Nature Search

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

Single-cell analysis of Drosophila development with Hi-M suggests that physical proximity between regulatory regions does not necessarily instruct transcriptional states. Multi-way analyses identify the existence of regulatory hubs that emerge before topologically associating domains.

Sergio Martin Espinola
Markus Götz
Marcelo Nollmann
Research01 Apr 2021
Nature Genetics

Volume: 53, P: 477-486
3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription

In Drosophila, insulators may be involved in the organization of Topological Associated Domains, but the mechanism of action is a still a matter of investigation. Here the authors investigate the role of insulators in the 3D organization of the Drosophila genome by combining bioinformatics analysis and Hi-M, an imaging-based methods developed to detect the 3D positions of multiple genomic loci in single cells.

Olivier Messina
Flavien Raynal
Marcelo Nollmann
ResearchOpen Access21 Oct 2023
Nature Communications

Volume: 14, P: 1-14
The mechanism of force transmission at bacterial focal adhesion complexes

The mystery of how bacteria that lack motile structures such as pili or flagella can ‘glide’ along surfaces is solved by a detailed description of the bacterial focal adhesion complex and its associated protein machinery.

Laura M. Faure
Jean-Bernard Fiche
Tâm Mignot
Research05 Oct 2016
Nature

Volume: 539, P: 530-535
Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila

Here the authors applied their recently developed multiplexed DNA-FISH Hi-M method to dissect the sources of heterogeneity in topologically associating ___domain (TAD)-like organization during Drosophila embryogenesis. This single-nucleus analysis allows them to reveal that multiple parameters contribute to shaping the trace of the chromatin path from a single nucleus.

Markus Götz
Olivier Messina
Marcelo Nollmann
ResearchOpen Access14 Sept 2022
Nature Communications

Volume: 13, P: 1-14
Multi-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria

Myxococcus xanthus forages and moves collectively to prey and feed on other bacterial species. Here, the authors challenge the conventional idea that during Myxococcus xanthus predation, A- and S-motilities are limited to specific forager and swarm roles and reveal a synergistic interaction between these motilities to enhance predation efficiency.

Sara Rombouts
Anna Mas
Marcelo Nollmann
ResearchOpen Access11 Sept 2023
Nature Communications

Volume: 14, P: 1-12
Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that exist at the kilo-megabase scale. Here Cattoni et al. combine super-resolution microscopy with DNA-labeling methods to quantify absolute frequencies of interactions within TADs.

Diego I. Cattoni
Andrés M. Cardozo Gizzi
Marcelo Nollmann
ResearchOpen Access24 Nov 2017
Nature Communications

Volume: 8, P: 1-10
Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque

Marcelo Nöllmann
Michael D Stone
Nicholas R Cozzarelli
Research04 Mar 2007
Nature Structural & Molecular Biology

Volume: 14, P: 264-271
Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis

Jerod L Ptacin
Marcelo Nollmann
Carlos Bustamante
Research06 Apr 2008
Nature Structural & Molecular Biology

Volume: 15, P: 485-493
Bacterial partition complexes segregate within the volume of the nucleoid

In most bacteria and archaea, a broadly conserved mitotic-like apparatus assures the inheritance of duplicated genetic material before cell division. Here, the authors use super-resolution microscopies to dissect the activities required for proper DNA segregation through the nucleoid interior.

Antoine Le Gall
Diego I. Cattoni
Marcelo Nollmann
ResearchOpen Access05 Jul 2016
Nature Communications

Volume: 7, P: 1-10
A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer–promoter communication

Combining genome engineering, epigenomics and multiplex three-dimensional microscopy approaches, the authors show that PRE chromatin loops form a topological scaffold, restricting promoter–enhancer communication and contributing to enhancer–promoter specificity.

