Insights into mammalian transcription control by systematic analysis of ChIP sequencing data

Abstract Background Transcription regulation is a major controller of gene expression dynamics during development and disease, where transcription factors (TFs) modulate expression of genes through direct or indirect DNA interaction. ChIP sequencing has become the most widely used technique to get a genome wide view of TF occupancy in a cell type of interest, mainly due to established standard protocols and a rapid decrease in the cost of sequencing. The number of available ChIP sequencing data sets in public domain is therefore ever increasing, including data generated by individual labs together with consortia such as the ENCODE project. Results A total of 1735 ChIP-sequencing datasets in mouse and human cell types and tissues were used to perform bioinformatic analyses to unravel diverse features of transcription control. 1- We used the Heat*seq webtool to investigate global relations across the ChIP-seq samples. 2- We demonstrated that factors have a specific genomic location preferences that are, for most factors, conserved across species. 3- Promoter proximal binding of factors was more conserved across cell types while the distal binding sites are more cell type specific. 4- We identified combinations of factors preferentially acting together in a cellular context. 5- Finally, by integrating the data with disease-associated gene loci from GWAS studies, we highlight the value of this data to associate novel regulators to disease. Conclusion In summary, we demonstrate how ChIP sequencing data integration and analysis is powerful to get new insights into mammalian transcription control and demonstrate the utility of various bioinformatic tools to generate novel testable hypothesis using this public resource

Carbon and nitrogen cycling through soil microbial biomass at various temperatures

International audienceC and N cycling were examined in a soil incubated at 4, 12, 20 or 28°C for 140 days. Before incubation the soil was amended with K15NO3, and either glucose-14C or holocellulose-14C. The kinetics of tracer and non-tracer C and N from the biomass, mineralized-C and inorganic-N were measured.C and N behaviours in soil were influenced by temperature, substrate and substrate-temperature interactions. Labelled-C mineralization rates after 140 days ranged from 41 to 58% for glucose and from 34 to 65% for holocellulose. Maximal immobilization was 21.8–31.6 mgN kg−1 soil for holocellulose and 24.3–33.5 mg N kg−1 soil for glucose. Re-mineralization began earlier with glucose and at higher temperatures: 6–23% of immobilized-N were re-mineralized for glucose and 0–19% for holocellulose. More labelled C and N were incorporated into the microbial biomass from both carbon sources at lower temperatures. The biomass turnover was highly influenced by temperature: 40–60% of labelled C or N incorporated in the biomass remained in this compartment at 20–28°C, while corresponding values at 4–12°C were only 0–40%.Organic-14C mineralization and immobilization rate constants were influenced by temperature, the different trends depending on the carbon source. Thus an overall temperature coefficient (Q10) could not be determined for these complex transformations. Variations in the rate constant with temperature were described using polynomial regressions

Decomposition of 15N-labelled catch-crop residues in soil: evaluation of N mineralization and plant-N uptake potentials under controlled conditions

International audienceThe decomposition of 15N‐labelled catch‐crop materials (rape, radish and rye), obtained from field experiments, was studied in a chalky Champagne soil during a 60‐week incubation at 28°C. Mineralized N was assumed to come from either labile or recalcitrant fractions of plant residues. The labile fraction represented about one‐third of the catch‐crop N; its mineralization rate constant varied from 0.06 to 0.12 d−1. The decomposition rate of the recalcitrant N fraction ranged from 0.03 × 10−2 to 0.06 × 10−2 d−1. Catch‐crop species and rate of incorporation had no effect on N residue mineralized at the end of incubation. The decomposition of labelled rye was monitored in the same soil during a 5‐month pot experiment to determine the N availability to an Italian ryegrass crop and the effect of plants on the decomposition processes. The 15N‐rye decomposed rapidly both in the presence or absence of Italian ryegrass, but the amounts of N mineralized were influenced by the presence of living roots: 42% of the 15N in labelled rye was present as inorganic N in the pots without plants after 5 months, compared with only 32% in the ryegrass crop. Comparison of microbial‐biomass dynamics in both treatments suggested that there had been preferential utilization by soil micro‐organisms of materials released from the living roots than the labelled plant residues

Differential Responses of Nitrate Reducer Community Size, Structure, and Activity to Tillage Systems▿ †

