3vem: Difference between revisions

Latest revision as of 10:35, 1 March 2024

Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1

Structural highlights

3vem is a 4 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MOM1_ARATH Required for the heritable maintenance of transcriptional gene silencing (TGS) in heterochromatin, and particularly in the intermediate bivalent heterochromatin, characterized by an unsual methylation pattern consisting in hypermethylated DNA and histone H3 'Lys-4' methylation (H3K4me) together with depletion of histone H3 'Lys-9' methylation (H3K9me), in a chromatin methylation-independent manner, in a non-CG methylation context. May play a role in the RNA polymerase IV/V (Pol-IV/V)-mediated RNA-directed DNA methylation (RdDM) leading to TGS (also called siRNA-mediated TGS pathway), probably by modulating small interfering RNA (siRNA) accumulation. Especially involved in the gene silencing of the transcriptionally silent information region (TSI), 5S ribosomal RNA genes (localized in the pericentromeric heterochromatin of chromosomes 3, 4, and 5) and of 180-bp satellite repeats and 106B long terminal repeat (LTR)-like repeats of the chromocenters. Prevents the aberrant mRNA transcriptional read-through.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

References

↑ Amedeo P, Habu Y, Afsar K, Mittelsten Scheid O, Paszkowski J. Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature. 2000 May 11;405(6783):203-6. PMID:10821279 doi:https://dx.doi.org/10.1038/35012108
↑ Steimer A, Amedeo P, Afsar K, Fransz P, Mittelsten Scheid O, Paszkowski J. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell. 2000 Jul;12(7):1165-78. PMID:10899982
↑ Mittelsten Scheid O, Probst AV, Afsar K, Paszkowski J. Two regulatory levels of transcriptional gene silencing in Arabidopsis. Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13659-62. Epub 2002 Oct 7. PMID:12370435 doi:https://dx.doi.org/10.1073/pnas.202380499
↑ Probst AV, Fransz PF, Paszkowski J, Mittelsten Scheid O. Two means of transcriptional reactivation within heterochromatin. Plant J. 2003 Feb;33(4):743-9. PMID:12609046
↑ Vaillant I, Schubert I, Tourmente S, Mathieu O. MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep. 2006 Dec;7(12):1273-8. Epub 2006 Nov 3. PMID:17082821 doi:https://dx.doi.org/10.1038/sj.embor.7400791
↑ Habu Y, Mathieu O, Tariq M, Probst AV, Smathajitt C, Zhu T, Paszkowski J. Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep. 2006 Dec;7(12):1279-84. Epub 2006 Nov 3. PMID:17082818 doi:https://dx.doi.org/10.1038/sj.embor.7400835
↑ Caikovski M, Yokthongwattana C, Habu Y, Nishimura T, Mathieu O, Paszkowski J. Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants. PLoS Genet. 2008 Aug 22;4(8):e1000165. doi: 10.1371/journal.pgen.1000165. PMID:18725928 doi:https://dx.doi.org/10.1371/journal.pgen.1000165
↑ Yokthongwattana C, Bucher E, Caikovski M, Vaillant I, Nicolet J, Mittelsten Scheid O, Paszkowski J. MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. EMBO J. 2010 Jan 20;29(2):340-51. doi: 10.1038/emboj.2009.328. Epub 2009 Nov 12. PMID:19910926 doi:https://dx.doi.org/10.1038/emboj.2009.328
↑ Mlotshwa S, Pruss GJ, Gao Z, Mgutshini NL, Li J, Chen X, Bowman LH, Vance V. Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing. Plant J. 2010 Nov;64(4):699-704. doi: 10.1111/j.1365-313X.2010.04358.x. Epub 2010, Oct 8. PMID:21070421 doi:https://dx.doi.org/10.1111/j.1365-313X.2010.04358.x
↑ Zhou Y, Zhang J, Lin H, Guo G, Guo Y. MORPHEUS' MOLECULE1 is required to prevent aberrant RNA transcriptional read-through in Arabidopsis. Plant Physiol. 2010 Nov;154(3):1272-80. doi: 10.1104/pp.110.162131. Epub 2010 Sep, 8. PMID:20826701 doi:https://dx.doi.org/10.1104/pp.110.162131
↑ Habu Y, Yoshikawa M. Locus-specific dependency of endogenous silent loci on MOM1 and non-CG methylation in Arabidopsis thaliana. Plant Signal Behav. 2010 Jun;5(6):724-6. Epub 2010 Jun 1. PMID:20404545

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Amedeo P, Habu Y, Afsar K, Mittelsten Scheid O, Paszkowski J. Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature. 2000 May 11;405(6783):203-6. PMID:10821279 doi:https://dx.doi.org/10.1038/35012108

[2] Steimer A, Amedeo P, Afsar K, Fransz P, Mittelsten Scheid O, Paszkowski J. Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell. 2000 Jul;12(7):1165-78. PMID:10899982

[3] Mittelsten Scheid O, Probst AV, Afsar K, Paszkowski J. Two regulatory levels of transcriptional gene silencing in Arabidopsis. Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13659-62. Epub 2002 Oct 7. PMID:12370435 doi:https://dx.doi.org/10.1073/pnas.202380499

[4] Probst AV, Fransz PF, Paszkowski J, Mittelsten Scheid O. Two means of transcriptional reactivation within heterochromatin. Plant J. 2003 Feb;33(4):743-9. PMID:12609046

[5] Vaillant I, Schubert I, Tourmente S, Mathieu O. MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep. 2006 Dec;7(12):1273-8. Epub 2006 Nov 3. PMID:17082821 doi:https://dx.doi.org/10.1038/sj.embor.7400791

