The extended AT-hook is a novel RNA binding motif

RNA Biology

Volumn 12, Issue 8, 2015, Pages 864-876

  Filarsky, Michael ^a,b   Zillner, Karina ^a   Araya, Ingrid ^a   Villar Garea, Ana ^a,c   Merkl, Rainer ^a   Längst, Gernot ^a   Németh, Attila ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b SWISS TROPICAL AND PUBLIC HEALTH INSTITUTE   (Switzerland)

^c UNIVERSITY OF MUNICH   (Germany)

Author keywords

AT hook; GPBP1; Microscale thermophoresis; Protein RNA interaction; PTOV1; RNA binding domain; Tip5

Indexed keywords

AMINO ACID; BINDING PROTEIN; DNA; GPBP1 PROTEIN; NUCLEIC ACID; NUCLEIC ACID BINDING PROTEIN; PTOV1 PROTEIN; RNA; RNA BINDING PROTEIN; TIP5 PROTEIN; UNCLASSIFIED DRUG; BAZ2A PROTEIN, HUMAN; DNA BINDING PROTEIN; NONHISTONE PROTEIN; PROTEIN BINDING; PTOV1 PROTEIN, HUMAN; TUMOR MARKER; TUMOR PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; AT HOOK MOTIF; BINDING AFFINITY; CELLULAR DISTRIBUTION; CONTROLLED STUDY; FEMALE; GEL MOBILITY SHIFT ASSAY; HELA CELL LINE; HUMAN; HUMAN CELL; IN VITRO STUDY; NUCLEOCYTOPLASMIC TRANSPORT; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN MOTIF; RNA BINDING; AMINO ACID SEQUENCE; ANIMAL; BINDING COMPETITION; BINDING SITE; CHEMISTRY; CONFORMATION; FLUORESCENCE MICROSCOPY; GENETICS; HCT 116 CELL LINE; METABOLISM; MOLECULAR GENETICS; MOLECULAR MODEL; MOUSE; MUTATION; NUCLEOTIDE MOTIF; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; BINDING, COMPETITIVE; BIOMARKERS, TUMOR; CHROMOSOMAL PROTEINS, NON-HISTONE; DNA; DNA-BINDING PROTEINS; HCT116 CELLS; HELA CELLS; HUMANS; MICE; MICROSCOPY, FLUORESCENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NEOPLASM PROTEINS; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MOTIFS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RNA;

EID: 84944448338     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.1080/15476286.2015.1060394     Document Type: Article

References (42)

