The extended AT-hook is a novel RNA binding motif

The AT-hook has been defined as a DNA binding peptide motif that contains a glycine-arginine-proline (G-R-P) tripeptide core flanked by basic amino acids. Recent reports documented variations in the sequence of AT-hooks and revealed RNA binding activity of some canonical AT-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. Here we describe the discovery and characterization of the extended AT-hook peptide motif (eAT-hook), in which basic amino acids appear symmetrical mainly at a distance of 12–15 amino acids from the G-R-P core. We identified 80 human and 60 mouse eAT-hook proteins and biochemically characterized the eAT-hooks of Tip5/BAZ2A, PTOV1 and GPBP1. Microscale thermophoresis and electrophoretic mobility shift assays reveal the nucleic acid binding features of this peptide motif, and show that eAT-hooks bind RNA with one order of magnitude higher affinity than DNA. In addition, cellular localization studies suggest a role for the N-terminal eAT-hook of PTOV1 in nucleocytoplasmic shuttling. In summary, our findings classify the eAT-hook as a novel nucleic acid binding motif, which potentially mediates various RNA-dependent cellular processes.

[1]  中山 幸輝.  A long noncoding RNA protects the heart from pathological hypertrophy , 2015 .

[2]  Jennifer A. Erwin,et al.  Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. , 2015, Molecular cell.

[3]  S. Gerstberger,et al.  A census of human RNA-binding proteins , 2014, Nature Reviews Genetics.

[4]  K. Morris,et al.  The rise of regulatory RNA , 2014, Nature Reviews Genetics.

[5]  Y. Fernández,et al.  Regulation of protein translation and c-Jun expression by prostate tumor overexpressed 1 , 2014, Oncogene.

[6]  M. Marz,et al.  pRNA: NoRC-associated RNA of rRNA operons. , 2014, RNA biology.

[7]  George M Church,et al.  pLogo: a probabilistic approach to visualizing sequence motifs , 2013, Nature Methods.

[8]  M. Rosenfeld,et al.  LncRNA-Dependent Mechanisms of Androgen Receptor-regulated Gene Activation Programs , 2013, Nature.

[9]  Timothy L Bailey,et al.  Defining the RGG/RG motif. , 2013, Molecular cell.

[10]  G. Längst,et al.  Large-scale organization of ribosomal DNA chromatin is regulated by Tip5 , 2013, Nucleic acids research.

[11]  Angela D. Wilkins,et al.  An AT-Hook Domain in MeCP2 Determines the Clinical Course of Rett Syndrome and Related Disorders , 2013, Cell.

[12]  V. Beneš,et al.  Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin. , 2012, Molecular cell.

[13]  Richard Bonneau,et al.  The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. , 2012, Molecular cell.

[14]  Norman E. Davey,et al.  Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins , 2012, Cell.

[15]  Sebastian Eilebrecht,et al.  7SK snRNA-mediated, gene-specific cooperativity of HMGA1 and P-TEFb , 2011, RNA biology.

[16]  H. Urlaub,et al.  7SK small nuclear RNA directly affects HMGA1 function in transcription regulation , 2010, Nucleic acids research.

[17]  Joaquín Dopazo,et al.  Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling , 2010, Nucleic Acids Res..

[18]  R. Reeves.  Nuclear functions of the HMG proteins. , 2010, Biochimica et biophysica acta.

[19]  I. Grummt,et al.  Reversible acetylation of the chromatin remodelling complex NoRC is required for non-coding RNA-dependent silencing , 2009, Nature Cell Biology.

[20]  Ronny Lorenz,et al.  The Vienna RNA Websuite , 2008, Nucleic Acids Res..

[21]  A. Villar-Garea,et al.  Fine Mapping of Posttranslational Modifications of the Linker Histone H1 from Drosophila melanogaster , 2008, PloS one.

[22]  D. Choi,et al.  The chili pepper CaATL1: an AT-hook motif-containing transcription factor implicated in defence responses against pathogens. , 2007, Molecular plant pathology.

[23]  Takashi Kubota,et al.  Identification of functional domains in TdIF1 and its inhibitory mechanism for TdT activity , 2007, Genes to cells : devoted to molecular & cellular mechanisms.

[24]  J. Dopazo,et al.  FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments , 2007, Nucleic Acids Res..

[25]  D. Wassarman,et al.  DNA Binding Properties of TAF1 Isoforms with Two AT-hooks* , 2006, Journal of Biological Chemistry.

[26]  Vladimir Vacic,et al.  Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments , 2006, Bioinform..

[27]  A. Engelman,et al.  A tripartite DNA-binding element, comprised of the nuclear localization signal and two AT-hook motifs, mediates the association of LEDGF/p75 with chromatin in vivo , 2006, Nucleic acids research.

[28]  J. Renau‐Piqueras,et al.  PTOV1 Enables the Nuclear Translocation and Mitogenic Activity of Flotillin-1, a Major Protein of Lipid Rafts , 2005, Molecular and Cellular Biology.

[29]  P. Cramer,et al.  The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity , 2004, BMC Cell Biology.

[30]  Shu Liu,et al.  The Murine G+C-Rich Promoter Binding Protein mGPBP Is Required for Promoter-Specific Transcription , 2003, Molecular and Cellular Biology.

[31]  Sylvia Heeneman,et al.  Vasculin, a novel vascular protein differentially expressed in human atherogenesis. , 2003, Blood.

[32]  J. Morote,et al.  PTOV-1, a novel protein overexpressed in prostate cancer, shuttles between the cytoplasm and the nucleus and promotes entry into the S phase of the cell division cycle. , 2003, The American journal of pathology.

[33]  E. Koonin,et al.  Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases , 2003, BMC Structural Biology.

[34]  Søren Brunak,et al.  NESbase version 1.0: a database of nuclear export signals , 2003, Nucleic Acids Res..

[35]  R Ohlsson,et al.  CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. , 2001, Trends in genetics : TIG.

[36]  X. Estivill,et al.  PTOV1, a novel protein overexpressed in prostate cancer containing a new class of protein homology blocks , 2001, Oncogene.

[37]  R. Rangel,et al.  Regulation of CD40 and CD40 ligand by the AT-hook transcription factor AKNA , 2001, Nature.

[38]  M. Yaniv,et al.  The Activity of Mammalian brm/SNF2α Is Dependent on a High-Mobility-Group Protein I/Y-Like DNA Binding Domain , 1999, Molecular and Cellular Biology.

[39]  D. Landsman,et al.  AT-hook motifs identified in a wide variety of DNA-binding proteins. , 1998, Nucleic acids research.

[40]  Jeffrey R. Huth,et al.  The solution structure of an HMG-I(Y)–DNA complex defines a new architectural minor groove binding motif , 1997, Nature Structural Biology.

[41]  Y. Lefebvre,et al.  Nuclear localization signals overlap DNA- or RNA-binding domains in nucleic acid-binding proteins. , 1995, Nucleic acids research.

[42]  M. Nissen,et al.  The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. , 1990, The Journal of biological chemistry.