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 …

CRISPR-Cas guides the future of genetic engineering

GJ Knott, JA Doudna - Science, 2018 - science.org
The diversity, modularity, and efficacy of CRISPR-Cas systems are driving a
biotechnological revolution. RNA-guided Cas enzymes have been adopted as tools to …

Lamina-associated domains: peripheral matters and internal affairs

N Briand, P Collas - Genome biology, 2020 - Springer
At the nuclear periphery, associations of chromatin with the nuclear lamina through lamina-
associated domains (LADs) aid functional organization of the genome. We review the …

Interchromosomal interactions: a genomic love story of kissing chromosomes

PG Maass, AR Barutcu, JL Rinn - Journal of Cell Biology, 2019 - rupress.org
Nuclei require a precise three-and four-dimensional organization of DNA to establish cell-
specific gene-expression programs. Underscoring the importance of DNA topology …

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus

AR Barutcu, PG Maass, JP Lewandowski… - Nature …, 2018 - nature.com
The binding of the transcriptional regulator CTCF to the genome has been implicated in the
formation of topologically associated domains (TADs). However, the general mechanisms of …

Imaging the unimaginable: leveraging signal generation of CRISPR-Cas for sensitive genome imaging

C Van Tricht, T Voet, J Lammertyn, D Spasic - Trends in Biotechnology, 2023 - cell.com
Fluorescence in situ hybridization (FISH) is the gold standard for visualizing genomic DNA in
fixed cells and tissues, but it is incompatible with live-cell imaging, and its combination with …

Approaches for understanding the mechanisms of long noncoding RNA regulation of gene expression

P McDonel, M Guttman - Cold Spring Harbor …, 2019 - cshperspectives.cshlp.org
Mammalian genomes encode tens of thousands of long noncoding RNAs (lncRNAs) that
have been implicated in a diverse array of biological processes and human diseases. In …

Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag

B Chen, W Zou, H Xu, Y Liang, B Huang - Nature communications, 2018 - nature.com
The lack of efficient tools to image non-repetitive genes in living cells has limited our ability
to explore the functional impact of the spatiotemporal dynamics of such genes. Here, we …

Monitoring the spatio-temporal organization and dynamics of the genome

HA Shaban, A Seeber - Nucleic acids research, 2020 - academic.oup.com
The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital
importance for transcription, DNA replication and genome maintenance. Each of these …

Directed evolution of CRISPR/Cas systems for precise gene editing

R Liu, L Liang, EF Freed, RT Gill - Trends in Biotechnology, 2021 - cell.com
CRISPR technology is a universal tool for genome engineering that has revolutionized
biotechnology. Recently identified unique CRISPR/Cas systems, as well as re-engineered …