A comparative analysis of transcribed genes in the mouse hypothalamus and neocortex reveals chromosomal clustering

An established kidney cell line from humpback grouper (Cromileptes altivelis) and its susceptibility to bacteria and heavy metals

Humpback grouper (Cromileptes altivelis), one kind of commercial fish with considerable economic value, has been recognized as a promising candidate for mariculture. In the wake of the development of aquaculture industry, the breeding density of C. altivelis has increased gradually, which gave rise to the occurrence of various pathogenic diseases. In our research, we established a new kidney cell line (designated as CAK) from humpback grouper and evaluated its susceptibility to bacteria and heavy metals. The results of our study showed that the optimal growth temperature was 26 °C, and optimal medium was L-15 supplemented with 20% fetal bovine serum (FBS). The sequencing of 18S rRNA gene indicated that CAK cell line was derived from C. altivelis. Chromosome analysis showed that the number of chromosome in CAK was 48. After being transfected of pEGFP-N3 plasmid, high transfection efficiency of CAK was observed, suggesting the potential to be used for the study of foreign functional genes. Moreover, the bacterial susceptibility results revealed that CAK cells were sensitive to Vibrio harveyi and Edwardsiella tarda, especially V. harveyi. Meanwhile, three heavy metals (Hg, Cu, and Cd) had toxic effects on the CAK cells with a dose-dependent manner. To sum up, the CAK cell line might be an ideal tool in vitro for analyzing the function of exogenous genes, bacterial susceptibility, and toxicity assay of heavy metals.

Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish

Background

Calcium ion is tightly regulated in body fluids and for euryhaline fish, which are exposed to rapid changes in environmental [Ca²⁺], homeostasis is especially challenging. The gill is the main organ of active calcium uptake and therefore plays a crucial role in the maintenance of calcium ion homeostasis. To study the molecular basis of the short-term responses to changing calcium availability, the whole gill transcriptome obtained by Super Serial Analysis of Gene Expression (SuperSAGE) of the euryhaline teleost green spotted puffer fish, Tetraodon nigroviridis, exposed to water with altered [Ca²⁺] was analysed.

Results

Transfer of T. nigroviridis from 10 ppt water salinity containing 2.9 mM Ca²⁺ to high (10 mM Ca²⁺ ) and low (0.01 mM Ca²⁺) calcium water of similar salinity for 2-12 h resulted in 1,339 differentially expressed SuperSAGE tags (26-bp transcript identifiers) in gills. Of these 869 tags (65%) were mapped to T. nigroviridis cDNAs or genomic DNA and 497 (57%) were assigned to known proteins. Thirteen percent of the genes matched multiple tags indicating alternative RNA transcripts. The main enriched gene ontology groups belong to Ca²⁺ signaling/homeostasis but also muscle contraction, cytoskeleton, energy production/homeostasis and tissue remodeling. K-means clustering identified co-expressed transcripts with distinct patterns in response to water [Ca²⁺] and exposure time.

Conclusions

The generated transcript expression patterns provide a framework of novel water calcium-responsive genes in the gill during the initial response after transfer to different [Ca²⁺]. This molecular response entails initial perception of alterations, activation of signaling networks and effectors and suggests active remodeling of cytoskeletal proteins during the initial acclimation process. Genes related to energy production and energy homeostasis are also up-regulated, probably reflecting the increased energetic needs of the acclimation response. This study is the first genome-wide transcriptome analysis of fish gills and is an important resource for future research on the short-term mechanisms involved in the gill acclimation responses to environmental Ca²⁺ changes and osmoregulation.

