Evidence map›Paper›PMID 25259844›Full record

ArticlePloS one2014

Does the upstream region possessing MULE-like sequence in rice upregulate PsbS1 gene expression?

Mohammed Nuruzzaman, Tatsuo Kanno, Rika Amada, Yoshiki Habu, Ichiro Kasajima, Toshiki Ishikawa, Maki Kawai-Yamada, Hirofumi Uchimiya

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

Article in PloS one, 2014. 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 26% 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, 6 citations in OpenAlex.

  1. Review
  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

8 authors at 3 institutions in 1 country.

Mohammed NuruzzamanInstitute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan; Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan.
Tatsuo KannoJapanese Science and Technology Agency, PRESTO, Saitama, Japan; Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Ibaraki, Japan.
Rika AmadaInstitute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan.
Yoshiki HabuPlant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Ibaraki, Japan.
Ichiro KasajimaNational Agriculture and Food Research Organization, Institute of Floricultural Science, Tsukuba, Japan.
Toshiki IshikawaGraduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan.
Maki Kawai-YamadaInstitute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan; Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama, Japan.
Hirofumi UchimiyaInstitute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan.
Saitama University · JPInstitute of Agrobiological Sciences · JPNational Agriculture and Food Research Organization · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The genomic nucleotide sequences of japonica rice (Sasanishiki and Nipponbare) contained about 2.7-kb unique region at the point of 0.4-kb upstream of the OsPsbS1 gene. In this study, we found that japonica rice with a few exceptions possessing such DNA sequences [denoted to OsMULE-japonica specific sequence (JSS)] is distinct by the presence of Mutator-like-element (MULE). Such sequence was absent in most of indica cultivars and Oryza glaberrima. In OsMULE-JSS1, we noted the presence of possible target site duplication (TSD; CTTTTCCAG) and about 80-bp terminal inverted repeat (TIR) near TSD. We also found the enhancement ofOsPsbS1 mRNA accumulation by intensified light, which was not associated with the DNA methylation status in OsMULE/JSS. In addition, O. rufipogon, possible ancestor of modern rice cultivars was found to compose PsbS gene of either japonica (minor) or indica (major) type. Transient gene expression assay showed that the japonica type promoter elevated a reporter gene activity than indica type.

Indexed as

Gene Expression Regulation, PlantGenes, PlantRegulatory Sequences, Nucleic AcidBase SequenceChromosomes, PlantDNA MethylationGene DosageGene ExpressionGene OrderGenes, ReporterGenome, PlantMolecular Sequence DataOryzaPromoter Regions, GeneticTerminal Repeat SequencesTranscriptional Activation

Identifiers

PMID25259844
PMCPMC4178011
OpenAlexW1990832129

What OpenQuestion holds

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LicenceCC BY
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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.