The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis

Author:

Diego-Martin Borja1,Pérez-Alemany Jaime1,Candela-Ferre Joan1,Corbalán-Acedo Antonio1,Pereyra Juan1,Alabadí David1ORCID,Jami-Alahmadi Yasaman2,Wohlschlegel James2,Gallego-Bartolomé Javier1ORCID

Affiliation:

1. Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València , Valencia, 46022 , Spain

2. Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, CA, 90095, USA

Abstract

Abstract Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of this SWI/SNF complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5′-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcription start site usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and 5′ transcript length change suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and transcription start site determination.

Publisher

Oxford University Press (OUP)

Subject

Genetics

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