Difference between revisions of "Os09g0442700"

From RiceWiki
Jump to: navigation, search
(→‎Structured Information)
Line 1: Line 1:
−
Please input one-sentence summary here.
+
The rice '''''Os09g0442700''''' was reported as '''''OsDDM1a''''' in 2012 <ref name="ref1" /> by researchers from Japan.  
  
 
==Annotated Information==
 
==Annotated Information==
 +
[[File:155-Os03g0722400.png|right|thumb|427px|'''Figure 1.''' ''Expression of OsDDM1 genes during development..<ref name="ref1" />.'']]
 +
===Gene Symbol===
 +
*'''''Os09g0442700''''' '''''<=>''''' '''''OsDDM1a'''''
 
===Function===
 
===Function===
−
The gene was suggested that to silence endogenous loci including those related to retrotransposons in the rice genome.But the roles on transposition of active transposons in the genome remains unknown.
+
* '''''OsDDM1''''' genes function to silence endogenous loci including those related to retrotransposons in the rice genome, however, their roles on transposition of active.
−
There are evidences suggested that the hypomethylation in the antisense of this gene lines is induced by the antisense transgene but not in the process of transformation that includes tissue culture for callus induction (Toki 1997).In the antisense of this gene lines, cytosine methylation is severely reduced in the repeated sequences.Reduction in cytosine methylation is more evident in the later generations.
+
transposons in the genome remains unknown.
−
Additional details suggest the gene occasional maintenance of the partial methylation state at the single copy locus.
+
* Hypomethylation induced by the antisense '''''OsDDM1''''' disturbs normal development.
 +
* Transgenic rice lines expressing '''''OsDDM1a''''' cDNA in antisense orientation exhibited the genomic DNA hypomethylation in repeated sequences similar to the pattern observed in Arabidopsis ddm1 mutants.
  
 
===Expression===
 
===Expression===
−
They observed dwarf phenotypes in the antisense gene lines(Hiromi Higo ''et al''.2012)[[File:Characterization_of_the_antisense_OsDDM1_lines.png|200px|thumb|right]]
+
* '''''OsDDM1a''''' and '''''OsDDM1b''''' are expressed during development with slight variations among various tissues, suggesting that there might be functional divergence of these two genes (Fig. 1c).
−
The figure shows A dwarf phenotype appeared in a later generation of line 17. Right wild
 
−
type; left line 17 (the fifth generation)
 
−
 
 
−
===Evolution===
 
−
*Relationship among DDM1-like proteins: a. An alignment(ClustalX) of the C-terminal portion of the deduced amino acid
 
−
sequences of OsDDM1a, OsDDM1b, ''Zea mays'' CHR101 ([www.chromdb.org]), ''Zea mays'' CHR106 ([www.chromdb.org]), ''Arabidopsis thaliana'' DDM1 (AAD28303), and ''Mus musculus'' LSH (NP 032260).
 
−
 
 
−
*Genomic Southern analysis and database search using this EST revealed that the genome of rice(''Oryza sativa'' var. Nipponbare) contains two sequences similar to DDM1 (Fig.a).
 
−
 
 
−
*The two nucleotide sequences,which we designated OsDDM1a (LOC_Os09g27060 or Os09g0442700) and OsDDM1b (LOC_Os03g51230 or
 
−
Os03g0722400),are 93% identical to each other in the predicted amino acid sequences and show 60 % identity to Arabidopsis DDM1 (AT5G66750).
 
−
 
 
−
*The EST clone C30395 covers from the 945th nucleotide to the end of the OsDDM1a.
 
−
The structures of these two genes are closely related to each other.
 
−
Both consist of 15 exons and 14 introns, and the DNA sequence similarity of these two genes is 81%even including
 
−
introns (Fig.b).
 
