Os04g0544100

Definition

SDG703, a 2712-bp rice gene located in chromosome 4 , encodes one of the Su(var)3–9 homologs(SUVH) which are evolutionarily conserved and whose H3K9 methyltransferase activity controls heterochromatin formation in eukaryotic organisms.

Phylogenetic tree

Phylogenetic analysis of rice and Arabidopsis SUVH proteins (also named as SET Domain Group, SDG) revealed four distinct clades (Figure 1A). Except clade 3 that has only one gene per species, each clade contains one to three pairs of sequences with high bootstrap values, which may correspond to duplications as a consequence of the polyploidization events that occurred 55–70 million years ago for rice or 20–30 million years ago for Arabidopsis (Paterson et al., 2004). Quantitative RT–PCR analysis of mRNA isolated from thee rice representative organs/tissues showed that although all of the genes were found to be more or less expressed in seedlings, flag leaves, and young panicles, the expression levels vary considerably among the different members(Figure 1B).

Function

Functional Analysis of Rice SVUH Genes

To study the function of rice SUVH proteins, the coding regions of the seven SUVH cDNA (SDG703, SDG704, SDG709, SDG713, SDG715, SDG726, and SDG728), of which the full lengths were available or obtained, were put under the control of the maize ubiquitin promoter in the overexpression vector pU1301 (Huang et al., 2007). Northern blot analysis revealed that many of the transgenic lines overexpressed the transgenes (Supplemental Figure 2). However, no obvious deviating phenotype compared to wild-type plants was observed (not shown). In parallel, we used gene-specific regions of SDG703, SDG704, SDG709, SDG710, SDG713, SDG714, SDG715, SDG726, SDG727, and SDG728 to construct RNA interference (RNAi) vector in pDS1301 (Huang et al., 2007). Real time RT–PCR analysis of 14–15 T0 plants per construct revealed several transgenic lines with reduced expression of the corresponding target gene (Supplemental Figure 3). Most of the RNAi plants (except that of SDG728) had no morphological phenotype, suggesting that rice SUVH genes may function redundantly to regulate plant growth.

Rice SUVH Proteins in Retrotransposon Repression

Tos17 is a copia-like retrotransposon that has heavy DNA methylation under normal growth conditions and can be activated under prolonged cell culture. The activated Tos17 is re-silenced during plant regeneration from explants (Cheng et al., 2006). It has been shown that SDG714 is involved in Tos17 DNA methylation and transposition (Ding et al., 2007). To study whether the expression of Tos17 was affected by deregulation of other rice SUVH genes, we compared Tos17 expression in wild-type, transgene negative and positive transgenic plants of SDG703, SDG704, SDG709, SDG713, and SDG728. In the RNAi plants of SDG703, SDG713, and SDG728, Tos17 expression was increased 4–20-fold compared to the controls (Figure 4A), with the highest expression observed in SDG728 RNAi plants. Conversely, overexpression of SDG703 and SDG728 repressed Tos17 expression (Figure 4A). Similarly, a Ty1-copia retrotransposon (Os08g03880) was also induced in SDG703 and SDG713 RNAi plants and repressed in SDG703 and SDG728 overexpression plants (Figure 4A).

Function of Histone Modification in Retrotransposon Repression in Rice

Besides DNA methylation, transcriptionally silenced retrotransposons are also maintained through histone methylation in Arabidopsis (Tran et al., 2005). The present data indicate that histone methylation may play a primary role in the retrotransposon repression. The chromatin immunoprecipitation results revealed an important role of H3K9me3 in retrotransposon repression. Similarly, previous results have shown that the rice SRT1 protein, a NAD+-dependent histone H3K9 deacetylase, is also required for transposon and retrotransposon repression. Therefore, it is likely that histone modifications(i.e. H3K9 deacetylation and methylation) may be an important mechanism that the rice genome uses to repress retrotransposons. Interplay between histone modification enzymes is suggested for epigenetic regulation of plant chromatin function (Zhou, 2009). Whether or not rice SUVH proteins functionally interact with SRT1 remains to be studied.

