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

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Abstract

Main Conclusion

Our study presents evidence for a novel mechanism for RBR function in transcriptional gene silencing by interacting with key players of the RdDM pathway in Arabidopsis and several plant clades.

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.

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Data availability

All data generated or analyzed during this study are included in this published article and its supplementary information files.

Abbreviations

AGO4:

Argonaute 4

DCL3:

Dicer-like 3

DRM2:

De novo DNA methyltransferase domains rearranged 2

LTR:

Long Terminal Repeat

NRPD:

Nuclear RNA Polymerase D

POLIV:

Polymerase IV

POLV:

Polymerase V

PRC2:

Polycomb repressor complex 2

RBR:

Retinoblastoma-related

RdDM:

RNA-directed DNA methylation pathway

RDM1:

RNA-directed DNA methylation 1

RDR2:

RNA-dependent RNA polymerase 2

SLiM:

Short linear motif

Y2H:

Yeast two-hybrid

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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.

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Author notes

  1. Jesús León-Ruiz and Annie Espinal-Centeno are contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Molecular and Developmental Complexity at Laboratorio Nacional de Genómica Para la Biodiversidad, Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional, (CINVESTAV-IPN), 36590, Irapuato, México

    Jesús León-Ruiz, Annie Espinal-Centeno & Alfredo Cruz-Ramírez

  2. Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia

    Ikram Blilou

  3. Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands

    Ben Scheres

  4. Group of Epigenetics and Developmental Biology, Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, 91090, Xalapa, México

    Mario Arteaga-Vázquez

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  1. Jesús León-Ruiz
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Correspondence to Mario Arteaga-Vázquez or Alfredo Cruz-Ramírez.

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León-Ruiz, J., Espinal-Centeno, A., Blilou, I. et al. RETINOBLASTOMA-RELATED interactions with key factors of the RNA-directed DNA methylation (RdDM) pathway and its influence on root development. Planta 257, 105 (2023). https://doi.org/10.1007/s00425-023-04135-x

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