Evidence map›Paper›PMID 39028505›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

High-Throughput Mapping of Chromosomal Conformations in E. coli Under Physiological Conditions Using Massively Multiplexed Mu Transposition.

Khang Ho, Sonya K Royzenblat, Brady Wilkins, Rasika Harshey, Lydia Freddolino

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. 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

5 · Who and what money

Authors and funding

5 authors.

Khang Ho *Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
Sonya K Royzenblat *Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.
Brady WilkinsDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
Rasika HarsheyDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
Lydia FreddolinoDepartment of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA. lydsf@umich.edu.

Funding

Virus-host interactions and microbial ecologyR35GM118085 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI HARSHEY, RASIKA M · 2016 to 2025
$5.6M
Cellular and Molecular Biology at MichiganT32GM145470 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI John Chadwick Brenner · 2022 to 2026
$4.1M
Bacteriophage Mu as Tool to Study Genome Organization in Bacteria and EukaryotesR21HG011838 · NHGRI · UNIVERSITY OF TEXAS AT AUSTIN · PI FREDDOLINO, LYDIA PETRA, HARSHEY, RASIKA M · 2021 to 2021
$447k
NHGRI NIH HHS R21 HG011838NIGMS NIH HHS R35 GM118085
6 · The paper itself

Abstract

Many approaches for measuring three-dimensional chromosomal conformations rely upon formaldehyde crosslinking followed by subsequent proximity ligation, a family of methods exemplified by 3C, Hi-C, etc. Here we provide an alternative crosslinking-free procedure for high-throughput identification of long-range contacts in the chromosomes of enterobacteria, making use of contact-dependent transposition of phage Mu to identify distant loci in close contact. The procedure described here will suffice to provide a comprehensive map of transposition frequencies between tens of thousands of loci in a bacterial genome, with the resolution limited by the diversity of the insertion site library used and the sequencing depth applied.

Indexed as

Chromosome MappingChromosomes, BacterialEscherichia coliBacteriophage muDNA Transposable ElementsHigh-Throughput Nucleotide SequencingDNA Transposable ElementsBacterial chromosome structureBacteriophage MuChromosome conformation captureHi-CMacrodomains

Identifiers

PMID39028505
PMCPMC11887985

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

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.