Evidence map›Paper›PMID 39080502›Full record

ArticleNature plants2024

Multilayered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm.

Kaoru Tonosaki, Daichi Susaki, Hatsune Morinaka, Akemi Ono, Hiroki Nagata, Hiroyasu Furuumi, Ken-Ichi Nonomura, Yutaka Sato, Keiko Sugimoto, Luca Comai and 3 more

Abstract read
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In one paragraph

Article in Nature plants, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Review
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.

Kaoru TonosakiKihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan. tonosaki@yokohama-cu.ac.jp.ORCID http://orcid.org/0000-0002-3530-5846
Daichi SusakiKihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan.ORCID http://orcid.org/0000-0002-9465-9222
Hatsune MorinakaRIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.ORCID http://orcid.org/0000-0003-3605-3887
Akemi OnoKihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan.
Hiroki NagataKihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan.ORCID http://orcid.org/0000-0002-3470-6066
Hiroyasu FuruumiGenetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan.ORCID http://orcid.org/0000-0003-0195-7018
Ken-Ichi NonomuraPlant Cytogenetics, National Institute of Genetics, Mishima, Shizuoka, Japan.ORCID http://orcid.org/0000-0002-2057-543X
Yutaka SatoGenetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan.
Keiko SugimotoRIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.ORCID http://orcid.org/0000-0002-9209-8230
Luca ComaiDepartment of Plant Biology and Genome Center, University of California, Davis, CA, USA.ORCID http://orcid.org/0000-0003-2642-6619
Katsunori HatakeyamaFaculty of Agriculture, Iwate University, Morioka, Iwate, Japan.
Taiji KawakatsuInstitute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan. riverwin@naro.affrc.go.jp.ORCID http://orcid.org/0000-0002-6871-9199
Tetsu KinoshitaKihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan. tkinoshi@yokohama-cu.ac.jp.ORCID http://orcid.org/0000-0001-9985-0870

Funding

Ministry of Education, Culture, Sports, Science and Technology (MEXT) 20K15504Ministry of Education, Culture, Sports, Science and Technology (MEXT) 21H02170Ministry of Education, Culture, Sports, Science and Technology (MEXT) 22H02320Ministry of Education, Culture, Sports, Science and Technology (MEXT) 22H05175Ministry of Education, Culture, Sports, Science and Technology (MEXT) 22K15145Ministry of Education, Culture, Sports, Science and Technology (MEXT) 23H04749Ministry of Education, Culture, Sports, Science and Technology (MEXT) 23H04756Ministry of Education, Culture, Sports, Science and Technology (MEXT) 23K23585
6 · The paper itself

Abstract

In angiosperms, epigenetic profiles for genomic imprinting are established before fertilization. However, the causal relationships between epigenetic modifications and imprinted expression are not fully understood. In this study, we classified 'persistent' and 'stage-specific' imprinted genes on the basis of time-course transcriptome analysis in rice (Oryza sativa) endosperm and compared them to epigenetic modifications at a single time point. While the levels of epigenetic modifications are relatively low in stage-specific imprinted genes, they are considerably higher in persistent imprinted genes. Overall trends revealed that the maternal alleles of maternally expressed imprinted genes are activated by DNA demethylation, while the maternal alleles of paternally expressed imprinted genes with gene body methylation (gbM) are silenced by DNA demethylation and H3K27me3 deposition, and these regions are associated with an enriched motif related to Tc/Mar-Stowaway. Our findings provide insight into the stability of genomic imprinting and the potential variations associated with endosperm development, different cell types and parental genotypes.

Indexed as

DNA MethylationEndospermEpigenesis, GeneticGene Expression Regulation, PlantGenomic ImprintingOryzaGenes, Plant

Identifiers

PMID39080502

What OpenQuestion holds

Textmetadata
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.