The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the literature supporting these data. The amount of information and the number of features provided by SGD have increased greatly following the release of the S.cerevisiae genomic sequence, which is currently the only complete sequence of a eukaryotic genome. SGD aids researchers by providing not only basic information, but also tools such as sequence similarity searching that lead to detailed information about features of the genome and relationships between genes. SGD presents information using a variety of user-friendly, dynamically created graphical displays illustrating physical, genetic and sequence feature maps. SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/

The entire DNA sequence of chromosome III of the yeast Saccharomyces cerevisiae has been determined. This is the first complete sequence analysis of an entire chromosome from any organism. The 315-kilobase sequence reveals 182 open reading frames for proteins longer than 100 amino acids, of which 37 correspond to known genes and 29 more show some similarity to sequences in databases. Of 55 new open reading frames analysed by gene disruption, three are essential genes; of 42 non-essential genes that were tested, 14 show some discernible effect on phenotype and the remaining 28 have no overt function.

The expression of some nuclear genes in Saccharomyces cerevisiae, such as the CIT2 gene, which encodes a glyoxylate cycle isoform of citrate synthase, is responsive to the functional state of mitochondria. Previous studies identified a basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor encoded by the RTG1 gene that is required for both basal expression of the CIT2 gene and its increased expression in respiratorydeficient cells. Here, we describe the cloning and characterization of RTG3, a gene encoding a 54-kDa bHLH/ Zip protein that is also required for CIT2 expression. Rtg3p binds together with Rtg1p to two identical sites oriented as inverted repeats 28 bp apart in a regulatory upstream activation sequence element (UAS r ) in the CIT2 promoter. The core binding site for the Rtg1p-Rtg3p heterodimer is 5-GGTCAC-3, which differs from the canonical E-box site, CANNTG, to which most other bHLH proteins bind. We demonstrate that both of the Rtg1p-Rtg3p binding sites in the UAS r element are required in vivo and act synergistically for CIT2 expression. The basic region of Rtg3p conforms well to the basic region of most bHLH proteins, whereas the basic region of Rtg1p does not. These findings suggest that the Rtg1p-Rtg3p complex interacts in a novel way with its DNA target sites.Cells of the yeast Saccharomyces cerevisiae are able to monitor and respond to changes in mitochondrial function through accommodating changes in nuclear gene expression (26). We have referred to this process as retrograde regulation, which can be thought of as a stress response to mitochondrial dysfunctions (reviewed by Shyjan and Butow [36]). One example of retrograde regulation is the elevated expression of the CIT2 gene in response to various mitochondrial lesions (17). CIT2 encodes a peroxisomal isoform of citrate synthase (CS2) (15, 21) that functions in the glyoxylate cycle. CS2 has 83% sequence similarity with the tricarboxylic acid (TCA) cycle isoform of citrate synthase, CS1, encoded by the CIT1 gene. Various mitochondrial lesions, such as a block in the TCA cycle or the loss of mitochondrial DNA, result in a transcriptional activation of CIT2 anywhere from 2-to 30-fold. This activation is dependent, in part, on the kind mitochondrial defect (4, 17). We have suggested that the corresponding increases in CS2 activity could compensate for decreases in TCA cycle activity (17) through the known metabolic interactions between the glyoxylate and TCA cycles (38).We have identified two genes, RTG1 and RTG2, that are central to this novel signaling pathway (16). Each is required for basal as well as retrograde-regulated CIT2 expression. Surprisingly, both RTG1 and RTG2 are also essential for peroxisome proliferation (4, 13), which can be induced in yeast cells by the presence of oleic acid in the growth medium (14,37,40). RTG1 and RTG2 are also required for the oleic acid-dependent increase in expression of POX genes (encoding enzymes of the ␤-oxidation pathway) and PMP27, which encodes a protein associated with peroxisoma...

Transcriptome analysis of human brain provides fundamental insight about development and disease, but largely relies on existing annotation. We sequenced transcriptomes of 72 prefrontal cortex samples across six life stages, and identified 50,650 differentially expression regions (DERs) associated with developmental and aging, agnostic of annotation. While many DERs annotated to non-exonic sequence (41.1%), most were similarly regulated in cytosolic mRNA extracted from independent samples. The DERs were developmentally conserved across 16 brain regions and within the developing mouse cortex, and were expressed in diverse cell and tissue types. The DERs were further enriched for active chromatin marks and clinical risk for neurodevelopmental disorders like schizophrenia. Lastly, we demonstrate quantitatively that these DERs associate with a changing neuronal phenotype related to differentiation and maturation. These data highlight conserved molecular signatures of transcriptional dynamics across brain development, some potential clinical relevance and the incomplete annotation of the human brain transcriptome.

