Evidence map›Paper›PMID 33176680›Full record

ArticleBMC genomics2020

Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns.

Yuan Lu, Mikki Boswell, William Boswell, Raquel Ybanez Salinas, Markita Savage, Jose Reyes, Sean Walter, Rebecca Marks, Trevor Gonzalez, Geraldo Medrano and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2020. 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

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

13 authors.

Yuan LuThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA. y_l54@txstate.edu.
Mikki BoswellThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
William BoswellThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Raquel Ybanez SalinasThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Markita SavageThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Jose ReyesThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Sean WalterThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Rebecca MarksThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Trevor GonzalezThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Geraldo MedranoThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Wesley C WarrenBond Life Sciences Center, University of Missouri, Columbia, MO, USA.
Manfred SchartlThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
Ronald B WalterThe Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.

Funding

Enhanced Development of the Xiphophorus Model System R24-OD-011120R24OD011120 · OD · TEXAS STATE UNIVERSITY · PI WALTER, RONALD B · 2012 to 2019
$5.3M
South Texas Doctoral Bridge ProgramR25GM102783 · NIGMS · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI OYAJOBI, BABATUNDE OLUKAYODE, WHITTEN, STEVEN T · 2013 to 2022
$3.1M
A genomic toolkit for functional interrogation of trait variation in an aquatic modelR24OD030214 · OD · UNIVERSITY OF MISSOURI-COLUMBIA · PI KEENE, ALEX C, WARREN, WESLEY CHARLES · 2022 to 2025
$2.8M
Development of Aquatic Model Resources for Therapeutic ScreensR24OD018555 · OD · UNIVERSITY OF OREGON · PI POSTLETHWAIT, JOHN H. · 2014 to 2017
$2.6M
Whole genome assembly resources for aquatic models of human diseaseR24OD011198 · OD · WASHINGTON UNIVERSITY · PI WARREN, WESLEY CHARLES · 2012 to 2019
$1.4M
Identification and Characterization of a Endogenous EGFR Regulatory Locus in Xiphophorus GenomeR15CA223964 · NCI · TEXAS STATE UNIVERSITY · PI LU, YUAN · 2018 to 2021
$887k
national institute of health R15-CA-223964national institute of health R24 OD-011120national institute of health R24 OD-018555national institute of health R25 GM 102783NCI NIH HHS R15 CA223964NIGMS NIH HHS R25 GM102783NIH HHS R24 OD011120NIH HHS R24 OD011198NIH HHS R24 OD018555NIH HHS R24 OD030214
6 · The paper itself

Abstract

backgroundStudying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period.

resultsOur results showed 1.3-21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs.

conclusionsThese observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.

Indexed as

Gene DuplicationGenes, DuplicateAnimalsEvolution, MolecularFishesGene ExpressionGenomePhylogenyBasal level gene expressionEvolutionGene expression profilingGenome duplicationLight responseOrganParalogProfilingXiphophorus

Identifiers

PMID33176680
PMCPMC7659085

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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.