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Table 1 Representative examples of protein, RNA and DNA motifs

From: Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation

Motif type Example motif Consensus sequencea Function
Protein short linear motifs
 Ligand - promote complex formation SH3 ligand PxxPx[KR] Complex formation with SH3 domains [195]
  Nuclear receptor box LxxLL Complex formation with Nuclear receptors [196]
  LD motif [LV][DE]x[LM][LM]xxL Complex formation with FAT domains [197]
  LxCxE motif [IL]xCxE Complex formation with Rb [198]
  RGD motif RGD Complex formation with Integrin family members [199]
 Localisation - recruit targeting and transport pathways to control protein localisation Nuclear Export Signal (NES) ΦxxΦxxxΦxxΦxΦ Translocation from the nucleus to the cytoplasm [200]
KDEL ER retrieval signal [KH]DEL-COOH Translocation from the Golgi to the endoplasmatic reticulum (ER) [201]
Ciliary targeting signal RVxP Transport to the plasma membrane of the cilia [202]
Peroxisomal targeting signal [KRH]xxΦ$ or [KRH]Φ$ Import into the peroxisomal lumen [203]
Tyrosine endocytic signal YxxΦ Directs endocytosis of membrane proteins [204]
 Enzyme recruitment - recruit enzymes to the protein/complex to modify/demodify a site distinct from the bound motif Cyclin docking motif [RK]xLx{0,1}[LF] Recruitment of the Cyclin-Cdk holoenzyme [205]
PP1 docking motif RVxF Recruitment of the PP1 phosphotase holoenzyme [206]
Tankyrase docking motif Rxx[PGAV][DEIP]G Recruitment of the Tankyrase poly-(ADP-ribose) polymerase [207]
USP7 docking motif PxxS Recruitment of the USP7 deubiquitylating enzyme [208]
NEDD4 docking motif PPxY Recruitment of the NEDD4 ubiquitylating enzyme [209]
 Stability - recruit E3 ubiquitin ligases and promote substrate polyubiquitylation to control protein stability APC/C D box degron RxxLxxΦ APC/C E3 ubiquitin ligase [210]
PIP degron Φ[ST]D[FY][FY]xxx[KR] Recruitment of the Cdt2 CRL4 E3 ubiquitin ligase [211]
Fbw7 degron pTPxxp[ST] Recruitment of the Fbw7 SCF E3 ubiquitin ligase [212]
Oxygen dependent VHL degron [IL]AoPx{6,8}ΦxΦ Recruitment of von Hippel-Lindau protein (pVHL) containing E3 ubiquitin ligase [213]
MDM2 degron FxxxWxxΦ Recruitment of the MDM2 ubiquitin ligase [214]
 Modification - act as sites of moiety attachment/removal, isomerisation or cleavage PIKK phosphorylation site ([ST])Q Phosphorylation by PIKK family kinases [215]
Pin1 isomerisation site p[ST](P) Isomerisation by the Pin1 phosphorylation-dependent prolyl isomerase [216]
N-Glycosylation site Nx([ST]) Glycosylation by Oligosaccharyltransferase [217]
Caspase-3 and −7 cleavage motif [DE]xxD|[AGS] Cleavage by Caspase family proteases [218]
Myristoylation site NH2-M(G)xxx[AGSTCN] Myristoylation by Myristoyl-CoA:protein N-myristoyltransferase [219]
RNA motifs
 Stability Adenosine and uridine (AU)-rich elements (ARE) AUUUA Recruits positive and negative regulators of mRNA stability [13]
 Splicing 5′ splice junction AG/GURAGU Recruits splice site recognising U1 snRNA component of the spliceosome [14]
 Modification Polyadenylation signal AUUAAA Recruits cleavage and polyadenylation specificity factor (CPSF) to cleave and polyadenylate 3′-UTRs [15]
 Localisation Muscleblind binding motifs YGCUKY Targets mRNAs to membranes [16]
 miRNA recruitment miR-125b miRNA response element CUCAGGG Regulates expression of mutiple proteins [17]
DNA regulatory elements
 Basal machinery recruitment TATA box TATAAAA Recruitment of the basal transcription machinery to the core gene promoter required for initiation of transcription [9]
 Promoters/Enhancers CCAAT/enhancer binding protein (C/EBP) site CCAAT Promotion of gene expression [10]
 Silencers/Insulators CCCTC-binding factor (CTCF) binding site CCGCGNGGNGGCAG Diverse functions including acting as a transcriptional repressor and insulator [11]
 Endonucleases EcoRI restriction site G|AATTC Sequence specific cleavage of DNA [12]
  1. aPatterns are representative and roughly define the specificity of the motif binding partner. Pattern syntax for proteins: letters denote a specific amino acid; “x” denotes any amino acid; square brackets denote a subset of allowed amino acids; curly brackets denote length variability; round brackets indicate a position targeted for post-translational modification after motif recognition; “p” denotes a phosphorylation site required for binding; “o” denotes a hydroxylation site required for binding; “|” denotes a cleavage site; “Φ” (phi) denotes a aliphatic residue; “NH2-” indicates the amino-terminus of the protein; “-COOH” indicates the carboxyl-terminus of the protein. Pattern syntax for DNA and RNA: “/” denotes a splice site. “K” denotes a guanine or a uracil; “Y” denotes an adenine or a cytosine; “R” denotes an adenine or a guanine; “N” denotes any base; “|” denotes a cleavage site