Evidence map›Paper›PMID 38062486›Full record

ArticleGenome biology2023

GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins.

Wandi S Zhu, Adam J Litterman, Harshaan S Sekhon, Robin Kageyama, Maya M Arce, Kimberly E Taylor, Wenxue Zhao, Lindsey A Criswell, Noah Zaitlen, David J Erle and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.5field-weighted citation impact, top 32% of its field
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

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Article
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

11 authors at 2 institutions in 2 countries.

Wandi S Zhu *Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
Adam J Litterman *Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
Harshaan S SekhonDepartment of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
Robin KageyamaDepartment of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
Maya M ArceDepartment of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
Kimberly E TaylorDepartment of Medicine, University of California San Francisco, San Francisco, USA.
Wenxue ZhaoDepartment of Medicine, University of California San Francisco, San Francisco, USA.
Lindsey A CriswellDepartment of Medicine, University of California San Francisco, San Francisco, USA.
Noah ZaitlenDepartment of Medicine, University of California San Francisco, San Francisco, USA.
David J ErleDepartment of Medicine, University of California San Francisco, San Francisco, USA.
K Mark AnselDepartment of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA. Mark.Ansel@ucsf.edu.ORCID 0000-0003-4840-9879
University of California, San Francisco · USSun Yat-sen University · CN

Funding

Role of miRNAs in Th2-Driven inflammation in AsthmaP01HL107202 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANSEL, KARL MARK · 2012 to 2023
$23.3M
MOLECULAR AND CELLULAR IMMUNOLOGYT32AI007334 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CYSTER, JASON G · 1988 to 2023
$11.0M
Airway epithelial cell gene regulation: new mechanisms and therapeutic strategiesR35HL145235 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ERLE, DAVID J · 2019 to 2025
$6.8M
Role of miRNAs in Th2-Driven inflammation in AsthmaR01HL109102 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Karl Mark Ansel · 2011 to 2026
$5.5M
Restorative practice in repairing harm and promoting safe and inclusive practices in the laboratory.T32GM136547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Adrian Erlebacher · 2020 to 2026
$4.5M
Massively parallel identification of functional 3' UTR variants in asthmaR01HL124285 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ERLE, DAVID J · 2014 to 2017
$2.2M
Empiric deconvolution of functional RNA elementsR01GM110251 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ERLE, DAVID J, MCMANUS, MICHAEL T · 2014 to 2017
$2.2M
Global analysis of T cell post-transcriptional regulatory elementsR21AI128047 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANSEL, KARL MARK · 2018 to 2019
$440k
NHLBI NIH HHS HL107202NHLBI NIH HHS HL109102NHLBI NIH HHS HL124285NHLBI NIH HHS P01 HL107202NHLBI NIH HHS R01 HL109102NHLBI NIH HHS R01 HL124285NHLBI NIH HHS R35 HL145235NIAID NIH HHS R21 AI128047NIAID NIH HHS T32 AI007334NIGMS NIH HHS GM110251NIGMS NIH HHS R01 GM110251NIGMS NIH HHS T32 GM136547
6 · The paper itself

Abstract

GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags correspond with known RBP binding sites and are enriched for sites detected by RBP-specific crosslinking immunoprecipitation (CLIP) for abundant cytosolic RBPs. Comparison of human Jurkat T cells and mouse primary T cells uncovers shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a conserved mRNA-destabilizing cis-regulatory element. GCLiPP signal overlapping with immune-related SNPs uncovers stabilizing cis-regulatory regions in CD5, STAT6, and IKZF1.

Indexed as

RNA-Binding ProteinsTranscriptomeAnimalsBinding SitesHumansImmunoprecipitationMiceProtein BindingRNARNARNA-Binding ProteinsCis-regulatory elementsPost-transcriptional regulationRNA-binding proteins (RBP)T cells

Identifiers

PMID38062486
PMCPMC10701951
OpenAlexW4389441844

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.