138+ plasma cells purified from bone marrow of the patients with MM and normal donors. Methods:Genomic DNA of CD138+ Plasma cell selected from both MM patients and normal primary bone marrow was extracted using QIAGEN genome isolation kit. Following extraction, methylated DNA was isolated by Chip and hybridized to Affymetrix Human 2.0 tiling arrays. Chip assay and array hybridization was performed by Genepathway Inc. CEL files were processed and normalized using the MAT program, and methylation peaks were called from the resulting MAT scores using a custom segmentation method. Peak annotation and characterization of different genomic regions was done with custom tools and using genome annotation files from the UCSC genome database. All peaks were visualized by IGB online software. Medip-PCR was done in human MM cell lines to validate the methylation status. Methylated gene expression was determined by both Semi-quantitative PCR and real-time PCR. 5′aza was used for demethylation in human MM cell lines. Methylated gene expression with or without 5′aza treatment was determined by both Semi-quantitative PCR and real-time PCR. Results:Genomic DNA from CD138+ plasma cells from bone marrow of MM patients showed a significant increase in methylation levels compared to normal controls. We demonstrated that the hypermethylated sites were distributed across the genome in the following proportions: 3.2% in the promoter region; 45.6% in the intragenic region; 5.4 % in the 3′ end region; and 46.8 % in the intergenic region. Furthermore, around 9 % promoter CpG islands (CGIs); 11% intragenic CGIs; 15 % CGIs in 3′end region; and 14.3 % intergenic CGIs of patients genomic DNA were methylated. Moreover 2.1% promoter CGIs; 2.3 % intragenic CGIs; 2.5% CGIs in 3′end region; and 4.7% intergenic CGIs were methylated for the normal control. Medip-PCR showed that the identified methylation pattern in MM patients showed similar results in MM cell lines. Expectedly, we also observed that suppressor of cytokine signaling 1 (SOCS1) was hypermethylated at the promoter region (MAT score=19.986) as has been reported in human cell lines. Importantly, another member of SOCS family SOCS3 showed much stronger signal in the promoter region with CpG island (MAT score=31.707) in MM patients compared to normal control. Notably, the expression of two members of TNFR superfamily TNFRSF18 and TNFRSF4 which play an important role in development and programmed cell death of lymphocyte significantly have increased 283 and 141-fold after treatment with 5′aza in MM cell lines. Conclusion:These findings enhance our understanding of the role of DNA methylation in MM, as one of the epigenetic changes that may contribute to the pathogenesis of this disease. The identification and functional characterization of novel key molecules affected by DNA methylation will provide deeper insight into the molecular basis of MM disease. Disclosures:Leleu:Celgene: Consultancy, Research Funding; Janssen Cilag: Consultancy, Research Funding; Leo Pharma: Consultancy; Amgen: Consultancy; Chugai: Research Funding; Roche: Consultancy, Research Funding; Novartis: Consultancy, Research Funding. Anderson:Millennium Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau.

Abstract 4048: Increased expression of PACS-1 in cervical cancer is associated with loss of microRNA449a

Abstract Cervical cancer is one of the leading causes of female death world wide with approximately 50,000 deaths per year. We identified a 300 kb deletion of chromosome 11q13 in cervical cancer and mapped eleven genes to this region. Of these, phosphofurin acidic cluster sorting −1 (PACS-1) gene encodes a multi-functional sorting protein involved in secretory pathway membrane traffic. Expression studies showed the presence of an abnormal PACS-1 transcript in tumorigenic cell lines. Protein expression studies in paired normal and cervical tumors showed over-expression of PACS-1 protein in tumor specimens. RT-PCR indicated that protein over-expression was related to over-expression at the RNA level. These findings together with the absence of detectable mutations in PACS-1 exons in HeLa or SiHa cervical carcinoma cell lines raised the possibility that dysregulation of a microRNA (miRNA) may alter PACS-1 expression in cervical cancer. Consistent with this possibility, a UCSC genome database search showed the presence of binding sites for miRNA449a in the 3′ UTR (untranslated region) of the PACS-1 RNA transcript. Co-transfection of PACS-1 3′UTR luciferase reporter with miRNA449a resulted in reduced expression of luciferase. Expression of miR449a in HeLa and SiHa cells led to reduced expression of PACS-1 and increased expression of p53 and p21 proteins. FACS analysis of HeLa cells transfected with miR449a showed a reduction in S phase indicating the growth suppressive effect of miR449a. These results indicate that miR449a regulates PACS-1 expression and loss of miR449a expression leads to over-expression of PACS-1. This in turn seems to result in the destabilization of p53 in cervical cancer. Our findings suggest PACS-1 plays a role in cervical cancer development and its expression is regulated post-transcriptionally by miRNA449a. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4048.

Parameters for accurate genome alignment

BackgroundGenome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters to use. Surprisingly, there has been no large-scale assessment of these choices using real genomic data. Moreover, rigorous procedures to control the rate of spurious alignment have not been employed.ResultsWe have assessed 495 combinations of score parameters for alignment of animal, plant, and fungal genomes. As our gold-standard of accuracy, we used genome alignments implied by multiple alignments of proteins and of structural RNAs. We found the HOXD scoring schemes underlying alignments in the UCSC genome database to be far from optimal, and suggest better parameters. Higher values of the X-drop parameter are not always better. E-values accurately indicate the rate of spurious alignment, but only if tandem repeats are masked in a non-standard way. Finally, we show that γ-centroid (probabilistic) alignment can find highly reliable subsets of aligned bases.ConclusionsThese results enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases. This study was made possible by our new software, LAST, which can align vertebrate genomes in a few hours http://last.cbrc.jp/.

Identification and characterization of human LYPD6, a new member of the Ly-6 superfamily

The Ly-6 protein superfamily is usually identified as a group of proteins with a LU protein domain. LU domain is about 80 amino acids long and characterized by a conserved pattern of 10 cysteine residues. Here we report the cloning and characterization of a novel human LU domain containing gene, LYPD6, isolated from human testis cDNA library, and mapped to 2q23.1-23.2 by searching the UCSC genomic database. The LYPD6 cDNA sequence of 3,501 base pairs contains an open reading frame encoding 171 amino acids. Subcellular localization of LYPD6 demonstrated that the protein was localized in the cytoplasm when overexpressed in COS-7 cells. RT-PCR analysis showed that LYPD6 was widely expressed in human tissues and the expression levels in brain and heart were relatively high. Furthermore, the subsequent analysis based on reporter gene assays suggested that overexpression of LYPD6 in HEK 293T cells was able to suppress the transcriptional activities of AP1.

Isolation and characterization of novel human short-chain dehydrogenase/reductase SCDR10B which is highly expressed in the brain and acts as hydroxysteroid dehydrogenase.

Hydroxysteroid dehydrogenase belongs to the subfamily of short-chain dehydrogenases/reductases (SDR), and 11-beta-hydroxysteroid dehydrogenase catalyzes the interconversion of inactive glucocorticoids (cortisone in human, dehydrocorticosterone in rodents) and active glucocorticoids (cortisol in human, corticosterone in rodents). We report here the cloning and characterization of a novel human SDR gene SCDR10B which encodes a protein with similarity to 11beta-hydroxysteroid dehydrogenase 1. SCDR10B was isolated from a human brain cDNA library, and was mapped to chromosome 19p13.3 by browsing the UCSC genomic database. It contains an ORF with a length of 858 bp, encoding a protein with a transmembrane helix and SDR domain. Its molecular mass and isoelectric point are predicted to be 30.8 kDa and 10.3 kDa, respectively. SCDR10B protein is highly conserved in mammals and fish. Phylogenetic tree analysis indicated that SCDR10B stands for a new subgroup in the 11beta-hydroxysteroid dehydrogenase family. Northern blot analysis showed that SCDR10B was highly expressed in brain, and a strong expression signal was detected in hippocampal neurons by immunohistochemical analysis. RT-PCR and immunohistochemical analysis showed that SCDR10B was up-regulated in lung-cancer cell lines and human lung cancer. SCDR10B can catalyze the dehydrogenation of cortisol in the presence of NADP(+), and therefore it is a hydroxysteroid dehydrogenase.

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks

Pairwise sequence alignment is a ubiquitous tool for inferring the evolution and function of DNA, RNA and protein sequences. It is therefore essential to identify alignments arising by chance alone, i.e. spurious alignments. On one hand, if an entire alignment is spurious, statistical techniques for identifying and eliminating it are well known. On the other hand, if only a part of the alignment is spurious, elimination is much more problematic. In practice, even the sizes and frequencies of spurious subalignments remain unknown. This article shows that some common scoring schemes tend to overextend alignments and generate spurious alignment flanks up to hundreds of base pairs/amino acids in length. In the UCSC genome database, e.g. spurious flanks probably comprise >18% of the human–fugu genome alignment. To evaluate the possibility that chance alone generated a particular flank on a particular pairwise alignment, we provide a simple ‘overalignment’ P-value. The overalignment P-value can identify spurious alignment flanks, thereby eliminating potentially misleading inferences about evolution and function. Moreover, by explicitly demonstrating the tradeoff between over- and under-alignment, our methods guide the rational choice of scoring schemes for various alignment tasks.

Cloning and characterization of a human LYPD7, a new member of the Ly-6 superfamily

Members of the Ly-6 (Lymphocyte Antigen 6) protein family share one or several repeat units of the LU domain that is defined by a distinct disulfide bonding pattern between 8 or 10 cysteine residues. Here we report the cloning and characterization of a novel human LU domain-containing gene, LYPD7 (LY6/PLAUR domain containing 7), isolated from human testis cDNA library, and mapped to 2q22.3-23.3 by searching the UCSC genomic database. The LYPD7 cDNA sequence consists of 1,600 nucleotides and contains an open reading frame of 624 bp, encoding a putative protein of 207 amino acid residues. RT-PCR analysis showed that LYPD7 was especially highly expressed in testis, lung, stomach, and prostate. Subcellular localization of LYPD7 demonstrated that the protein was localized in the cytoplasm when overexpressed in Hela cells. Furthermore, the subsequent analysis based on reporter gene assays suggested that overexpression of LYPD7 in HEK 293T cells was able to activate the transcriptional activities of AP1 (PMA).

Identification of a novel human lactate dehydrogenase gene LDHAL6A, which activates transcriptional activities of AP1(PMA)

L-lactate dehydrogenase is a crucial enzyme in the process of glycolysis. Here we report the cloning and characterization of another novel lactate dehydrogenase gene, named as LDHAL6A (lactate dehydrogenase A-like 6A), which encodes a 332-amino-acid protein. The LDHAL6A gene consists of seven exons, and is mapped to 11p15.1 by searching the UCSC genomic database. By RT-PCR analysis in various tissues, LDHAL6A was found to be exclusively expressed in human testis. Subcellular localization demonstrated that LDHAL6A protein was located in the cytoplasm when overexpressed in COS7 cells. Furthermore, we found that the recombinant protein GST-LDHAL6A can catalyze the pyruvate convert into the lactate with NADH as its coenzyme. And in the dual luciferase reporter system, expression of LDHAL6A was able to activate transcriptional activities of AP1(PMA).

Cloning and characterization of a novel humanSPRYD4gene encoding a putative SPRY domain-containing protein

We report here the cloning and characterization of a novel human SPRYD4 gene which encodes a SPRY domain containing protein. The SPRYD4 gene is isolated from the human brain cDNA library, and mapped to 12q13.2 by searching the UCSC genomic database. The SPRYD4 cDNA is 1201 base pairs in length and contains an open reading frame encoding 207 amino acids. The SPRYD4 gene consists of two exons and encodes a putative protein with a SPRY domain ranging from 86 to 203 amino acids. The RT-PCR analysis reveals that SPRYD4 is ubiquitously expressed in 18 human tissues. However, it is strongly expressed in kidney, bladder, brain, thymus and stomach, while weakly expressed liver, testis, uterus, spleen and lung. Subcellular localization demonstrates that SPRYD4 protein is localized in the nuclear when overexpressed in COS-7 cell.

Cloning and characterization of a human GDPD domain-containing protein GDPD5

Glycerophosphodiester phosphodiesterase (GDPD) catalyzes the hydrolysis of deacylated glycerophospholipids to glycerol phosphate and alcohol. GDPD5 has been reported in Mus musculus and Gallus gallus, but not in Homo sapiens. Here we report the cloning and characterization of a novel human GDPD domain-containing gene, GDPD5, isolated from human testis cDNA library, and mapped to 11q13.4-13.5 by searching the UCSC genomic database. The GDPD5 cDNA sequence of 3442 base pairs contains an open reading frame encoding 605 amino acids. The GDPD5 gene consists of 17 exons and encodes a putative protein with six transmembrane regions and a GDPD motif. Subcellular localization of GDPD5 demonstrated that the protein was localized in the cytoplasm when overexpressed in COS-7 cells. RT-PCR analysis showed that GDPD5 was widely expressed in human tissues and the expression levels in kidney and prostate were relatively low.

Cloning and characterization of the human gene RAP2C, a novel member of Ras family, which activates transcriptional activities of SRE

The Ras family regulates a wide variety of cellular functions that include cell growth, differentiation, and apoptosis. In this study, we identified a novel human gene named RAP2C, isolated from human testis cDNA library, and mapped to Xq26.2 by searching the UCSC genomic database. The RAP2C cDNA contains an open reading frame of 552 bp, encoding a putative protein of 183 amino acid residues. The predicted protein contains a RAS domain. By RT-PCR analysis in various tissues, RAP2C was found to be principally expressed in the liver, skeletal muscle, prostate, uterus, rectum, stomach, and bladder and to a less extent in brain, kidney, pancreas, and bone marrow. RAP2C protein was located in cytoplasm when overexpressed in COS-7 cells. Reporter gene assays showed that overexpression of RAP2C in HEK293T cells activated the transcriptional activities of serum response element (SRE). These results indicate that RAP2C is a novel member of the Ras family, belonging to the Rap branch of small GTPase proteins and may be involved in SRE-mediated gene transcription.

Molecular cloning and expression analysis of a new gene for short-chain dehydrogenase/reductase 9.

We report here the cloning and characterization of a novel human short-chain dehydrogenases/reductase gene SCDR9, isolated from a human liver cDNA library, and mapped to 4q22.1 by browsing the UCSC genomic database. SCDR9 containing an ORF with a length of 900 bp, encoding a protein with a signal peptide sequence and an adh_short domain. GFP localization shows SCDR9 protein concentrated in some site of the cytoplasm, but not in the ER. Expression pattern in eighteen tissues revealed that SCDR9 is expressed highly in liver. Soluble recombinant protein was successfully purified from Escherichia coli using pET28A(+) expression vector. Our data provides important information for further study of the function of the SCDR9 gene and its products.

Isolation and Characterization of a Novel Four-Transmembrane Protein PMP22CD Specifically Expressed in the Testis

PMP22_Claudin family proteins play important roles in cell tight junction. In thisstudy, we have identified a novel member of this family, PMP22CD. Human PMP22CD wasfirst discovered by database sequence mining and analysis, and verified by cloning andsequencing. PMP22CD was isolated from the human testis cDNA library and mapped tochromosome 11q24.1 by browsing the UCSC genomic database. It contains an ORF with alength of 675bp, encoding a protein that contains a putative PMP22_Claudin domain withfour transmembrane helices. Its molecular weight and isoelectric point are predicted to be25.8kDa and 8.42, respectively. The PMP22CD protein is highly conservative in mammalanimals. Phylogenetic tree analysis indicated that PMP22CD stands for a new subgroup inthe PMP22/EMP/Claudin family. RT-PCR analysis showed that PMP22CD was specificallyexpressed in the testis. Green fluorescence protein localization analysis showed thatPMP22CD mainly surrounded the nuclear membrane, with a minority distribution in thecytoplasm. These results suggested that PMP22CD is a distant member of thePMP22/EMP/Claudin family and that it may have a novel function that does not involve celltight junction because it is not located at the cell membrane.