SAGE is far more sensitive than EST for detecting low-abundance transcripts

Genetic Databases and Gene Editing Tools for Enhancing Crop Resistance against Abiotic Stress

Abiotic stresses extensively reduce agricultural crop production globally. Traditional breeding technology has been the fundamental approach used to cope with abiotic stresses. The development of gene editing technology for modifying genes responsible for the stresses and the related genetic networks has established the foundation for sustainable agriculture against environmental stress. Integrated approaches based on functional genomics and transcriptomics are now expanding the opportunities to elucidate the molecular mechanisms underlying abiotic stress responses. This review summarizes some of the features and weblinks of plant genome databases related to abiotic stress genes utilized for improving crops. The gene-editing tool based on clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has revolutionized stress tolerance research due to its simplicity, versatility, adaptability, flexibility, and broader applications. However, off-target and low cleavage efficiency hinder the successful application of CRISPR/Cas systems. Computational tools have been developed for designing highly competent gRNA with better cleavage efficiency. This powerful genome editing tool offers tremendous crop improvement opportunities, overcoming conventional breeding techniques' shortcomings. Furthermore, we also discuss the mechanistic insights of the CRISPR/Cas9-based genome editing technology. This review focused on the current advances in understanding plant species' abiotic stress response mechanism and applying the CRISPR/Cas system genome editing technology to develop crop resilience against drought, salinity, temperature, heavy metals, and herbicides.

Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco (Nicotiana tabacum)

The basic helix-loop-helix (bHLH) is the second-largest TF family in plants that play important roles in plant growth, development, and stress responses. In this study, a total of 100 bHLHs were identified using Hidden Markov Model profiles in the Nicotiana tabacum genome, clustered into 15 major groups (I-XV) based on their conserved domains and phylogenetic relationships. Group VIII genes were found to be the most abundant, with 27 NtbHLH members. The expansion of NtbHLHs in the genome was due to segmental and tandem duplication. The purifying selection was found to have an important role in the evolution of NtHLHs. Subsequent qRT-PCR validation of five selected genes from transcriptome data revealed that NtbHLH3.1, NtbHLH3.2, NtbHLH24, NtbHLH50, and NtbHLH59.2 have higher expressions at 12 and 24 h in comparison to 0 h (control) of chilling stress. The validated results demonstrated that NtbHLH3.2 and NtbHLH24 genes have 3 and fivefold higher expression at 12 h and 2 and threefold higher expression at 24 h than control plant, shows high sensitivity towards chilling stress. Moreover, the co-expression of positively correlated genes of NtbHLH3.2 and NtbHLH24 confirmed their functional significance in chilling stress response. Therefore, suggesting the importance of NtbHLH3.2 and NtbHLH24 genes in exerting control over the chilling stress responses in tobacco.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01042-x.

Estimation of metabolic fluxes distribution in Saccharomyces cerevisiae during the production of volatile compounds of Tequila

A stoichiometric model for Saccharomyces cerevisiae is reconstructed to analyze the continuous fermentation process of agave juice in Tequila production. The metabolic model contains 94 metabolites and 117 biochemical reactions. From the above set of reactions, 93 of them are linked to internal biochemical reactions and 24 are related to transport fluxes between the medium and the cell. The central metabolism of S. cerevisiae includes the synthesis for 20 amino-acids, carbohydrates, lipids, DNA and RNA. Using flux balance analysis (FBA), different physiological states of S. cerevisiae are shown during the fermentative process; these states are compared with experimental data under different dilution rates (0.04-0.12 h$ ^{-1} $). Moreover, the model performs anabolic and catabolic biochemical reactions for the production of higher alcohols. The importance of the Saccharomyces cerevisiae genomic model in the area of alcoholic beverage fermentation is due to the fact that it allows to estimate the metabolic fluxes during the beverage fermentation process and a physiology state of the microorganism.

Microfluidic Transfection for High-Throughput Mammalian Protein Expression

Mammalian synthetic biology and cell biology would greatly benefit from improved methods for highly parallel transfection, culturing, and interrogation of mammalian cells. Transfection is routinely performed on high-throughput microarrays, but this setup requires manual cell culturing and precludes precise control over the cell environment. As an alternative, microfluidic transfection devices streamline cell loading and culturing. Up to 280 transfections can be implemented on the chip at high efficiency. The culturing environment is tightly regulated and chambers physically separate the transfection reactions, preventing cross-contamination. Unlike typical biological assays that rely on end-point measurements, the microfluidic chip can be integrated with high-content imaging, enabling the evaluation of cellular behavior and protein expression dynamics over time.

Advances in Fasciola hepatica research using 'omics' technologies

The liver fluke Fasciola hepatica is an economically important pathogen of livestock worldwide, as well as being an important neglected zoonosis. Parasite control is reliant on the use of drugs, particularly triclabendazole, which is effective against multiple parasite stages. However, the spread of parasites resistant to triclabendazole has intensified the pursuit for novel control strategies. Emerging 'omics' technologies are helping advance our understanding of liver fluke biology, specifically the molecules that act at the host-parasite interface and are central to infection, virulence and long-term survival within the definitive host. This review discusses the technological sequencing advances that have facilitated the unbiased analysis of liver fluke biology, resulting in an extensive range of 'omics' datasets. In addition, we highlight the 'omics' studies of host responses to F. hepatica infection that, when combined with the parasite datasets, provide the opportunity for integrated analyses of host-parasite interactions. These extensive datasets will form the foundation for future in-depth analysis of F. hepatica biology and development, and the search for new drug or vaccine interventions.