[6] Habu Y, Mathieu O, Tariq M, Probst AV, Smathajitt C, Zhu T, Paszkowski J. Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep. 2006 Dec;7(12):1279-84. Epub 2006 Nov 3. PMID:17082818 doi:https://dx.doi.org/10.1038/sj.embor.7400835

[7] Caikovski M, Yokthongwattana C, Habu Y, Nishimura T, Mathieu O, Paszkowski J. Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants. PLoS Genet. 2008 Aug 22;4(8):e1000165. doi: 10.1371/journal.pgen.1000165. PMID:18725928 doi:https://dx.doi.org/10.1371/journal.pgen.1000165

[8] Yokthongwattana C, Bucher E, Caikovski M, Vaillant I, Nicolet J, Mittelsten Scheid O, Paszkowski J. MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. EMBO J. 2010 Jan 20;29(2):340-51. doi: 10.1038/emboj.2009.328. Epub 2009 Nov 12. PMID:19910926 doi:https://dx.doi.org/10.1038/emboj.2009.328

[9] Mlotshwa S, Pruss GJ, Gao Z, Mgutshini NL, Li J, Chen X, Bowman LH, Vance V. Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing. Plant J. 2010 Nov;64(4):699-704. doi: 10.1111/j.1365-313X.2010.04358.x. Epub 2010, Oct 8. PMID:21070421 doi:https://dx.doi.org/10.1111/j.1365-313X.2010.04358.x

[10] Zhou Y, Zhang J, Lin H, Guo G, Guo Y. MORPHEUS' MOLECULE1 is required to prevent aberrant RNA transcriptional read-through in Arabidopsis. Plant Physiol. 2010 Nov;154(3):1272-80. doi: 10.1104/pp.110.162131. Epub 2010 Sep, 8. PMID:20826701 doi:https://dx.doi.org/10.1104/pp.110.162131

[11] Habu Y, Yoshikawa M. Locus-specific dependency of endogenous silent loci on MOM1 and non-CG methylation in Arabidopsis thaliana. Plant Signal Behav. 2010 Jun;5(6):724-6. Epub 2010 Jun 1. PMID:20404545

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@@ Line 1: / Line 1: @@
-[[Image:3vem.jpg|left|200px]]
-<!--
+==Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1==
-The line below this paragraph, containing "STRUCTURE_3vem", creates the "Structure Box" on the page.
+<StructureSection load='3vem' size='340' side='right'caption='[[3vem]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3vem]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEM FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
--->
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vem OCA], [https://pdbe.org/3vem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vem RCSB], [https://www.ebi.ac.uk/pdbsum/3vem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vem ProSAT]</span></td></tr>
-{{STRUCTURE_3vem|  PDB=3vem  |  SCENE=  }}
+</table>
+== Function ==
-===Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1===
+[https://www.uniprot.org/uniprot/MOM1_ARATH MOM1_ARATH] Required for the heritable maintenance of transcriptional gene silencing (TGS) in heterochromatin, and particularly in the intermediate bivalent heterochromatin, characterized by an unsual methylation pattern consisting in hypermethylated DNA and histone H3 'Lys-4' methylation (H3K4me) together with depletion of histone H3 'Lys-9' methylation (H3K9me), in a chromatin methylation-independent manner, in a non-CG methylation context. May play a role in the RNA polymerase IV/V (Pol-IV/V)-mediated RNA-directed DNA methylation (RdDM) leading to TGS (also called siRNA-mediated TGS pathway), probably by modulating small interfering RNA (siRNA) accumulation. Especially involved in the gene silencing of the transcriptionally silent information region (TSI), 5S ribosomal RNA genes (localized in the pericentromeric heterochromatin of chromosomes 3, 4, and 5) and of 180-bp satellite repeats and 106B long terminal repeat (LTR)-like repeats of the chromocenters. Prevents the aberrant mRNA transcriptional read-through.<ref>PMID:10821279</ref> <ref>PMID:10899982</ref> <ref>PMID:12370435</ref> <ref>PMID:12609046</ref> <ref>PMID:17082821</ref> <ref>PMID:17082818</ref> <ref>PMID:18725928</ref> <ref>PMID:19910926</ref> <ref>PMID:21070421</ref> <ref>PMID:20826701</ref> <ref>PMID:20404545</ref>
+== References ==
+<references/>
-<!--
+__TOC__
-The line below this paragraph, {{ABSTRACT_PUBMED_22346760}}, adds the Publication Abstract to the page
+</StructureSection>
-(as it appears on PubMed at http://www.pubmed.gov), where 22346760 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_22346760}}
-==About this Structure==
-[[3vem]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VEM OCA].
-==Reference==
-<ref group="xtra">PMID:022346760</ref><references group="xtra"/>
 [[Category: Arabidopsis thaliana]]
-[[Category: Halazonetis, T.]]
+[[Category: Large Structures]]
-[[Category: Nishikura, T.]]
+[[Category: Halazonetis T]]
-[[Category: Paszkowski, J.]]
+[[Category: Nishikura T]]
-[[Category: Petty, T J.]]
+[[Category: Paszkowski J]]
-[[Category: Thore, S.]]
+[[Category: Petty TJ]]
-[[Category: Chromatin]]
+[[Category: Thore S]]
-[[Category: Coiled-coil]]
-[[Category: Hendecad]]
-[[Category: Nucleus]]
-[[Category: Sirna]]
-[[Category: Transcription]]
-[[Category: Transcriptional gene silencing]]

3vem: Difference between revisions

Latest revision as of 10:35, 1 March 2024

Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1

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