ChIP–seq: advantages and challenges of a maturing technology

PJ Park - Nature reviews genetics, 2009 - nature.com
Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for
genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes …

The biology of chromatin remodeling complexes

CR Clapier, BR Cairns - Annual review of biochemistry, 2009 - annualreviews.org
The packaging of chromosomal DNA by nucleosomes condenses and organizes the
genome, but occludes many regulatory DNA elements. However, this constraint also allows …

Nucleosome positioning and gene regulation: advances through genomics

C Jiang, BF Pugh - Nature Reviews Genetics, 2009 - nature.com
Knowing the precise locations of nucleosomes in a genome is key to understanding how
genes are regulated. Recent'next generation'ChIP–chip and ChIP–Seq technologies have …

[HTML][HTML] The DNA-encoded nucleosome organization of a eukaryotic genome

N Kaplan, IK Moore, Y Fondufe-Mittendorf, AJ Gossett… - Nature, 2009 - nature.com
Nucleosome organization is critical for gene regulation. In living cells this organization is
determined by multiple factors, including the action of chromatin remodellers, competition …

Bidirectional promoters generate pervasive transcription in yeast

Z Xu, W Wei, J Gagneur, F Perocchi… - Nature, 2009 - nature.com
Genome-wide pervasive transcription has been reported in many eukaryotic organisms,,,,,,,
revealing a highly interleaved transcriptome organization that involves hundreds of …

H3. 3/H2A. Z double variant–containing nucleosomes mark'nucleosome-free regions' of active promoters and other regulatory regions

C Jin, C Zang, G Wei, K Cui, W Peng, K Zhao… - Nature …, 2009 - nature.com
To understand how chromatin structure is organized by different histone variants, we have
measured the genome-wide distribution of nucleosome core particles (NCPs) containing the …

Histones: annotating chromatin

EI Campos, D Reinberg - Annual review of genetics, 2009 - annualreviews.org
Chromatin is a highly regulated nucleoprotein complex through which genetic material is
structured and maneuvered to elicit cellular processes, including transcription, cell division …

[HTML][HTML] A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling

VR Ramirez-Carrozzi, D Braas, DM Bhatt, CS Cheng… - Cell, 2009 - cell.com
We describe a broad mechanistic framework for the transcriptional induction of mammalian
primary response genes by Toll-like receptors and other stimuli. One major class of primary …

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

JR Hesselberth, X Chen, Z Zhang, PJ Sabo… - Nature …, 2009 - nature.com
The orchestrated binding of transcriptional activators and repressors to specific DNA
sequences in the context of chromatin defines the regulatory program of eukaryotic …

The logic of chromatin architecture and remodelling at promoters

BR Cairns - Nature, 2009 - nature.com
The regulation of gene transcription involves a dynamic balance between packaging
regulatory sequences into chromatin and allowing transcriptional regulators access to these …