The 4D nucleome project
Abstract The 4D Nucleome Network aims to develop and apply approaches to map the
structure and dynamics of the human and mouse genomes in space and time with the goal …
structure and dynamics of the human and mouse genomes in space and time with the goal …
The quest for mammalian Polycomb response elements: are we there yet?
M Bauer, J Trupke, L Ringrose - Chromosoma, 2016 - Springer
A long-standing mystery in the field of Polycomb and Trithorax regulation is how these
proteins, which are highly conserved between flies and mammals, can regulate several …
proteins, which are highly conserved between flies and mammals, can regulate several …
Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance
DNA double-strand break (DSB) repair is mediated by multiple pathways. It is thought that
the local chromatin context affects the pathway choice, but the underlying principles are …
the local chromatin context affects the pathway choice, but the underlying principles are …
Promoter-intrinsic and local chromatin features determine gene repression in LADs
C Leemans, MCH van der Zwalm, L Brueckner… - Cell, 2019 - cell.com
It is largely unclear whether genes that are naturally embedded in lamina-associated
domains (LADs) are inactive due to their chromatin environment or whether LADs are …
domains (LADs) are inactive due to their chromatin environment or whether LADs are …
Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons
Q Wu, J Wu, K Karim, X Chen, T Wang, S Iwama… - Molecular Cell, 2023 - cell.com
CRISPR activation (CRISPRa) is an important tool to perturb transcription, but its
effectiveness varies between target genes. We employ human pluripotent stem cells with …
effectiveness varies between target genes. We employ human pluripotent stem cells with …
Enhancer-gene specificity in development and disease
T Pachano, E Haro, A Rada-Iglesias - Development, 2022 - journals.biologists.com
Enhancers control the establishment of spatiotemporal gene expression patterns throughout
development. Over the past decade, the development of new technologies has improved our …
development. Over the past decade, the development of new technologies has improved our …
Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus
Selective recruitment and concentration of signalling proteins within membraneless
compartments is a ubiquitous mechanism for subcellular organization,–. The dynamic flow of …
compartments is a ubiquitous mechanism for subcellular organization,–. The dynamic flow of …
Local rewiring of genome–nuclear lamina interactions by transcription
L Brueckner, PA Zhao, T van Schaik, C Leemans… - The EMBO …, 2020 - embopress.org
Transcriptionally inactive genes are often positioned at the nuclear lamina (NL), as part of
large lamina‐associated domains (LADs). Activation of such genes is often accompanied by …
large lamina‐associated domains (LADs). Activation of such genes is often accompanied by …
Cause and consequence of tethering a SubTAD to different nuclear compartments
PJ Wijchers, PHL Krijger, G Geeven, Y Zhu, A Denker… - Molecular cell, 2016 - cell.com
Detailed genomic contact maps have revealed that chromosomes are structurally organized
in megabase-sized topologically associated domains (TADs) that encompass smaller …
in megabase-sized topologically associated domains (TADs) that encompass smaller …
Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency
S Gisler, JP Gonçalves, W Akhtar, J de Jong… - Nature …, 2019 - nature.com
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9
activity is crucial to design effective gene editing assays. However, it is challenging to profile …
activity is crucial to design effective gene editing assays. However, it is challenging to profile …