RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development.

Jesús León-Ruiz; Espinal-Centeno Annie; Ikram Blilou; Scheres Ben; Arteaga-Vázquez Mario; Luis Alfredo Cruz-Ramirez

doi:10.1007/s00425-023-04135-x

RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development.

Jesús León-Ruiz, Espinal-Centeno Annie, Ikram Blilou, Scheres Ben, Arteaga-Vázquez Mario, Luis Alfredo Cruz-Ramirez

Research output: Contribution to journal › Article › peer-review

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Abstract

Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double-stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24-nt siRNAs) by DCL3. 24-nt siRNAs serve as guides to direct AGO4–siRNA complexes to chromatin-bound POLV-derived transcripts generated from the template/target DNA. The interaction between POLV, AGO4, DMS3, DRD1, RDM1 and DRM2 promotes DRM2-mediated de novo DNA methylation. The Arabidopsis Retinoblastoma protein homolog (RBR) is a master regulator of the cell cycle, stem cell maintenance, and development. We in silico predicted and explored experimentally the protein–protein interactions (PPIs) between RBR and members of the RdDM pathway. We found that the largest subunits of POLIV and POLV (NRPD1 and NRPE1), the shared second largest subunit of POLIV and POLV (NRPD/E2), RDR1, RDR2, DCL3, DRM2, and SUVR2 contain canonical and non-canonical RBR binding motifs and several of them are conserved since algae and bryophytes. We validated experimentally PPIs between Arabidopsis RBR and several of the RdDM pathway proteins. Moreover, seedlings from loss-of-function mutants in RdDM and RBR show similar phenotypes in the root apical meristem. We show that RdDM and SUVR2 targets are up-regulated in the 35S:AmiGO–RBR background.

Original language	English (US)
Journal	Planta
Volume	257
Issue number	6
DOIs	https://doi.org/10.1007/s00425-023-04135-x
State	Published - Apr 30 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-05-02
Acknowledged KAUST grant number(s): OSR-2020-CRG9-4381
Acknowledgements: We wish to thank Vicki Chandler, Steve Jacobsen, Fred Berger and Pauline Jullien for sharing published plant materials. We also thank Dr. Juan Caballero-Pérez for initial advice on bioinformatics. J L-R (CVU 858608) was supported by Consejo Nacional de Ciencia y Tecnología (CONACYT) with a PhD Fellowship. A C-R was supported by EMBO-ALTF 1114-2006 and CONACYT 000000000092916 grants. Colaborative work between A C-R and IB groups is supported by King Abdullah University of Science and Technology (KAUST), Award No. OSR-2020-CRG9-4381. M A-V was supported by CONACYT grants 158550 and A1-S-38383, UCMEXUS-CONACYT Collaborative Grant CN-20-166 and Newton Fund of the Royal Society grant NA150181.

ASJC Scopus subject areas

Plant Science
Genetics

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10.1007/s00425-023-04135-x

Cite this

@article{ee5b25990f7b42b7beb3b6391d6094b7,

title = "RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development.",

abstract = "Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double-stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24-nt siRNAs) by DCL3. 24-nt siRNAs serve as guides to direct AGO4–siRNA complexes to chromatin-bound POLV-derived transcripts generated from the template/target DNA. The interaction between POLV, AGO4, DMS3, DRD1, RDM1 and DRM2 promotes DRM2-mediated de novo DNA methylation. The Arabidopsis Retinoblastoma protein homolog (RBR) is a master regulator of the cell cycle, stem cell maintenance, and development. We in silico predicted and explored experimentally the protein–protein interactions (PPIs) between RBR and members of the RdDM pathway. We found that the largest subunits of POLIV and POLV (NRPD1 and NRPE1), the shared second largest subunit of POLIV and POLV (NRPD/E2), RDR1, RDR2, DCL3, DRM2, and SUVR2 contain canonical and non-canonical RBR binding motifs and several of them are conserved since algae and bryophytes. We validated experimentally PPIs between Arabidopsis RBR and several of the RdDM pathway proteins. Moreover, seedlings from loss-of-function mutants in RdDM and RBR show similar phenotypes in the root apical meristem. We show that RdDM and SUVR2 targets are up-regulated in the 35S:AmiGO–RBR background.",

author = "Jes{\'u}s Le{\'o}n-Ruiz and Espinal-Centeno Annie and Ikram Blilou and Scheres Ben and Arteaga-V{\'a}zquez Mario and Cruz-Ramirez, {Luis Alfredo}",

note = "KAUST Repository Item: Exported on 2023-05-02 Acknowledged KAUST grant number(s): OSR-2020-CRG9-4381 Acknowledgements: We wish to thank Vicki Chandler, Steve Jacobsen, Fred Berger and Pauline Jullien for sharing published plant materials. We also thank Dr. Juan Caballero-P{\'e}rez for initial advice on bioinformatics. J L-R (CVU 858608) was supported by Consejo Nacional de Ciencia y Tecnolog{\'i}a (CONACYT) with a PhD Fellowship. A C-R was supported by EMBO-ALTF 1114-2006 and CONACYT 000000000092916 grants. Colaborative work between A C-R and IB groups is supported by King Abdullah University of Science and Technology (KAUST), Award No. OSR-2020-CRG9-4381. M A-V was supported by CONACYT grants 158550 and A1-S-38383, UCMEXUS-CONACYT Collaborative Grant CN-20-166 and Newton Fund of the Royal Society grant NA150181.",

