Michal Lapidot

Genome‐wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms

Many genomic loci contain transcription units on both strands, therefore two oppositely oriented transcripts can overlap. Often, one strand codes for a protein, whereas the transcript from the other strand is non‐encoding. Such natural antisense transcripts (NATs) can negatively regulate the conjugated sense transcript. NATs are highly prevalent in a wide range of species—for example, around 15% of human protein‐encoding genes have an associated NAT. The regulatory mechanisms by which NATs act are diverse, as are the means to control their expression. Here, we review the current understanding of NAT function and its mechanistic basis, which has been gathered from both individual gene cases and genome‐wide studies. In parallel, we survey findings about the regulation of NAT transcription. Finally, we hypothesize that the regulation of antisense transcription might be tailored to its mode of action. According to this model, the observed relationship between the expression patterns of NATs and their targets might indicate the regulatory mechanism that is in action.

Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE

Recent enhancements and current research in the GeneCards (GC) (http://bioinfo.weizmann.ac.il/cards/) project are described, including the addition of gene expression profiles and integrated gene locations. Also highlighted are the contributions of specialized associated human gene-centric databases developed at the Weizmann Institute. These include the Unified Database (UDB) (http://bioinfo.weizmann.ac.il/udb) for human genome mapping, the human Chromosome 21 database at the Weizmann Insti-tute (CroW 21) (http://bioinfo.weizmann.ac.il/crow21), and the Human Olfactory Receptor Data Explora-torium (HORDE) (http://bioinfo.weizmann.ac.il/HORDE). The synergistic relationships amongst these efforts have positively impacted the quality, quantity and usefulness of the GeneCards gene compendium.

GeneCards™ 2002: towards a complete, object-oriented, human gene compendium

MOTIVATION In the post-genomic era, functional analysis of genes requires a sophisticated interdisciplinary arsenal. Comprehensive resources are challenged to provide consistently improving, state-of-the-art tools. RESULTS GeneCards (Rebhan et al., 1998) has made innovative strides: (a). regular updates and enhancements incorporating new genes enriched with sequences, genomic locations, cDNA assemblies, orthologies, medical information, 3D protein structures, gene expression, and focused SNP summaries; (b). restructured software using object-oriented Perl, migration to schema-driven XML, and (c). pilot studies, introducing methods to produce cards for novel and predicted genes.

Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription

We have generated a WWW interface for automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles. The server provides a wide spectrum of analysis tools that allow de novo discovery of regulatory motifs, along with refinement and in-depth investigation of fully or partially characterized motifs. The presented discovery and analysis tools are fundamentally different from existing tools in their basic rational, statistical background and specificity and sensitivity towards true regulatory elements. We thus anticipate that the service will be of great importance to the experimental and computational biology communities alike. The motif discovery and diagnosis workbench is available at http://longitude.weizmann.ac.il/rMotif/.

Nucleotide variation of regulatory motifs may lead to distinct expression patterns

MOTIVATION Current methodologies for the selection of putative transcription factor binding sites (TFBS) rely on various assumptions such as over-representation of motifs occurring on gene promoters, and the use of motif descriptions such as consensus or position-specific scoring matrices (PSSMs). In order to avoid bias introduced by such assumptions, we apply an unsupervised motif extraction (MEX) algorithm to sequences of promoters. The extracted motifs are assessed for their likely cis-regulatory function by calculating the expression coherence (EC) of the corresponding genes, across a set of biological conditions. RESULTS Applying MEX to all Saccharomyces cerevisiae promoters, followed by EC analysis across 40 biological conditions, we obtained a high percentage of putative cis-regulatory motifs. We clustered motifs that obtained highly significant EC scores, based on both their sequence similarity and similarity in the biological conditions these motifs appear to regulate. We describe 20 clusters, some of which regroup known TFBS. The clusters display different mRNA expression profiles, correlated with typical changes in the nucleotide composition of their relevant motifs. In several cases, a variation of a single nucleotide is shown to lead to distinct differences in expression patterns. These results are confronted with additional information, such as binding of transcription factors to groups of genes. Detailed analysis is presented for clusters related to MCB/SCB, STRE and PAC. In the first two cases, we provide evidence for different binding mechanisms of different clusters of motifs. For PAC-related motifs we uncover a new cluster that has so far been overshadowed by the stronger effects of known PAC motifs. SUPPLEMENTARY INFORMATION Supplementary data are available at http://adios.tau.ac.il/regmotifs and at Bioinformatics online.

GeneCards/spl trade/ 2002: an evolving human gene compendium

GeneCards/spl trade/ (http://bioinfo.weizmann.ac.il/cards/) is an automated, integrated database of human genes, genomic maps, proteins, and diseases, with software that retrieves, consolidates, searches, and displays human genome information. Over the past few years, the system has consistently, added new features including sequence accessions, genomic locations, cDNA assemblies, orthologies, medical information, 3D protein structures, SNP summaries, and gene expression. In parallel, its infrastructure is being upgraded to use object-oriented Perl to produce, display, and search data that is formatted in Extensible Markup Language (XML, (http://www.w3.org/XML), providing a basis for schema-driven display code and context-specific searches.

Characterization of the effects of TF binding site variations on gene expression towards predicting the functional outcomes of regulatory SNPs

This work addresses a central question in medical genetics - the distinction between disease-causing SNPs and neutral variations. Unlike previous studies that focused mainly on coding SNPs, our efforts were centered around variations in regulatory regions and specifically within transcription factor (TF) binding sites. We have compiled a comprehensive collection of genome wide TF binding sites and developed computational measures to estimate the effects of binding site variations on the expression profiles of the regulated genes. Applying these measures to binding sites of known TFs, we were able to make predictions that were in line with published experimental evidence and with structural data on DNA-protein interactions. We attempted to generalize the properties of expression-altering substitutions by accumulating statistics from many substitutions across multiple binding sites. We found that in the yeast genome substitutions that abolish a G or a C are on average more severe than substitutions that abolish an A or a T. This may be attributed to the low GC content of the yeast genome, in which G and C may be important for conferring specificity. We found additional factors that are correlated with the severity of a substitution. Such factors can be integrated in order to create a set of rules for the prioritization of regulatory SNPs according to their disease-causing potential.