The Mediator complex as a master regulator of transcription by RNA polymerase II

WF Richter, S Nayak, J Iwasa, DJ Taatjes - Nature Reviews Molecular …, 2022 - nature.com
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits,
controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining …

Chromatin accessibility and the regulatory epigenome

SL Klemm, Z Shipony, WJ Greenleaf - Nature Reviews Genetics, 2019 - nature.com
Physical access to DNA is a highly dynamic property of chromatin that plays an essential
role in establishing and maintaining cellular identity. The organization of accessible …

[HTML][HTML] Loss of epigenetic information as a cause of mammalian aging

JH Yang, M Hayano, PT Griffin, JA Amorim… - Cell, 2023 - cell.com
All living things experience an increase in entropy, manifested as a loss of genetic and
epigenetic information. In yeast, epigenetic information is lost over time due to the …

Effective gene expression prediction from sequence by integrating long-range interactions

Ž Avsec, V Agarwal, D Visentin, JR Ledsam… - Nature …, 2021 - nature.com
How noncoding DNA determines gene expression in different cell types is a major unsolved
problem, and critical downstream applications in human genetics depend on improved …

The evolution, evolvability and engineering of gene regulatory DNA

ED Vaishnav, CG de Boer, J Molinet, M Yassour, L Fan… - Nature, 2022 - nature.com
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal
phenotype and fitness,–. Constructing complete fitness landscapes, in which DNA …

Brain cell type–specific enhancer–promoter interactome maps and disease-risk association

A Nott, IR Holtman, NG Coufal, JCM Schlachetzki, M Yu… - Science, 2019 - science.org
Noncoding genetic variation is a major driver of phenotypic diversity, but functional
interpretation is challenging. To better understand common genetic variation associated with …

[HTML][HTML] Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases

M Ota, Y Nagafuchi, H Hatano, K Ishigaki, C Terao… - Cell, 2021 - cell.com
Genetic studies have revealed many variant loci that are associated with immune-mediated
diseases. To elucidate the disease pathogenesis, it is essential to understand the function of …

The post-GWAS era: from association to function

MD Gallagher, AS Chen-Plotkin - The American Journal of Human …, 2018 - cell.com
During the past 12 years, genome-wide association studies (GWASs) have uncovered
thousands of genetic variants that influence risk for complex human traits and diseases. Yet …

Niche-specific reprogramming of epigenetic landscapes drives myeloid cell diversity in nonalcoholic steatohepatitis

JS Seidman, TD Troutman, M Sakai, A Gola, NJ Spann… - Immunity, 2020 - cell.com
Tissue-resident and recruited macrophages contribute to both host defense and pathology.
Multiple macrophage phenotypes are represented in diseased tissues, but we lack deep …

Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

AW Turner, SS Hu, JV Mosquera, WF Ma… - Nature …, 2022 - nature.com
Coronary artery disease (CAD) is a complex inflammatory disease involving genetic
influences across cell types. Genome-wide association studies have identified over 200 loci …