FindING a phosphoinositide receptor

Phosphoinositides (PtdInsPs) have diverse roles in cytoplasmic signaling, but so far their function in the nucleus has been unclear. Or Gozani and colleagues have now found that ING2, a PHD finger protein associated with chromatin complexes, is in fact a nuclear receptor for PtdInsPs (Cell 114, 99–111; 2003). Previous studies have shown that overexpression of ING2 stimulates acetylation of p53 and induces apoptosis. Indeed, mutant ING2 that lacks the ability to interact with PtdInsPs through its PHD fingers is unable to induce either. By overexpressing PIKIIβ and effectively reducing levels of PtdIns(5)P, the group eliminated detectable ING2 from chromatin and the nuclear matrix, indicating that PtdInsPs are necessary for subcellular localization of the protein. Gozani et al. then took the work a step further and showed that PHD finger motifs from several proteins can bind PtdInsPs with varying affinities and specificities. Finally, through RNAi-mediated knock-down of ING2, they rendered cells resistant to etoposide-induced cell death. The work suggests an important regulatory role for PtdInsPs—possibly linking them to DNA repair and regulation of p53 function—and identifies a function for PHD finger motifs. MS

Mouse Genes Volume I

Move over, J. K. Rowling. The international FANTOM consortium (Functional Annotation of the Mouse) has put together a special issue of Genome Research (13, 1265–1561; 2003) in which they describe, among other features of the second phase of cDNA annotation, the 'DNA Book.' With 60,770 mouse cDNAs spotted on the pages, the book aims at solving a big problem for the FANTOM project, namely, the predictable increase in requests for cDNAs. Unlike the science required to sequence and categorize, cDNAs still have to be shipped the old-fashioned way. The high cost of shipping every individual cDNA requested on dry ice led the group to consider alternative ways of getting clones to researchers. Jun Kawai and Yoshihide Hayashizaki (Genome Res. 13, 1488–1495; 2003) describe how they plan to distribute the entire RIKEN Mouse Genome Encyclopedia of cDNA clones in a single book or on individual sheets to those in need of a specific clone. To test their hypothesis that cDNAs can be shipped en masse to researchers on water-soluble paper, the group included a sampling of 12 genes from the TCA cycle in the issue. They ask that researchers extract the DNA, amplify the clones using PCR and report their successes and failures back to the RIKEN website. MS

Refining cancer models

The RB/E2F pathway is essential for initiating DNA synthesis and controlling cell proliferation. Somatic inactivation of RB has been implicated in a wide array of cancers. To provide a more accurate model of the occurrence of sporadic cancer in humans, Tyler Jacks and colleagues studied the effect of conditionally knocking out Rb (Nature 424, 223–228; 2003). Experiments compared the conditional elimination of Rb, using the Cre/loxP system, with germline loss of Rb. In cells arrested at G0 owing to low serum concentration, about 20% of the cells incorporated BrdU in germline Rb−/− cells as compared with 50% of cells in which Rb was knocked out after Cre treatment. Thus, somatic disruption of Rb results in a burst of DNA synthesis and re-entry into the cell cycle. The functionally related protein p107 is upregulated in germline Rb−/− cells and seems to compensate for Rb. By contrast, levels of p107 are initially low in conditionally inactivated Rb−/− cells, thereby allowing cell cycle re-entry on Rb deletion. These experiments show that the effect of Rb deletion depends on the timing of the event and provide a more accurate picture of the molecular events after somatic mutation of RB that lead to human cancer. DG

Distantly determined

Sonic hedgehog (SHH) expression is a crucial determinant of limb bud development and the antero-posterior pattern of digits. In a recent study published in Human Molecular Genetics (12, 1725–1735; 2003), Laura Lettice and colleagues characterized an enhancer of SHH that sits inside the gene Lmbr1, fully 1 Mb distant from SHH. An earlier study from some of the same authors (Proc. Natl. Acad. Sci. USA 99, 7548–7553; 2002) provided genetic evidence that a cis-regulator of Shh sits in intron 5 of Lmbr1. In the new study, the authors used transgenics and comparative genomics to refine and define the regulatory element. In mice, a 1.7-kb fragment incorporated into a transgenic reporter construct drove expression patterns similar to normal Shh expression. Moving onto Fugu rubripes, the authors identified a region of approximately 400 bp that is conserved between fish, mice and humans, which also drove an Shh-like expression pattern in mice, thereby further refining the regulatory region. Preaxial polydactyly (PPD) is a relatively common limb deformation syndrome in humans. In four families with PPD, the authors identified mutations in the regulatory element that they propose results in the disorder by affecting SHH expression. Further studies should illuminate how such a distantly located regulatory element controls the expression of SHH. DG

Corals of many colors

Credit: Photo: Mikhail Matz

The pleasingly diverse array of colors displayed by coral reefs is a functional and evolutionary mystery. Ilya Kelmanson and Mikhail Matz have now made some progress by studying color variation in the great star coral Montastraea cavernosa (Mol. Biol. Evol. 20, 1125–1133; 2003). The specific question the authors addressed is whether the basis of intraspecific color variation is due to polymorphism or polyphenism. A polyphenic origin of color diversity would imply epigenetic or environmental influences. M. cavernosa, one of the most common reef-building corals in the Caribbean, has several color variants, and Kelmanson and Matz took advantage of this to search for mutations and differences in expression levels in the genes encoding the GFP-like proteins that are responsible for reef colors. Distinct color morphs of M. cavernosa were found to encode between four and seven such genes, with no sequence differences of consequence in the coding regions. The relative abundances of the gene products, however, were clearly different between morphs. Although regulatory polymorphisms cannot yet be ruled out, the authors favor an environmental explanation for color diversity, given their observation that red-colored colonies are more abundant at greater depths. AP

Research notes written by David Gresham, Alan Packer and Michael Stebbins.