A serial analysis of gene expression profile of the Alzheimer's disease Tg2576 mouse model

Serial analysis of gene expression (SAGE), a technique that allows for the simultaneous detection of expression levels of the entire genome without a priori knowledge of gene sequences, was used to examine the transcriptional expression pattern of the Tg2576 mouse model of Alzheimer's disease (AD). Pairwise comparison between the Tg2576 and nontransgenic SAGE libraries identified a number of differentially expressed genes in the Tg2576 SAGE library, some of which were not previously revealed by the microarray studies. Real-time PCR was used to validate a panel of genes selected from the SAGE analysis in the Tg2576 mouse brain, as well as the hippocampus and temporal cortex of sporadic AD and normal age-matched controls. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 5 (NDUFA5) and FXYD domain-containing ion transport regulator 6 (FXYD6) were found to be significantly decreased in the Tg2576 mouse brain and AD hippocampus. PTEN-induced putative kinase 1 (PINK1), phosphatidylethanolamine binding protein (PEBP), crystalline mu (CRYM), and neurogranin (NRGN) were significantly decreased in AD tissues. The gene ontologies represented in the Tg2576 data were statistically analyzed and demonstrated a significant under-representation of genes involved with G-protein-coupled receptor signaling and odorant binding, while genes significantly over-represented were focused on cellular communication and cellular physiological processes. The novel approach of profiling the Tg2576 mouse brain using SAGE has identified different genes that could subsequently be examined for their potential as peripheral diagnostic and prognostic markers for Alzheimer's disease.

Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling

BACKGROUND

Development of the cerebral cortex requires highly specific spatio-temporal regulation of gene expression. It is proposed that transcriptome profiling of the cerebral cortex at various developmental time points or regions will reveal candidate genes and associated molecular pathways involved in cerebral corticogenesis.

RESULTS

Serial analysis of gene expression (SAGE) libraries were constructed from C57BL/6 mouse cerebral cortices of age embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4 to 6 months. Hierarchical clustering analysis of 561 differentially expressed transcripts showed regionalized, stage-specific and co-regulated expression profiles. SAGE expression profiles of 70 differentially expressed transcripts were validated using quantitative RT-PCR assays. Ingenuity pathway analyses of validated differentially expressed transcripts demonstrated that these transcripts possess distinctive functional properties related to various stages of cerebral corticogenesis and human neurological disorders. Genomic clustering analysis of the differentially expressed transcripts identified two highly transcribed genomic loci, Sox4 and Sox11, during embryonic cerebral corticogenesis. These loci feature unusual overlapping sense and antisense transcripts with alternative polyadenylation sites and differential expression. The Sox4 and Sox11 antisense transcripts were highly expressed in the brain compared to other mouse organs and are differentially expressed in both the proliferating and differentiating neural stem/progenitor cells and P19 (embryonal carcinoma) cells.

CONCLUSIONS

We report validated gene expression profiles that have implications for understanding the associations between differentially expressed transcripts, novel targets and related disorders pertaining to cerebral corticogenesis. The study reports, for the first time, spatio-temporally regulated Sox4 and Sox11 antisense transcripts in the brain, neural stem/progenitor cells and P19 cells, suggesting they have an important role in cerebral corticogenesis and neuronal/glial cell differentiation.

Modified PCR methods for 3' end amplification from serial analysis of gene expression (SAGE) tags

Serial analysis of gene expression (SAGE) is a powerful technique to study gene expression at the genome level. However, a disadvantage of the shortness of SAGE tags is that it prevents further study of SAGE library data, thus limiting extensive application of the SAGE method in gene expression studies. However, this problem can be solved by extension of the SAGE tags to 3' cDNAs. Therefore, several methods based on PCR have been developed to generate a 3' longer fragment cDNA corresponding to a SAGE tag. The list of modified methods is extensive, and includes rapid RT-PCR analysis of unknown SAGE tags (RAST-PCR), generation of longer cDNA fragments from SAGE tags for gene identification (GLGI), a high-throughput GLGI procedure, reverse SAGE (rSAGE), two-step analysis of unknown SAGE tags (TSAT-PCR), etc. These procedures are constantly being updated because they have characteristics and advantages that can be shared. Development of these methods has promoted the widespread use of the SAGE technique, and has accelerated the speed of studies of large-scale gene expression.

Feeding induced changes in the hypothalamic transcriptome

BACKGROUND

Obesity is a complex multifactorial disorder which needs a comprehensive approach for prevention and treatment. We investigated the modifications in the hypothalamic gene expression induced by high-fat (HF) and low-fat (LF) meal ingestion in mice, in order to identify the signals rapidly mediating the hypothalamic control on energy intake.

METHODS

After fasting, 1 group of mice was sacrificed and the others were fed ad libitum with HF or LF diet, and sacrificed 3 h after the beginning of the meal. The hypothalamus was sampled and the serial analysis of gene expression method was performed.

