Evidence map›Paper›PMID 39678350›Full record

ArticleResearch square2024

DNA sequence-induced solid phase transition as a solution to the genome folding paradox.

Joan M Pulupa, Natalie G McArthur, Olga Stathi, Miao Wang, Marianna Zazhytska, Isabella D Pirozzolo, Ahana Nayar, Lawrence Shapiro, Stavros Lomvardas

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2024. 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

5 · Who and what money

Authors and funding

9 authors.

Joan M PulupaDepartment of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Natalie G McArthurDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA.
Olga StathiMortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY 10027, USA.
Miao WangDepartment of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Marianna ZazhytskaDepartment of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Isabella D PirozzoloMedical Scientist Training Program, Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.ORCID https://orcid.org/0000-0003-0025-8549
Ahana NayarBarnard College, New York, NY, 10025, USA.
Lawrence ShapiroDepartment of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Stavros LomvardasDepartment of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.ORCID https://orcid.org/0000-0002-7668-3026

Funding

Tumor Biology and Microenvironment ProgramP30CA013696 · NCI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Anil K Rustgi · 1985 to 2026
$115.3M
Medical Scientist Training ProgramT32GM145440 · NIGMS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI STEVEN L REINER · 2022 to 2026
$7.3M
Understanding how opioids affect the experiential and neural signatures of feelings of social connection with close othersR01DA052883 · NIDA · SAN DIEGO STATE UNIVERSITY · PI Tristen K. Inagaki · 2021 to 2026
$3.0M
Principles of zonal olfactory receptor gene expressionR01DC018745 · NIDCD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI LOMVARDAS, STAVROS · 2020 to 2024
$2.3M
The "olfactosome" as a biomolecular condensateR21DA056348 · NIDA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI LOMVARDAS, STAVROS · 2022 to 2023
$452k
Identifying the mechanism of olfactory receptor gene regulation in olfactory neurons with live-cell imagingK99DC021219 · NIDCD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI PULUPA, JOAN M. · 2023 to 2024
$326k
NCI NIH HHS P30 CA013696NIDA NIH HHS R01 DA052883NIDA NIH HHS R21 DA056348NIDCD NIH HHS K99 DC021219NIDCD NIH HHS R01 DC018745NIGMS NIH HHS T32 GM145440
6 · The paper itself

Abstract

Ultra long-range genomic contacts, which emerge as prominent components of genome architecture, constitute a biochemical paradox. This is because regulatory DNA elements make selective and stable contacts with DNA sequences located megabases away, instead of interacting with proximal sequences occupied by the same exact transcription factors (TF). This is exemplified in olfactory sensory neurons (OSNs), where only a fraction of Lhx2/Ebf1/Ldb1-bound sites interact with each other, converging into highly selective multi-chromosomal enhancer hubs.

Identifiers

PMID39678350
PMCPMC11643329

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Registered trials

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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.