Identification of six new box C/D snoRNA gene clusters from rice

Li, Wei; Jiang, Ge; Zeng, Dabo; Jin, Youxin

doi:10.1080/15216540701589312

Cited by 6 publications

(2 citation statements)

References 25 publications

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“…However, multi-GO genes predicted for the functionality of any plant QTL have never been validated. Similarly, genes in the functional gene clusters representing gene families 46 , biosynthetic pathways 47 or certain traits 48 49 belong to a single GO category. The plant self-incompatibility (SI) S-locus is a unique case of multi-GO locus in which SI is governed in different plant families through genes of different GO categories, i.e.…”

Section: Discussionmentioning

confidence: 99%

Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

Dixit

Biswal

Min

et al. 2015

Sci Rep

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Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security.

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Section: Discussionmentioning

confidence: 99%

Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

Dixit

Biswal

Min

et al. 2015

Sci Rep

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“…The global studies of the snoRNA content in A. thaliana were complemented by the analysis of the RNA family in rice [ 45 , 46 ]. This has led to the extension of predicted snoRNAome by optimizing the search algorithms [ 47 ].…”

Section: Introductionmentioning

confidence: 99%

The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited

Streit

Shanmugam

Garbelyanski

et al. 2020

Plants

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Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.

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Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

Goyal

Kumar

Shukla

et al. 2011

Planta

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Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.

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Identification of six new box C/D snoRNA gene clusters from rice

Cited by 6 publications

References 25 publications

Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited

Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

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