ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

<p>Abstract</p> <p>Background</p> <p>Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of <it>Drosophila melanogaster</it>.</p> <p>Results</p> <p>Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis.</p> <p>Conclusions</p> <p>Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis.</p

Assessment of the Food Habits of the Moroccan Dorcas Gazelle in M’Sabih Talaa, West Central Morocco, Using the trnL Approach

Food habits of the Moroccan dorcas gazelle, Gazella dorcas massaesyla, previously investigated in the 1980s using microhistological fecal analysis, in the M’Sabih Talaa Reserve, west central Morocco, were re-evaluated over three seasons (spring, summer and autumn 2009) using the trnL approach to determine the diet composition and its seasonal variation from fecal samples. Taxonomic identification was carried out using the identification originating from the database built from EMBL and the list of plant species within the reserve. The total taxonomic richness in the reserve was 130 instead of 171 species in the 1980s. The diet composition revealed to be much more diversified (71 plant taxa belonging to 57 genus and 29 families) than it was 22 years ago (29 identified taxa). Thirty-four taxa were newly identified in the diet while 13 reported in 1986–87 were not found. Moroccan dorcas gazelle showed a high preference to Acacia gummifera, Anagallis arvensis, Glebionis coronaria, Cladanthus arabicus, Diplotaxis tenuisiliqua, Erodium salzmannii, Limonium thouini, Lotus arenarius and Zizyphus lotus. Seasonal variations occurred in both number (40–41 taxa in spring-summer and 49 taxa in autumn vs. respectively 23–22 and 26 in 1986–1987) and taxonomic type of eaten plant taxa. This dietary diversification could be attributed either to the difference in methods of analysis, trnL approach having a higher taxonomic resolution, or a potential change in nutritional quality of plants over time

Français, méthodes lycées toutes séries / livre du professeur, programme 2007

National audienc

Français, méthodes lycées toutes séries / livre du professeur, programme 2007

National audienc

Conséquences sur la fertilité de l'inactivation de Raptor au niveau de l'hypothalamus de souris

National audienc

Negative regulation of transcription by the type II arginine methyltransferase PRMT5

We have identified previously a repressor element in the transcription start site region of the cyclin E1 promoter that periodically associates with an atypical, high molecular weight E2F complex, termed CERC. Purification of native CERC reveals the presence of the type II arginine methyltransferase PRMT5, which can mono- or symetrically dimethylate arginine residues in proteins. Chromatin immunoprecipitations (ChIPs) show that PRMT5 is associated specifically with the transcription start site region of the cyclin E1 promoter. ChIP analyses also show that this correlates with the presence on the same promoter region of arginine-methylated proteins including histone H4, an in vitro substrate of PRMT5. Consistent with its presence within the repressor complex, forced expression of PRMT5 negatively affects cyclin E1 promoter activity and cellular proliferation, effects that require its methyltransferase activity. These data provide the first direct experimental evidence that a type II arginine methylase is involved in the control of transcription and proliferation

Agroecological practices supporting food production and reducing food insecurity in developing countries: A study on scientific literature in 17 countries

This report represents the initial effort to structure existing knowledge about agroecology as farming and food system in support of the EC Knowledge Centre on Food and Nutrition Security (https://ec.europa.eu/knowledge4policy/global-food-nutrition-security_en). Scientific literature has been screened on a selection of developing countries in which food and nutrition security and sustainable agriculture represent a focal sector for EU intervention (Benin, Burkina Faso, Cuba, Ethiopia, Ghana, Guatemala, Kenya, Lao PDR, Madagascar, Malawi, Mali, Nicaragua, Niger, Senegal, Tanzania, Togo, Zimbabwe). In total, 172 documents have been synthesised, a country brief has been prepared for each investigated country, and some general conclusions have been drawn. Overall, the majority of analysed publications focuses on small scale, extensive farming systems that produce food at subsistence levels and for sale on local markets. This includes smallholder farming producing staple crops (millet, sorghum, yam, etc.) or vegetable gardening for local markets. The agroecological practices that are mostly studied are: agroforestry, intercropping (or mixed cropping), introduction of legumes in rotations, soil and water conservation practices (mulching, return of crop residues, zaï holes etc.), use of animal manure, biocontrol methods to mitigate chemical pesticide use. At least 50% of the analysed papers report a positive contribution of agroecological practices to food security, mostly due to improved yields and/or a better economic situation of producers. The improvement of soil quality is key to improve yields and consequently income and food security; this can be achieved using various practices including the use of residue mulch from tree leaves in agroforestry, as well as crop mixtures or intercropping and longer more diversified crop rotations. Moreover, higher on-farm crop species diversity often results in more diversified diets. Diversified crop systems, including the introduction of agroforestry, improve household nutritional status and have positive links to better health conditions. On the other hand, the lack of access to inputs is an important limitation to the improvement of soil fertility (manure, mineral fertilizer, leaf litter, etc.), which remains a major hindrance for food security. The agroecological cultivation of cash crops, post-harvest practices and crop-livestock integration were overall lacking in the scientific analyses, as well as the assessments of fully agroecological systems compared to individual agroecological practices or groups of practices. The report identifies three factors required for the substantial development of agroecology at the farm level: more financial support from the government, greater scientific knowledge on novel agroecological practices, and a higher market value for agroecological products