Os05g0196500 - Revision history

192.168.72.52: /* Structured Information */

2015-06-12T07:32:06Z

‎Structured Information

Sdzhangjie1989: /* Function */

2014-06-08T14:34:02Z

‎Function

Sdzhangjie1989: /* Crystal Structure */

2014-05-15T03:28:16Z

‎Crystal Structure

Sdzhangjie1989: /* Knowledge Extension */

2014-05-15T03:19:07Z

‎Knowledge Extension

Sdzhangjie1989: /* Function */

2014-05-15T02:54:34Z

‎Function

Sdzhangjie1989: /* Function */

2014-05-15T02:53:40Z

‎Function

Sdzhangjie1989: /* References */

2014-05-15T02:49:03Z

‎References

Sdzhangjie1989: /* Annotated Information */

2014-05-15T02:46:37Z

‎Annotated Information

Sdzhangjie1989 at 02:34, 15 May 2014

2014-05-15T02:34:36Z

Sdzhangjie1989: /* Expression */

2014-05-14T15:15:35Z

‎Expression

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 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

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 ===Function===
 [[File:jmj703 mutants.PNG|right|thumb|500px|''jmj703 mutants display pleiotropic defective phenotypes (from reference <ref name="ref1" />).'']]
-This gene encodes a histone H3K4 demethylase —JMJ703 which involves in both transposon(TE) silencing and stem elongation in rice. ''jmj703'' mutants displayed pleiotropic phenotypes such as erect leaves, significantly decreased secondary panicle branches and abnormal phenotypes of grains, the most obvious of which was dwarfism.<ref name="ref1" /> JMJ703 is a JmjC domain-containing protein, which can specifically demethylate methylated histone H3 lysine 4 and reverse all three forms of H3K4me(mono-, di-, or trimethylation).<ref name="ref2" /> It is required for TEs silencing. Impaired JMJ703 activity leads to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons(''Karma'' and ''LINE1''). However, loss of JMJ703 does not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways, indicating that different subsets of TEs may be regulated by distinct epigenetic pathways.<ref name="ref1" /> Besides, loss-of-function mutation of the gene reduces cell division rate of the stem and size of plant stature, showing the importance of this protein in plant growth. The mechanism may be that JMJ703 regulates H3K4me3 on CKX genes and that the mutant phenotype might be due to cytokinin deficiency caused by increased H3K4me3 and increased expression of CKX genes.<ref name="ref2" />
+This gene encodes a histone H3K4 demethylase —JMJ703 which involves in both transposon(TE) silencing and stem elongation in rice. ''jmj703'' mutants displayed pleiotropic phenotypes such as erect leaves, significantly decreased secondary panicle branches and abnormal phenotypes of grains, the most obvious of which was dwarfism.<ref name="ref1" /> JMJ703 is a JmjC domain-containing protein, which can specifically demethylate methylated histone H3 lysine 4 and reverse all three forms of H3K4me(mono-, di-, or trimethylation).<ref name="ref2" /> It is required for TEs silencing. Impaired JMJ703 activity leads to elevated levels of H3K4me3, misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons(''Karma'' and ''LINE1''). These changes enhance the movement of transposons that are normally silenced and immobile. So we can conclude from these findings that plants use H3K4me3 demethylase to constitutively remove active chromatin marks and maintain the silent status of a subset of retrotransposons to preserve genome integrity. However, loss of JMJ703 does not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways, indicating that different subsets of TEs may be regulated by distinct epigenetic pathways.<ref name="ref1" /> Besides, loss-of-function mutation of the gene reduces cell division rate of the stem and size of plant stature, showing the importance of this protein in plant growth. The mechanism may be that JMJ703 regulates H3K4me3 on CKX genes and that the mutant phenotype might be due to cytokinin deficiency caused by increased H3K4me3 and increased expression of CKX genes.<ref name="ref2" />
 ===Expression===

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 [[File:crystal structure.PNG|right|thumb|150px|''Overall structure of c-JMJ703. Separate domains are colored differently and labeled. (from reference <ref name="ref2" />).'']]
 Gel filtration reveals that c-JMJ703 exists as a monomer in solution, suggesting that the monomer may be the biological unit. The c-JMJ703 molecule presents a canonical overall folding of JMJD2 proteins and contains four of the five domains defined in the structure of c-JMJD2A: the JmjN domain (A139-K199), the long b-hairpin (D200-T271), the mixed domain (L272-V377) and the JmjC domain (L378-A498). The JmjC domain, sandwiched by the JmjN and the long b-hairpin with the
-mixed domain, adopts a jellyroll-like structure with two fourstranded b-sheets as a cupin fold.<ref name="ref2" />
+mixed domain, adopts a jellyroll-like structure with two fourstranded b-sheets as a cupin fold. Although c-JMJ703 shares low primary sequence similarity (less
 ===Knowledge Extension===
 Numerous epigenetic marks, including acetylation, methylation, phosphorylation, and ubiquitination, are introduced at particular sites on histone tails. Posttranslational modifications of histone tails are critical epigenetic marks that regulate diverse cellular processes. Histone lysine methylation activates or represses transcription, depending on the site and degree of these modifications. Two classes of histone lysine demethylases remove histone methylation. Lysine demethylase 1 (KDM1, also known as LSD1) is a flavin adenine dinucleotide (FAD)-containing enzyme that removes mono-/di-methylation. The Jumonji C-terminal domain (JmjC) family of histone demethylases uses Fe2+ and α-ketoglutarate as cofactors to remove all methylation states. Like all other histone modifications, histone lysine methylation is dynamic and reversible. Its addition and removal are catalyzed by histone methyltransferases and demethylases, respectively. Histone demethylases contribute to the regulation of the steady-state levels of histone methylation and are thus crucial for many chromatin-based cellular processes.<ref name="ref3" />

