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 …

DNA methylation and de-methylation using hybrid site-targeting proteins

Y Lei, YH Huang, MA Goodell - Genome biology, 2018 - Springer
DNA methylation plays important roles in determining cellular identity, disease, and
environmental responses, but little is known about the mechanisms that drive methylation …

Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes

F Li, M Papworth, M Minczuk, C Rohde… - Nucleic acids …, 2007 - academic.oup.com
Gene silencing by targeted DNA methylation has potential applications in basic research
and therapy. To establish targeted methylation in human cell lines, the catalytic domains …

Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery

AP Siegenfeld, SA Roseman, H Roh, NZ Lue… - Nature …, 2022 - nature.com
The genome can be divided into two spatially segregated compartments, A and B, which
partition active and inactive chromatin states. While constitutive heterochromatin is …

In vivo methylation of mtDNA reveals the dynamics of protein–mtDNA interactions

AP Rebelo, SL Williams, CT Moraes - Nucleic acids research, 2009 - academic.oup.com
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 …

Site‐selective in vivo targeting of cytosine‐5 DNA methylation by zinc‐finger proteins

CD Carvin, RD Parr, MP Kladde - Nucleic acids research, 2003 - academic.oup.com
Cytosine‐5 DNA methylation is a critical signal defining heritable epigenetic states of
transcription. As aberrant methylation patterns often accompany disease states, the ability to …

Correlation between small-scale methylation changes and gene expression during the development of myopia

K Thomson, J Game, C Karouta… - FASEB …, 2022 - researchprofiles.canberra.edu.au
Visually induced changes in the expression of early growth response-1 (EGR1), FBJ
osteosarcoma oncogene (FOS), and NGFI-A binding protein-2 (NAB2) appear to form a part …

Single-molecule and population probing of chromatin structure using DNA methyltransferases

JA Kilgore, SA Hoose, TL Gustafson, W Porter… - Methods, 2007 - Elsevier
Probing chromatin structure with DNA methyltransferases offers advantages over more
commonly used nuclease-based and chromatin immunoprecipitation methods for detection …

Effectors of lysine 4 methylation of histone H3 in Saccharomyces cerevisiae are negative regulators of PHO5 and GAL1-10

CD Carvin, MP Kladde - Journal of Biological Chemistry, 2004 - ASBMB
Post-translational modifications of histone amino-terminal tails are a key determinant in
gene expression. Histone methylation plays a dual role in gene regulation. Methylation of …

Directed evolution of improved zinc finger methyltransferases

B Chaikind, M Ostermeier - PLoS One, 2014 - journals.plos.org
The ability to target DNA methylation toward a single, user-designated CpG site in vivo may
have wide applicability for basic biological and biomedical research. A tool for targeting …