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Correction: Corrigendum: Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster

Bas Tolhuis
Inhua Muijrers
Maarten van Lohuizen
Amendments and Corrections01 Jul 2006
Nature Genetics

Volume: 38, P: 850
Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

Chromatin crosslinking facilitates the detection in selected genomic regions of structural variants missed by existing approaches

Paula J P de Vree
Elzo de Wit
Wouter de Laat
Research17 Aug 2014
Nature Biotechnology

Volume: 32, P: 1019-1025
SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors

The regulatory landscape of malignant rhabdoid tumor (MRT) due to SMARCB1 loss remains to be explored. Here, the authors perform multi-omics analysis using patient-derived MRT organoids and characterise the epigenetic reprogramming events underlying SMARCB1 loss.

Ning Qing Liu
Irene Paassen
Jarno Drost
ResearchOpen Access01 Dec 2023
Nature Communications

Volume: 14, P: 1-14
Variegated gene expression caused by cell-specific long-range DNA interactions

How regulatory elements spatially interact with their target DNA sequences is unclear. The β-globin locus control region (LCR) is found to take part in interchromosomal interactions with a few genes controlled by shared transcription factors, and to transcriptionally upregulate β-globin mRNA in a subset of cells.

Daan Noordermeer
Elzo de Wit
Wouter de Laat
Research26 Jun 2011
Nature Cell Biology

Volume: 13, P: 944-951
Distinct roles for CKM–Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction

Here, Dimitrova et al. examine how CKM–Mediator and Polycomb shape 3D chromosome interactions in ESCs and discover that gene activation during differentiation is independent of pre-formed interactions but depends on recruitment of the core Mediator.

Emilia Dimitrova
Angelika Feldmann
Robert J. Klose
ResearchOpen Access11 Oct 2022
Nature Structural & Molecular Biology

Volume: 29, P: 1000-1010
Characterization of the Drosophila melanogaster genome at the nuclear lamina

Helen Pickersgill
Bernike Kalverda
Bas van Steensel
Research30 Jul 2006
Nature Genetics

Volume: 38, P: 1005-1014
Limitations and possibilities of small RNA digital gene expression profiling

Sam E V Linsen
Elzo de Wit
Edwin Cuppen
Correspondence01 Jul 2009
Nature Methods

Volume: 6, P: 474-476
The structural basis for cohesin–CTCF-anchored loops

The crystal structure of the SA2–SCC1 subunits of human cohesin in complex with CTCF reveals the molecular basis of the cohesin–CTCF interaction that enables the dynamic regulation of chromatin folding.

Yan Li
Judith H. I. Haarhuis
Daniel Panne
Research06 Jan 2020
Nature

Volume: 578, P: 472-476
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation

WAPL creates a pool of free cohesin that binds to cell-type-specific sites. This cohesin turnover is important for maintaining promoter–enhancer loops.

Ning Qing Liu
Michela Maresca
Elzo de Wit
Research14 Dec 2020
Nature Genetics

Volume: 53, P: 100-109
Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster

Bas Tolhuis
Inhua Muijrers
Maarten van Lohuizen
Research20 Apr 2006
Nature Genetics

Volume: 38, P: 694-699
A Mediator-cohesin axis controls heterochromatin ___domain formation

The link between 3D genome architecture and gene expression is still far from resolved. Here the authors show that loss of the CDK catalytic subunit of the Mediator complex results in heterochromatic silencing, which can be rescued by stabilization of cohesin on chromatin.

Judith H. I. Haarhuis
Robin H. van der Weide
Elzo de Wit
ResearchOpen Access08 Feb 2022
Nature Communications

Volume: 13, P: 1-10
High-throughput identification of human SNPs affecting regulatory element activity

Application of SuRE reporter technology to survey the effect of 5.9 million SNPs in the human genome on enhancer and promoter activity identifies over 30,000 SNPs that alter the activity of putative regulatory elements.

Joris van Arensbergen
Ludo Pagie
Bas van Steensel
Research28 Jun 2019
Nature Genetics

Volume: 51, P: 1160-1169
The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism

Here, the authors use gene editing combined with Hi-C to show that cohesin acetylation restricts the length of chromatin loops through enhanced binding of cohesin to PDS5A.

Marjon S. van Ruiten
Démi van Gent
Benjamin D. Rowland
ResearchOpen Access16 Jun 2022
Nature Structural & Molecular Biology

Volume: 29, P: 586-591
The pluripotent genome in three dimensions is shaped around pluripotency factors

Using 4C technology, higher-order topological features of the pluripotent genome are identified; in pluripotent stem cells, Nanog clusters specifically with other pluripotency genes and this clustering is centred around Nanog-binding sites, suggesting that Nanog helps to shape the three-dimensional structure of the pluripotent genome and thereby contributes to the robustness of the pluripotent state.

