Characterizing cis-regulatory elements using single-cell epigenomics

S Preissl, KJ Gaulton, B Ren - Nature Reviews Genetics, 2023 - nature.com
Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …

[HTML][HTML] The self-organizing genome: principles of genome architecture and function

T Misteli - Cell, 2020 - cell.com
Genomes have complex three-dimensional architectures. The recent convergence of
genetic, biochemical, biophysical, and cell biological methods has uncovered several …

Understanding 3D genome organization by multidisciplinary methods

I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention

X Zhu, Z Chen, W Shen, G Huang, JM Sedivy… - Signal transduction and …, 2021 - nature.com
Remarkable progress in ageing research has been achieved over the past decades.
General perceptions and experimental evidence pinpoint that the decline of physical …

Advances in epigenetics link genetics to the environment and disease

G Cavalli, E Heard - Nature, 2019 - nature.com
Epigenetic research has accelerated rapidly in the twenty-first century, generating justified
excitement and hope, but also a degree of hype. Here we review how the field has evolved …

Long-range enhancer–promoter contacts in gene expression control

S Schoenfelder, P Fraser - Nature Reviews Genetics, 2019 - nature.com
Spatiotemporal gene expression programmes are orchestrated by transcriptional
enhancers, which are key regulatory DNA elements that engage in physical contacts with …

Origins of DNA replication in eukaryotes

Y Hu, B Stillman - Molecular cell, 2023 - cell.com
Errors occurring during DNA replication can result in inaccurate replication, incomplete
replication, or re-replication, resulting in genome instability that can lead to diseases such as …

Integrative single-cell analysis

T Stuart, R Satija - Nature reviews genetics, 2019 - nature.com
The recent maturation of single-cell RNA sequencing (scRNA-seq) technologies has
coincided with transformative new methods to profile genetic, epigenetic, spatial, proteomic …

Methods for mapping 3D chromosome architecture

R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

Organizational principles of 3D genome architecture

MJ Rowley, VG Corces - Nature Reviews Genetics, 2018 - nature.com
Studies of 3D chromatin organization have suggested that chromosomes are hierarchically
organized into large compartments composed of smaller domains called topologically …