The main objective of this study was to determine how the size, structure, and activity of the nitrate reducer community were affected by adoption of a conservative tillage system as an alternative to conventional tillage. The experimental field, established in Madagascar in 1991, consists of plots subjected to conventional tillage or direct-seeding mulch-based cropping systems (DM), both amended with three different fertilization regimes. Comparisons of size, structure, and activity of the nitrate reducer community in samples collected from the top layer in 2005 and 2006 revealed that all characteristics of this functional community were affected by the tillage system, with increased nitrate reduction activity and numbers of nitrate reducers under DM. Nitrate reduction activity was also stimulated by combined organic and mineral fertilization but not by organic fertilization alone. In contrast, both negative and positive effects of combined organic and mineral fertilization on the size of the nitrate reducer community were observed. The size of the nitrate reducer community was a significant predictor of the nitrate reduction rates except in one treatment, which highlighted the inherent complexities in understanding the relationships the between size, diversity, and structure of functional microbial communities along environmental gradients

Decomposition of 15 N-labelled catch-crop residues in soil : evaluation of N mineralization and plant-N uptake potentials under controlled conditions

73 ref.International audienc

Dynamics of the diazotroph Bacillus polymyxa in the rhizosphere of wheat (Triticum aestivum L.) after inoculation and its effect on uptake of 15N-labelled fertilizer

International audienceAn experiment under glasshouse conditions with a sandy soil was conducted to evaluate the effect of the inoculation of wheat (Triticum aestivum L.) roots with Bacillus polymyxa on N uptake by plants and to investigate the effect of N fertilization on the dynamics of this strain. Different treatments were considered: (i) amended (l00 kg N ha -I) or not with 15N labelled ammonium nitrate ; (ii) inoculated (2.5 107 spores per seed and 0.5 109 spores kg-I soil) or not with B. polymyxa CF43. No promoting effect on wheat growth (dry yield) or N uptake was observed after inoculation under these experimental conditions; 62 per cent of the N fertilizer was assimilated by plants during the first 33 days. Inoculation had no effect on the quantity of soil adhering to the roots. Soluble organic C and inorganic N concentrations were higher in the soil adhering to the roots than in bulk soil. However, the nitrate concentration in soil adhering to the roots was influenced by inoculation at the beginning of plant growth, nitrate supply to the root system being delayed by its probable retention in the rhizosphere. Furthermore, total bacteria in roots, soil adhering to the roots and bulk soil was not affected by N fertilization. The number of B. polymyxa cells measured by an AB-ELISA method increased first in the bulk soil and later in the soil adhering to the roots after inoculation. Fertilization with N decreased the B. polymyxa population in adhering soil, competitive suppression of diazotrophs by non-fixing bacteria probably being induced by the presence of large amounts of nutrients in the rhizosphere when N was added

Role of Plant Residues in Determining Temporal Patterns of the Activity, Size, and Structure of Nitrate Reducer Communities in Soil ▿ †

The incorporation of plant residues into soil not only represents an opportunity to limit soil organic matter depletion resulting from cultivation but also provides a valuable source of nutrients such as nitrogen. However, the consequences of plant residue addition on soil microbial communities involved in biochemical cycles other than the carbon cycle are poorly understood. In this study, we investigated the responses of one N-cycling microbial community, the nitrate reducers, to wheat, rape, and alfalfa residues for 11 months after incorporation into soil in a field experiment. A 20- to 27-fold increase in potential nitrate reduction activity was observed for residue-amended plots compared to the nonamended plots during the first week. This stimulating effect of residues on the activity of the nitrate-reducing community rapidly decreased but remained significant over 11 months. During this period, our results suggest that the potential nitrate reduction activity was regulated by both carbon availability and temperature. The presence of residues also had a significant effect on the abundance of nitrate reducers estimated by quantitative PCR of the narG and napA genes, encoding the membrane-bound and periplasmic nitrate reductases, respectively. In contrast, the incorporation of the plant residues into soil had little impact on the structure of the narG and napA nitrate-reducing community determined by PCR-restriction fragment length polymorphism (RFLP) fingerprinting. Overall, our results revealed that the addition of plant residues can lead to important long-term changes in the activity and size of a microbial community involved in N cycling but with limited effects of the type of plant residue itself

Changement d'usage des terres et fonctionnement microbien : le cas du semis direct sous couverture végétale à Madagascar

National audienc

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package