SUMOylation by Pias1 Regulates the Activity of the Hedgehog Dependent Gli Transcription Factors

Hedgehog (Hh) signaling, a vital signaling pathway for the development and homeostasis of vertebrate tissues, is mediated by members of the Gli family of zinc finger transcription factors. Hh signaling increases the transcriptional activity of Gli proteins, at least in part, by inhibiting their proteolytic processing. Conversely, phosphorylation by cAMP-dependent protein kinase (PKA) inhibits Gli transcriptional activity by promoting their ubiquitination and proteolysis. Whether other post-translational modifications contribute to the regulation of Gli protein activity has been unclear.Here we provide evidence that all three Gli proteins are targets of small ubiquitin-related modifier (SUMO)-1 conjugation. Expression of SUMO-1 or the SUMO E3 ligase, Pias1, increased Gli transcriptional activity in cultured cells. Moreover, PKA activity reduced Gli protein SUMOylation. Strikingly, in the embryonic neural tube, the forced expression of Pias1 increased Gli activity and induced the ectopic expression of the Gli dependent gene Nkx2.2. Conversely, a point mutant of Pias1, that lacks ligase activity, blocked the endogenous expression of Nkx2.2.Together, these findings provide evidence that Pias1-dependent SUMOylation influences Gli protein activity and thereby identifies SUMOylation as a post-translational mechanism that regulates the hedgehog signaling pathway

Microarray-Based Sketches of the HERV Transcriptome Landscape

Human endogenous retroviruses (HERVs) are spread throughout the genome and their long terminal repeats (LTRs) constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA) and revealed that (i) autonomous active LTRs are broadly subjected to operational determinism (ii) the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii) the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects

From the peas of Gregor Mendel to the human genome and beyond

In the middle of the 19th century, Gregor Mendel conducted his experiments with peas. This took place in the Augustinian monastery in Brno (now the Czech Republic), where he was the abbot. These experiments laid the foundations of modern genetics. At around the same time Charles Darwin formulated his theory of evolution. Through their work, these two men inaugurated the age of modern biology. The next most important step came in 1953 when James Watson and Francis Crick solved the elusive DNA structure. Since then methods for ‘reading’ genetic information have developed quickly, and genomes of many organisms have been analysed, including our own. The human genome consists of 3 billion letters (nucleotides) and it comprises approximately 25,000 genes. The smallest natural genome is the genome of Mycoplasma genitalium. It consists of a mere 500,000 nucleotides and is composed of 500 genes. Yet, mycoplasma is capable of a completely independent life. It would appear from this fact that basic life itself is not overwhelmingly complicated. The human genome is now being compared with the genome of our closest relative, the chimpanzee, with the aim of identifying the basic principles of humanity. A gene was identified that is involved in skull growth (and subsequently in brain growth), and another gene important in the ability to articulate. These two genes mutated at approximately the time when Homo sapiens appeared. However, they can hardly explain the humanization of our predecessor. Only two per cent of the human genome are genes that we need for our life. It is interesting that eight per cent of our genome, i.e., four times more, are genes of viral origin, in other words genes that viruses integrated into the human DNA. We analysed these genes in the human genome and compared them with the viral genes in the chimpanzee genome. Did viral infections and the integration of viral genes in the mammalian genomes contribute to the humanization of our predecessor