The Role of Phospholipase D and MAPK Signaling Cascades in the Adaption of Lichen Microalgae to Desiccation: Changes in Membrane Lipids and Phosphoproteome

Classically, lichen phycobionts are described as poikilohydric organisms able to undergo desiccation due to the constitutive presence of molecular protection mechanisms. However, little is known about the induction of cellular responses in lichen phycobionts during drying. The analysis of the lipid composition of the desiccated lichen microalga Asterochloris erici revealed the unusual accumulation of highly polar lipids (oligogalactolipids and phosphatidylinositol), which prevents the fusion of membranes during stress, but also the active degradation of cone-shaped lipids (monogalactosyldiacylglycerol and phosphatidylethanolamine) to stabilize membranes in desiccated cells. The level of phosphatidic acid increased 7-fold during desiccation, implicating a possible role for phospholipase D (PLD) in the response to osmotic stress. Inhibition of PLD with 1-butanol markedly impaired the recovery of photosynthesis activity in A. erici upon desiccation and salt stress (2 M NaCl). These two hyperosmotic stresses caused the phosphorylation of c-Jun N-terminal kinase (JNK) and p38-like mitogen-activated protein kinase (MAPK) and the dephosphorylation of extracellular signal-regulated kinase (ERK). The incubation with 1-butanol reduced the phosphorylation of JNK-like proteins and increased the dephosphorylation of ERK-like proteins, which indicates an upstream control of MAPK cascades by PLD. The phosphoproteome showed that desiccation caused the phosphorylation of several proteins in A. erici, most of them involved in protein turnover. The results demonstrate that lichen phycobionts possess both constitutive and inducible protective mechanisms to acquire desiccation tolerance. Among others, these responses are controlled by the PLD pathway through the activation of MAPK cascades.

A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing

Mammalian synthetic biology could be augmented through the development of high-throughput microfluidic systems that integrate cellular transfection, culturing, and imaging. We created a microfluidic chip that cultures cells and implements 280 independent transfections at up to 99% efficiency. The chip can perform co-transfections, in which the number of cells expressing each protein and the average protein expression level can be precisely tuned as a function of input DNA concentration and synthetic gene circuits can be optimized on chip. We co-transfected four plasmids to test a histidine kinase signaling pathway and mapped the dose dependence of this network on the level of one of its constituents. The chip is readily integrated with high-content imaging, enabling the evaluation of cellular behavior and protein expression dynamics over time. These features make the transfection chip applicable to high-throughput mammalian protein and synthetic biology studies.

The Compass-like locus, exclusive to the Ambulacrarians, encodes a chromatin insulator binding protein in the sea urchin embryo

Chromatin insulators are eukaryotic genome elements that upon binding of specific proteins display barrier and/or enhancer-blocking activity. Although several insulators have been described throughout various metazoans, much less is known about proteins that mediate their functions. This article deals with the identification and functional characterization in Paracentrotus lividus of COMPASS-like (CMPl), a novel echinoderm insulator binding protein. Phylogenetic analysis shows that the CMPl factor, encoded by the alternative spliced Cmp/Cmpl transcript, is the founder of a novel ambulacrarian-specific family of Homeodomain proteins containing the Compass domain. Specific association of CMPl with the boxB cis-element of the sns5 chromatin insulator is demonstrated by using a yeast one-hybrid system, and further corroborated by ChIP-qPCR and trans-activation assays in developing sea urchin embryos. The sns5 insulator lies within the early histone gene cluster, basically between the H2A enhancer and H1 promoter. To assess the functional role of CMPl within this locus, we challenged the activity of CMPl by two distinct experimental strategies. First we expressed in the developing embryo a chimeric protein, containing the DNA-binding domain of CMPl, which efficiently compete with the endogenous CMPl for the binding to the boxB sequence. Second, to titrate the embryonic CMPl protein, we microinjected an affinity-purified CMPl antibody. In both the experimental assays we congruently observed the loss of the enhancer-blocking function of sns5, as indicated by the specific increase of the H1 expression level. Furthermore, microinjection of the CMPl antiserum in combination with a synthetic mRNA encoding a forced repressor of the H2A enhancer-bound MBF1 factor restores the normal H1 mRNA abundance. Altogether, these results strongly support the conclusion that the recruitment of CMPl on sns5 is required for buffering the H1 promoter from the H2A enhancer activity, and this, in turn, accounts for the different level of accumulation of early linker and nucleosomal transcripts.

Mounting evidence in several model organisms collectively demonstrates a role for the DNA-protein complexes known as chromatin insulators in orchestrating the functional domain organization of the eukaryotic genome. Several DNA elements displaying features of insulators, viz barrier and/or directional enhancer-blocking activity, have been identified in yeast, Drosophila, sea urchin, vertebrates and plants; however, proteins that bind these DNA sequences eliciting insulator activities are far less known. Here we identify a novel protein, COMPASS-like (CMPl), which is expressed exclusively by the ambulacrarian group of metazoans and interacts directly with the sea urchin sns5 insulator. Sns5 lies within the early histone gene cluster, basically between the H2A enhancer and H1 promoter, where it acts buffering the H1 promoter from the H2A enhancer influence. Intriguingly, we find that CMPl role is absolutely required for the sns5 activity, therefore imposing the different level of accumulation of the linker and nucleosomal transcripts. Overall, our findings add an interesting and novel facet to the chromatin insulator field, highlighting the surprisingly low evolutionary conservation of trans-acting factors binding to chromatin insulators. This opens the possibility that multiple lineage-specific factors modulate chromatin organization in different metazoans.

Minimizing the unpredictability of transgene expression in plants: the role of genetic insulators

The genetic transformation of plants has become a necessary tool for fundamental plant biology research, as well as the generation of engineered plants exhibiting improved agronomic and industrial traits. However, this technology is significantly hindered by the fact that transgene expression is often highly variable amongst independent transgenic lines. Two of the major contributing factors to this type of inconsistency are inappropriate enhancer-promoter interactions and chromosomal position effects, which frequently result in mis-expression or silencing of the transgene, respectively. Since the precise, often tissue-specific, expression of the transgene(s) of interest is often a necessity for the successful generation of transgenic plants, these undesirable side effects have the potential to pose a major challenge for the genetic engineering of these organisms. In this review, we discuss strategies for improving foreign gene expression in plants via the inclusion of enhancer-blocking insulators, which function to impede enhancer-promoter communication, and barrier insulators, which block the spread of heterochromatin, in transgenic constructs. While a complete understanding of these elements remains elusive, recent studies regarding their use in genetically engineered plants indicate that they hold great promise for the improvement of transgene expression, and thus the future of plant biotechnology.

