Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome

In vivo and transcriptome-wide identification of RNA binding protein target sites

Animal mRNAs are regulated by hundreds of RNA binding proteins (RBPs). The identification of RBP targets is crucial for understanding their function. A recent method, PAR-CLIP, uses photoreactive nucleosides to crosslink RBPs to target RNAs in cells prior to immunoprecipitation. Here, we establish iPAR-CLIP (in vivo PAR-CLIP) to determine, at nucleotide resolution, transcriptome-wide binding sites of GLD-1, a conserved, germline-specific translational repressor in C. elegans. We identified 439 reproducible target mRNAs and demonstrate an excellent dynamic range of target detection by iPAR-CLIP. Upon GLD-1 knockdown, protein but not mRNA expression of the 439 targets was specifically upregulated, demonstrating functionality. Finally, we discovered strongly conserved GLD-1 binding sites near the start codon of target genes. These sites are functional in vitro and likely confer strong repression in vivo. We propose that GLD-1 interacts with the translation machinery near the start codon, a so-far-unknown mode of gene regulation in eukaryotes

Comunidade arbórea de uma floresta estacional decídua sobre afloramento calcário na Bacia do rio Paraná Arboreal community of a seasonal deciduous forest on limestone outcrop in São Domingos - Goiás, Parana river Basin, Brazil

A bacia do rio Paraná (GO e TO), com 5.940.382 ha, tem alta diversidade de fitofisionomias, com sua flora pouco conhecida. As atividades de extração de madeira e implantação de pastagem contribuíram decisivamente para a remoção da vegetação. Este estudo foi conduzido em uma floresta estacional decídua sobre afloramento calcário (aproximadamente 13º41'16"S e 46º44'20"W e 462 m de altitude) - fazenda Canadá (São Domingos-GO). Foram demarcadas cinco linhas paralelas, a intervalos de 100 m, onde foram distribuídas aleatoriamente 25 parcelas de 20 x 20 m (total de 1 ha). Em cada parcela foram amostradas todas as árvores com diâmetro do caule a 1,3 m de altura do solo (DAP) > 5 cm, nos quais foi medido o DAP, estimada a altura máxima e identificada a espécie. Foram amostrados 924 indivíduos de 48 espécies, 38 gêneros e 24 famílias e obtidos o índice de Shannon-Wienner de 2,99 nats/ind. e a equabilidade de 0,77. As espécies que apresentaram maior valor de importância (VI) foram Myracrodruon urundeuva (36,09), Pseudobombax tomentosum (34,75), Dilodendron bipinnatum (26,61), Combretum duarteanum (22,19), Jacaranda brasiliana (21,57), Commiphora leptophloeos (19,18), Astronium fraxinifolium (13,84), Tabebuia impetiginosa (13,79), Pseudobombax longiflorum (11,64) e Machaerium scleroxylon (10,00), que juntas somaram 69,9% do VI total. A diversidade foi próxima à encontrada em outros trabalhos em floresta estacional decídua sobre solo e afloramento na região.<br>The Parana River basin - an area of 5,940,382 ha located in Brazil- has a highly diverse phytophysiognomy and scarce flora information. Wood extraction and pasture activities have decisively contributed to the removal of vegetation in this area. This study was carried out in a seasonal deciduous forest on limestone outcrop (approximately 13º41'16" S and 46º44'20" W) on Canada Farm (São Domingos-GO.) Twenty -five plots of 20 m x 20m (1 ha) were randomly allocated on parallel lines 100 m apart. Trees with stem diameter at 1.3 m breast height (DBH) > 5 cm were sampled and their DBH, maximum height and species determined. In the phytosociological study, 924 individuals comprising 48 species, 38 genera and 24 families were sampled. The species with the highest importance value (IV) were Myracrodruon urundeuva (36.09%), Pseudobombax tomentosum (34.75%), Dilodendron bipinnatum (26.61%), Combretum duarteanum (22.19%), Jacaranda brasiliana (21.57%), Commiphora leptophloeos (19.18%), Astronium fraxinifolium (13.84%), Tabebuia impetiginosa (13.79%), Pseudobombax longiflorum (11.64%) and Machaerium scleroxylon (10.00%), comprising 69.9% of the total IV. Diversity was close to that found in other seasonal deciduous forest studies in the region