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month = apr,

day = "30",

doi = "10.1007/s00425-023-04135-x",

language = "English (US)",

volume = "257",

journal = "Planta",

issn = "0032-0935",

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T1 - RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development.

AU - León-Ruiz, Jesús

AU - Annie, Espinal-Centeno

AU - Blilou, Ikram

AU - Ben, Scheres

AU - Mario, Arteaga-Vázquez

AU - Cruz-Ramirez, Luis Alfredo

N1 - KAUST Repository Item: Exported on 2023-05-02 Acknowledged KAUST grant number(s): OSR-2020-CRG9-4381 Acknowledgements: We wish to thank Vicki Chandler, Steve Jacobsen, Fred Berger and Pauline Jullien for sharing published plant materials. We also thank Dr. Juan Caballero-Pérez for initial advice on bioinformatics. J L-R (CVU 858608) was supported by Consejo Nacional de Ciencia y Tecnología (CONACYT) with a PhD Fellowship. A C-R was supported by EMBO-ALTF 1114-2006 and CONACYT 000000000092916 grants. Colaborative work between A C-R and IB groups is supported by King Abdullah University of Science and Technology (KAUST), Award No. OSR-2020-CRG9-4381. M A-V was supported by CONACYT grants 158550 and A1-S-38383, UCMEXUS-CONACYT Collaborative Grant CN-20-166 and Newton Fund of the Royal Society grant NA150181.

PY - 2023/4/30

Y1 - 2023/4/30

N2 - Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double-stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24-nt siRNAs) by DCL3. 24-nt siRNAs serve as guides to direct AGO4–siRNA complexes to chromatin-bound POLV-derived transcripts generated from the template/target DNA. The interaction between POLV, AGO4, DMS3, DRD1, RDM1 and DRM2 promotes DRM2-mediated de novo DNA methylation. The Arabidopsis Retinoblastoma protein homolog (RBR) is a master regulator of the cell cycle, stem cell maintenance, and development. We in silico predicted and explored experimentally the protein–protein interactions (PPIs) between RBR and members of the RdDM pathway. We found that the largest subunits of POLIV and POLV (NRPD1 and NRPE1), the shared second largest subunit of POLIV and POLV (NRPD/E2), RDR1, RDR2, DCL3, DRM2, and SUVR2 contain canonical and non-canonical RBR binding motifs and several of them are conserved since algae and bryophytes. We validated experimentally PPIs between Arabidopsis RBR and several of the RdDM pathway proteins. Moreover, seedlings from loss-of-function mutants in RdDM and RBR show similar phenotypes in the root apical meristem. We show that RdDM and SUVR2 targets are up-regulated in the 35S:AmiGO–RBR background.

AB - Transposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double-stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24-nt siRNAs) by DCL3. 24-nt siRNAs serve as guides to direct AGO4–siRNA complexes to chromatin-bound POLV-derived transcripts generated from the template/target DNA. The interaction between POLV, AGO4, DMS3, DRD1, RDM1 and DRM2 promotes DRM2-mediated de novo DNA methylation. The Arabidopsis Retinoblastoma protein homolog (RBR) is a master regulator of the cell cycle, stem cell maintenance, and development. We in silico predicted and explored experimentally the protein–protein interactions (PPIs) between RBR and members of the RdDM pathway. We found that the largest subunits of POLIV and POLV (NRPD1 and NRPE1), the shared second largest subunit of POLIV and POLV (NRPD/E2), RDR1, RDR2, DCL3, DRM2, and SUVR2 contain canonical and non-canonical RBR binding motifs and several of them are conserved since algae and bryophytes. We validated experimentally PPIs between Arabidopsis RBR and several of the RdDM pathway proteins. Moreover, seedlings from loss-of-function mutants in RdDM and RBR show similar phenotypes in the root apical meristem. We show that RdDM and SUVR2 targets are up-regulated in the 35S:AmiGO–RBR background.

UR - http://hdl.handle.net/10754/691360

UR - https://link.springer.com/10.1007/s00425-023-04135-x

U2 - 10.1007/s00425-023-04135-x

DO - 10.1007/s00425-023-04135-x

M3 - Article

C2 - 37120771

SN - 0032-0935

VL - 257

JO - Planta

JF - Planta

IS - 6

ER -

RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development.

Abstract

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