Related labs

• Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, National 430070 Wuhan, China
• Institut de Biotechnologie des Plantes, UMR8618, CNRS, Universite´ Paris sud 11, 91405 Orsay, France
• Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
• Division of Molecular Biology, Department of Biology, University of Oslo, PO Box 1031 Blindern, N-0315 Norway
• Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
• Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7295, USA.
• National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China

Reference

• Qin F J, Sun Q W, Huang L M, et al. Rice SUVH histone methyltransferase genes display specific functions in chromatin modification and retrotransposon repression[J]. Molecular plant, 2010, 3(4): 773-782.
• Huang L, Sun Q, Qin F, et al. Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice[J]. Plant physiology, 2007, 144(3): 1508-1519.
• Paterson A H, Bowers J E, Chapman B A. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics[J]. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(26): 9903-9908.
• Baumbusch L O, Thorstensen T, Krauss V, et al. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes[J]. Nucleic Acids Research, 2001, 29(21): 4319-4333.
• Tran R K, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis[J]. Genome biology, 2005, 6(11): R90.

Structured information

GenBank: AK066297 LOCUS AK066297 2712 bp mRNA linear PLN 04-DEC-2008 DEFINITION Oryza sativa Japonica Group cDNA clone:J013059A21, full insert sequence. ACCESSION AK066297 VERSION AK066297.1 GI:32976315 KEYWORDS FLI_CDNA; CAP trapper. SOURCE Oryza sativa Japonica Group (Japanese rice)

    ORGANISM  Oryza sativa Japonica Group           Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;            Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP            clade; Ehrhartoideae; Oryzeae; Oryza.

REFERENCE 1 AUTHORS Kikuchi,S., Satoh,K., Nagata,T., Kawagashira,N., Doi,K., Kishimoto,N., Yazaki,J., Ishikawa,M., Yamada,H., Ooka,H., Hotta,I., Kojima,K., Namiki,T., Ohneda,E., Yahagi,W., Suzuki,K., Li,C.J., Ohtsuki,K., Shishiki,T., Otomo,Y., Murakami,K., Iida,Y., Sugano,S., Fujimura,T., Suzuki,Y., Tsunoda,Y., Kurosaki,T., Kodama,T., Masuda,H., Kobayashi,M., Xie,Q., Lu,M., Narikawa,R., Sugiyama,A., Mizuno,K., Yokomizo,S., Niikura,J., Ikeda,R., Ishibiki,J., Kawamata,M., Yoshimura,A., Miura,J., Kusumegi,T., Oka,M., Ryu,R., Ueda,M., Matsubara,K., Kawai,J., Carninci,P., Adachi,J., Aizawa,K., Arakawa,T., Fukuda,S., Hara,A., Hashizume,W., Hayatsu,N., Imotani,K., Ishii,Y., Itoh,M., Kagawa,I., Kondo,S., Konno,H., Miyazaki,A., Osato,N., Ota,Y., Saito,R., Sasaki,D., Sato,K., Shibata,K., Shinagawa,A., Shiraki,T., Yoshino,M., Hayashizaki,Y. and Yasunishi,A.