SpliceAid 2: a database of human splicing factors expression data and RNA target motifs

Splicing is the most frequently altered biological process by mutations within gene regions. Information for splicing is recognized by several factors that bind pre-mRNA sequence and, through coordinated interaction, yield mature transcripts. Some in silico methods have been developed to predict if a mutation leads to aberrant splicing patterns. We previously created SpliceAid tool that is able to minimize false positive predictions because it adopts strictly experimental RNA target motifs bound by splicing proteins in humans. In order to improve prediction accuracy and better understand the splicing outcome, the tissue specificity of each splicing regulatory factor has to be taken into account. Here, we have developed SpliceAid 2 by adding the expression data related to the splicing factors extracted from the main proteomic and transcriptomic databases, true 5' and 3' splice sites, polypyrimidine tracts, and branch point sequences. The new version collects 2,220 target sites of 62 human splicing proteins and their expression data in 320 tissues per cell. SpliceAid 2 can be useful to foresee the splicing pattern alteration, to guide the identification of the molecular effect due to the mutations and to understand the tissue-specific alternative splicing. SpliceAid 2 is freely accessible at www.introni.it/spliceaid.html.

Enhancer-promoter interference and its prevention in transgenic plants

Biotechnology has several advantages over conventional breeding for the precise engineering of gene function and provides a powerful tool for the genetic improvement of agronomically important traits in crops. In particular, it has been exploited for the improvement of multiple traits through the simultaneous introduction or stacking of several genes driven by distinct tissue-specific promoters. Since transcriptional enhancer elements have been shown to override the specificity of nearby promoters in a position- and orientation-independent manner, the co-existence of multiple enhancers/promoters within a single transgenic construct could be problematic as it has the potential to cause the mis-expression of transgene product(s). In order to develop strategies with, which to prevent such interference, a clear understanding of the mechanisms underlying enhancer-mediated activation of target promoters, as well as the identification of DNA sequences that function to block these interactions in plants, will be necessary. To date, little is known concerning enhancer function in plants and only a very limited number of enhancer-blocking insulators that operate in plant species have been identified. In this review, we discuss the current knowledge surrounding enhancer-promoter interactions, as well as possible means of minimizing such interference during plant transformation experiments.

Identification and characterization of gene expression involved in the coloration of cichlid fish using microarray and qRT-PCR approaches

It has been suggested that speciation on the basis of sexual selection is an important mechanism for the generation of new species for East African cichlids, where male body coloration is one of the major discriminatory factors used by females in mate choice. To gain insight into the molecular basis of cichlid coloration, we studied the Lake Malawi cichlid Pseudotropheus saulosi, comparing transcription in the bright blue skin of males to the yellow skin of females. Our cDNA microarray experiments identified 46 clones that exhibited expression differences between the two sexes, of which five were confirmed to be differentially expressed by relative quantitative real-time PCR (qRT-PCR). This gene list includes a representative from the endosomal-to-Golgi vesicle trafficking pathway, Coatomer protein complex, subunit zeta-1 (Copz-1), which is known to be a critical determinant of pigmentation in humans and zebrafish. With the support of microscopic images of the skin of these specimens, we interpret the transcriptional differences between the blue males and yellow females. Here, we provide insight into the putative functional diversification of genes involved in the coloration of cichlids and by extension, on the evolution of coloration in teleost fish.

Differentially expressed genes during bovine intramuscular adipocyte differentiation profiled by serial analysis of gene expression

Beef marbling or intramuscular fat deposition is an economically important carcass trait in Japanese Black cattle. To investigate genes involved in intramuscular adipogenesis, differential gene expression during adipogenesis in a clonal bovine intramuscular preadipocyte (BIP) cell line was profiled with serial analysis of gene expression (SAGE). We sequenced 75 283 tags for the proliferation phase (day 0) and 81 878 tags for the differentiation phase (4 days after adipogenic stimulation: day 4). A comparison of the unique SAGE tag frequencies between the day 0- and day 4-libraries revealed that 878 (2.8%) of the 30 989 unique putative transcripts were expressed at significantly different levels (P < 0.05); 401 tags (1.4%) were up-regulated and 477 tags (1.2%) were down-regulated in the day 4-library relative to the day 0-library. We confirmed up-regulation of 10 tags of the genes that were up-regulated in the previous subtraction cloning studies in BIP cells [Animal Science Journal, 76 (2005) 479]. Of the 878 differentially expressed tags, 377 were identified in the bovine RefSeq library and 356 were assigned a bovine draft genomic sequence. Fifteen tags were mapped in previously detected beef marbling quantitative trait loci (QTL) regions [Mammalian Genome, 18 (2007) 125]. These genes may be involved in the adipogenic processes of beef marbling.

Deep SAGE analysis of the Caenorhabditis elegans transcriptome

We employed the Tag-seq technique to generate global transcription profiles for different strains and life stages of the nematode C. elegans. Tag-seq generates cDNA tags as does Serial Analysis of Gene Expression (SAGE), but the method yields a much larger number of tags, generating much larger data sets than SAGE. We examined differences in the performance of SAGE and Tag-seq by comparing gene expression data for 13 pairs of libraries. We identified genes for which expression was consistently changed in long-lived worms. Additional genes emerged in the deeper Tag-seq profiles, including several ‘signature’ genes found among those zup-regulated in long-lived dauer larvae (cki-1, aak-2 and daf-16). Fifty to sixty percent of the genes differentially expressed in daf-2(−) versus daf-2(+) adults had fragmentary or no functional annotation, suggesting the involvement of as yet unstudied pathways in aging. We were able to distinguish between changes in gene expression associated with altered genotype or altered growth conditions. We found 62 cases of possible mRNA isoform switching in the 13 Tag-seq libraries, whereas the 13 SAGE libraries allowed detection of only 15 such occurrences. We observed strong expression of anti-sense transcripts for several mitochondrial genes, but nuclear anti-sense transcripts were neither abundant nor consistently expressed among the libraries.

