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Publisher Correction: Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

Luca Fiorillo
Francesco Musella
Mario Nicodemi
Amendments and CorrectionsOpen Access03 Sept 2021
Nature Methods

Volume: 18, P: 1266
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

Multiplex-genome architecture mapping (multiplex-GAM) enables rapid, unbiased, ligation-free mapping of genome-wide chromatin interactions.

Robert A. Beagrie
Christoph J. Thieme
Ana Pombo
ResearchOpen Access19 Jun 2023
Nature Methods

Volume: 20, P: 1037-1047
Complex multi-enhancer contacts captured by genome architecture mapping

A technique called genome architecture mapping (GAM) involves sequencing DNA from a large number of thin nuclear cryosections to develop a map of genome organization without the limitations of existing 3C-based methods.

Robert A. Beagrie
Antonio Scialdone
Ana Pombo
Research08 Mar 2017
Nature

Volume: 543, P: 519-524
Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells

In this work, the authors apply polymer models to reconstruct the 3D structure of the genome during SARS-CoV-2 infection and examine how the virus impacts key mechanisms of chromatin organization.

Andrea M. Chiariello
Alex Abraham
Mario Nicodemi
ResearchOpen Access13 May 2024
Nature Communications

Volume: 15, P: 1-13
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

Two main mechanisms have been proposed to shape 3D genome architecture - loop extrusion and phase separation. Here the authors combine these mechanisms in polymer models in a manner that best fits 3D genome, based on both Hi-C and super-resolution locus imaging data, proposing that these two physical processes can indeed coexist simultaneously within cells to define loops and TADs.

Mattia Conte
Ehsan Irani
Mario Nicodemi
ResearchOpen Access13 Jul 2022
Nature Communications

Volume: 13, P: 1-13
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

This Analysis reports a computational approach to implement Hi-C, SPRITE and GAM, which allows researchers to assess the performances of the three technologies to capture DNA contacts in chromatin three-dimensional models.

Luca Fiorillo
Francesco Musella
Mario Nicodemi
ResearchOpen Access07 May 2021
Nature Methods

Volume: 18, P: 482-490
Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

The molecular and physical mechanisms underlying chromatin folding at the single DNA molecule level remain poorly understood. Here, the authors use polymer modeling to investigate the conformations of two 2Mb-wide DNA loci in normal and cohesin depleted cells, and provide evidence that the architecture of the studied loci is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules.

Mattia Conte
Luca Fiorillo
Mario Nicodemi
ResearchOpen Access03 Jul 2020
Nature Communications

Volume: 11, P: 1-13
Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Homotypic interactions between active and Polycomb-repressed promoters co-occurring in the same DNA fiber, rather than CTCF occupancy, explain the 3D HoxB folding pattern.

Mariano Barbieri
Sheila Q Xie
Ana Pombo
Research24 Apr 2017
Nature Structural & Molecular Biology

Volume: 24, P: 515-524
Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations

Release of paused Pol II at specific intronic loci or chromatin domains favors the formation of abnormal DNA recombination, leading to cancer-associated chromosomal translocations.

Gaetano Ivan Dellino
Fernando Palluzzi
Pier Giuseppe Pelicci
Research20 May 2019
Nature Genetics

Volume: 51, P: 1011-1023
RNA-mediated symmetry breaking enables singular olfactory receptor choice

Messenger RNAs transcribed from olfactory-receptor genes may have non-coding functions that include recruitment of transcriptional enhancers and inhibition of potentially thousands of competing alleles to ensure stable transcription of a single allele.

Ariel D. Pourmorady
Elizaveta V. Bashkirova
Stavros Lomvardas
ResearchOpen Access20 Dec 2023
Nature

Volume: 625, P: 181-188
Polymer physics predicts the effects of structural variants on chromatin architecture

The authors present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer–promoter contacts. PRISMR correctly predicts ectopic contacts induced by pathogenic SVs at the mouse Epha4 locus.

Simona Bianco
Darío G. Lupiáñez
Mario Nicodemi
Research16 Apr 2018
Nature Genetics

Volume: 50, P: 662-667
Polymer physics of chromosome large-scale 3D organisation

Andrea M. Chiariello
Carlo Annunziatella
Mario Nicodemi
ResearchOpen Access13 Jul 2016
Scientific Reports

Volume: 6, P: 1-8
Cell-type specialization is encoded by specific chromatin topologies

A new technique called immunoGAM, which combines genome architecture mapping (GAM) with immunoselection, enabled the discovery of specialized chromatin conformations linked to gene expression in specific cell populations from mouse brain tissues.

Warren Winick-Ng
Alexander Kukalev
Ana Pombo
ResearchOpen Access17 Nov 2021
Nature

Volume: 599, P: 684-691
CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

The insulation potency of CTCF depends on the number of binding sites in tandem and on upstream flanking sequences. Insulators form local chromatin domain boundaries and weaken enhancer–promoter contacts.

Hui Huang
Quan Zhu
Bing Ren
Research17 May 2021
Nature Genetics

Volume: 53, P: 1064-1074
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Acute loss of CTCF disproportionately affects the transcription of genes that display promoter-proximal CTCF binding and are dependent on long-distance enhancers.

Naoki Kubo
Haruhiko Ishii
Bing Ren
Research04 Jan 2021
Nature Structural & Molecular Biology

Volume: 28, P: 152-161
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

A Pitx1 enhancer shows activity in forelimbs and hindlimbs but only interacts with Pitx1 in hindlimbs because of its three-dimensional configuration. Structural variants that affect three-dimensional conformation induce Pitx1 expression in forelimbs and cause partial arm-to-leg transformation in mice and humans.

Bjørt K. Kragesteen
Malte Spielmann
Guillaume Andrey
Research27 Sept 2018
Nature Genetics

Volume: 50, P: 1463-1473
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

Tri-C is a new 3C approach to identify concurrent chromatin interactions at individual alleles. The authors observe specific higher-order structures involving simultaneous interactions between multiple enhancers and promoters, called regulatory hubs.

A. Marieke Oudelaar
James O. J. Davies
Jim R. Hughes
Research29 Oct 2018
Nature Genetics

Volume: 50, P: 1744-1751
Challenges and guidelines toward 4D nucleome data and model standards

Marc A. Marti-Renom
Genevieve Almouzni
Maria-Elena Torres-Padilla
Reviews27 Sept 2018
Nature Genetics

Volume: 50, P: 1352-1358
Slow relaxation and compaction of granular systems

Patrick Richard
Mario Nicodemi
Daniel Bideau
Reviews01 Feb 2005
Nature Materials

Volume: 4, P: 121-128
A stochastic model dissects cell states in biological transition processes

Jonathan W. Armond
Krishanu Saha
Sach Mukherjee
ResearchOpen Access17 Jan 2014
Scientific Reports

Volume: 4, P: 1-9

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Publisher Correction: Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

Complex multi-enhancer contacts captured by genome architecture mapping

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells

Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations

RNA-mediated symmetry breaking enables singular olfactory receptor choice

Polymer physics predicts the effects of structural variants on chromatin architecture

Polymer physics of chromosome large-scale 3D organisation

Cell-type specialization is encoded by specific chromatin topologies

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

Challenges and guidelines toward 4D nucleome data and model standards

Slow relaxation and compaction of granular systems

A stochastic model dissects cell states in biological transition processes

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