TITLE Direct Submission JOURNAL Submitted (05-DEC-2001) Contact: Shoshi Kikuchi National Institute of Agrobiological Sciences, Department of Molecular Genetics, Head of Laboratory of Gene Expression; 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan COMMENT This clone is one of the 28K full-length cDNA clones from japonica rice. URL : http://cdna01.dna.affrc.go.jp/cDNA/ NIAS Rice Full-Length cDNA Project Team: Kikuchi,S., Satoh,K., Nagata,T., Kawagashira,N., Doi,K., Kishimoto,N., Yazaki,J., Ishikawa,M., Yamada,H., Ooka,H., Hotta,I., Kojima,K., Namiki,T., Ohneda,E., Yahagi,W., Suzuki,K., Li,C., Ohtsuki,K., Shishiki,T. And Yamamoto,M. FAIS Genome Sequencing & Analysis Group: Otomo,Y., Iida,Y., Fujimura,T., Ikeda,R., Ishibiki,J., Kawamata,M., Kobayashi,M., Kodama,T., Kurosaki,T., Kusumegi,T., Lu,M., Masuda,H., Miura,J., Mizuno,K., Narikawa,R., Niikura,J., Oka,M., Ryu,R., Sugano,S., Sugiyama,A., Suzuki,Y., Tsunoda,Y., Ueda,M., Xie,Q., Yokomizo,S., Yoshimura,A., Matsubara,K. and Murakami,K.

Genome Exploration Research Group in Riken Genomic Sciences Center and Genome Science Laboratory in Riken: Adachi,J., Aizawa,K., Akimura,T., Arakawa,T., Carninci,P., Fukuda,S., Hanagaki,T., Hara,A., Hashizume,W., Hayashida,K., Hayatsu,N., Hiramoto,K., Hiraoka,T., Hori,F., Iida,J., Imamura,K., Imotani,K., Ishii,Y., Itoh,M., Kagawa,I., Kanagawa,S., Katoh,H., Kawai,J., Kishikawa-Hirozane,T., Kojima,Y., Kondo,S., Konno,H., Kouda,M., Koya,S., Kurihara,C., Matsuyama,T., Miyazaki,A., Murata,M., Nakamura,M., Nishi,K., Nomura,K., Numasaki,R., Ohno,M., Osato,N., Ota,Y., Saitoh,H., Sakai,C., Sakai,K., Sakazume,N., Sano,H., Sasaki,D., Sato,K., Shibata,K., Shinagawa,A., Shiraki,T., Sogabe,Y., Tagami,M., Tagami-Takeda,Y., Tagawa,A., Takahashi,F., Takaku-Akahira,S., Tanaka,T., Tomaru,A., Toya,T., Waki,K., Yasunishi,A. and Hayashizaki,Y.

FEATURES Location/Qualifiers Source 1..2712/organism="Oryza sativa Japonica Group" /mol_type="mRNA" /cultivar="Nipponbare" /db_xref="taxon:39947" /clone="J013059A21" misc_feature 1..2712

/note="(RAP Annotation release2) Similar to SET      	domain-containing protein SET104;

(Rice Genome Annotation Project) histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6, putative, expressed; mapping to R04-TIGRv4S1-000851R (Chr.4: short arm=27024994, long arm=27027704, direction=reverse) for TIGR Pseudomol ver4" ORIGIN

