Characterizing the genetic programs that specify development and evolution of the cerebral cortex is a central challenge in neuroscience. Stem cells in the transient embryonic ventricular and subventricular zones generate neurons that migrate across the intermediate zone to the overlying cortical plate, where they differentiate and form the neocortex. It is clear that not one but a multitude of molecular pathways are necessary to progress through each cellular milestone, yet the underlying transcriptional programs remain unknown. Here, we apply differential transcriptome analysis on microscopically isolated cell populations, to define five transcriptional programs that represent each transient embryonic zone and the progression between these zones. The five transcriptional programs contain largely uncharacterized genes in addition to transcripts necessary for stem cell maintenance, neurogenesis, migration, and differentiation. Additionally, we found intergenic transcriptionally active regions that possibly encode unique zone-specific transcripts. Finally, we present a highresolution transcriptome map of transient zones in the embryonic mouse forebrain.radial glia | pyramidal neurons | cortical development | laser microdissection

We report a new strategy for cell-type-specific delivery of functional siRNAs into cells. The method involves the noncovalent attachment of siRNAs to ligand-conjugated oligodeoxynucleotides via nucleic acid base-paired interactions. The resulting complexes can be directly applied to cells, leading to specific cellular uptake and gene silencing. The method is simple, economical, and can be easily adapted for other cell surface receptors. Here we show the application of this method for the delivery of siRNAs to folate receptor-expressing cells.

We have exploited the ability of transmembrane domains to engage in highly specific protein-protein interactions to construct a new class of small proteins that inhibit HIV infection. By screening a library encoding hundreds of thousands of artificial transmembrane proteins with randomized transmembrane domains (termed “traptamers,” for transmembrane aptamers), we isolated six 44- or 45-amino-acid proteins with completely different transmembrane sequences that inhibited cell surface and total expression of the HIV coreceptor CCR5. The traptamers inhibited transduction of human T cells by HIV reporter viruses pseudotyped with R5-tropic gp120 envelope proteins but had minimal effects on reporter viruses with X4-tropic gp120. Optimization of two traptamers significantly increased their activity and resulted in greater than 95% inhibition of R5-tropic reporter virus transduction without inhibiting expression of CD4, the primary HIV receptor, or CXCR4, another HIV coreceptor. In addition, traptamers inhibited transduction mediated by a mutant R5-tropic gp120 protein resistant to maraviroc, a small-molecule CCR5 inhibitor, and they dramatically inhibited replication of an R5-tropic laboratory strain of HIV in a multicycle infection assay. Genetic experiments suggested that the active traptamers specifically interacted with the transmembrane domains of CCR5 and that some of the traptamers interacted with different portions of CCR5. Thus, we have constructed multiple proteins not found in nature that interfere with CCR5 expression and inhibit HIV infection. These proteins may be valuable tools to probe the organization of the transmembrane domains of CCR5 and their relationship to its biological activities, and they may serve as starting points to develop new strategies to inhibit HIV infection.

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eThe 44-amino-acid E5 protein of bovine papillomavirus is a dimeric transmembrane protein that exists in a stable complex with the platelet-derived growth factor (PDGF) ␤ receptor, causing receptor activation and cell transformation. The transmembrane domain of the PDGF ␤ receptor is required for complex formation, but it is not known if the two proteins contact one another directly. Here, we studied a PDGF ␤ receptor mutant containing a leucine-to-isoleucine substitution in its transmembrane domain, which prevents complex formation with the wild-type E5 protein in mouse BaF3 cells and inhibits receptor activation by the E5 protein. We selected E5 mutants containing either a small deletion or multiple substitution mutations that restored binding to the mutant PDGF ␤ receptor, resulting in receptor activation and growth factor independence. These E5 mutants displayed lower activity with PDGF ␤ receptor mutants containing other transmembrane substitutions in the vicinity of the original mutation, and one of them cooperated with a receptor mutant containing a distal mutation in the juxtamembrane domain. These results provide strong genetic evidence that the transmembrane domains of the E5 protein and the PDGF ␤ receptor contact one another directly. They also demonstrate that different mutations in the E5 protein allow it to tolerate the same mutation in the PDGF ␤ receptor transmembrane domain and that a mutation in the E5 protein can allow it to tolerate different mutations in the PDGF ␤ receptor. Thus, the rules governing direct interactions between transmembrane helices are complex and not restricted to local interactions. Proteins that span cellular membranes are thought to comprise up to 30% of the proteome (1). The membrane-spanning segments of most of these transmembrane proteins adopt an ␣-helical conformation and can undergo highly specific, lateral interactions to form oligomeric protein complexes or properly folded multipass transmembrane proteins (2, 3). These helical interactions are often essential for biological activity, but the structural basis of the vast majority of transmembrane interactions is not understood because of difficulties in obtaining high-resolution structures of transmembrane helical bundles. Mutational analysis showed that homodimeric helix-helix interactions can be determined by highly specific interactions between amino acid side chains (4). Formation of heteromeric transmembrane complexes can be mediated by interactions between hydrophilic amino acid side chains (5-7), but the structural basis for the specificity of heteromeric transmembrane interactions has not been studied in detail. In our laboratory, we have developed genetic methods to analyze heteromeric transmembrane interactions in mammalian cells and showed that artificial transmembrane proteins can undergo specific functional interactions with native transmembrane proteins (8-12).The 44-amino-acid E5 oncoprotein of bovine papillomavirus type 1 (BPV) is essentially an isolated transmembrane domain that forms a homodime...