Evidence map›Paper›PMID 36087152›Full record

ArticleMarine biotechnology (New York, N.Y.)2022

Comparative Methylome Analysis Reveals Epigenetic Signatures Associated with Growth and Shell Color in the Pacific Oyster, Crassostrea gigas.

Chao Tan, Chenyu Shi, Yin Li, Wen Teng, Yongjing Li, Huiru Fu, Liting Ren, Hong Yu, Qi Li, Shikai Liu

Abstract read
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In one paragraph

Article in Marine biotechnology (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
1.2field-weighted citation impact, top 22% 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

6 citing papers in PubMed, 14 citations in OpenAlex.

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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

10 authors at 2 institutions in 1 country.

Chao Tan *Key Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Chenyu Shi *Key Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Yin LiKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Wen TengKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Yongjing LiKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Huiru FuKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Liting RenKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Hong YuKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Qi LiKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China.
Shikai LiuKey Laboratory of Mariculture, Ministry of Education College of Fisheries, Ocean University of China, Ocean University of China, 266003, Qingdao, China. liushk@ouc.edu.cn.
Ocean University of China · CNQingdao National Laboratory for Marine Science and Technology · CN

Funding

National Natural Science Foundation of China 41976098
6 · The paper itself

Abstract

Fast growth is one of the most important breeding goals for all economic species such as the Pacific oyster (Crassostrea gigas), an aquaculture mollusk with top global production. Although the genetic basis and molecular mechanisms of growth-related traits have been widely investigated in the oyster, the role of DNA methylation involved in growth regulation remains largely unexplored. In this study, we performed a comparative DNA methylome analysis of two selectively bred C. gigas strains with contrasted phenotypes in growth and shell color based on whole-genome bisulfite sequencing (WGBS). Genome-wide profiling of DNA methylation at the single-base resolution revealed that DNA methylations were widely spread across the genome with obvious hotspots, coinciding with the distribution of genes and repetitive elements. Higher methylation levels were observed within genic regions compared with intergenic and promoter regions. Comparative analysis of DNA methylation allowed the identification of 339,604 differentially methylated CpG sites (DMCs) clustering in 27,600 differentially methylated regions (DMRs). Functional annotation analysis identified 11,033 genes from DMRs which were enriched in biological processes including cytoskeleton system, cell cycle, signal transduction, and protein biosynthesis. Integrative analysis of methylome and transcriptome profiles revealed a positive correlation between gene expression and DNA methylation within gene-body regions. Protein-protein interaction (PPI) analysis of differentially expressed and methylated genes allowed for the identification of integrin beta-6 (homolog of human ITGB3) as a hub modulator of the PI3K/Akt signaling pathway that was involved in various growth-related processes. This work provided insights into epigenetic regulation of growth in oysters and will be valuable resources for studying DNA methylation in invertebrates.

Indexed as

Biological PhenomenaCrassostreaAnimalsDNA MethylationEpigenesis, GeneticEpigenomeHumansIntegrinsPhosphatidylinositol 3-KinasesProto-Oncogene Proteins c-aktIntegrinsPhosphatidylinositol 3-KinasesProto-Oncogene Proteins c-aktCrassostrea gigasDNA methylationGrowthTranscriptional regulationWGBS

Identifiers

PMID36087152
OpenAlexW4295095232

What OpenQuestion holds

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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.