Citation: Yin Xinqiang, Hu Jialiang, Xu Hanmei. Distribution of micropeptide-coding sORFs in transcripts[J]. Chinese Chemical Letters, ;2018, 29(7): 1029-1032. doi: 10.1016/j.cclet.2018.04.027 shu

Distribution of micropeptide-coding sORFs in transcripts

Yin Xinqiang ^a,b ,
Hu Jialiang ^a,c ,
Xu Hanmei ^a,c,,

a.
The Engineering Research Center of Peptide Drug Discovery and Development, China Pharmaceutical University, Nanjing 210009, China
b.
The Basic Medical School, North Sichuan Medical College, Nanchong 673000, China
c.
State Key Laboratory of Natural Medicines, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China

Corresponding author: Xu Hanmei, 13913925346@126.com
Received Date: 19 March 2018
Revised Date: 30 March 2018
Accepted Date: 9 April 2018
Available Online: 24 July 2018

Figures(2)

Small open reading frames (sORFs) are distributed over a wide variety of transcripts.sORFs encoding functional peptides have been identified in various configurations within apparently long noncoding RNAs. Many translated sORFs have been identified across mRNAs, including 5'-upstream, coding domain, and 3'-downstream. sORFs have also been found in circular RNAs, pri-miRNAs, and ribosomal RNAs. Here, we present an overview of the wide distribution of the sORFs in transcripts and their functional roles in organisms.
- Micropeptide,
- sORFs,
- uORFs,
- ncRNA,
- circRNAs,
- Pri-miRNAs
1. [1]
  M.A. Basrai, P. Hieter, J.D. Boeke, Genome Res. 7(1997) 768-771. doi: 10.1101/gr.7.8.768
2. [2]
  M.A. Mumtaz, J.P. Couso, Biochem. Soc. Trans. 43(2015) 1271-1276. doi: 10.1042/BST20150170
3. [3]
  M.I. Galindo, J.I. Pueyo, S. Fouix, S.A. Bishop, J.P. Couso, PLoS Biol. 5(2007) e106. doi: 10.1371/journal.pbio.0050106
4. [4]
  Y. Hashimoto, T. Kondo, Y. Kageyama, Dev. Growth Differ. 50(2008) S269-S276. doi: 10.1111/j.1440-169X.2008.00994.x
5. [5]
  J. Crappe, W.V. Criekinge, G. Menschaert, EuPA Open Proteom. 3(2014) 128-137. doi: 10.1016/j.euprot.2014.02.006
6. [6]
  I.P. Ivanov, A.E. Firth, A.M. Michel, et al., Nucleic Acids Res. 39(2011) 4220-4234. doi: 10.1093/nar/gkr007
7. [7]
  G. Menschaert, W. Van Criekinge, T. Notelaers, et al., Mol. Cell Proteom. 12(2013) 1780-1790. doi: 10.1074/mcp.M113.027540
8. [8]
  S.J. Andrews, J.A. Rothnagel, Nat. Rev. Genet. 15(2014) 193-204. doi: 10.1038/nrg3520
9. [9]
  L. Kong, Y. Zhang, Z.Q. Ye, et al., Nucleic Acids Res. 35(2007) W345-W349. doi: 10.1093/nar/gkm391
10. [10]
  Y. Ina, J. Mol. Evol. 40(1997) 190-226.
11. [11]
  L.D. Hurst, Trends Genet. 18(2002) 486. doi: 10.1016/S0168-9525(02)02722-1
12. [12]
  M.F. Lin, J.W. Carlson, M.A. Crosby, et al., Genome Res. 17(2007) 1823-1836. doi: 10.1101/gr.6679507
13. [13]
  A. Stark, M.F. Lin, P. Kheradpour, et al., Nature 450(2007) 219-232. doi: 10.1038/nature06340
14. [14]
  G. Butler, M.D. Rasmussen, M.F. Lin, et al., Nature 459(2007) 657-662.
15. [15]
  M. Clamp, B. Fry, M. Kamal, et al., Proc. Natl. Acad. Sci. U. S. A. 104(2007) 19428-19433. doi: 10.1073/pnas.0709013104
16. [16]
  M. Guttman, I. Amit, M. Garber, et al., Nature 458(2009) 223-227. doi: 10.1038/nature07672
