Evidence map›Paper›PMID 34415544›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

The 3D Organization of Chromatin Colors in Mammalian Nuclei.

Leopold Carron, Jean-Baptiste Morlot, Annick Lesne, Julien Mozziconacci

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Leopold CarronSorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France.
Jean-Baptiste MorlotSorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France.
Annick LesneSorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France. lesne@lptmc.jussieu.fr.
Julien MozziconacciSorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, Paris, France. julien.mozziconacci@mnhn.fr.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

While many computational methods have been proposed for 3D chromosome reconstruction from chromosomal contact maps, these methods are rarely used for the interpretation of such experimental data, in particular Hi-C data. We posit that this is due to the lack of an easy-to-use implementation of the proposed algorithms, as well as to the important computational cost of most methods. We here give a detailed implementation of the fast ShRec3D algorithm. We provide a tutorial that will enable the reader to reconstruct 3D consensus structures for human chromosomes and to decorate these structures with chromatin epigenetic states. We use this methodology to show that the bivalent chromatin, including Polycomb-rich domains, is spatially segregated and located in between the active and the quiescent chromatin compartments.

Indexed as

ChromatinChromosomesAlgorithmsAnimalsChromosomes, HumanColorHumansPolycomb-Group ProteinsChromatinPolycomb-Group Proteins3D reconstructionChromatinContact networkEpigenetic marksHi-CMultidimensional scalingShortest-path distance

Identifiers

PMID34415544

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.