Evidence map›Paper›PMID 37986839›Full record

ArticlebioRxiv : the preprint server for biology2023

Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1.

Cheng Xu, Holly Kleinschmidt, Jianyu Yang, Erik Leith, Jenna Johnson, Song Tan, Shaun Mahony, Lu Bai

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors at 1 institution in 1 country.

Cheng XuDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Holly KleinschmidtDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Jianyu YangDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Erik LeithDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Jenna JohnsonDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Song TanDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Shaun MahonyDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Lu BaiDepartment of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Pennsylvania State University · US

Funding

Structural studies of chromatin complexesR35GM127034 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI SONG TAN · 2018 to 2026
$4.8M
Mechanism of Chromatin Accessibility, 3D Chromosome Organization, and Their Functions in Gene RegulationR35GM139654 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI Lu Bai · 2021 to 2026
$3.8M
Understanding the predeterminants of transcription factor regulatory activityR35GM144135 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI Shaun Aengus Mahony · 2022 to 2026
$2.4M
Eukaryotic Gene Regulation (EGR) Predoctoral Training ProgramT32GM125592 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI REESE, JOSEPH C · 2018 to 2022
$920k
NIGMS NIH HHS R35 GM127034NIGMS NIH HHS R35 GM139654NIGMS NIH HHS R35 GM144135NIGMS NIH HHS T32 GM125592
6 · The paper itself

Abstract

Despite the unique ability of pioneer transcription factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called ChIP-ISO to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1. Combining ChIP-ISO with

Identifiers

PMID37986839
PMCPMC10659273
OpenAlexW4388613611

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.