17. [17]
  M. Guttman, M. Garber, J.Z. Levin, et al., Nat. Biotechnol. 28(2010) 503-510. doi: 10.1038/nbt.1633
18. [18]
  M.F. Lin, I. Jungreis, M. Kellis, Bioinformatics 27(2011) i275-i282. doi: 10.1093/bioinformatics/btr209
19. [19]
  N.T. Ingolia, S. Ghaemmaghami, J.R. Newman, et al., Science 324(2009) 218-223. doi: 10.1126/science.1168978
20. [20]
  S. Lee, B. Liu, S.X. Huang, et al., Proc. Natl. Acad. Sci. U. S. A. 109(2012) E2424-E2432. doi: 10.1073/pnas.1207846109
21. [21]
  N.T. Ingolia, G.A. Brar, S. Rouskin, et al., Nat. Protoc. 7(2012) 1534-1550. doi: 10.1038/nprot.2012.086
22. [22]
  S. Iwasaki, N.T. Ingolia, Trends Biochem. Sci. 42(2017) 612-624. doi: 10.1016/j.tibs.2017.05.004
23. [23]
  M.V. Gerashchenko, V.N. Gladyshev, Nucleic Acids Res. 45(2017) e6. doi: 10.1093/nar/gkw822
24. [24]
  M. Guttman, P. Russell, N.T. Ingolia, et al., Cell 154(2013) 240-251. doi: 10.1016/j.cell.2013.06.009
25. [25]
  N.T. Ingolia, G.A. Brar, N. Stern-Ginossar, et al., Cell Rep. 8(2014) 1365-1379. doi: 10.1016/j.celrep.2014.07.045
26. [26]
  A.A. Bazzini, T.G. Johnstone, R. Christiano, et al., EMBO J. 33(2014) 981-993. doi: 10.1002/embj.201488411
27. [27]
  J. Crappé, E. Ndah, A. Koch, et al., Nucleic Acids Res. 43(2015) e29. doi: 10.1093/nar/gku1283
28. [28]
  L. Calviello, N. Mukherjee, E. Wyler, et al., Nat. Methods 13(2016) 165-170. doi: 10.1038/nmeth.3688
29. [29]
  J.L. Aspden, Y.C. Eyre-Walker, R.J. Phillips, et al., Elife 3(2014) e03528.
30. [30]
  S.A. Slavoff, A.J. Mitchell, A.G. Schwaid, et al., Nat. Chem. Biol. 9(2013) 59-64. doi: 10.1038/nchembio.1120
31. [31]
  Q. Chu, J. Ma, A. Saghatelian, Crit. Rev. Biochem. Mol. Biol. 50(2015) 134-141. doi: 10.3109/10409238.2015.1016215
32. [32]
  J.A. Vizcaino, A. Csordas, N. Del-Toro, et al., Nucleic Acids Res. 44(2016) 11033. doi: 10.1093/nar/gkw880
33. [33]
  T.T. Cech, J.A. Steitz, Cell 157(2014) 77-94. doi: 10.1016/j.cell.2014.03.008
34. [34]
  E.G. Magny, J.I. Pueyo, F.M. Pearl, et al., Science 341(2013) 1116-1120. doi: 10.1126/science.1238802
35. [35]
  D.M. Anderson, K.M. Anderson, C.L. Chang, et al., Cell 160(2015) 595-606. doi: 10.1016/j.cell.2015.01.009
36. [36]
  B.R. Nelson, C.A. Makarewich, D.M. Anderson, et al., Science 351(2016) 271-275. doi: 10.1126/science.aad4076
37. [37]
  A. Pauli, M.L. Norris, E. Valen, et al., Science 343(2014) 1248636. doi: 10.1126/science.1248636
38. [38]
  G. Menschaert, W. Van Criekinge, T. Notelaers, et al., Mol. Cell. Proteom. 12(2013) 1780-1790. doi: 10.1074/mcp.M113.027540
39. [39]
  N.G. D'Lima, J. Ma, L. Winkler, et al., Nat. Chem. Biol. 13(2017) 174-180. doi: 10.1038/nchembio.2249
40. [40]
  A.M. Michel, D.E. Andreev, P.V. Baranov, BMC Bioinform. 15(2014) 380. doi: 10.1186/s12859-014-0380-4
41. [41]
  A. Matsumoto, A. Pasut, M. Matsumoto, et al., Nature 541(2017) 228-232. doi: 10.1038/nature21034
42. [42]
  S.E. Calvo, D.J. Pagliarini, V.K. Mootha, PNAS 106(2009) 7507-7512. doi: 10.1073/pnas.0810916106
43. [43]
  L.E. Cabrera-Quio, S. Herberg, A. Pauli, RNA Biol. 13(2016) 1051-1059. doi: 10.1080/15476286.2016.1218589
