Identification and characterization of sORF-encoded polypeptides

Critical Reviews in Biochemistry and Molecular Biology

Volumn 50, Issue 2, 2015, Pages 134-141

  Chu, Qian ^a   Ma, Jiao ^a,b   Saghatelian, Alan ^a  

^a SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Bioactive polypeptides; Next generation sequencing; Novel genes; Proteomics; Short small open reading frames

Indexed keywords

AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; MESSENGER RNA; POLYPEPTIDE; TRANSCRIPTION FACTOR; UNTRANSLATED RNA; PEPTIDE; RNA;

ALTERNATIVE RNA SPLICING; CELL FUNCTION; GENE EXPRESSION PROFILING; GENOMICS; HUMAN; MASS SPECTROMETRY; MOLECULAR BIOLOGY; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEOMICS; REVIEW; RIBOSOME; SITE DIRECTED MUTAGENESIS; SUGAR TRANSPORT; GENETICS;

GENOMICS; HUMANS; OPEN READING FRAMES; PEPTIDES; PROTEOMICS; RIBOSOMES; RNA;

EID: 84928819339     PISSN: 10409238     EISSN: 15497798     Source Type: Journal    
DOI: 10.3109/10409238.2015.1016215     Document Type: Review

References (59)

1. Ambros V. (2004). The functions of animal microRNAs. Nature 431: 350-5
2. Andrews SJ, Rothnagel JA. (2014). Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 15: 193-204
3. Aspden JL, Eyre-Walker YC, Phillips RJ, et al. (2014). Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. Elife 3: e03528
4. Bazzini AA, Johnstone TG, Christiano R, et al. (2014). Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33: 981-93
5. Brent MR, Guigo R. (2004). Recent advances in gene structure prediction. Curr Opin Struct Biol 14: 264-72
6. Calvo SE, Pagliarini DJ, Mootha VK. (2009). Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci USA 106: 7507-12
7. Chew GL, Pauli A, Rinn JL, et al. (2013). Ribosome profiling reveals resemblance between long non-coding RNAs and 50 leaders of coding RNAs. Development 140: 2828-34
8. Crappe J, Van Criekinge W, Trooskens G, et al. (2013). Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs. BMC Genomics 14: 648
9. De Coninck B, Carron D, Tavormina P, et al. (2013). Mining the genome of Arabidopsis thaliana as Abasis for the identification of novel bioactive peptides involved in oxidative stress tolerance. J Exp Bot 64: 5297-307
10. Dinger ME, Pang KC, Mercer TR, et al. (2008). Differentiating proteincoding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol 4: e1000176
11. Dong X, Wang DX, Liu P, et al. (2013). Zm908p11, encoded by a short open reading frame (sORF) gene, functions in pollen tube growth as a profilin ligand in maize. J Exp Bot 64: 2359-72
12. Falth M, Skold K, Norrman M, et al. (2006). SwePep, a database designed for endogenous peptides and mass spectrometry. Mol Cell Proteomics 5: 998-1005
13. Fatica A, Bozzoni I. (2014). Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet 15: 7-21
14. Ferguson JT, Wenger CD, Metcalf WW, et al. (2009). Top-down proteomics reveals novel protein forms expressed in Methanosarcina acetivorans. J Am Soc Mass Spectrom 20: 1743-50
15. Galindo MI, Pueyo JI, Fouix S, et al. (2007). Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol 5: e106
16. Gleason CA, Liu QL, Williamson VM. (2008). Silencing a candidate nematode effector gene corresponding to the tomato resistance gene Mi-1 leads to acquisition of virulence. Mol Plant Microbe Interact 21: 576-85
17. Guo B, Zhai D, Cabezas E, et al. (2003). Humanin peptide suppresses apoptosis bYinterfering with Bax activation. Nature 423: 456-61
18. Guttman M, Russell P, Ingolia NT, et al. (2013). Ribosome profiling provides evidence that large noncoding RNAs do notencode proteins. Cell 154: 240-51
19. hashimoto Y, Kondo T, Kageyama Y. (2008). Lilliputians get into the limelight: novel class of small peptide genes in morphogenesis. Dev Growth Differ 50: S269-76
20. hashimoto Y, Niikura T, Tajima H, et al. (2001). A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer's disease genes and Abeta. Proc Natl Acad Sci USA 98: 6336-41
21. holst JJ. (2007). The physiology of glucagon-like peptide 1. Physiol Rev 87: 1409-39
22. Ingolia NT. (2014). Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15: 205-13
23. Ingolia NT, Brar GA, Rouskin S, et al. (2012). The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7: 1534-50
24. Ingolia NT, Brar GA, Stern-Ginossar N, et al. (2014). Ribosome profiling reveals pervasive translation outside of annotated proteincoding genes. Cell Rep 8: 1365-79
25. Ingolia NT, Ghaemmaghami S, Newman JRS, et al. (2009). Genomewide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-23
26. Ingolia NT, Lareau LF, Weissman JS. (2011). Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147: 789-802
