The relationship between genome structure and function

AM Oudelaar, DR Higgs - Nature Reviews Genetics, 2021 - nature.com
Precise patterns of gene expression in metazoans are controlled by three classes of
regulatory elements: promoters, enhancers and boundary elements. During differentiation …

Interplay between genetics and epigenetics in osteoarthritis

SJ Rice, F Beier, DA Young, J Loughlin - Nature Reviews …, 2020 - nature.com
Research into the molecular genetics of osteoarthritis (OA) has been substantially bolstered
in the past few years by the implementation of powerful genome-wide scans that have …

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease

R Nativio, Y Lan, G Donahue, S Sidoli, A Berson… - Nature …, 2020 - nature.com
Protein aggregation is the hallmark of neurodegeneration, but the molecular mechanisms
underlying late-onset Alzheimer's disease (AD) are unclear. Here we integrated …

Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale

X Li, Z Li, H Zhou, SM Gaynor, Y Liu, H Chen, R Sun… - Nature …, 2020 - nature.com
Large-scale whole-genome sequencing studies have enabled the analysis of rare variants
(RVs) associated with complex phenotypes. Commonly used RV association tests have …

Transposable elements drive widespread expression of oncogenes in human cancers

HS Jang, NM Shah, AY Du, ZZ Dailey, EC Pehrsson… - Nature …, 2019 - nature.com
Transposable elements (TEs) are an abundant and rich genetic resource of regulatory
sequences,–. Cryptic regulatory elements within TEs can be epigenetically reactivated in …

Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability

Z Zhang, K Luo, Z Zou, M Qiu, J Tian, L Sieh, H Shi… - Nature …, 2020 - nature.com
Abstract N 6-methyladenosine (m6A) plays important roles in regulating messenger RNA
processing. Despite rapid progress in this field, little is known about the genetic …

Targeted Perturb-seq enables genome-scale genetic screens in single cells

D Schraivogel, AR Gschwind, JH Milbank, DR Leonce… - Nature …, 2020 - nature.com
The transcriptome contains rich information on molecular, cellular and organismal
phenotypes. However, experimental and statistical limitations constrain sensitivity and …

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes

I Miguel-Escalada, S Bonàs-Guarch, I Cebola… - Nature …, 2019 - nature.com
Genetic studies promise to provide insight into the molecular mechanisms underlying type 2
diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer …

Landscape of stimulation-responsive chromatin across diverse human immune cells

D Calderon, MLT Nguyen, A Mezger, A Kathiria… - Nature …, 2019 - nature.com
A hallmark of the immune system is the interplay among specialized cell types transitioning
between resting and stimulated states. The gene regulatory landscape of this dynamic …

DNA G-quadruplex structures mold the DNA methylome

SQ Mao, AT Ghanbarian, J Spiegel… - Nature structural & …, 2018 - nature.com
Control of DNA methylation level is critical for gene regulation, and the factors that govern
hypomethylation at CpG islands (CGIs) are still being uncovered. Here, we provide evidence …