Dynamic regulation of nucleosome positioning in the human genome

DE Schones, K Cui, S Cuddapah, TY Roh, A Barski… - Cell, 2008 - cell.com
The positioning of nucleosomes with respect to DNA plays an important role in regulating
transcription. However, nucleosome map** has been performed for only limited genomic …

Nucleosome positioning in Saccharomyces cerevisiae

A Jansen, KJ Verstrepen - Microbiology and molecular biology …, 2011 - Am Soc Microbiol
The DNA of eukaryotic cells is spooled around large histone protein complexes, forming
nucleosomes that make up the basis for a high-order packaging structure called chromatin …

Characterization of enhancer function from genome-wide analyses

GA Maston, SG Landt, M Snyder… - Annual review of …, 2012 - annualreviews.org
There has been a recent surge in the use of genome-wide methodologies to identify and
annotate the transcriptional regulatory elements in the human genome. Here we review …

A region of the human HOXD cluster that confers polycomb-group responsiveness

CJ Woo, PV Kharchenko, L Daheron, PJ Park… - Cell, 2010 - cell.com
Polycomb group (PcG) proteins are essential for accurate axial body patterning during
embryonic development. PcG-mediated repression is conserved in metazoans and is …

Nucleosome positioning signals in genomic DNA

HE Peckham, RE Thurman, Y Fu… - Genome …, 2007 - genome.cshlp.org
Although histones can form nucleosomes on virtually any genomic sequence, DNA
sequences show considerable variability in their binding affinity. We have used DNA …

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

JS Pedersen, E Valen, AMV Velazquez… - Genome …, 2014 - genome.cshlp.org
Epigenetic information is available from contemporary organisms, but is difficult to track back
in evolutionary time. Here, we show that genome-wide epigenetic information can be …

[HTML][HTML] Epigenetic changes in fetal hypothalamic energy regulating pathways are associated with maternal undernutrition and twinning

G Begum, A Stevens, EB Smith, K Connor… - The FASEB …, 2012 - ncbi.nlm.nih.gov
Undernutrition during pregnancy is implicated in the programming of offspring for the
development of obesity and diabetes. We hypothesized that maternal programming causes …

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

JA West, A Cook, BH Alver, M Stadtfeld… - Nature …, 2014 - nature.com
Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in
mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs) and …

Predicting human nucleosome occupancy from primary sequence

S Gupta, J Dennis, RE Thurman… - PLoS computational …, 2008 - journals.plos.org
Nucleosomes are the fundamental repeating unit of chromatin and comprise the structural
building blocks of the living eukaryotic genome. Micrococcal nuclease (MNase) has long …

Epigenetic silencing in Friedreich ataxia is associated with depletion of CTCF (CCCTC-binding factor) and antisense transcription

I De Biase, YK Chutake, PM Rindler, SI Bidichandani - PloS one, 2009 - journals.plos.org
Background Over 15 inherited diseases are caused by expansion of triplet-repeats.
Friedreich ataxia (FRDA) patients are homozygous for an expanded GAA triplet-repeat …