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Nicolas Nègre

Publications and source records attributed to Nicolas Nègre.

6 recordsLinked to original sources
PubMed2006

Chromosomal distribution of PcG proteins during Drosophila development.

Polycomb group (PcG) proteins are able to maintain the memory of silent transcriptional states of homeotic genes throughout development. In Drosophila, they form multimeric complexes that bind to specific DNA regulatory elements named PcG response elements (PREs). To date, few PREs have been identified and the chromosomal distribution of PcG proteins during development is unknown. We used chromatin immunoprecipitation (ChIP) with genomic tiling path microarrays to analyze the binding profile of the PcG proteins Polycomb (PC) and Polyhomeotic (PH) across 10 Mb of euchromatin. We also analyzed the distribution of GAGA factor (GAF), a sequence-specific DNA binding protein that is found at most previously identified PREs. Our data show that PC and PH often bind to clustered regions within large loci that encode transcription factors which play multiple roles in developmental patterning and in the regulation of cell proliferation. GAF co-localizes with PC and PH to a limited extent, suggesting that GAF is not a necessary component of chromatin at PREs. Finally, the chromosome-association profile of PC and PH changes during development, suggesting that the function of these proteins in the regulation of some of their target genes might be more dynamic than previously anticipated.

Animals↗
PubMed2006

From genetics to epigenetics: the tale of Polycomb group and trithorax group genes.

The Polycomb gene was discovered 60 years ago as a mutation inducing a particular homeotic phenotype. Subsequent work showed that Polycomb is a general repressor of homeotic genes. Other genes with similar function were identified and named Polycomb group (PcG) genes, while trithorax group (trxG) genes were shown to counteract PcG-mediated repression of homeotic genes. We now know that PcG and trxG proteins are conserved factors that regulate hundreds of different genomic loci. A sophisticated pathway is responsible for recruitment of these proteins at regulatory regions that were named PcG and trxG response elements (PRE and TRE). Once recruited to their targets, multimeric PcG and trxG protein complexes regulate transcription by modulating chromatin structure, in particular via deposition of specific post-translational histone modification marks and control of chromatin accessibility, as well as regulation of the three-dimensional nuclear organization of PRE and TRE. Here, we recapitulate the history of PcG and trxG gene discovery, we review the current evidence on their molecular function and, based on this evidence, we propose a revised classification of genes involved in PcG and trxG regulatory pathways.

Animals↗
PubMed2006

PRE-mediated bypass of two Su(Hw) insulators targets PcG proteins to a downstream promoter.

Drosophila Polycomb group response elements (PRE) silence neighboring genes, but silencing can be blocked by one copy of the Su(Hw) insulator element. We show here that Polycomb group (PcG) proteins can spread from a PRE in the flanking chromatin region and that PRE blocking depends on a physical barrier established by the insulator to PcG protein spreading. On the other hand, PRE-mediated silencing can bypass two Su(Hw) insulators to repress a downstream reporter gene. Strikingly, insulator bypass involves targeting of PcG proteins to the downstream promoter, while they are completely excluded from the intervening insulated domain. This shows that PRE-dependent silencing is compatible with looping of the PRE in order to bring PcG proteins in contact with the promoter and does not require the coating of the whole chromatin domain between PRE and promoter.

Animals↗
PubMed2006

Mapping the distribution of chromatin proteins by ChIP on chip.

The ChIP on chip method combines chromatin immunoprecipitation (ChIP) with hybridization on DNA microarrays (chip). The ChIP technique allows one to obtain a DNA sample enriched in sequences bound by transcription factors or chromatin-associated proteins. Usually, ChIP is used to test whether specific candidate sequences are bound by a transcription factor, but microarrays are a powerful tool that allows testing large pools of sequences at once. This chapter presents the pipeline of a ChIP on chip method that can be applied to map the binding sites of chromatin-associated proteins along Drosophila chromosomes at different developmental stages. This chapter provides protocols for ChIP, for quality control tests of ChIP samples, for microarray design, for hybridization of the ChIP samples onto microarrays, and for initial analysis of the data. In addition, this chapter discusses the most important steps in each of the protocols as well as the importance of bioinformatic analysis in order to extract valuable biological information from the data sets.

Chromatin↗
PubMed2003

Mitotic G2-arrest is required for neural cell fate determination in Drosophila.

In the wing discs of Drosophila, the mecanosensory precursor cells are singled out from clusters of cells blocked at the G2 phase of the cell cycle. This mitotic quiescence and the selection of the precursors are under strict spatio-temporal control. We forced G2 cells to enter mitosis by overexpression of string, the Drosophila homologue of the cdc25 gene. Premature entrance in the cell cycle is associated to a loss of precursor cells. Precursors are lost consecutively to a transcriptional down-regulation of the determinant proneural achaete/scute genes. This down-regulation results from an over-activation of the Enhancer of Split genes, known as effectors of the Notch signalling pathway. We conclude that exit from the cell cycle is required for proper neural cell fate determination.

Animals↗