    1 gaggagaacc cccaccccac ccacctcgcc ccactccgcc gcgccccctc cccgctgcct
   61 ccgtggagcg tcatctccac gtgcagggtt agaggcttct ggtggtggtg ggggcagtgc
  121 ggggggcgtt ggatggggat cccggaggtg gtggtgccgc cgagggcggc cggcccgcgg
  181 aggtacaagg ggctcgtgcc gtggcgcttc cagccgggct tcgtcaggcc gcctccggtc
  241 aagccccctg ccgccgccgc cgccgttgcc ggaggagggg tcgcgggcac gcccggcggc
  301 aagggtcgcg ggttgggggc gtcgggggaa ggcgtcgggt ccagtggagg ccggggagat
  361 cctcaatcga ggagatgcac ccacagcgcg agcgcgaagg gctctggtga tgcgcggagc
  421 gtggaggagg gcggtccccg tgttgccgga gacgacggcg gttcgggcaa atccggcgtc
  481 gcggcggagg gctccggatt tgagggtttg aggaatggca ggggcggtgg cgttggaacg
  541 gcagctgccg aagattgtgg tttggagaag tccaaccccg atggcatcgt cggagatgct
  601 gatgtgcatc ttgagagcgg cagcgatgca agagatgggg aatgcgtttc tgagggtttg
  661 aagaagcctt gtgtaaataa tagcaatggt tcttctgccg cggattgcgc gccgaaggtg
  721 aaaaagggaa atgacagtgg caatggaggt gccgatgagt gtaatgctgc agccaaaagt
  781 agcaacttag catgtcctgg caacaatggc gacgaaacga atcgtaaggg gcggaaggta
  841 gtacttccat ggaggttcca ggttgggttc aagcggtcgt tctcgaaagc tttctgctcc
  901 gatagtgaat cttcagggcc ctctggtact caattctaca gagcccaaga ctcttcgaca
  961 ccgtgcactc cagcaacaag aagttctgtc cggtgttatg cgagtgctca ttctggtgtt
 1021 agagtctcgg ccatgcgtga tttctcagtg aaaggtgaga aggaaacatc aactccatat
 1081 aagaagagca aaactggcat ggatggtcct agtcaaggga tgccaaagaa tggagttgtc
 1141 ctcgctaggg aaaacattat gggatctctg cagaattttc gcttaattta cagggacctt
 1201 ttggatgaag aagaagagaa gtcgacagaa gcagtgatta gacctgatct acaagcttac
 1261 agaattttca gggagcggtt catcacagac tgcgatgaga agaaatatat tggcaatgtg
 1321 cctggaatca aagttggtga tatcttccac ttgagggtag agctttgtgt tgttggtctt
 1381 catcgcccac accgggtggg tgtagatcat atcaaacagg aggatgggac ttgcatagct
 1441 gttagcattg tatcatatgc acaatcttcc gatattaaga ataatttgga tgtcttggtg
 1501 tattctggag caatgacagc tatagccaat cagaagatag agggtaccaa cttagcactc
 1561 aagaagagta tggacactaa cacaccagtc cgtgttatcc atggtttcgt cactcacctc
 1621 aatggaaact gccagcgaaa gaagatccct acttatatat atgggggttt atatatagtc
 1681 gagaaatact ggagggagaa agagggtaat gatcgttatg tttatatgtt ccgactgaga
 1741 agaatggcag gtcagaaaca cattgacatc caagacattc tgaattcagg acaagctgaa
 1801 tcatatggtg gtattatcat aaaagatata tcccgaggat tggagaagat ccctgtatct
 1861 gttgttaatt caatatctga tgagtaccca atgccctatc gctacattgc acacctgcag
 1921 tacccccgta actaccagcc agcacctcca gcaggctgtg gttgtgttgg tggatgctca
 1981 gattctaaaa ggtgtgcatg tgcagtgaaa aatggtgggg agattccttt caatgataaa
 2041 ggccgcatct tagaagcaaa acctcttgtt tatgagtgtg gaccttcatg caagtgccct
 2101 cctacatgtc ataacagagt tggtcaacat ggccttaggt ttcgtttgca agtcttcaaa
 2161 accaaattga tgggctgggg agtaagaact cttgacttca taccatctgg aagctttgta
 2221 tgtgaataca ttggagaagt gttggaggat gaagaggcac agaaaaggtc gaccgatgaa
 2281 tacttattcg ctattggtca taattattat gatgaagccc tttgggaggg cctatcaaga
 2341 tccataccct cacttcagaa gggtcctgat aaagatgagg aagctggctt tgctgttgat
 2401 gcttcaaaga tgggcaactt tgcaaaattc atcaaccata gttgcacccc taacctttat
 2461 gcacaaaatg tcctatatga tcatgacgac aagagtgtac ctcacattat gttctttgcc
 2521 tgtgaggaca ttccaccccg ccaagaactt tcataccact acaactatac aatagatcag
 2581 gttcatgatg ccaatggtaa catcaagaag aaaaaatgtc tctgtggctc tatagagtgt
 2641 gatggttggt tgtattaggc ttgagagtgt actatttcca gaggcataat tgaacttctt
 2701tcattgggca tg

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