title: Reader interactome of epigenetic histone marks in birds.
abstract: Lysine methylation is part of the posttranscriptional histone code employed to recruit modification specific readers to chromatin. Unbiased, quantitative mass spectrometry approaches combined with peptide pull-downs have been used to study histone methylation-dependent binders in mammalian cells. Here, we extend the study to birds by investigating the interaction partners for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 in chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) using label-free quantitative proteomics. In general, we find very strong overlap in interaction partners for the trimethyl marks in birds compared to mammals, underscoring the known conserved function of these modifications. In agreement with their epigenetic role, we find binding of PHF2 and members of the TFIID, SAGA, SET1 and NURF complex to the activation mark H3K4me3. Our data furthermore supports the existence of a LID complex in vertebrates recruited to the H3K4me3 mark. The repressive marks are bound by the HP1 proteins and the EED subunit of the PRC2 complex as well as by WIZ. Like reported in the previous mammalian screens, we found ZNF462, ZNF828 and POGZ enriched at H3K9me3. However, we noted some unexpected differences. N-PAC (also known as GLYR1), an H3K36me3 interactor in mammals, is reproducible not enriched at this modification in our screen in birds. This initial finding suggests that despite strong conservation of the histone tail sequence, a few species-specific differences in epigenetic readers may have evolved between birds and mammals. All MS data have been deposited in the ProteomeXchange with identifier PXD002282 (http://proteomecentral.proteomexchange.org/dataset/PXD002282).
authors.affiliation: Institute of Molecular Biology (IMB), Mainz, Germany.
authors.forename: Alina
authors.initials: A
authors.lastname: Bluhm
authors.affiliation: Institute of Molecular Biology (IMB), Mainz, Germany.
authors.forename: Nuria
authors.initials: N
authors.lastname: Casas-Vila
authors.affiliation: Institute of Molecular Biology (IMB), Mainz, Germany.
authors.forename: Marion
authors.initials: M
authors.lastname: Scheibe
authors.affiliation: Institute of Molecular Biology (IMB), Mainz, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Butter
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030161:Avian Proteins / Q000235:genetics / Q000378:metabolism*; D002460:Cell Line; D002645:Chickens; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism*; D044127:Epigenesis, Genetic; D046369:Finches; D042421:Histone Code; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008239:Lysine / Q000378:metabolism; D008745:Methylation; D008969:Molecular Sequence Data; D063146:Polycomb-Group Proteins / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D016415:Sequence Alignment; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D019895:Transposases / Q000235:genetics / Q000378:metabolism; D016335:Zinc Fingers
chemical_list: D030161:Avian Proteins; D002843:Chromatin; D006657:Histones; D063146:Polycomb-Group Proteins; D014157:Transcription Factors; D019895:Transposases; D008239:Lysine
keywords: Cell biology; Epigenetics; Histone; Interactomics; Mass spectrometry; Methylation