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 …

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 …

Mitochondrial base editor induces substantial nuclear off-target mutations

Z Lei, H Meng, L Liu, H Zhao, X Rao, Y Yan, H Wu… - Nature, 2022 - nature.com
DddA-derived cytosine base editors (DdCBEs)—which are fusions of split DddA halves and
transcription activator-like effector (TALE) array proteins from bacteria—enable targeted C• …

Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges

AQ Nguyen, HP Vu, LN Nguyen, Q Wang… - Science of the Total …, 2021 - Elsevier
Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in
molecular biology has revealed new and significant challenges for AMR mitigation given the …

Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data

X Zhang, S Zhang, Q Zhao, R Ming, H Tang - Nature plants, 2019 - nature.com
Construction of chromosome-level assembly is a vital step in achieving the goal of a
'Platinum'genome, but it remains a major challenge to assemble and anchor sequences to …

Effects of emerging pollutants on the occurrence and transfer of antibiotic resistance genes: A review

G Feng, H Huang, Y Chen - Journal of Hazardous Materials, 2021 - Elsevier
The emergence and spread of antibiotic resistance genes (ARGs) have become major
concerns for both public health and environmental ecosystems. Emerging pollutants (EPs) …

Network enhancement as a general method to denoise weighted biological networks

B Wang, A Pourshafeie, M Zitnik, J Zhu… - Nature …, 2018 - nature.com
Networks are ubiquitous in biology where they encode connectivity patterns at all scales of
organization, from molecular to the biome. However, biological networks are noisy due to …

Systematic evaluation of chromosome conformation capture assays

B Akgol Oksuz, L Yang, S Abraham, SV Venev… - Nature …, 2021 - nature.com
Chromosome conformation capture (3C) assays are used to map chromatin interactions
genome-wide. Chromatin interaction maps provide insights into the spatial organization of …

Computational methods for analysing multiscale 3D genome organization

Y Zhang, L Boninsegna, M Yang, T Misteli… - Nature Reviews …, 2024 - nature.com
Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

Regulation of genome organization and gene expression by nuclear mechanotransduction

C Uhler, GV Shivashankar - Nature reviews Molecular cell biology, 2017 - nature.com
It is well established that cells sense chemical signals from their local microenvironment and
transduce them to the nucleus to regulate gene expression programmes. Although a number …