Incorporating Domain-Specific Information Quality Constraints into Database Queries

The range of information now available in queryable repositories opens up a host of possibilities for new and valuable forms of data analysis. Database query languages such as SQL and XQuery offer a concise and high-level means by which such analyses can be implemented, facilitating the extraction of relevant data subsets into either generic or bespoke data analysis environments. Unfortunately, the quality of data in these repositories is often highly variable. The data is still useful, but only if the consumer is aware of the data quality problems and can work around them. Standard query languages offer little support for this aspect of data management. In principle, however, it should be possible to embed constraints describing the consumer’s data quality requirements into the query directly, so that the query evaluator can take over responsibility for enforcing them during query processing.

Most previous attempts to incorporate information quality constraints into database queries have been based around a small number of highly generic quality measures, which are defined and computed by the information provider. This is a useful approach in some application areas but, in practice, quality criteria are more commonly determined by the user of the information not by the provider. In this article, we explore an approach to incorporating quality constraints into database queries where the definition of quality is set by the user and not the provider of the information. Our approach is based around the concept of a quality view , a configurable quality assessment component into which domain-specific notions of quality can be embedded. We examine how quality views can be incorporated into XQuery, and draw from this the language features that are required in general to embed quality views into any query language. We also propose some syntactic sugar on top of XQuery to simplify the process of querying with quality constraints.

Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis

Normalization of mRNA levels using endogenous reference genes (ERGs) is critical for an accurate comparison of gene expression between different samples. Despite the popularity of traditional ERGs (tERGs) such as GAPDH and ACTB, their expression variability in different tissues or disease status has been reported. Here, we first selected candidate housekeeping genes (HKGs) using human gene expression data from different platforms including EST, SAGE, and microarray, and 13 novel ERGs (nERGs) (ARL8B, CTBP1, CUL1, DIMT1L, FBXW2, GPBP1, LUC7L2, OAZ1, PAPOLA, SPG21, TRIM27, UBQLN1, ZNF207) were further identified from these HKGs. The mean coefficient variation (CV) values of nERGs were significantly lower than those of tERGs and the expression level of most nERGs was relatively lower than high expressing tERGs in all dataset. The higher expression stability and lower expression levels of most nERGs were validated in 108 human samples including formalin-fixed paraffin-embedded (FFPE) tissues, frozen tissues and cell lines, through quantitative real-time RT-PCR (qRT-PCR). Furthermore, the optimal number of nERGs required for accurate normalization was as few as two, while four genes were required when using tERGs in FFPE tissues. Most nERGs identified in this study should be better reference genes than tERGs, based on their higher expression stability and fewer numbers needed for normalization when multiple ERGs are required.

LongSAGE analysis of the early response to cold stress in Arabidopsis leaf

The initial events involved in signal transduction generated by cold exposure are poorly known in plants. We were interested in the characterization of early response to cold stress in Arabidopsis leaves. So we examined plants exposed to 0 degrees C for 1 h. Using LongSAGE at the level of transcription, a total of 27,612 tags, including 11,089 unique tags were sequenced and analyzed. By adopting LongSAGE methods, the ambiguity of tag identification was reduced by about 10%. Only 46% of identified tags in the 1-h cold-stressed plants matched existing Arabidopsis UniGene entries. A comparison of the tags derived from the cold-treated leaves with those identified in the non-treated leaves revealed 315 differentially expressed genes (P < 0.01). Functional classification of expressed genes during the early cold response indicated that genes were involved in light harvesting, the Calvin cycle, and photorespiration were expressed at relatively low levels compared to their presence in non-cold-stressed plants. On other hand, genes involved in mitochondrial electron transport and ATP synthesis showed an increased expression. Some orphan LongSAGE tags uniquely matched pri-miRNA, suggesting the existence of miRNA in our SAGE library. These findings suggest that diverse protection strategies appear in the early response of leaves exposed to cold stress. First of all, several genes included in signal transduction through calcium mediated signal sensing, and cascades of several kinases, and transcription factors, were distinguished in the early cold response. Furthermore, genes affecting the synthesis of salicylic acid, nitrate assimilation, ammonia assimilation, the gluconeogenesis pathway, and glucosinolate biosynthesis were newly detected in relationship with cold stress. Finally, our results in the present work provide new insights into the molecular mechanisms involved in transcriptional regulation in response to cold exposure in plants.

The marker SCK13(603) associated with resistance to ascochyta blight in chickpea is located in a region of a putative retrotransposon

The sequence characterized amplified region (SCAR) marker SCK13(603), associated with ascochyta blight resistance in a chickpea recombinant inbred line (RIL) population, was used as anchored sequence for genome walking. The PCRs performed in the walking steps to walk in the same direction produced eight bands in 5' direction and five bands in 3' direction with a length ranking from 530 to 2,871 bp. The assembly of the bands sequences along with the sequence of SCK13(603) resulted in 7,815 bp contig. Blastn analyses showed stretches of DNA sequence mainly distributed from the nucleotides 1,500 to 4,500 significantly similar to Medicago truncatula genomic DNA. Three open reading frames (ORFs) were identified and blastp analysis of predicted amino acids sequences revealed that ORF1, ORF2 and ORF3 had significant similarity to a CCHC zinc finger protein, to an integrase, and to a precursor of the glucoamylase s1/s2, respectively, from M. truncatula. The high homology of the putative proteins derived from ORF1 and ORF2 with retrotransposon proteins and the prediction of the existence of conserved domains usually present in retrotransposon proteins indicate that the marker SCK13(603) is located in a region of a putative retrotransposon. The information generated in this study has contributed to increase the knowledge of this important region for blight resistance in chickpea.

What would you do if you could sequence everything?

It could be argued that the greatest transformative aspect of the Human Genome Project has been not the sequencing of the genome itself, but the resultant development of new technologies. A host of new approaches has fundamentally changed the way we approach problems in basic and translational research. Now, a new generation of high-throughput sequencing technologies promises to again transform the scientific enterprise, potentially supplanting array-based technologies and opening up many new possibilities. By allowing DNA/RNA to be assayed more rapidly than previously possible, these next-generation platforms promise a deeper understanding of genome regulation and biology. Significantly enhancing sequencing throughput will allow us to follow the evolution of viral and bacterial resistance in real time, to uncover the huge diversity of novel genes that are currently inaccessible, to understand nucleic acid therapeutics, to better integrate biological information for a complete picture of health and disease at a personalized level and to move to advances that we cannot yet imagine.