RESULTS

Approximately 254,588 tags, which correspond to 65,548 tag species were isolated from the 3 groups. The data showed twelve transcripts regulated by food intake. Among these, 2 transcripts have mitochondrial functions (MtCo1, Ppid), 3 are involved in protein transport and regulation (Ube2q2, Mup1, Sec13), 1 in cellular pH control (Slc4a3) and another 1 has a role in the epigenetic control of gene expression (Setd3). In addition, 5 potentially novel transcripts were differentially modulated.

CONCLUSION

We identified genes that may regulate hypothalamic circuits governing the early response to food intake. 3 genes were specifically modulated by high-fat intake.

Gene expression atlas of the mouse central nervous system: impact and interactions of age, energy intake and gender

The transcriptional profiles of five regions of the central nervous system (CNS) of mice varying in age, gender and dietary intake were measured by microarray. The resulting data provide insights into the mechanisms of age-, diet- and gender-related CNS plasticity and vulnerability in mammals.

Background

The structural and functional complexity of the mammalian central nervous system (CNS) is organized and modified by complicated molecular signaling processes that are poorly understood.

Results

We measured transcripts of 16,896 genes in 5 CNS regions from cohorts of young, middle-aged and old male and female mice that had been maintained on either a control diet or a low energy diet known to retard aging. Each CNS region (cerebral cortex, hippocampus, striatum, cerebellum and spinal cord) possessed its own unique transcriptome fingerprint that was independent of age, gender and energy intake. Less than 10% of genes were significantly affected by age, diet or gender, with most of these changes occurring between middle and old age. The transcriptome of the spinal cord was the most responsive to age, diet and gender, while the striatal transcriptome was the least responsive. Gender and energy restriction had particularly robust influences on the hippocampal transcriptome of middle-aged mice. Prominent functional groups of age- and energy-sensitive genes were those encoding proteins involved in DNA damage responses (Werner and telomere-associated proteins), mitochondrial and proteasome functions, cell fate determination (Wnt and Notch signaling) and synaptic vesicle trafficking.

Conclusion

Mouse CNS transcriptomes responded to age, energy intake and gender in a regionally distinctive manner. The systematic transcriptome dataset also provides a window into mechanisms of age-, diet- and sex-related CNS plasticity and vulnerability.

CREB binding and activity in brain: regional specificity and induction by electroconvulsive seizure

BACKGROUND

The transcription factor cyclic adenosine monophosphate response element binding protein (CREB) orchestrates diverse neurobiological processes including cell differentiation, survival, and plasticity. Alterations in CREB-mediated transcription have been implicated in numerous central nervous system (CNS) disorders including depression, anxiety, addiction, and cognitive decline. However, it remains unclear how CREB contributes to normal and aberrant CNS function, as the identity of CREB-regulated genes in brain and the regional and temporal dynamics of CREB function remain largely undetermined.

METHODS

We combined microarray and chromatin immunoprecipitation technology to analyze CREB-DNA interactions in brain. We compared the occupancy and activity of CREB at gene promoters in rat frontal cortex, hippocampus, and striatum before and after a rodent model of electroconvulsive therapy.

RESULTS

Our analysis identified >860 CREB binding sites in rat brain. We identified multiple genomic loci enriched with CREB binding sites and find that CREB-occupied transcripts interact extensively to promote cell proliferation, plasticity, and resiliency. We discovered regional differences in CREB occupancy and activity that explain, in part, the diverse biological and behavioral outputs of CREB activity in frontal cortex, hippocampus, and striatum. Electroconvulsive seizure rapidly increased CREB occupancy and/or phosphorylation at select promoters, demonstrating that both events contribute to the temporal regulation of the CREB transcriptome.

CONCLUSIONS

Our data provide a mechanistic basis for CREB's ability to integrate regional and temporal cues to orchestrate state-specific patterns of transcription in the brain, indicate that CREB is an important mediator of the biological responses to electroconvulsive seizure, and provide global mechanistic insights into CREB's role in psychiatric and cognitive function.

Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models

Using serial analysis of gene expression, we collected quantitative transcriptome data in 11 regions of the adult wild-type mouse brain: the orbital, prelimbic, cingulate, motor, somatosensory, and entorhinal cortices, the caudate-putamen, the nucleus accumbens, the thalamus, the substantia nigra, and the ventral tegmental area. With >1.2 million cDNA tags sequenced, this database is a powerful resource to explore brain functions and disorders. As an illustration, we performed interregional comparisons and found 315 differential transcripts. Most of them are poorly characterized and 20% lack functional annotation. For 78 differential transcripts, we provide independent expression level measurements in mouse brain regions by real-time quantitative RT-PCR. We also show examples where we used in situ hybridization to achieve infrastructural resolution. For 30 transcripts, we next demonstrated that regional enrichment is conserved in the human brain. We then quantified the expression levels of region-enriched transcripts in the R6/2 mouse model of Huntington disease and the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of Parkinson disease and observed significant alterations in the striatum, cerebral cortex, thalamus and substantia nigra of R6/2 mice and in the striatum of MPTP-treated mice. These results show that the gene expression data provided here for the mouse brain can be used to explore pathophysiological models and disclose transcripts differentially expressed in human brain regions.

Transcriptome analysis reveals season-specific rbcS gene expression profiles in diploid perennial ryegrass (Lolium perenne L.)

Perennial ryegrass (Lolium perenne L.) is a major grass species used for forage and turf throughout the world, and gains by conventional breeding have reached a plateau. Perennial ryegrass is an outcrossing, self-incompatible diploid (2n = 2x = 14) with a relatively large genome (4067 Mbp/diploid genome; Evans, G.M., Rees, H., Snell, C.L. and Sun, S. (1972) The relation between nuclear DNA amount and the duration of the mitotic cycle. Chrom. Today, 3, 24-31). Using tissues sourced from active pastures during the peak of the autumn, winter, spring and summer seasons, we analysed the ryegrass transcriptome employing a Serial Analysis of Gene Expression (SAGE) protocol, with the dual goals of understanding the seasonal changes in perennial ryegrass gene expression and enhancing our ability to select genes for genetic manipulation. A total of 159,002 14-mer SAGE tags was sequenced and mapped to the perennial ryegrass DNA database, comprising methyl-filtered (GeneThresher) and expressed sequence tag (EST) sequences. The analysis of 14,559 unique SAGE tags, which were present more than once in our SAGE library, revealed 964, 1331, 346 and 131 exclusive transcripts to autumn, winter, spring and summer, respectively. Intriguingly, our analysis of the SAGE tags revealed season-specific expression profiles for the small subunit of ribulose-1,5-bisphosphate carboxylase (Rubisco), LprbcS. The transcript level for LprbcS was highest in spring, and then decreased gradually between summer and winter. Five different copies of LprbcS were revealed in ryegrass, with one possibly producing splice variant transcripts. Two highly expressed LprbcS genes were reported, one of which was not active in autumn. Another LprbcS gene showed an inverse expression profile to the autumn inactive LprbcS in a manner to compensate the expression level.

Nedd4-WW domain-binding protein 5 (Ndfip1) is associated with neuronal survival after acute cortical brain injury

Understanding the transcriptional response to neuronal injury after trauma is a necessary prelude to formulation of therapeutic strategies. We used Serial Analysis of Gene Expression (SAGE) to identify 50,000 sequence tags representing 18,000 expressed genes in the cortex 2 h after traumatic brain injury (TBI). A similar tag library was obtained from sham-operated cortex. The SAGE data were validated on biological replicates using quantitative real-time-PCR on multiple samples at 2, 6, 12, and 24 h after TBI. This analysis revealed that the vast majority of genes showed a downward trend in their pattern of expression over 24 h. This was confirmed for a subset of genes using in situ hybridization and immunocytochemistry on brain sections. Of the overexpressed genes in the trauma library, Nedd4-WW (neural precursor cell expressed, developmentally downregulated) domain-binding protein 5 (N4WBP5) (also known as Ndfip1) is strongly expressed in surviving neurons around the site of injury. Overexpression of N4WBP5 in cultured cortical neurons increased the number of surviving neurons after gene transfection and growth factor starvation compared with control transfections. These results identify N4WBP5 as a neuroprotective protein and, based on its known interaction with the ubiquitin ligase Nedd4, would suggest protein ubiquitination as a possible survival strategy in neuronal injury.

