Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome

PLoS Genetics
Paja SijacicRoger B Deal

Abstract

The SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z into nucleosomes, has been well characterized in yeast and animals, but its composition in plants has remained uncertain. We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 (ARP6) as bait in tandem affinity purification experiments to isolate associated proteins from Arabidopsis thaliana. We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes, demonstrating that this complex is conserved in plants. We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9) and three members of the Alfin1-like protein family, all of which have been shown to bind modified histone tails. Since mbd9 mutant plants were phenotypically similar to arp6 mutants, we explored a potential role for MBD9 in H2A.Z deposition. We found that MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites, which represent a subset of the genomic regions normally enriched with H2A.Z. We also discovered that MBD9 preferentially interacts with acetylated histone H4 peptides, as well as those carrying mono- or dimethylated H3 lysine 4, or dimethylated H3 ar...Continue Reading

References

Jun 1, 1992·Molecular Biology of the Cell·A van Daal, S C Elgin
Aug 1, 1996·Molecular and Cellular Biology·X Liu GorovskyMA
Mar 9, 1999·The Plant Journal : for Cell and Molecular Biology·S J Clough, A F Bent
Jun 29, 1999·Nature·M J ClarksonD J Tremethick
Aug 23, 2001·Current Biology : CB·R FaastI Lyons
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Oct 14, 2003·Plant Physiology·Mark D Curtis, Ueli Grossniklaus
Dec 24, 2003·Molecular Cell·Nevan J KroganJack F Greenblatt
Feb 18, 2004·Molecular and Cellular Biology·Yannick DoyonJacques Côté
Sep 24, 2004·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Xiang-Jiao Yang
Jan 14, 2005·The Journal of Biological Chemistry·Yong CaiJoan Weliky Conaway
Apr 5, 2005·Nature Genetics·Markus SchmidJan U Lohmann
Sep 17, 2005·Nature Methods·Anne-Valérie GendrelVincent Colot
Mar 1, 2006·Current Opinion in Genetics & Development·Ryan M Raisner, Hiten D Madhani
Mar 18, 2006·Genes & Development·Michael-Christopher KeoghStephen Buratowski
Mar 18, 2006·Genes & Development·Catherine B MillarMichael Grunstein
Apr 21, 2006·The Plant Journal : for Cell and Molecular Biology·Mingsheng PengSteven J Rothstein
Nov 15, 2006·Methods : a Companion to Methods in Enzymology·Yong CaiRonald C Conaway
May 29, 2007·Molecular and Cellular Biology·Melissa Durant, B Franklin Pugh
Jul 10, 2007·The Journal of Biological Chemistry·Madeline M WongJohn C Chrivia
Aug 3, 2007·Genes & Development·Nicolas GévryLuc Gaudreau
Nov 9, 2007·The Plant Journal : for Cell and Molecular Biology·Rosana March-DíazJosé C Reyes
Feb 16, 2008·Structure·Jordanka Zlatanova, Amit Thakar
Nov 6, 2008·PloS One·Francesca MartinatoErnesto Guccione
May 8, 2009·The Plant Journal : for Cell and Molecular Biology·Mahmoud W F YaishSteven J Rothstein
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Oct 15, 2009·Molecular Plant·Rosana March-Díaz, Jose C Reyes
Nov 10, 2009·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Phoebe Y T LuMichael S Kobor

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Citations

May 12, 2020·Journal of Experimental Botany·Aline V ProbstCrisanto Gutierrez
Mar 11, 2020·Frontiers in Plant Science·Loreto Espinosa-CoresManuel Piñeiro
Sep 20, 2019·International Journal of Molecular Sciences·Jianhao WangSongguang Yang
Jan 13, 2021·Current Opinion in Plant Biology·Michael BorgFrédéric Berger
Dec 14, 2019·Plant Communications·Bingkun Lei, Frédéric Berger
Feb 14, 2021·Current Opinion in Plant Biology·Ray ScheidXuehua Zhong
Aug 30, 2021·The New Phytologist·Adam Hannan ParkerJurriaan Ton

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Datasets Mentioned

BETA
GSE117391
GSM2752981

Methods Mentioned

BETA
Tandem Affinity Purification
transgenic
affinity purification
affinity
immunoprecipitation
ChIP
ChIP-seq
acetylation
RNA-seq
peptide array

Software Mentioned

htseq
Bowtie2
PeakAnnotator
SeqPlots
Samtools
samtools view
deepTools
Array Analyze
Proteome Discoverer
HOMER package

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