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 mixed domain, adopts a jellyroll-like structure with two fourstranded b-sheets as a cupin fold.<ref name="ref2" />
 ===Knowledge Extension===
-Posttranslational modifications of histone tails are critical epigenetic marks that regulate diverse cellular processes. Histone lysine methylation activates or represses transcription, depending on the site and degree of these modifications. Two classes of histone lysine demethylases remove histone methylation. Lysine demethylase 1 (KDM1, also known as LSD1) is a flavin adenine dinucleotide (FAD)-containing enzyme that removes mono-/di-methylation. The Jumonji C-terminal domain (JmjC) family of histone demethylases uses Fe2+ and α-ketoglutarate as cofactors to remove all methylation states.<ref name="ref3" />
+Numerous epigenetic marks, including acetylation, methylation, phosphorylation, and ubiquitination, are introduced at particular sites on histone tails. Posttranslational modifications of histone tails are critical epigenetic marks that regulate diverse cellular processes. Histone lysine methylation activates or represses transcription, depending on the site and degree of these modifications. Two classes of histone lysine demethylases remove histone methylation. Lysine demethylase 1 (KDM1, also known as LSD1) is a flavin adenine dinucleotide (FAD)-containing enzyme that removes mono-/di-methylation. The Jumonji C-terminal domain (JmjC) family of histone demethylases uses Fe2+ and α-ketoglutarate as cofactors to remove all methylation states. Like all other histone modifications, histone lysine methylation is dynamic and reversible. Its addition and removal are catalyzed by histone methyltransferases and demethylases, respectively. Histone demethylases contribute to the regulation of the steady-state levels of histone methylation and are thus crucial for many chromatin-based cellular processes.<ref name="ref3" />
 ==Labs working on this gene==

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 ===Function===
 [[File:jmj703 mutants.PNG|right|thumb|500px|''jmj703 mutants display pleiotropic defective phenotypes (from reference <ref name="ref1" />).'']]
-This gene encodes a histone H3K4 demethylase —JMJ703 which involves in both transposon(TE) silencing and stem elongation in rice. ''jmj703'' mutants displayed pleiotropic phenotypes(including erect leaves, significantly decreased secondary panicle branches and abnormal phenotypes of grains), the most obvious of which was dwarfism.<ref name="ref1" /> JMJ703 is a JmjC domain-containing protein, which can specifically demethylate methylated histone H3 lysine 4 and reverse all three forms of H3K4me(mono-, di-, or trimethylation).<ref name="ref2" /> It is required for TEs silencing. Impaired JMJ703 activity leads to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons(''Karma'' and ''LINE1''). However, loss of JMJ703 does not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways, indicating that different subsets of TEs may be regulated by distinct epigenetic pathways.<ref name="ref1" /> Besides, loss-of-function mutation of the gene reduces cell division rate of the stem and size of plant stature, showing the importance of this protein in plant growth. The mechanism may be that JMJ703 regulates H3K4me3 on CKX genes and that the mutant phenotype might be due to cytokinin deficiency caused by increased H3K4me3 and increased expression of CKX genes.<ref name="ref2" />
+This gene encodes a histone H3K4 demethylase —JMJ703 which involves in both transposon(TE) silencing and stem elongation in rice. ''jmj703'' mutants displayed pleiotropic phenotypes such as erect leaves, significantly decreased secondary panicle branches and abnormal phenotypes of grains, the most obvious of which was dwarfism.<ref name="ref1" /> JMJ703 is a JmjC domain-containing protein, which can specifically demethylate methylated histone H3 lysine 4 and reverse all three forms of H3K4me(mono-, di-, or trimethylation).<ref name="ref2" /> It is required for TEs silencing. Impaired JMJ703 activity leads to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons(''Karma'' and ''LINE1''). However, loss of JMJ703 does not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways, indicating that different subsets of TEs may be regulated by distinct epigenetic pathways.<ref name="ref1" /> Besides, loss-of-function mutation of the gene reduces cell division rate of the stem and size of plant stature, showing the importance of this protein in plant growth. The mechanism may be that JMJ703 regulates H3K4me3 on CKX genes and that the mutant phenotype might be due to cytokinin deficiency caused by increased H3K4me3 and increased expression of CKX genes.<ref name="ref2" />
 ===Expression===

@@ Line 28: / Line 28: @@
 <ref name="ref1">Cui X, Jin P, Cui X, et al. Control of transposon activity by a histone H3K4 demethylase in rice[J]. Proceedings of the National Academy of Sciences, 2013, 110(5): 1953-1958.</ref>
 <ref name="ref2"> Chen Q, Chen X, Wang Q, et al. Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice[J]. PLoS genetics, 2013, 9(1): e1003239.</ref>
 </references>

← Older revision		Revision as of 02:34, 15 May 2014
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−	~~Please input one-sentence summary here~~.	+	This is a gene which encodes a histone H3K4 demethylase in rice.

	==Annotated Information==		==Annotated Information==

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 ===Expression===
 JMJ703 is expressed at relatively high levels in leaves of 7 d-after-germination (DAG) seedlings compared with all of the other tissues tested.<ref name="ref1" />
 ===Evolution===