Chromosomal losses are associated with hypomethylation of the gene-control regions in the stomach with a low number of active genes

Transitional-CpG methylation between unmethylated promoters and nearby methylated retroelements plays a role in the establishment of tissue-specific transcription. This study examined whether chromosomal losses reducing the active genes in cancers can change transitional-CpG methylation and the transcription activity in a cancer-type-dependent manner. The transitional-CpG sites at the CpG-island margins of nine genes and the non-island-CpG sites round the transcription start sites of six genes lacking CpG islands were examined by methylation-specific polymerase chain reaction (PCR) analysis. The number of active genes in normal and cancerous tissues of the stomach, colon, breast, and nasopharynx were analyzed using the public data in silico. The CpG-island margins and non-island CpG sites tended to be hypermethylated and hypomethylated in all cancer types, respectively. The CpG-island margins were hypermethylated and a low number of genes were active in the normal stomach compared with other normal tissues. In gastric cancers, the CpG-island margins and non-island-CpG sites were hypomethylated in association with high-level chromosomal losses, and the number of active genes increased. Colon, breast, and nasopharyngeal cancers showed no significant association between the chromosomal losses and methylation changes. These findings suggest that chromosomal losses in gastric cancers are associated with the hypomethylation of the gene-control regions and the increased number of active genes.

Applications of next-generation sequencing technologies in functional genomics

A new generation of sequencing technologies, from Illumina/Solexa, ABI/SOLiD, 454/Roche, and Helicos, has provided unprecedented opportunities for high-throughput functional genomic research. To date, these technologies have been applied in a variety of contexts, including whole-genome sequencing, targeted resequencing, discovery of transcription factor binding sites, and noncoding RNA expression profiling. This review discusses applications of next-generation sequencing technologies in functional genomics research and highlights the transforming potential these technologies offer.

Gene expression studies of the dikaryotic mycelium and primordium of Lentinula edodes by serial analysis of gene expression

Lentinula edodes (Shiitake mushroom) is a common edible mushroom that has high nutritional and medical value. Although a number of genes involved in the fruit of the species have been identified, little is known about the process of differentiation from dikaryotic mycelium to primordium. In this study, serial analysis of gene expression (SAGE) was applied to determine the gene expression profiles of the dikaryotic mycelium and primordium of L. edodes in an effort to advance our understanding of the molecular basis of fruit body development. A total of 6363 tags were extracted (3278 from the dikaryotic mycelium and 3085 from the primordium), 164 unique tags matched the in-house expressed sequence tag (EST) database. The difference between the expression profiles of the dikaryotic mycelium and primordium suggests that a specific set of genes is required for fruit body development. In the transition from the mycelium to the primordium, different hydrophobins were expressed abundantly, fewer structural genes were expressed, transcription and translation became active, different genes became involved in intracellular trafficking, and stress responses were expressed. These findings advance our understanding of fruit body development. We used cDNA microarray hybridization and Northern blotting to verify the SAGE results, and found SAGE to be highly efficient in the performance of transcriptome analysis. To our knowledge, this is the first SAGE study of a mushroom.

Robust-LongSAGE (RL-SAGE): an improved LongSAGE method for high-throughput transcriptome analysis

Serial analysis of gene expression (SAGE) is a powerful technique for large-scale transcriptome analysis in eukaryotes. However, technical difficulties in the SAGE library construction, such as low concatemer cloning efficiency, small concatemer size, and a high level of empty clones, has prohibited its widespread use as a routine technique for expression profiling in many laboratories. We recently improved the LongSAGE library construction method considerably and developed a modified version called Robust-LongSAGE, or RL-SAGE. In RL-SAGE, concatemer cloning efficiency and clone insert size were increased significantly. About 20 PCR reactions are sufficient to make a library with more than 150,000 clones. Using RL-SAGE, we have made 10 libraries of rice, maize, and the rice blast fungus Magnaporthe grisea.

Serial analysis of gene expression

Serial analysis of gene expression (SAGE) is a method used to obtain comprehensive, unbiased and quantitative gene-expression profiles. Its major advantage over arrays is that it does not require a priori knowledge of the genes to be analyzed and reflects absolute mRNA levels. Since the original SAGE protocol was developed in a short-tag (10-bp) format, several modifications have been made to produce longer SAGE tags for more precise gene identification and to decrease the amount of starting material necessary. Several SAGE-like methods have also been developed for the genome-wide analysis of DNA copy-number changes and methylation patterns, chromatin structure and transcription factor targets. In this protocol, we describe the 17-bp longSAGE method for transcriptome profiling optimized for a small amount of starting material. The generation of such libraries can be completed in 7-10 d, whereas sequencing and data analysis require an additional 2-3 wk.

SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages

SAGE (Serial Analysis of Gene Expression) experiments generate short nucleotide sequences called ‘tags’ which are assumed to map unambiguously to their original transcripts (1 tag to 1 transcript mapping). Nevertheless, many tags are generated that do not map to any transcript or map to multiple transcripts. Current bioinformatics resources, such as SAGEmap and TAGmapper, have focused on reducing the number of unmapped tags. Here, we describe SAGETTARIUS, a new high-throughput program that performs successive precise Nla3 and Sau3A tag to transcript mapping, based on specifically designed Virtual Tag (VT) libraries. First, SAGETTARIUS decreases the number of tags mapped to multiple transcripts. Among the various mapping resources compared, SAGETTARIUS performed the best in this respect by decreasing up to 11% the number of multiply mapped tags. Second, SAGETTARIUS allows the establishment of a guideline for SAGE experiment sequencing efforts through efficient mapping of the CRT (Cytoplasmic Ribosomal protein Transcripts)-specific tags. Using all publicly available human and mouse Nla3 SAGE experiments, we show that sequencing 100 000 tags is sufficient to map almost all CRT-specific tags and that four sequencing stages can be identified when carrying out a human or mouse SAGE project. SAGETTARIUS is web interfaced and freely accessible to academic users.

SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation

We describe a web server for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE). The core of the server relies on a database of genomic virtual tags built by a recently described method that attempts to reduce the amount of ambiguous assignments for those tags that are not unique in the genome. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. The output of the server consists of a table in HTML format that contains links to a graphic representation of the results and to some external servers and databases, facilitating the tasks of analysis of gene expression and gene discovery. Also, a table in tab delimited text format is produced, allowing the user to export the results into custom databases and software for further analysis. The current server version provides the most accurate and complete SAGE tag mapping source that is available for the yeast organism. In the near future, this server will also allow the accurate mapping of experimental SAGE-tags from other model organisms such as human, mouse, frog and fly. The server is freely available on the web at: http://dna.bio.puc.cl/SAGExplore.html.

Ancient conserved domain protein-1 binds copper and modifies its retention in cells

The ancient conserved domain protein (ACDP) family are a recently identified group of homologous mammalian proteins. Some family members have been suggested to have roles in the metabolism of metals. We investigated the capacity of ACDP-1 to bind metals. Using immobilised metal affinity chromatography and isothermal titration calorimetry we determined that ACDP-1 is a high affinity copper binding protein able to bind copper at nanomolar concentrations. In addition the promoter of ACDP-1 contains metal response elements and the cellular expression of ACDP-1 alters cellular retention of copper. However, cellular expression of ACDP-1 does not alter cellular resistance to the toxicity of copper or other metals. As our findings place the subcellular localisation of ACDP-1 in the cytoplasm it is possible that ACDP-1 represent a novel copper chaperone or storage protein.

Single molecule transcription profiling with AFM

Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

Influence of the transposable element neighborhood on human gene expression in normal and tumor tissues

Transposable elements (TEs) are genomic sequences able to replicate themselves, and to move from one chromosomal position to another within the genome. Many TEs contain their own regulatory regions, which means that they may influence the expression of neighboring genes. TEs may also be activated and transcribed in various cancers. We therefore tested whether gene expression in normal and tumor tissues is influenced by the neighboring TEs. To do this, we associated all human genes to the nearest TEs. We analyzed the expression of these genes in normal and tumor tissues using SAGE and EST data, and related this to the presence and type of TEs in their vicinity. We confirmed that TEs tend to be located in antisense orientation relative to their hosting genes. We found that the average number of tissues where a gene is expressed varies depending on the type of TEs located near the gene, and that the difference in expression level between normal and tumor tissues is greatest for genes that host SINE elements. This deregulation increases with the number of SINE copies in the gene vicinity. This suggests that SINE elements might contribute to the cascade of gene deregulation in cancer cells.

Influence of temperature on the ontogenetic expression of neural development-related genes from developing tilapia brain expressed sequence tags

The developing central neural circuits in teleosts are genetically controlled and temperature-initiated. We compiled a list of transcripts expressed in the developing tilapia (Oreochromis mossambicus) brain using expressed sequence tags derived from the developing brain, and investigated genes with thermosensitive ontogenetic expression. Of 1084 clones, 893 were unique genes, 445 of which were known. Fourteen of the latter were neural development-related, and the ontogenetic expression of nine was temperature-influenced. Discs large homolog 5, myelin expression factor 2, plasticity-related protein-2, tsc2 gene product-related genes, and an inhibitor of differentiation protein 2 (Id2) were differentially temperature-influenced according to their developmental stages. Endothelial differentiation-related factor 1, midkine-related growth factor b, and mitogen-activated protein kinase 14b were specifically influenced by elevated temperature, and beta-catenin-like isoform 1 by lower temperature. Neural development-related genes, particularly those with thermosensitive ontogenetic expression, might be important for developing central neural circuits in teleosts.

Robust analysis of 5'-transcript ends: a high-throughput protocol for characterization of sequence diversity of transcription start sites

The structure and diversity at the 3' ends of mRNA transcripts have been extensively characterized using several tag-based techniques in eukaryotes. However, the 5' ends of mRNA transcripts are not well understood, owing to a lack of efficient experimental approaches. We developed a new gene expression profiling method, called robust analysis of 5'-transcript ends (5' RATE), to rapidly isolate the 5' ends of mRNA transcripts. After ligating RNA oligo linkers to the 5' regions of decapped mRNA, cDNA is synthesized and digested with the restriction enzyme NlaIII. Ditags are formed by ligating two individual NlaIII tags, and are then PCR-amplified, purified and sequenced using a pyrosequencing approach. The 5'-RATE procedure is simple, fast and cost-effective because the complicated steps in comparative methods such as serial analysis of gene expression (including the formation of concatemers and their subsequent cloning and sequencing) have been eliminated. The longer 5'-RATE tags (>80 bp) provide more accurate matching to reference sequences for gene annotation and allow in-depth analysis of sequence diversity at the 5' regions of mRNA transcripts. Using our procedure, a 5'-RATE library with about 180,000 end sequences can be generated within a week. We have successfully applied the 5'-RATE method to characterize the transcriptome of various plant species including maize, rice and soybean. This method can be easily adapted to other eukaryotic organisms using the detailed procedures described in this protocol.

Identification of candidate mRNAs associated with gonadotropin-induced maturation of murine cumulus oocyte complexes using serial analysis of gene expression

In cultured cumulus oocyte complexes (COC), FSH induces gene transcription required for germinal vesicle breakdown (GVBD). Experiments were performed to determine the critical period when gene transcription is required for GVBD and to identify candidate mRNAs involved. Experiment I: murine COC were cultured 4 h in the presence of FSH with 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB) added at different intervals after the start of culture. COC cultured with FSH underwent GVBD (82 ± 7%). When DRB was added at 0, 5, or 10 min after culture initiation, oocyte maturation was blocked (17 ± 7, 14 ± 6, and 21 ± 6% GVBD, respectively). When DRB was added after 15, 20, or 30 min, progressively more COC underwent GVBD (37 ± 6, 39 ± 6, and 66 ± 6%, respectively). The critical period of transcription required for GVBD occurred between 15 and 30 min after culture initiation. Experiment II: COC were cultured for 25 min in the presence (plusDRB) or absence (minusDRB) of DRB. SAGE libraries were generated from COC RNA of each treatment group. A total of 48,431 and 45,367 tags were sequenced for the plusDRB and minusDRB libraries, respectively. Criteria used to identify transcripts of interest included a total tag count of at least 10 across both libraries and a threefold or greater difference in expression between libraries. Using these criteria, 39 and 27 transcripts were identified as differentially expressed at the P ≤ 0.01 and P ≤ 0.001 levels, respectively. Differentially expressed transcripts were classed into major categories that included cell growth, development, and regulation of gene expression. Differentially expressed transcripts represent candidates potentially involved in regulating maturation of murine COC.

Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

BACKGROUND

In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE). The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome.

RESULTS

We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T) priming to internal poly-(A) regions during reverse transcription.

CONCLUSION

We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications.

Robust analysis of 5'-transcript ends (5'-RATE): a novel technique for transcriptome analysis and genome annotation

Complicated cloning procedures and the high cost of sequencing have inhibited the wide application of serial analysis of gene expression and massively parallel signature sequencing for genome-wide transcriptome profiling of complex genomes. Here we describe a new method called robust analysis of 5'-transcript ends (5'-RATE) for rapid and cost-effective isolation of long 5' transcript ends (approximately 80 bp). It consists of three major steps including 5'-oligocapping of mRNA, NlaIII tag and ditag generation, and pyrosequencing of NlaIII tags. Complicated steps, such as purification and cloning of concatemers, colony picking and plasmid DNA purification, are eliminated and the conventional Sanger sequencing method is replaced with the newly developed pyrosequencing method. Sequence analysis of a maize 5'-RATE library revealed complex alternative transcription start sites and a 5' poly(A) tail in maize transcripts. Our results demonstrate that 5'-RATE is a simple, fast and cost-effective method for transcriptome analysis and genome annotation of complex genomes.

Applying the SAGE technique to study the effects of electromagnetic field on biological systems

Identification of genes alternatively expressed in electromagnetic field (EMF)-exposed cells could provide direct evidence for biological effects of EMF. As there are a few indications so far for certain genes to be influenced by EMF, genome-wide scans of the transcriptome appear to be necessary. Among the several technologies used for genome-wide gene expression analysis, serial analysis of gene expression (SAGE) is one promising method, which seems particularly applicable for EMF research. This review provides a brief description of the features of gene expression, illustrates the basic principle of SAGE, and discusses the advantages and limitations of SAGE as well as examples of application. This information should help investigators determine if the SAGE technique is an optimal method for evaluating the biological effects of EMF.

Abundant transcripts of malting barley identified by serial analysis of gene expression (SAGE)

Serial analysis of gene expression (SAGE) was applied to the major cereal crop barley (Hordeum vulgare) to characterize the transcriptional profile of grain during the malting process. Seven SAGE libraries were generated from seed at different time points during malting, in addition to one library from dry mature seed. A total of 155,206 LongSAGE tags, representing 41,909 unique sequences, was generated. This study reports an in-depth analysis of the most abundant transcripts from each of eight specific time points in a malting barley time course. The 100 most abundant tags from each library were analysed to identify the putative functional role of highly abundant transcripts. The largest functional groups included transcripts coding for stress response and cell defence, ribosomal proteins and storage proteins. The most abundant tag represented B22EL8, a barley metallothionein, which showed significant up-regulation across the malting time course. Considerable changes in the abundance profiles of some of the highly abundant tags occurred at 24 h post-steeping, indicating that it may be an important time point for gene expression changes associated with barley seed germination.

The canine genome

The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.

Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips

Background

Serial Analysis of Gene Expression (SAGE) and microarrays have found awidespread application, but much ambiguity exists regarding the evaluation of these technologies. Cross-platform utilization of gene expression data from the SAGE and microarray technology could reduce the need for duplicate experiments and facilitate a more extensive exchange of data within the research community. This requires a measure for the correspondence of the different gene expression platforms. To date, a number of cross-platform evaluations (including a few studies using SAGE and Affymetrix GeneChips) have been conducted showing a variable, but overall low, concordance. This study evaluates these overall measures and introduces the between-ratio difference as a concordance measure pergene.

Results

In this study, gene expression measurements of Unigene clusters represented by both Affymetrix GeneChips HG-U133A and SAGE were compared using two independent RNA samples. After matching of the data sets the final comparison contains a small data set of 1094 unique Unigene clusters, which is unbiased with respect to expression level. Different overall correlation approaches, like Up/Down classification, contingency tables and correlation coefficients were used to compare both platforms. In addition, we introduce a novel approach to compare two platforms based on the calculation of differences between expression ratios observed in each platform for each individual transcript. This approach results in a concordance measure per gene (with statistical probability value), as opposed to the commonly used overall concordance measures between platforms.

Conclusion

We can conclude that intra-platform correlations are generally good, but that overall agreement between the two platforms is modest. This might be due to the binomially distributed sampling variation in SAGE tag counts, SAGE annotation errors and the intensity variation between probe sets of a single gene in Affymetrix GeneChips. We cannot identify or advice which platform performs better since both have their (dis)-advantages. Therefore it is strongly recommended to perform follow-up studies of interesting genes using additional techniques. The newly introduced between-ratio difference is a filtering-independent measure for between-platform concordance. Moreover, the between-ratio difference per gene can be used to detect transcripts with similar regulation on both platforms.

Detecting novel low-abundant transcripts in Drosophila

Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue. From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies.

Sociogenomics: social life in molecular terms

Spectacular progress in molecular biology, genome-sequencing projects and genomics makes this an appropriate time to attempt a comprehensive understanding of the molecular basis of social life. Promising results have already been obtained in identifying genes that influence animal social behaviour and genes that are implicated in social evolution. These findings - derived from an eclectic mix of species that show varying levels of sociality - provide the foundation for the integration of molecular biology, genomics, neuroscience, behavioural biology and evolutionary biology that is necessary for this endeavour.

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

A number of methods are currently used for gene expression profiling. They differ in scale, economy and sensitivity. We present the results of a direct comparison between serial analysis of gene expression (SAGE) and the Barley1 Affymetrix GeneChip. Both technology platforms were used to obtain quantitative measurements of transcript abundance using identical RNA samples and assessed for their ability to quantify differential gene expression. For SAGE, a total of 82,122 tags were generated from two independent libraries representing whole developing barley caryopsis and dissected embryos. The Barley1 GeneChip contains 22,791 probe sets. Results obtained from both methods are generally comparable, indicating that both will lead to similar conclusions regarding transcript levels and differential gene expression. However, excluding singletons, 24.4% of the unique SAGE tags had no corresponding probe set on the Barley1 array indicating that a broader snapshot of gene expression was obtained by SAGE. Discrepancies were observed for a number of "genes" and these are discussed.

