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Title: INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

Abstract

At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsismore » genome.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ;  [1];  [2];  [2]
  1. (UCLA)
  2. (
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
FOREIGNUNIVERSITYOTHER U.S. GOVERNMENT
OSTI Identifier:
1048574
Resource Type:
Journal Article
Journal Name:
Proc. Natl. Acad. Sci. USA
Additional Journal Information:
Journal Volume: 109; Journal Issue: (22) ; 05, 2012; Journal ID: ISSN 1091-6490
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ARABIDOPSIS; CYTOSINE; DNA; GENES; GENETICS; IN VIVO; MACHINERY; MAINTENANCE; MASS SPECTROSCOPY; METHYLATION; MIRRORS; MUTANTS; MUTATIONS; PHENOTYPE; PROTEINS; RNA

Citation Formats

Ausin, Israel, Greenberg, Maxim V.C., Simanshu, Dhirendra K., Hale, Christopher J., Vashisht, Ajay A., Simon, Stacey A., Lee, Tzuu-fen, Feng, Suhua, Española, Sophia D., Meyers, Blake C., Wohlschlegel, James A., Patel, Dinshaw J., Jacobsen, Steven E., MSKCC), and Delaware). INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. United States: N. p., 2012. Web. doi:10.1073/pnas.1206638109.
Ausin, Israel, Greenberg, Maxim V.C., Simanshu, Dhirendra K., Hale, Christopher J., Vashisht, Ajay A., Simon, Stacey A., Lee, Tzuu-fen, Feng, Suhua, Española, Sophia D., Meyers, Blake C., Wohlschlegel, James A., Patel, Dinshaw J., Jacobsen, Steven E., MSKCC), & Delaware). INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. United States. doi:10.1073/pnas.1206638109.
Ausin, Israel, Greenberg, Maxim V.C., Simanshu, Dhirendra K., Hale, Christopher J., Vashisht, Ajay A., Simon, Stacey A., Lee, Tzuu-fen, Feng, Suhua, Española, Sophia D., Meyers, Blake C., Wohlschlegel, James A., Patel, Dinshaw J., Jacobsen, Steven E., MSKCC), and Delaware). Tue . "INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis". United States. doi:10.1073/pnas.1206638109.
@article{osti_1048574,
title = {INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis},
author = {Ausin, Israel and Greenberg, Maxim V.C. and Simanshu, Dhirendra K. and Hale, Christopher J. and Vashisht, Ajay A. and Simon, Stacey A. and Lee, Tzuu-fen and Feng, Suhua and Española, Sophia D. and Meyers, Blake C. and Wohlschlegel, James A. and Patel, Dinshaw J. and Jacobsen, Steven E. and MSKCC) and Delaware)},
abstractNote = {At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.},
doi = {10.1073/pnas.1206638109},
journal = {Proc. Natl. Acad. Sci. USA},
issn = {1091-6490},
number = (22) ; 05, 2012,
volume = 109,
place = {United States},
year = {2012},
month = {10}
}