Elzo de Wit
Britta A. M. Bouwman
Wouter de Laat
Research24 Jul 2013
Nature

Volume: 501, P: 227-231
Enhancer hubs and loop collisions identified from single-allele topologies

Multi-contact 4C (MC-4C) sequencing analyzes multi-way conformations of individual alleles. MC-4C identifies the β-globin superenhancer as a hub that can accommodate two genes simultaneously and shows that CTCF-anchored loops collide in WAPL-depleted cells.

Amin Allahyar
Carlo Vermeulen
Wouter de Laat
Research09 Jul 2018
Nature Genetics

Volume: 50, P: 1151-1160
Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer

Glucocorticoids (GC) are reported to block cancer cell proliferation, but the mode of action is unclear. Here the authors show that glucocorticoid receptor activation induces cancer cell dormancy in lung cancer by regulating CDKN1C expression through a distal enhancer, and these dormant cells are addicted to IGF-1R signalling pathway.

Stefan Prekovic
Karianne Schuurman
Wilbert Zwart
ResearchOpen Access16 Jul 2021
Nature Communications

Volume: 12, P: 1-18
The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

Swapping the Xist/Tsix transcriptional units and placing their promoters in each other’s topologically associating ___domain shows that the topological partitioning of the X-inactivation center is critical to ensure proper X inactivation during development.

Joke G. van Bemmel
Rafael Galupa
Edith Heard
Research27 May 2019
Nature Genetics

Volume: 51, P: 1024-1034
A transient absence of SMC-mediated loops after mitosis

After mitosis chromosomes are drastically reshaped. A study now charts the dynamics of this conformational change at high temporal resolution. During the shift from one loop-forming complex (condensin) to another (cohesin), an intermediate chromosome folding state exists in which neither of these complexes are associated with chromatin.

Ning Qing Liu
Elzo de Wit
News & Views04 Nov 2019
Nature Cell Biology

Volume: 21, P: 1303-1304
A natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis

Cdkn2ab knockout mice develop skin tumours but this phenotype is lost on backcrossing of the mice. Here, the authors describe a genetic variant encompassing Wnt7b that synergises with Cdkn2ab loss and is required for tumour formation in these mice.

Paul Krimpenfort
Margriet Snoek
Anton Berns
ResearchOpen Access29 Mar 2019
Nature Communications

Volume: 10, P: 1-10
New insights into genome folding by loop extrusion from inducible degron technologies

Inducible protein degradation technologies enable the depletion of loop extrusion factors within short time frames, leading to the rapid reconfiguration of the 3D genome. Nora and de Wit review insights from degron approaches into the molecular factors controlling genome folding and how these findings have changed our understanding of genome organization, including its role in transcription.

Elzo de Wit
Elphège P. Nora
Reviews30 Sept 2022
Nature Reviews Genetics

Volume: 24, P: 73-85
Capturing heterogeneity: single-cell structures of the 3D genome

One of the striking features of cells seen through a microscope is the heterogeneous organization of the nuclei. A combination of molecular methods and computational modeling has now been used to reconstruct accurate 3D structures of the genome inside single nuclei.

Elzo de Wit
News & Views04 May 2017
Nature Structural & Molecular Biology

Volume: 24, P: 437-438
Robust 4C-seq data analysis to screen for regulatory DNA interactions

A high-resolution 4C-seq protocol involving two restriction digests and a revised analysis pipeline allows robust detection of physical interactions between regulatory DNA elements.

Harmen J G van de Werken
Gilad Landan
Wouter de Laat
Research09 Sept 2012
Nature Methods

Volume: 9, P: 969-972
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)

Marieke Simonis
Petra Klous
Wouter de Laat
Research08 Oct 2006
Nature Genetics

Volume: 38, P: 1348-1354

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Correction: Corrigendum: Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster

Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors

Variegated gene expression caused by cell-specific long-range DNA interactions

Distinct roles for CKM–Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction

Characterization of the Drosophila melanogaster genome at the nuclear lamina

Limitations and possibilities of small RNA digital gene expression profiling

The structural basis for cohesin–CTCF-anchored loops

WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation

Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster

A Mediator-cohesin axis controls heterochromatin ___domain formation

High-throughput identification of human SNPs affecting regulatory element activity

The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism

The pluripotent genome in three dimensions is shaped around pluripotency factors

Enhancer hubs and loop collisions identified from single-allele topologies

Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

A transient absence of SMC-mediated loops after mitosis

A natural WNT signaling variant potently synergizes with Cdkn2ab loss in skin carcinogenesis

New insights into genome folding by loop extrusion from inducible degron technologies

Capturing heterogeneity: single-cell structures of the 3D genome

Robust 4C-seq data analysis to screen for regulatory DNA interactions

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)

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