A novel RNA binding surface of the TAM domain of TIP5/BAZ2A mediates epigenetic regulation of rRNA genes.
The chromatin remodeling complex NoRC, comprising the subunits SNF2h and TIP5/BAZ2A, mediates heterochromatin formation at major clusters of repetitive elements, including rRNA genes, centromeres and telomeres. Association with chromatin requires the interaction of the TAM (TIP5/ARBP/MBD) domain of TIP5 with noncoding RNA, which targets NoRC to specific genomic loci. Here, we show that the NMR structure of the TAM domain of TIP5 resembles the fold of the MBD domain, found in methyl-CpG binding proteins. However, the TAM domain exhibits an extended MBD fold with unique C-terminal extensions that constitute a novel surface for RNA binding. Mutation of critical amino acids within this surface abolishes RNA binding in vitro and in vivo. Our results explain the distinct binding specificities of TAM and MBD domains to RNA and methylated DNA, respectively, and reveal structural features for the interaction of NoRC with non-coding RNA.
Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany Biomolecular NMR and Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Garching D-85747, Germany.
Irina
I
Anosova
Division of Molecular Biology of the Cell II, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg D-69120, Germany.
Svitlana
S
Melnik
Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany Biomolecular NMR and Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Garching D-85747, Germany.
Konstantinos
K
Tripsianes
Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany Biomolecular NMR and Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Garching D-85747, Germany.
Fatiha
F
Kateb
Division of Molecular Biology of the Cell II, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg D-69120, Germany I.Grummt@dkfz.de.
Ingrid
I
Grummt
Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg D-85764, Germany Biomolecular NMR and Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Garching D-85747, Germany sattler@helmholtz-muenchen.de.
Michael
M
Sattler
D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D020459:Genes, rRNA; D057809:HEK293 Cells; D006801:Humans; D008958:Models, Molecular; D017354:Point Mutation; D011485:Protein Binding; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D000092468:Bromodomain Containing Proteins
D002868:Chromosomal Proteins, Non-Histone; D012313:RNA; D016601:RNA-Binding Proteins; C436708:BAZ2A protein, human; D000092468:Bromodomain Containing Proteins