Evidence map›Paper›PMID 37292896›Full record

ArticlebioRxiv : the preprint server for biology2023

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.

Fairlie Reese, Brian Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Elisabeth Rebboah, Narges Rezaie, Diane Trout, Milad Razavi-Mohseni, Yunzhe Jiang and 35 more

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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. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed, 61 citations in OpenAlex.

  1. 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

45 authors at 10 institutions in 2 countries.

Fairlie ReeseDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Brian WilliamsDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Gabriela Balderrama-GutierrezDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Dana WymanCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Muhammed Hasan ÇelikCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Elisabeth RebboahCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Narges RezaieCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Diane TroutDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Milad Razavi-MohseniDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.
Yunzhe JiangProgram in Computational Biology and Bioinformatics, Yale University, New Haven, USA.
Beatrice BorsariProgram in Computational Biology and Bioinformatics, Yale University, New Haven, USA.
Samuel MorabitoCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Heidi Yahan LiangCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Cassandra J McGillDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Sorena RahmanianCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Jasmine SakrCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Shan JiangDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Weihua ZengDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
Klebea CarvalhoCenter for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Annika K WeimerDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Louise A DionneThe Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA.
Ariel McShaneCellular and Molecular Biology Program, University of Michigan, Ann Arbor, USA.
Karan BediDepartment of Biostatistics, University of Michigan, Ann Arbor, USA.
Shaimae I ElhajjajyProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA.
Sean UpchurchDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Jennifer JouDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Ingrid YoungworthDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Idan GabdankDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Paul SudDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Otto JolankiDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
J Seth StrattanDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Meenakshi S KagdaDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Michael P SnyderDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Ben C HitzDepartment of Genetics, Stanford University School of Medicine, Palo Alto, USA.
Jill E MooreProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA.
Zhiping WengProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA.
David BennettRush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA.
Laura ReinholdtThe Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA.
Mats LjungmanCenter for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, USA.
Michael A BeerDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.
Mark B GersteinProgram in Computational Biology and Bioinformatics, Yale University, New Haven, USA.
Lior PachterDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Roderic GuigóCentre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
Barbara J WoldDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Ali MortazaviDevelopmental and Cell Biology, University of California, Irvine, Irvine, USA.
University of California, Irvine · USStanford University · USCalifornia Institute of Technology · USUniversity of Massachusetts Chan Medical School · USUniversity of Michigan · USYale University · USJackson Laboratory · USJohns Hopkins University · USRush University Medical Center · USUniversitat Pompeu Fabra · ES

Funding

SUPPLEMENT TO RUSH ALZHEIMERS DISEASE CENTER COREP30AG010161 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI LEURGANS, SUE E. · 1991 to 2020
$49.1M
EPIDEMIOLOGY OF NEURAL RESERVE AND NEUROBIOLOGY IN AGINGR01AG017917 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 2001 to 2023
$43.3M
A Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0M
Rush Alzheimer's Disease Research CenterP30AG072975 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI Lisa L Barnes, Julie A. Schneider · 2021 to 2026
$24.7M
RISK FACTORS, PATHOLOGY, AND CLINICAL EXPRESSIONS OF ADR01AG015819 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1998 to 2024
$21.4M
The Mutant Mouse Resource and Research Center at The Jackson LaboratoryU42OD010921 · OD · JACKSON LABORATORY · PI LAURA G REINHOLDT · 2012 to 2026
$21.4M
Higher Precision Human and Mouse TranscriptomesUM1HG009443 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI MORTAZAVI, SEYED ALI, WOLD, BARBARA J · 2017 to 2021
$15.5M
Multi-omic network-directed proteoform discovery, dissection and functional validation to prioritize novel AD therapeutic targetsU01AG061356 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BENNETT, DAVID ALAN, DE JAGER, PHILIP L · 2018 to 2022
$13.7M
Pathway discovery, validation and compound identification for Alzheimer's disease - SupplementU01AG046152 · NIA · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BENNETT, DAVID ALAN, DE JAGER, PHILIP L · 2013 to 2017
$13.6M
EDAC: ENCODE Data Analysis CenterU24HG009446 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2017 to 2022
$10.4M
Resources for Comparative Mendelian Disease GenomicsR24OD021325 · OD · JACKSON LABORATORY · PI BERGSTROM, DAVID ERIC, REINHOLDT, LAURA G · 2016 to 2023
$6.5M
Systematic Identification of Core Regulatory Circuitry from ENCODE DataU01HG009380 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI BEER, MICHAEL A · 2017 to 2021
$2.6M
NHGRI NIH HHS R01 HG012367NHGRI NIH HHS U01 HG009380NHGRI NIH HHS U24 HG009397NHGRI NIH HHS U24 HG009446NHGRI NIH HHS UM1 HG009382NHGRI NIH HHS UM1 HG009443NIA NIH HHS P30 AG010161NIA NIH HHS P30 AG072975NIA NIH HHS R01 AG015819NIA NIH HHS R01 AG017917NIA NIH HHS U01 AG046152NIA NIH HHS U01 AG061356NIH HHS R24 OD021325NIH HHS U42 OD010921
6 · The paper itself

Abstract

The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3' end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives the complete structure of most transcripts. We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1 billion circular consensus reads (CCS) for 81 unique human and mouse samples. We detect at least one full-length transcript from 87.7% of annotated human protein coding genes and a total of 200,000 full-length transcripts, 40% of which have novel exon junction chains. To capture and compute on the three sources of transcript structure diversity, we introduce a gene and transcript annotation framework that uses triplets representing the transcript start site, exon junction chain, and transcript end site of each transcript. Using triplets in a simplex representation demonstrates how promoter selection, splice pattern, and 3' processing are deployed across human tissues, with nearly half of multi-transcript protein coding genes showing a clear bias toward one of the three diversity mechanisms. Evaluated across samples, the predominantly expressed transcript changes for 74% of protein coding genes. In evolution, the human and mouse transcriptomes are globally similar in types of transcript structure diversity, yet among individual orthologous gene pairs, more than half (57.8%) show substantial differences in mechanism of diversification in matching tissues. This initial large-scale survey of human and mouse long-read transcriptomes provides a foundation for further analyses of alternative transcript usage, and is complemented by short-read and microRNA data on the same samples and by epigenome data elsewhere in the ENCODE4 collection.

Identifiers

PMID37292896
PMCPMC10245583
OpenAlexW4376876239

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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.