Sentences with word «nucleosome»

O'Sullivan came to the Karlseder lab seven years ago to explore whether histone / DNA interactions in nucleosomes altered telomere function.

Chromatin is built when DNA winds around millions of spool - like protein structures called nucleosomes.

Using super-resolution fluorescence microscopy (stochastic optical reconstruction microscopy; STORM)(Rust et al., Nature Methods, 2006) in collaboration with the group of Melike Lakadamyali (Institute of Photonic Sciences, Barcelona) we have dissected out the nanoscale organization of nucleosome assembly, with high molecular specificity and spatial resolution in a variety of somatic and stem / reprogrammed cells.

(A) and (B) show the distribution of nucleosome formation potential scores at 400 and 2000 bp upstream from the gene start site respectively.

Correlation coefficients of total expression levels (log10) with nucleosome formation potential scores in housekeeping (Hkg) and tissue specific genes (Tsg).

Li M, Hada A, Sen P, Olufemi L, Hall MA, Smith BY, Forth S, McKnight JN, Patel A, Bowman GD, Bartholomew B, Wang MD. (2015) Dynamic regulation of transcription factors by nucleosome remodeling.

Why the CENP - A nucleosome exhibits flexible DNA ends is totally unknown.

Nagaki et al. [6] used anti-CenH3 antibodies to immunoprecipitate chromatin (ChIP) comprising DNA bound to CenH3 - containing nucleosomes, confirming that CenH3 is associated with both the CentO repeats and the CRR family of retrotransposons.

Although it has not been established that CenH3 alone determines centromere identity, the sequence of a complete centromere should at the least include the entire region that is wound around nucleosomes containing CenH3.

The team observed a relative scarcity of nucleosomes at telomeres from ASF1 - depleted cells, as one might expect once a histone chaperone is lost.

«Namely, when the way cells package DNA into nucleosomes breaks down, damage occurs.»

The ability of PARP1 to control cellular processes is regulated by nucleosomes — the basic unit of DNA packaging, consisting of a segment of DNA wound in sequence around eight histone protein cores, similar to a thread wrapped around a spool.

Comparison of the level of correlation between nucleosome formation potential scores and contrasting expression levels of genes.

This will be done using deuterium exchange mass spectrometry to identify the structural characteristics and conformational rigidity of nucleosomes assembled from 1) CENP - A, 2) histone H3 or 3) histone H3 carrying the centromere targeting domain of CENP - A.

They discovered all promoters could be classified into two distinct types differing by their state of nucleosome stability.

Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS Canonical nucleosome organization at promoters forms during genome activation.

Little is known about the biological function of BAZ2B but it has been suggested to regulate nucleosome mobilization by the ATP - dependent chromatin remodeling factor ISWI.

Researchers from the University of Geneva (UNIGE) and the Ecole polytechnique fédérale de Lausanne (EPFL), Switzerland, are studying the mechanisms controlling nucleosome dynamics and how this affects gene expression.

This assay enabled us to elucidate the mechanism of action of the chromatin assembly factor 1 (CAF - 1), leading to the first described molecular model for nucleosome assembly (Figure 3)(1)(2).

In this way the binding of the DNA to the corresponding nucleosome is changed so that the DNA for example becomes accessible for transcription enzymes and activates a particular gene.

, can lock nucleosome interactions and compact chromatin even more, thereby preventing the gene expression machinery to access the DNA.

«Our paper shows that suppressing ASF1 induces ALT by affecting nucleosome assembly,» he says.

We have made an important step forward in our general understanding of how gene regulators can bind to and recognize nucleosomes.»

The helix winds onto nucleosomes to form chromatin, which winds and winds in its turn into formations similar to what you get when you keep twisting the two ends of a string.

This technique, developed as a collaboration between the Babraham Institute, the European Bioinformatics Institute (EMBL - EBI) and the University of Edinburgh and reported today (22nd February 2018) in Nature Communications, is called single - cell nucleosome, methylation, transcription sequencing or scNMT - seq.

In a study published in Molecular Cell this month, Alexei V. Tulin, PhD, Associate Professor at Fox Chase Cancer Center, and colleagues reported that chemical modification of one type of histone — called H2Av — leads to substantial changes in nucleosome shape.

When we modified one histone, we changed the whole nucleosome.»

We believe that the presence of dynamic nucleosomes at highly expressed genes helps to unwind this spring rapidly and as often as necessary,» comments David Shore.

The interplay of different molecular actors involved in nucleosome destabilization is described in the journal Molecular Cell.

In collaboration with researchers at the Department of Computer Science (UNIGE) and the Swiss Institute of Bioinformatics at EPFL, David Shore's team has undertaken to characterize nucleosomes present in every gene promoter of yeast DNA.

Centromeric chromatin includes a centromere - specific histone H3 variant (CenH3) that is incorporated into nucleosomes underlying the kinetochore.

«It is important to understand how nucleosomes are moved, ejected or restructured, as this will affect the accessibility of promoter DNA, which in turn influences the expression of the corresponding genes,» explains David Shore, professor at the Department of Molecular Biology of the Faculty of Science at UNIGE.

They speculate that the dynamic nature of the «fragile» nucleosome plays an important role in increasing access of the proteins initiating the transcription to the promoter.

«It's the packing density that could change and limit the accessibility of chromatin, providing a local and global structural basis through which different combinations of DNA sequences, nucleosome variations and modifications could be integrated in the nucleus to exquisitely fine - tune the functional activity and accessibility of our genomes.»

The other type, which contains well - known stable nucleosomes, is located at less frequently expressed genes.

Using this dominant TSS, the authors searched for phased dinucleotides associated with nucleosome location (AA / AT / TA / TT).

The forward - and reverse - oriented peaks were usually separated by around 180 base pairs, and corresponded to nucleosome boundaries.

Chromatin structure is defined by several parameters such as combination of histone post-translational marks, nucleosome occupancy, DNA methylation or incorporation of histone variants.

Chromatin remodelers are sophisticated nano - machines, which are able to alter histone - DNA interactions and to mobilize nucleosomes.

The DNase I data exploits a structural feature of regulatory DNA that's been known for decades: the binding of sequence - specific transcriptional regulators in place of nucleosomes creates DNase I hypersensitive sites, or DHSs.

Sequencing of DNase I hypersensitive sites in (125 cell types), FAIRE analysis of reduced nucleosome crosslinking (25 cell types), and genomic DNase I footprinting (41 cell types).

The four histones create a new nucleosome spool for that section of DNA.

In a second study, published in 2016 in the EMBO Journal, the Panne group reported on the second nucleosome assembly step.