Genome-wide association studies (GWASs) have reported many single nucleotide polymorphisms (SNPs) associated with psychiatric disorders, but knowledge is lacking regarding molecular mechanisms. Here we show that risk alleles spanning multiple genes across the 10q24.32 schizophrenia-related locus are associated in the human brain selectively with an increase in the expression of both BLOC-1 related complex subunit 7 (BORCS7) and a previously uncharacterized, human-specific arsenite methyltransferase (AS3MT) isoform (AS3MT(d2d3)), which lacks arsenite methyltransferase activity and is more abundant in individuals with schizophrenia than in controls. Conditional-expression analysis suggests that BORCS7 and AS3MT(d2d3) signals are largely independent. GWAS risk SNPs across this region are linked with a variable number tandem repeat (VNTR) polymorphism in the first exon of AS3MT that is associated with the expression of AS3MT(d2d3) in samples from both Caucasians and African Americans. The VNTR genotype predicts promoter activity in luciferase assays, as well as DNA methylation within the AS3MT gene. Both AS3MT(d2d3) and BORCS7 are expressed in adult human neurons and astrocytes, and they are upregulated during human stem cell differentiation toward neuronal fates. Our results provide a molecular explanation for the prominent 10q24.32 locus association, including a novel and evolutionarily recent protein that is involved in early brain development and confers risk for psychiatric illness.

A pharmacogenetics-based dosing algorithm has been developed for improvement in the time to reach the stable dosing of warfarin. This model may be useful in helping the clinicians to prescribe warfarin with greater safety and efficiency.

RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on highquality RNA. We demonstrate here that statistical adjustment using existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. Using RNA-seq data from molecular degradation experiments of human primary tissues, we introduce a methodquality surrogate variable analysis (qSVA)-as a framework for estimating and removing the confounding effect of RNA quality in differential expression analysis. We show that this approach results in greatly improved replication rates (>3×) across two large independent postmortem human brain studies of schizophrenia and also removes potential RNA quality biases in earlier published work that compared expression levels of different brain regions and other diagnostic groups. Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from human tissue.RNA sequencing | differential expression analysis | statistical modeling | RNA quality M icroarrays and RNA sequencing (RNA-seq) can measure gene expression levels across hundreds of samples in a single experiment. As gene expression levels are measured with error, normalization procedures have been implemented for both microarray (1) and RNA sequencing (2) data to reduce technical variability, including controlling for variability associated with how and when the samples are run, so-called "batch" effects (3). Recent research has further characterized this expression variability in RNA-seq data (4-6), including demonstrating variability associated with technical factors involved in the preparation, sequencing, and analysis of samples. Variability in gene expression is particularly influenced by RNA quality (7) because accurately measuring gene expression levels strongly depends on the quality of the input RNA. This suggests that a portion of traditionally measured latent "batch" effects could actually be attributed to the underlying quality of the input RNA.Postmortem studies typically extract RNA from tissue that has been susceptible to a wide variety of antemortem and postmortem factors. Several approaches exist for quantifying the quality of the input RNA before sequencing library construction, including UV absorption ratios of 280 nm to 260 nm and RNA integrity numbers (RINs). RIN is a machine learning-derived measurement resulting from placing RNA on a Bioanalyzer and obtaining a tracing of fragment sizes per sample. RIN ranges from 10 (very high quality RNA) to 0 (completely degraded RNA), and the apparent intactness of ribosomal RNAs (which are two large peaks in the fragment size tracing) is one of the most discriminating factors that distinguishes very high quality from moderate quality RNA (8). Recommended RIN thresholds for sample exclusion before data generation have been suggested as low as 5.0 for PCR (7) and 7.0 for RNA-seq. (9). However, even high quality samples (RIN ...

We have adapted a LacZ promoter trap screen developed by Burns et al.(1994) to search for genes whose expression is dependent on Rtg2p, a protein with an N‐terminal hsp70/actin/sugar kinase ATP binding domain. Rtg2p acts upstream of the basic helix–loop–helix/leucine zipper transcription factors, Rtg1p and Rtg3p. All three proteins are known to be required for the expression of the CIT2 gene, which encodes a peroxisomal isoform of citrate synthase whose expression is also dependent on the functional state of mitochondria. Using this screen, we have identified a previously uncharacterized gene, YEL071w, predicted to encode a protein of 496 amino acids that shares 80% homology and 60% sequence identity with actin interacting protein 2, encoded by the AIP2 gene; both proteins also share sequence similarity to aD‐lactate dehydrogenase encoded by the DLD1 gene. Expression of YEL071w is dependent on the functional state of mitochondria and on all three of the Rtg proteins, whereas AIP2 expression is independent of the Rtg proteins and the functional state of mitochondria. Like CIT2, the 5′ flanking region of YEL071w contains two R box binding sites for the Rtg1p/Rtg3p heterodimeric transcription complex. Both R boxes are necessary for full YEL071w expression. We show that YEL071w and AIP2 encode proteins withD‐lactate dehydrogenase activity, the former located in the cytoplasm and the latter in the mitochondrial matrix. Our data thus provide gene assignments for two previously unrecognizedD‐lactate dehydrogenase activities in yeast. Copyright © 1999 John Wiley & Sons, Ltd.