27. Ivanov IP, Firth AE, Michel AM, et al. (2011). Identification of evolutionarily conserved non-AUG-initiated N-Terminal extensions in human coding sequences. Nucleic Acids Res 39: 4220-34
28. Kastenmayer JP, Ni L, Chu A, et al. (2006). Functional genomics of genes with small open reading frames (sORFs) in S-cerevisiae. Genome Res 16: 365-73
29. Kondo T, Hashimoto Y, Kato K, et al. (2007). Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nat Cell Biol 9: 660-5
30. Kondo T, Plaza S, Zanet J, et al. (2010). Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science 329: 336-9
31. Kozak M. (1986). Point mutations define a sequence flanking the Aug initiator codon that modulates translation by eukaryotic ribosomes. Cell 44: 283-92
32. Ladoukakis E, Pereira V, Magny EG, et al. (2011). Hundreds of putatively functional small open reading frames in Drosophila. Genome Biol 12: R118
33. Lin MF, Jungreis I, Kellis M. (2011). PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27: i275-82
34. Lo WS, Gardiner E, Xu Z, et al. (2014). Human tRNA synthetase catalytic nulls with diverse functions. Science 345: 328-32
35. Ma J, Ward CC, Jungreis I, et al. (2014). Discovery of human sORFencoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res 13: 1757-65
36. Magny EG, Pueyo JI, Pearl FM, et al. (2013). Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames. Science 341: 1116-20
37. Maki K, Morita T, Otaka H, et al. (2010). A minimal base-pairing region of Abacterial small RNA SgrS required for translational repression of ptsG mRNA. Mol Microbiol 76: 782-92
38. Margolis RN, Evans RM, O'Malley BW, et al. (2005). The Nuclear Receptor Signaling Atlas: development of a functional atlas of nuclear receptors. Mol Endocrinol 19: 2433-6
39. Menschaert G, Van Criekinge W, Notelaers T, et al. (2013). Deep proteome coverage baseDon ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events. Mol Cell Proteomics 12: 1780-90
40. Oyama M, Kozuka-Hata H, Suzuki Y, et al. (2007). Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics 6: 1000-6
41. Pauli A, Norris ML, Valen E, et al. (2014). Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science 343: 1248636
42. Regard JB, Sato IT, Coughlin SR. (2008). Anatomical profiling of G protein-coupled receptor expression. Cell 135: 561-71
43. Rice JB, Vanderpool CK. (2011). The small RNA SgrS controls sugarphosphate accumulation by regulating multiple PTS genes. Nucleic Acids Res 39: 3806-19
44. Rohrig H, Schmidt J, Miklashevichs E, et al. (2002). Soybean ENOD40 encodes two peptides that bind to sucrose synthase. Proc Natl Acad Sci USA 99: 1915-20
45. Saltiel AR, Kahn CR. (2001). Insulin signalling and the regulation of glucose and lipid metabolism. Nature 414: 799-806
46. Slavoff SA, Heo J, Budnik BA, et al. (2014). A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining. J Biol Chem 289: 10950-7
47. Slavoff SA, Mitchell AJ, Schwaid AG, et al. (2013). Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 9: 59-64
48. Smith JE, Alvarez-Dominguez JR, Kline N, et al. (2014). Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae. Cell Rep 7: 1858-66
49. Steiner DF. (1998). The proprotein convertases. Curr Opin Chem Biol 2: 31-9
50. Van Damme P, Gawron D, Van Criekinge W, et al. (2014). N-Terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol Cell Proteomics 13: 1245-61
51. van den Pol AN. (2012). Neuropeptide transmission in brain circuits. Neuron 76: 98-115
52. Vander Heiden MG. (2011). Targeting cancer metabolism: a therapeutic window opens. Nat Rev Drug Discov 10: 671-84
53. Vanderperre B, Lucier JF, Bissonnette C, et al. (2013). Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One 8: e70698
54. Wadler CS, Vanderpool CK. (2007). A dual function for Abacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. Proc Natl Acad Sci USA 104: 20454-9
55. Wilson BA, Masel J. (2011). Putatively noncoding transcripts show extensive association with ribosomes. Genome Biol Evol 3: 1245-52
56. Yang XH, Tschaplinski TJ, Hurst GB, et al. (2011). Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res 21: 634-41
57. Yore MM, Syed I, Moraes-Vieira PM, et al. (2014). Discovery of a class of endogenous mammalian lipids with anti-diabetic and anti-inflammatory effects. Cell 159: 318-32
58. Zhai D, Luciano F, Zhu X, et al. (2005). Humanin binds and nullifies Bid activity by blocking its activation of Bax and Bak. J Biol Chem 280: 15815-24
59. Zhang MQ. (2002). Computational prediction of eukaryotic proteincoding genes. Nat Rev Genet 3: 698-709