1. Reeves R, Nissen MS. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem 1990; 265:8573-82; PMID:1692833
2. Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM. The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif. Nat Struct Biol 1997; 4:657-65; PMID:9253416; http://dx.doi.org/10.1038/nsb0897-657
3. Reeves R. Nuclear functions of the HMG proteins. Biochim Biophys Acta 2010; 1799:3-14; PMID:19748605
4. Aravind L, Landsman D. AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res 1998; 26:4413-21; PMID:9742243; http://dx.doi.org/10.1093/nar/26.19.4413
5. Iyer LM, Koonin EV, Aravind L. Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Struct Biol 2003; 3:1; PMID:12553882; http://dx.doi.org/10.1186/1472-6807-3-1
6. Metcalf CE, Wassarman DA. DNA binding properties of TAF1 isoforms with two AT-hooks. J Biol Chem 2006; 281:30015-23; PMID:16893881; http://dx.doi.org/10.1074/jbc.M606289200
7. Siddiqa A, Sims-Mourtada JC, Guzman-Rojas L, Rangel R, Guret C, Madrid-Marina V, Sun Y, Martinez-Valdez H. Regulation of CD40 and CD40 ligand by the AT-hook transcription factor AKNA. Nature 2001; 410:383-7; PMID:11268217; http://dx.doi.org/10.1038/35066602
8. Cikala M, Alexandrova O, David CN, Pröschel M, Stiening B, Cramer P, Böttger A. The phosphatidylserine receptor from Hydra is a nuclear protein with potential Fe(II) dependent oxygenase activity. BMC Cell Biol 2004; 5:26; PMID:15193161; http://dx.doi.org/10.1186/1471-2121-5-26
9. Kim S-Y, Kim Y-C, Seong ES, Lee Y-H, Park JM, Choi D. The chili pepper CaATL1: an AT-hook motif-containing transcription factor implicated in defence responses against pathogens. Mol Plant Pathol 2007; 8:761-71; PMID:20507536; http://dx.doi.org/10.1111/j.1364-3703.2007.00427.x
10. Kubota T, Maezawa S, Koiwai K, Hayano T, Koiwai O. Identification of functional domains in TdIF1 and its inhibitory mechanism for TdT activity. Genes Cells 2007; 12:941-59; PMID:17663723; http://dx.doi.org/10.1111/j.1365-2443.2007.01105.x
11. Turlure F, Maertens G, Rahman S, Cherepanov P, Engelman A. A tripartite DNA-binding element, comprised of the nuclear localization signal and two AThook motifs, mediates the association of LEDGF/p75 with chromatin in vivo. Nucleic Acids Res 2006; 34:1653-65; PMID:16549878; http://dx.doi.org/10.1093/nar/gkl052
12. Baker SA, Chen L, Wilkins AD, Yu P, Lichtarge O, Zoghbi HY. An AT-Hook Domain in MeCP2 Determines the Clinical Course of Rett Syndrome and Related Disorders. Cell 2013; 152:984-96; PMID:23452848; http://dx.doi.org/10.1016/j.cell.2013.01.038
13. Zillner K, Filarsky M, Rachow K, Weinberger M, Längst G, Németh A. Large-scale organization of ribosomal DNA chromatin is regulated by Tip5. Nucleic Acids Res 2013; 41:5251-62; PMID:23580549; http://dx.doi.org/10.1093/nar/gkt218
14. Bourachot B, Yaniv M, Muchardt C. The activity of mammalian brm/SNF2alpha is dependent on a highmobility-group protein I/Y-like DNA binding domain. Mol Cell Biol 1999; 19:3931-9; PMID:10330133
15. O'Shea JP, Chou MF, Quader SA, Ryan JK, Church GM, Schwartz D. pLogo: a probabilistic approach to visualizing sequence motifs. Nat Methods 2013; 10:1211-2; PMID:24097270; http://dx.doi.org/10.1038/nmeth.2646
16. Vacic V, Iakoucheva LM, Radivojac P. Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics 2006; 22:1536-7; PMID:16632492; http://dx.doi.org/10.1093/bioinformatics/btl151
17. Al-Shahrour F, Minguez P, Tarraga J, Medina I, Alloza E, Montaner D, Dopazo J. FatiGO C: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 2007; 35:W91-6; PMID:17478504; http://dx.doi.org/10.1093/nar/gkm260
18. Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tarraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, et al. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res 2010; 38:W210-3; PMID:20478823; http://dx.doi.org/10.1093/nar/gkq388
19. Benedit P, Paciucci R, Thomson TM, Valeri M, Nadal M, Caceres C, de Torres I, Estivill X, Lozano JJ, Morote J. PTOV1, a novel protein overexpressed in prostate cancer containing a new class of protein homology blocks. Oncogene 2001; 20:1455; PMID:11313889; http://dx.doi.org/10.1038/sj.onc.1204233
20. Santamaría A, Fernández PL, Farré X, Benedit P, Reventós J, Morote J, Paciucci R, Thomson TM. 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. Am J Pathol 2003; 162:897-905; http://dx.doi.org/10.1016/S0002-9440(10)63885-0
21. Hsu LC, Liu S, Abedinpour F, Beech RD, Lahti JM, Kidd VJ, Greenspan JA, Yeung CY. The Murine GCC-Rich Promoter Binding Protein mGPBP Is Required for Promoter-Specific Transcription. Mol Cell Biol 2003; 23:8773-85; PMID:14612417; http://dx.doi.org/10.1128/MCB.23.23.8773-8785.2003
