Nucleosome | EPFL Graph Search

A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins H2A, H2B, H3, and H4. DNA must be compacted into nucleosomes to fit within the cell nucleus. In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome. Each human cell contains about 30 million nucleosomes. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosome positions in the genome are n

Evolution of nucleosomes position in yeasts: conservation of global pattern and divergence of gene-specific patterns

Sébastien Dubuis

This master project describes computational analysis of nucleosomes positioning in four yeast species: S. cerevisiae, S. kudriavzevii, S. bayanus (three relatively close species, ~75% of sequence similarity) and C. glabrata (more distant, ~57% of sequence similarity). We found that the global organization of nucleosomes previously described in S. cerevisiae (Nucleosome Depleted Region followed by an array of nucleosomes) was largely conserved among the different species also with the conservation of occupied/depleted promoters' classification from previous works redefined here in a more specific way. However, this conservation of general pattern does not reflect the evolution of gene specific pattern. Indeed, we show that nucleosome pattern diverged rapidly leaving practically no similarities between S. cerevisiae and C. glabrata orthologs. This was confirmed by different analysis and additional data from other species. In contrast, the pattern of gene expression and the response to stress were largely conserved among this species. Together, these results suggest that the general properties of nucleosome patterns and some specific features are conserved even if the gene specific patterns diverge much faster than the DNA sequence and the expression patterns. This argues strongly in favor of a model where different configurations of nucleosomes positions can encode the same expression output and where nucleosomes features evolve mainly by neutral drift

2010

High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites

Ludovica Vanzan

Binding of mammalian transcription factors (TFs) to regulatory regions is hindered by chromatin compaction and DNA methylation of their binding sites. Nevertheless, pioneer transcription factors (PFs), a distinct class of TFs, have the ability to access nucleosomal DNA, leading to nucleosome remodelling and enhanced chromatin accessibility. Whether PFs can bind to methylated sites and induce DNA demethylation is largely unknown. Using a highly parallelized approach to investigate PF ability to bind methylated DNA and induce DNA demethylation, we show that the interdependence between DNA methylation and TF binding is more complex than previously thought, even within a select group of TFs displaying pioneering activity; while some PFs do not affect the methylation status of their binding sites, we identified PFs that can protect DNA from methylation and others that can induce DNA demethylation at methylated binding sites. We call the latter super pioneer transcription factors (SPFs), as they are seemingly able to overcome several types of repressive epigenetic marks. Finally, while most SPFs induce TET-dependent active DNA demethylation, SOX2 binding leads to passive demethylation, an activity enhanced by the co-binding of OCT4. This finding suggests that SPFs could interfere with epigenetic memory during DNA replication. The functional relevance of epigenetic modifications on transcription regulation has been an important question since their discovery. Here, the authors investigate the effect of DNA methylation on Pioneer Transcription Factor (PF) binding and distinguish between PFs that protect their binding sites from methylation and those that bind to methylated DNA and induce DNA demethylation.

NATURE RESEARCH2021

Developement of a gateway compatible system for speciﬁc DNA integration in mouse embryonic stem cells and evaluation of the effect of nucleosome positioning on gene expression

Julien Bryois

An emerging model views gene regulation as a competition for regulatory sequences between transcription factors and nucleosomes at thermodynamic equilibrium. A computational model of the DNA affinity of nucleosomes was recently developed allowing to predict the nucleosome occupancy of DNA sequences. The aim of this project was to investigate the effect of different predicted nucleosome occupancies of an important transcription factor binding site on mammalian gene expression. To this end, a two site and three site gateway compatible system allowing integration of DNA at a speciﬁc locus of two mouse embryonic stem cell lines was developed. An important POU5F1 (previously known as OCT4)/SOX2 binding site located in the Nanog promoter was chosen to be the transcription factor binding site of interest as it was shown to play a major role for Nanog expression. A 2kb sequence from the Nanog proximal promoter (-1585 to +415) was cloned upstream of two different minimal promoters and a GFP reporter using three site gateway cloning. These constructs were integrated in both cell lines and expressed low to medium levels of GFP. Next, several variants of a 1kb sequence from the Nanog promoter (-933 to +53), previously shown to be functional, were constructed. 35bp surrounding the POU5F1/SOX2 binding site were altered resulting in differential predicted nucleosome occupancy of the binding site. These promoters were linked to GFP with or without the addition of a kozak consensus sequence and a SV40 polyadenylation signal. Surprisingly, all these variants showed low GFP expression after transfection. This was not caused by biases introduced by the gateway system as a gateway construct containing the CMV promoter linked to GFP was shown to be functional. Furthermore, direct cloning of the 1kb Nanog promoter in a GFP expressing vector without gateway showed similar GFP expression as gateway cloning. Results indicate that both 2kb and 1kb Nanog promoters express GFP at low levels and that the constructs produced may be useful to measure differences in GFP expression using ﬂow cytometry

2010

Developement of a gateway compatible system for speciﬁc DNA integration in mouse embryonic stem cells and evaluation of the effect of nucleosome positioning on gene expression

Julien Bryois

2010