Sandrine Denaud
Marion Bardou
Giacomo Cavalli
ResearchOpen Access16 Aug 2024
Nature Structural & Molecular Biology

Volume: 31, P: 1942-1954
Identification of the FtsK sequence-recognition ___domain

Jerod L Ptacin
Marcelo Nöllmann
Nicholas R Cozzarelli
Research15 Oct 2006
Nature Structural & Molecular Biology

Volume: 13, P: 1023-1025
Mechanochemical analysis of DNA gyrase using rotor bead tracking

Jeff Gore
Zev Bryant
Carlos Bustamante
Research05 Jan 2006
Nature

Volume: 439, P: 100-104
DNA overwinds when stretched

Physical intuition predicts that DNA should unwind under tension as it is pulled towards a denatured structure, but this is not the case. Pulling of a single DNA molecule first leads to overwinding, which causes it to lengthen, not shorten. These results can be explained by a coupling between stretch and twist, such that the DNA inner radius changes under tension.

Jeff Gore
Zev Bryant
Carlos Bustamante
Research12 Jul 2006
Nature

Volume: 442, P: 836-839
Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M

Here, the authors provide detailed experimental and analytical procedures for Hi-M, a method that enables simultaneous imaging of 3D genome folding and RNA localization in single cells.

Andrés M. Cardozo Gizzi
Sergio M. Espinola
Marcelo Nollmann
Protocols22 Jan 2020
Nature Protocols

Volume: 15, P: 840-876
Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

Nikolaus Rajewsky
Geneviève Almouzni
Frauke Zipp
Amendments and CorrectionsOpen Access17 Mar 2021
Nature

Volume: 592, P: E8
Giant proteins that move DNA: bullies of the genomic playground

Proteins that move and manipulate DNA share certain properties that are crucial for the preservation of the genetic material. Such proteins are often large and multimeric, they require energy to enforce the reaction directionality, they move stochastically and their activity changes DNA topology.

Nicholas R. Cozzarelli
Gregory J. Cost
James E. Stray
Reviews01 Aug 2006
Nature Reviews Molecular Cell Biology

Volume: 7, P: 580-588
Highly efficient multicolor multifocus microscopy by optimal design of diffraction binary gratings

Bassam Hajj
Laura Oudjedi
Marcelo Nollmann
ResearchOpen Access13 Jul 2017
Scientific Reports

Volume: 7, P: 1-9
LifeTime and improving European healthcare through cell-based interceptive medicine

The LifeTime initiative is an ambitious, multidisciplinary programme that aims to improve healthcare by tracking individual human cells during disease processes and responses to treatment in order to develop and implement cell-based interceptive medicine in Europe.

Nikolaus Rajewsky
Geneviève Almouzni
Frauke Zipp
Reviews07 Sept 2020
Nature

Volume: 587, P: 377-386
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
Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues

This protocol describes how to perform single-particle tracking photoactivated localization microscopy (sptPALM) of membrane proteins in living plant tissues. The procedure covers all stages, from sample preparation to data analysis.

Vincent Bayle
Jean-Bernard Fiche
Yvon Jaillais
Protocols24 Feb 2021
Nature Protocols

Volume: 16, P: 1600-1628
Sequence-dependent catalytic regulation of the SpoIIIE motor activity ensures directionality of DNA translocation

Osvaldo Chara
Augusto Borges
Diego I. Cattoni
ResearchOpen Access27 Mar 2018
Scientific Reports

Volume: 8, P: 1-10

Search

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription

The mechanism of force transmission at bacterial focal adhesion complexes

Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila

Multi-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque

Sequence-directed DNA export guides chromosome translocation during sporulation in Bacillus subtilis

Bacterial partition complexes segregate within the volume of the nucleoid

A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer–promoter communication

Identification of the FtsK sequence-recognition ___domain

Mechanochemical analysis of DNA gyrase using rotor bead tracking

DNA overwinds when stretched

Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

Giant proteins that move DNA: bullies of the genomic playground

Highly efficient multicolor multifocus microscopy by optimal design of diffraction binary gratings

LifeTime and improving European healthcare through cell-based interceptive medicine

Challenges and guidelines toward 4D nucleome data and model standards

Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues

Sequence-dependent catalytic regulation of the SpoIIIE motor activity ensures directionality of DNA translocation

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