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 …

Enhancer RNAs are an important regulatory layer of the epigenome

V Sartorelli, SM Lauberth - Nature structural & molecular biology, 2020 - nature.com
Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development
and disease through their regulation of transcription, RNA processing and translation …

Machine learning meets omics: applications and perspectives

R Li, L Li, Y Xu, J Yang - Briefings in Bioinformatics, 2022 - academic.oup.com
The innovation of biotechnologies has allowed the accumulation of omics data at an
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

W Li, D Notani, MG Rosenfeld - Nature Reviews Genetics, 2016 - nature.com
Networks of regulatory enhancers dictate distinct cell identities and cellular responses to
diverse signals by instructing precise spatiotemporal patterns of gene expression. However …

The Mediator complex: a central integrator of transcription

BL Allen, DJ Taatjes - Nature reviews Molecular cell biology, 2015 - nature.com
Abstract The RNA polymerase II (Pol II) enzyme transcribes all protein-coding and most non-
coding RNA genes and is globally regulated by Mediator—a large, conformationally flexible …

The selection and function of cell type-specific enhancers

S Heinz, CE Romanoski, C Benner… - Nature reviews Molecular …, 2015 - nature.com
The human body contains several hundred cell types, all of which share the same genome.
In metazoans, much of the regulatory code that drives cell type-specific gene expression is …

Long noncoding RNAs in cardiovascular diseases

S Uchida, S Dimmeler - Circulation research, 2015 - Am Heart Assoc
In recent year, increasing evidence suggests that noncoding RNAs play important roles in
the regulation of tissue homeostasis and pathophysiological conditions. Besides small …

Genome-wide mapping and analysis of chromosome architecture

AD Schmitt, M Hu, B Ren - Nature reviews Molecular cell biology, 2016 - nature.com
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in
the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects …

3D chromosome regulatory landscape of human pluripotent cells

X Ji, DB Dadon, BE Powell, ZP Fan, D Borges-Rivera… - Cell stem cell, 2016 - cell.com
In this study, we describe the 3D chromosome regulatory landscape of human naive and
primed embryonic stem cells. To devise this map, we identified transcriptional enhancers …

dbSUPER: a database of super-enhancers in mouse and human genome

A Khan, X Zhang - Nucleic acids research, 2016 - academic.oup.com
Super-enhancers are clusters of transcriptional enhancers that drive cell-type-specific gene
expression and are crucial to cell identity. Many disease-associated sequence variations are …