Structure and function of the human genome

The human genome project has had an impact on both biological research and its political organization; this review focuses primarily on the scientific novelty that has emerged from the project but also touches on its political dimensions. The project has generated both anticipated and novel information; in the later category are the description of the unusual distribution of genes, the prevalence of non-protein-coding genes, and the extraordinary evolutionary conservation of some regions of the genome. The applications of the sequence data are just starting to be felt in basic, rather than therapeutic, biomedical research and in the vibrant human origins and variation debates. The political impact of the project is in the unprecedented extent to which directed funding programs have emerged as drivers of basic research and the organization of the multidisciplinary groups that are needed to utilize the human DNA sequence.

Interpreting experimental results using gene ontologies

High-throughput experimental techniques, such as microarrays, produce large amounts of data and knowledge about gene expression levels. However, interpretation of these data and turning it into biologically meaningful knowledge can be challenging. Frequently the output of such an analysis is a list of significant genes or a ranked list of genes. In the case of DNA microarray studies, data analysis often leads to lists of hundreds of differentially expressed genes. Also, clustering of gene expression data may lead to clusters of tens to hundreds of genes. These data are of little use if one is not able to interpret the results in a biological context. The Gene Ontology Consortium provides a controlled vocabulary to annotate the biological knowledge we have or that is predicted for a given gene. The Gene Ontologies (GOs) are organized as a hierarchy of annotation terms that facilitate an analysis and interpretation at different levels. The top-level ontologies are molecular function, biological process, and cellular component. Several annotation databases for genes of different organisms exist. This chapter describes how to use GO in order to help biologically interpret the lists of genes resulting from high-throughput experiments. It describes some statistical methods to find significantly over- or underrepresented GO terms within a list of genes and describes some tools and how to use them in order to do such an analysis. This chapter focuses primarily on the tool GOstat (http://gostat.wehi.edu.au). Other tools exist that enable similar analyses, but are not described in detail here.

Cancer in xeroderma pigmentosum and related disorders of DNA repair

Nucleotide-excision repair diseases exhibit cancer, complex developmental disorders and neurodegeneration. Cancer is the hallmark of xeroderma pigmentosum (XP), and neurodegeneration and developmental disorders are the hallmarks of Cockayne syndrome and trichothiodystrophy. A distinguishing feature is that the DNA-repair or DNA-replication deficiencies of XP involve most of the genome, whereas the defects in CS are confined to actively transcribed genes. Many of the proteins involved in repair are also components of dynamic multiprotein complexes, transcription factors, ubiquitylation cofactors and signal-transduction networks. Complex clinical phenotypes might therefore result from unanticipated effects on other genes and proteins.

Global analysis of IL-2 target genes: identification of chromosomal clusters of expressed genes

T lymphocytes play a central role in controlling adaptive immune responses. IL-2 critically regulates both T cell growth and death and is involved in maintaining peripheral tolerance, but the molecules involved in these and other IL-2 actions are only partially known. We now provide a comprehensive compendium of the genes expressed in T cells and of those regulated by IL-2 based on a combination of DNA microarrays and serial analysis of gene expression (SAGE). The newly identified IL-2 target genes include many genes previously linked to apoptosis in other cellular systems that may contribute to IL-2-dependent survival functions. We also studied the mRNA expression of known regulators of signaling pathways for their induction in response to IL-2 in order to identify potential novel positive and/or negative feedback regulators of IL-2 signaling. We show that IL-2 regulates only a limited number of these genes. These include suppressors of cytokine signaling (SOCS) 1, SOCS2, dual-specificity phosphatase (DUSP) 5, DUSP6 and non-receptor type phosphatase-7 (PTPN7). Additionally, we provide evidence that many genes expressed in T cells locate in chromosomal clusters, and that select IL-2-regulated genes are located in at least two clusters, one at 5q31, a known cytokine gene cluster, and the other at 6p21.3, a region that contains genes encoding the tumor necrosis factor (TNF) superfamily members TNF, LT-alpha and LT-beta.