Serial analysis of gene expression during elongation of the peri-implantation porcine trophectoderm (conceptus)

Conceptus loss during the preimplantation and early postimplantation period hinders the efficiency of swine reproduction. Significant conceptus loss occurs during trophectoderm elongation between gestational day 11 ( D11) and day 12 ( D12). Elongation of the porcine conceptus is a key stage of development during which maternal recognition of pregnancy, initial placental development, and preparation for implantation occurs. The objective of this study was to establish comparative transcriptome profiles of D11 ovoid and D12 filamentous conceptuses and thereby identify temporally regulated genes essential for developmental progression during conceptus elongation. Serial analysis of gene expression (SAGE) libraries were constructed from in vivo derived ovoid and filamentous swine conceptuses to yield a total of 42,389 tags (ovoid) and 42,391 tags (filamentous) representing 14,464 and 13,098 putative unique transcripts, respectively. Statistical analysis of tag frequencies revealed the differential expression of 431 tags between libraries ( P < 0.05). Nucleotide sequence alignment searches on public databases provided SAGE tag annotation and gene ontology assignments. Comparisons between the SAGE profiles of ovoid and filamentous conceptuses revealed increased expression of key genes in the steroidogenesis [cytochrome P-450scc ( CYP11A1), aromatase ( CYP19A), and steroidogenic acute regulatory protein ( STAR)] and oxidative stress response pathways [microsomal glutathione S-transferase 1 ( MGST1) and copper-zinc superoxide dismutase ( SOD1)]. Differential expression of these genes in the steroidogenic and oxidative stress response pathways was confirmed by real-time PCR. These results validate the utility of SAGE in the pig and establish an initial model linking gene expression profiles at the pathway level with phenotypic progression from ovoid to filamentous stages of conceptus development.

Exercise training increases electron and substrate shuttling proteins in muscle of overweight men and women with the metabolic syndrome

Aerobic conditioned muscle shows increased oxidative metabolism or glucose relative to untrained muscle at a given absolute exercise intensity. The studies of a targeted risk reduction intervention through defined exercise (STRRIDE) study is an aerobic exercise intervention in men and women with features of metabolic syndrome (Kraus WE, Torgan CE, Duscha BD, Norris J, Brown SA, Cobb FR, Bales CW, Annex BH, Samsa GP, Houmard JA, and Slentz CA, Med Sci Sports Exerc 33: 1774–1784, 2001), with four muscle biopsies taken during training and detraining time points. Here, we expanded a previous study (Hittel DS, Kraus WE, and Hoffman EP, J Physiol 548: 401–410, 2003) and used mRNA profiling to investigate gene transcripts associated with energy and substrate metabolism in STRRIDE participants. We found coordinate regulation of key metabolic enzymes with aerobic training in metabolic syndrome (aspartate aminotransferase 1, lactate dehydrogenase B, and pyruvate dehydrogenase-α1). All were also quickly downregulated by detraining, although the induction was not an acute response to activity. Protein and enzymatic assays were used to validate mRNA induction with aerobic training and loss with detraining (96 h to 2 wk) in 10 male and 10 female STRRIDE subjects. We propose that training coordinately increases the levels of aspartate aminotransferase 1, lactate dehydrogenase B, and pyruvate dehydrogenase-α1subunit, increasing glucose metabolism in muscle by liberating pyruvate for oxidative metabolism and, therefore, limiting lactate efflux. Serial measurement of fasting plasma lactate from 62 subjects from the same exercise group demonstrated a significant decrease of circulating lactate with training. We also found evidence for sex-specific molecular remodeling of muscle with ubiquinol-cytochrome c reductase core protein II, a component of mitochondrial respiratory complex III, which showed an increase after training that was specific to women. These biochemical adaptations complement existing molecular models for improved glucose tolerance with exercise intervention in prediabetic individuals.

LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse

MOTIVATION

Owing to its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries.

RESULTS

A fraction of LongSAGE tags could not be unambiguously assigned to its gene, due to the presence of widely conserved sequences downstream of particular CATG anchor sites. The presence of alternative forms of transcripts was confirmed in 45% of all detected genes. Surprisingly, a large fraction of LongSAGE tags with hits to the genome (66%) could not be assigned to any gene annotated in EnsEMBL. Among such cases, 2098 LongSAGE tags fell into a region containing a putative gene predicted by GenScan, providing experimental evidence for the presence of real genes, while 9112 genes were found out to be left out or wrongly annotated by the EnsEMBL pipeline.

CONCLUSIONS

LongSAGE transcriptome data can significantly improve the genome annotation by identifying novel genes and alternative transcripts, even in the case of thus far best-characterized organisms like the mouse.

CONTACT

imai@gsf.de.

LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome

MOTIVATION

Despite the increasing notions of the functional importance of antisense transcripts in gene regulation, the genome-wide overview on the ontology of antisense genes has not been obtained. Therefore, we tried to find novel antisense genes genome-wide by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries.

RESULTS

We identified 1260 potential antisense genes, of which 1001 are not annotated in EnsEMBL, thereby being regarded as novel. Interestingly their sense counterparts were co-expressed in the majority of the cases.

CONCLUSIONS

The use of LongSAGE transcriptome data is extremely powerful in the identification of thus-far unknown antisense transcripts, even in the case of well-characterized organisms like the mouse.

CONTACT

imai@gsf.de.

From differential gene expression to differential gene function and back

Following the decoding of several plant and animal genomes, the identification of all corresponding transcripts and proteins and understanding how their expression corresponds to physiological and pathological states is the obvious next step. Nucleic acid quantification methods have become increasingly high-throughput and relatively low-cost, and moving ahead, combinations of technologies monitoring differential gene expression and those defining differential cellular function will yield maximum benefit in furthering biology and for drug target identification and validation.: