Chromatin accessibility profiling methods
L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
High-resolution digital profiling of the epigenome
GE Zentner, S Henikoff - Nature Reviews Genetics, 2014 - nature.com
The widespread adoption of short-read DNA sequencing as a digital epigenomic readout
platform has motivated the development of genome-wide tools that achieve base-pair …
platform has motivated the development of genome-wide tools that achieve base-pair …
Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
DNA methylation and nucleosome positioning work together to generate chromatin
structures that regulate gene expression. Nucleosomes are typically mapped using …
structures that regulate gene expression. Nucleosomes are typically mapped using …
Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
It is well established that cancer-associated epigenetic repression occurs concomitant with
CpG island hypermethylation and loss of nucleosomes at promoters, but the role of …
CpG island hypermethylation and loss of nucleosomes at promoters, but the role of …
Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level
M Fatemi, MM Pao, S Jeong, EN Gal-Yam… - Nucleic acids …, 2005 - academic.oup.com
Promoters are molecular 'modules', which are controlled as individual entities yet are often
analyzed by nuclease digestion methodologies which, a priori, destroy this modularity …
analyzed by nuclease digestion methodologies which, a priori, destroy this modularity …
Cooperative binding between distant transcription factors is a hallmark of active enhancers
Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation.
While cooperative binding of TFs at enhancers is known to be critical for transcriptional …
While cooperative binding of TFs at enhancers is known to be critical for transcriptional …
Partitioned usage of chromatin remodelers by nucleosome-displacing factors
Summary Nucleosome-displacing-factors (NDFs) in yeast, similar to pioneer factors in
higher eukaryotes, can open closed chromatin and generate nucleosome-depleted regions …
higher eukaryotes, can open closed chromatin and generate nucleosome-depleted regions …
Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
E Oberbeckmann, M Wolff, N Krietenstein… - Genome …, 2019 - genome.cshlp.org
Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for
understanding genome regulation because nucleosomes modulate DNA access by their …
understanding genome regulation because nucleosomes modulate DNA access by their …
In vivo methylation of mtDNA reveals the dynamics of protein–mtDNA interactions
To characterize the organization of mtDNA–protein complexes (known as nucleoids) in vivo,
we have probed the mtDNA surface exposure using site-specific DNA methyltransferases …
we have probed the mtDNA surface exposure using site-specific DNA methyltransferases …
DNA methylation and nucleosome occupancy regulate the cancer germline antigen gene MAGEA11
MAGEA11 is a cancer germline (CG) antigen and androgen receptor co-activator. Its
expression in cancers other than prostate, and its mechanism of activation, has not been …
expression in cancers other than prostate, and its mechanism of activation, has not been …