David J. Clark

Long-read DNA sequencing reveals global hypomethylation and focal hypermethylation in SDHx-deficient pheochromocytoma and paraganglioma

The paper uses long-read sequencing to analyze DNA methylation patterns in SDHx-deficient PPGLs and finds global hypomethylation with focal hypermethylation at specific CpG islands.

Histone H3K9 methylation and Heterochromatin Protein 1 do not limit DNA accessibility in living S. pombe cells

The paper shows that chromatin in living S. pombe cells is generally accessible, challenging the idea that heterochromatin represses DNA access.

Sir proteins impede, but do not prevent, access to silent chromatin in living Saccharomyces cerevisiae

The paper shows Sir proteins impede but do not prevent access to silent chromatin in yeast, using DNA methylation rates as a measure.

The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells

The paper assesses the roles of ISW1 and CHD1 chromatin remodelers in suppressing nucleosome dynamics in living yeast cells, finding that their depletion increases DNA methylation rates.

Nucleosome dynamics render heterochromatin accessible in living human cells

The paper measures genome accessibility in living human cells and finds that heterochromatin is more accessible than previously thought due to dynamic nucleosome behavior.

Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m6A detection efficiency and calling bias correcting pipeline

The paper develops a pipeline to correct m6A detection biases in PacBio long-read sequencing of M.EcoGII-treated yeast nuclei, revealing chromatin heterogeneity at the single-molecule level.

The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution

This study shows that the ISW1b complex is essential for nucleosome spacing and resolving dinucleosomes, while ISW1a has a minor role, and Set2-mediated H3-K36 methylation supports ISW1b function.

DNA accessibility is not the primary determinant of chromatin-mediated gene regulation

The paper challenges the idea that DNA accessibility is the main factor in gene regulation by showing that accessibility varies between cells and does not strongly correlate with gene activity.