22. Bijnens APJJ. Vasculin, a novel vascular protein differentially expressed in human atherogenesis. Blood 2003; 102:2803-10; PMID:12842993; http://dx.doi.org/10.1182/blood-2003-01-0306
23. Eilebrecht S, Brysbaert G, Wegert T, Urlaub H, Benecke BJ, Benecke A. 7SK small nuclear RNA directly affects HMGA1 function in transcription regulation. Nucleic Acids Res 2011; 39:2057-72; PMID:21087998; http://dx.doi.org/10.1093/nar/gkq1153
24. Zhou Y, Schmitz K-M, Mayer C, Yuan X, Akhtar A, Grummt I. Reversible acetylation of the chromatin remodelling complex NoRC is required for non-coding RNA-dependent silencing. Nat Cell Biol 2009; 11:1010-6; PMID:19578370; http://dx.doi.org/10.1038/ncb1914
25. Marqués N, Sesé M, Cánovas V, Valente F, Bermudo R, de Torres I, Fernández Y, Abasolo I, Fernández PL, Contreras H, et al. Regulation of protein translation and c-Jun expression by prostate tumor overexpressed 1. Oncogene 2014; 33:1124-34; http://dx.doi.org/10.1038/onc.2013.51
26. Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, Längst G. Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin. Mol Cell 2012; 48:434-44; PMID:23022379; http://dx.doi.org/10.1016/j.molcel.2012.08.021
27. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL. The Vienna RNA Websuite. Nucleic Acids Res 2008; 36:W70-4; PMID:18424795; http://dx.doi.org/10.1093/nar/gkn188
28. Santamaria A, Castellanos E, Gomez V, Benedit P, Renau-Piqueras J, Morote J, Reventos J, Thomson TM, Paciucci R. PTOV1 Enables the Nuclear Translocation and Mitogenic Activity of Flotillin-1, a Major Protein of Lipid Rafts. Mol Cell Biol 2005; 25:1900-11; PMID:15713644; http://dx.doi.org/10.1128/MCB.25.5.1900-1911.2005
29. la Cour T, Gupta R, Rapacki K, Skriver K, Poulsen FM, Brunak S. NESbase version 1.0: a database of nuclear export signals. Nucleic Acids Res 2003; 31:393-6; PMID:12520031; http://dx.doi.org/10.1093/nar/gkg101
30. LaCasse EC, Lefebvre YA. Nuclear localization signals overlap DNA- or RNA-binding domains in nucleic acid-binding proteins. Nucleic Acids Res 1995; 23:1647-56; PMID:7540284; http://dx.doi.org/10.1093/nar/23.10.1647
31. Thandapani P, O'Connor TR, Bailey TL, Richard S. Defining the RGG/RG Motif. Mol Cell 2013; 50:613-23; PMID:23746349; http://dx.doi.org/10.1016/j.molcel.2013.05.021
32. Morris KV, Mattick JS. The rise of regulatory RNA. Nat Rev Genet 2014; 15:423-37; PMID:24776770; http://dx.doi.org/10.1038/nrg3722
33. Eilebrecht S, Benecke B-J, Benecke A. 7SK snRNA-mediated, gene-specific cooperativity of HMGA1 and PTEFb. RNA Biol 2011; 8:1084-93; ; PMID:21957495; http://dx.doi.org/10.4161/rna.8.6.17015
34. Wehner S, Dörrich AK, Ciba P, Wilde A, Marz M. pRNA: NoRC-associated RNA of rRNA operons. RNA Biol 2014; 11:3-9; PMID:24440945; http://dx.doi.org/10.4161/rna.27448
35. Kung JT, Kesner B, An JY, Ahn JY, Cifuentes-Rojas C, Colognori D, Jeon Y, Szanto A, Del Rosario BC, Pinter SF, et al. Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Mol Cell 2015; 57:361-75; PMID:25578877; http://dx.doi.org/10.1016/j.molcel.2014.12.006
36. Ohlsson R, Renkawitz R, Lobanenkov V. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 2001; 17:520-7; PMID:11525835; http://dx.doi.org/10.1016/S0168-9525(01)02366-6
37. Yang L, Lin C, Jin C, Yang JC, Tanasa B, Li W, Merkurjev D, Ohgi KA, Da Meng, Zhang J, et al. lncRNA-dependent mechanisms of androgenreceptor-regulated gene activation programs. Nature 2014; 500:598-602; http://dx.doi.org/10.1038/nature12451
38. Han P, Li W, Lin C-H, Yang J, Shang C, Nurnberg ST, Jin KK, Xu W, Lin C-Y, Lin C-J, et al. A long noncoding RNA protects the heart from pathological hypertrophy. Nature 2014; 514:102-6; PMID:25119045; http://dx.doi.org/10.1038/nature13596
39. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, et al. The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts. Mol Cell 2012; 46:674-90; PMID:22681889; http://dx.doi.org/10.1016/j.molcel.2012.05.021
40. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, et al. Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins. Cell 2012; 149:1393-406; PMID:22658674; http://dx.doi.org/10.1016/j.cell.2012.04.031
41. Gerstberger S, Hafner M, Tuschl T. A census of human RNA-binding proteins. Nat Rev Genet 2014; 15:829-45; PMID:25365966; http://dx.doi.org/10.1038/nrg3813
42. Villar-Garea A, Imhof A. Fine Mapping of Posttranslational Modifications of the Linker Histone H1 from Drosophila melanogaster. PLoS ONE 2008; 3:e1553; PMID:18253500; http://dx.doi.org/10.1371/journal.pone.0001553