−
[[File:Relationship among DDM1-like proteins.png]]
 
−
 
 
−
*The exon–intron structure is similar,
 
−
although not identical, to that of the Arabidopsis DDM1,which is composed of 16 exons. The OsDDM1 genes lack the
 
−
introns corresponding to the eighth intron of the Arabidopsis DDM1 gene (Fig. b).
 
−
The start codon of the Arabidopsis DDM1 is in the first exon, while it is in the second exon in the OsDDM1 genes. OsDDM1a and OsDDM1b are transcribed during development with slight variations in their relative abundance among different issues.Both OsDDM1 transcripts are more abundant in proliferating young tissues than in mature tissues that are consistent with the expected function of DDM1 for maintenance of DNA methylation on newly replicated DNA strands.
 
  
 
==Labs working on this gene==
 
==Labs working on this gene==
−
*Japan Science and Technology Agency,Kawaguchi 332-0012, Japan
+
* CREST, Japan Science and Technology Agency,Kawaguchi 332-0012, Japan
−
*Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
+
* Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
−
*Department of Plant Science, University of Manitoba,Winnipeg R3T 2N2, Canada
+
* Department of Plant Science, University of Manitoba,Winnipeg R3T 2N2, Canada
−
*Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan
+
* Department of Integrated Genetics, National Institute of Genetics, Mishima 411-0801, Japan
−
*Genetic Strains Research Center, National Institute of Genetics,Mishima 411-0801, Japan
 
  
 
==References==
 
==References==
−
*Hiromi Higo ''et al.''DDM1 (Decrease in DNA Methylation) genes in rice (''Oryza sativa'').Mol Genet Genomics (2012) 287:785–792
+
<references>
 +
* <ref name="ref1">
 +
Higo H, Tahir M, Takashima K, Miura A, Watanabe K, Tagiri A, Ugaki M, Ishikawa
 +
R, Eiguchi M, Kurata N, Sasaki T, Richards E, Takano M, Kishimoto N, Kakutani T,
 +
Habu Y. DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa). Mol
 +
Genet Genomics. 2012 Oct;287(10):785-92. Epub 2012 Aug 24. PubMed PMID: 22915302.
 +
</ref>
 +
</references>
  
 
==Structured Information==
 
==Structured Information==

Revision as of 13:30, 21 October 2016

The rice Os09g0442700 was reported as OsDDM1a in 2012 [1] by researchers from Japan.

Annotated Information

Figure 1. Expression of OsDDM1 genes during development..[1].

Gene Symbol

  • Os09g0442700 <=> OsDDM1a

Function

  • OsDDM1 genes function to silence endogenous loci including those related to retrotransposons in the rice genome, however, their roles on transposition of active.

transposons in the genome remains unknown.

  • Hypomethylation induced by the antisense OsDDM1 disturbs normal development.
  • Transgenic rice lines expressing OsDDM1a cDNA in antisense orientation exhibited the genomic DNA hypomethylation in repeated sequences similar to the pattern observed in Arabidopsis ddm1 mutants.

Expression

  • OsDDM1a and OsDDM1b are expressed during development with slight variations among various tissues, suggesting that there might be functional divergence of these two genes (Fig. 1c).

Labs working on this gene

  • CREST, Japan Science and Technology Agency,Kawaguchi 332-0012, Japan
  • Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
  • Department of Plant Science, University of Manitoba,Winnipeg R3T 2N2, Canada
  • Department of Integrated Genetics, National Institute of Genetics, Mishima 411-0801, Japan

References

  1. ↑ 1.0 1.1 Higo H, Tahir M, Takashima K, Miura A, Watanabe K, Tagiri A, Ugaki M, Ishikawa R, Eiguchi M, Kurata N, Sasaki T, Richards E, Takano M, Kishimoto N, Kakutani T, Habu Y. DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa). Mol Genet Genomics. 2012 Oct;287(10):785-92. Epub 2012 Aug 24. PubMed PMID: 22915302.

Structured Information

Retrieved from "https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0442700&oldid=275120"