Quantifying ChIP-seq data:A spiking method providing an internal reference for sample-to-sample normalization

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This "spike" chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes

Le tissu adipeux (un nouveau site hématopoïétique ?)

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

Developmental changes in integrin beta-subunits in rat cerebral cortex.

International audienc

Altered macrophage-like functions of preadipocytes in inflammation and genetic obesity

International audienc

Choosing an Adipose Tissue Depot for Sampling. Factors in selection and depot specificity

Part of the Methods in Molecular Biology™ book series (MIMB, volume 456).International audienc

Adipose-derived stromal cells: Their identity and uses in clinical trials, an update

In adults, adipose tissue is abundant and can be easily sampled using liposuction. Largely involved in obesity and associated metabolic disorders, it is now described as a reservoir of immature stromal cells. These cells, called adipose-derived stromal cells (ADSCs) must be distinguished from the crude stromal vascular fraction (SVF) obtained after digestion of adipose tissue. ADSCs share many features with mesenchymal stem cells derived from bone marrow, including paracrine activity, but they also display some specific features, including a greater angiogenic potential. Their angiogenic properties as well as their paracrine activity suggest a putative tumor-promoting role for ADSCs although contradictory data have been published on this issue. Both SVF cells and ADSCs are currently being investigated in clinical trials in several fields (chronic inflammation, ischemic diseases, etc.). Apart from a phase III trial on the treatment of fistula, most of these are in phase I and use autologous cells. In the near future, the end results of these trials should provide a great deal of data on the safety of ADSC use

Le recrutement et l’activation d’adipocytes bruns et/ou BRITE

Chez les mammifères, on distingue classiquement deux types de tissus adipeux : le blanc et le brun (TAB). Le tissu adipeux blanc représente le principal site de stockage de l’énergie dans l’organisme ; le TAB quant à lui dissipe cette énergie sous forme de chaleur grâce à l’expression de la protéine découplante UCP1 (uncoupling protein-1) qui permet le découplage du fonctionnement de la chaîne respiratoire de celui de l’ATP synthase. Alors que les adipocytes blancs et bruns ont longtemps été considérés comme deux types cellulaires très proches et dérivés d’un précurseur commun, des données récentes ont cependant remis en cause ces conclusions et identifé un nouveau type possible d’adipocyte : l’adipocyte BRITE (brown-in-white). En parallèle, la découverte récente de la présence de TAB en quantité notable chez l’homme adulte a relancé l’intérêt de la communauté scientifique pour ce tissu. Étant donné sa capacité considérable à dissiper des substrats, le TAB est redevenu une cible thérapeutique d’intérêt dans la lutte contre les maladies métaboliques, comme le diabète ou l’obésité. L’objectif de cette revue est de résumer la littérature sur ce sujet et d’identifier certains points à clarifie

A role for preadipocytes as macrophage-like cells

International audienc