44. [44]
  Y. Ye, Y. Liang, Q. Yu, et al., Hum. Genet. 134(2015) 605-612. doi: 10.1007/s00439-015-1544-7
45. [45]
  S.E. Calvo, D.J. Pagliarini, V.K. Mootha, PNAS 106(2009) 7507-7512. doi: 10.1073/pnas.0810916106
46. [46]
  J.T. Mendell, N.A. Sharifi, J.L. Meyers, et al., Nat. Genet. 36(2004) 1073-1078. doi: 10.1038/ng1429
47. [47]
  H. Yepiskoposyan, F. Aeschimann, D. Nilsson, et al., RNA 17(2011) 2108-2118. doi: 10.1261/rna.030247.111
48. [48]
  K.A. Spriggs, M. Bushell, A.E. Willis, Mol. Cell 40(2010) 228-237. doi: 10.1016/j.molcel.2010.09.028
49. [49]
  C. Jousse, et al., Nucleic Acids Res. 29(2001) 4341-4351. doi: 10.1093/nar/29.21.4341
50. [50]
  C. Akimoto, E. Sakashita, K. Kasashima, et al., Biochim. Biophs. Acta1830(2013) 2728-2738. doi: 10.1016/j.bbagen.2012.12.010
51. [51]
  G.L. Yosten, J. Liu, H. Ji, et al., J. Physiol. 594(2016) 1601-1605. doi: 10.1113/JP270567
52. [52]
  B. Vanderperre, J.F. Lucier, C. Bissonnette, et al., PLoS One 8(2013) e70698. doi: 10.1371/journal.pone.0070698
53. [53]
  H. Mouilleron, V. Delcourt, X. Roucou, Nucleic Acids Res. 44(2016) 14-23. doi: 10.1093/nar/gkv1218
54. [54]
  S.A. Slavoff, et al., Nature Chem. Biol. 9(2013) 59-64. doi: 10.1038/nchembio.1120
55. [55]
  B. Vanderperre, et al., FASEB J. 25(2011) 2373-2386. doi: 10.1096/fj.10-173815
56. [56]
  D. Bergeron, et al., J. Biol. Chem. 288(2013) 21824-21835. doi: 10.1074/jbc.M113.472654
57. [57]
  L.J. Li, Q. Huang, H.F. Pan, et al., Exp. Cell Res. 346(2016) 248-254. doi: 10.1016/j.yexcr.2016.07.021
58. [58]
  D. van Rossum, B.M. Verheijen, R.J. Pasterkamp, Front. Mol. Neurosci. 9(2016) 74.
59. [59]
  M. Cortés-López, P. Miura, Yale J. Biol. Med. 89(2016) 527-537.
60. [60]
  D. Rong, H. Sun, Z. Li, et al., Oncotarget 8(2017) 73271-73281.
61. [61]
  S. Qu, Z. Liu, X. Yang, Cancer Lett. 414(2018) 301-309. doi: 10.1016/j.canlet.2017.11.022
62. [62]
  M.M. Jiang, Z.T. Mai, S.Z. Wan, et al., J. Cancer Res. Clin. Oncol. 144(2018) 667-674. doi: 10.1007/s00432-017-2576-2
63. [63]
  N.R. Pamudurti, O. Bartok, M. Jens, et al., Mol. Cell 66(2017) 9-21. doi: 10.1016/j.molcel.2017.02.021
64. [64]
  I. Legnini, G. Di Timoteo, F. Rossi, et al., Mol. Cell 66(2017) 22-37. doi: 10.1016/j.molcel.2017.02.017
65. [65]
  D. Lauressergues, J.M. Couzigou, H.S. Clemente, et al., Nature 520(2015) 90-93. doi: 10.1038/nature14346
66. [66]
  Y. Hashimoto, T. Niikura, H. Tajima, et al., Proc. Natl. Acad. Sci. U. S. A. 98(2001) 6336-6341. doi: 10.1073/pnas.101133498
67. [67]
  C. Lee, J. Zeng, G.B. Drew, et al., Cell Metab. 21(2015) 443-454. doi: 10.1016/j.cmet.2015.02.009
68. [68]
  B. Guo, D. Zhai, E. Cabezas, et al., Nature 423(2003) 456-461. doi: 10.1038/nature01627
69. [69]
  D. Zhai, F. Luciano, X. Zhu, et al., J. Biol. Chem. 280(2005) 15815-15824. doi: 10.1074/jbc.M411902200
70. [70]
  C. Lee, K. Yen, P. Cohen, et al., Trends Endocrinol. Metab. 24(2013) 222-228. doi: 10.1016/j.tem.2013.01.005

Get Citation

PDF

XML

Metrics

PDF Downloads(1)
Abstract views(1566)
HTML views(86)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142