Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association.
Down-Regulation
/ genetics
Genome, Human
HEK293 Cells
Half-Life
Humans
Models, Biological
Nucleotidyltransferases
/ metabolism
Protein Binding
RNA Processing, Post-Transcriptional
/ genetics
RNA Stability
/ genetics
RNA, Messenger
/ genetics
RNA-Binding Proteins
/ metabolism
Signal Transduction
Transcriptome
/ genetics
Up-Regulation
/ genetics
3′-end processing
HITS-CLIP
RBM10
RNA-turnover
Star-PAP
mRNA metabolism
polyadenylation
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
15 Sep 2021
15 Sep 2021
Historique:
received:
17
07
2021
revised:
08
08
2021
accepted:
19
08
2021
entrez:
28
9
2021
pubmed:
29
9
2021
medline:
21
10
2021
Statut:
epublish
Résumé
Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3'-UTR processing, we observed a high association of Star-PAP at the 3'-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3'-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.
Identifiants
pubmed: 34576144
pii: ijms22189980
doi: 10.3390/ijms22189980
pmc: PMC8469156
pii:
doi:
Substances chimiques
RBM10 protein, human
0
RNA, Messenger
0
RNA-Binding Proteins
0
Nucleotidyltransferases
EC 2.7.7.-
TUT1 protein, human
EC 2.7.7.-
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Déclaration de conflit d'intérêts
The authors declare no conflicts of interest.
Références
J Biol Chem. 2008 May 2;283(18):12665-73
pubmed: 18305108
Nature. 2009 Jul 23;460(7254):479-86
pubmed: 19536157
FEBS Lett. 2014 Mar 18;588(6):942-7
pubmed: 24530524
EMBO J. 2003 Jun 2;22(11):2821-30
pubmed: 12773396
Genes Dev. 1999 Jul 15;13(14):1884-97
pubmed: 10421639
Nucleic Acids Res. 2017 Sep 6;45(15):8930-8942
pubmed: 28911096
EMBO Mol Med. 2013 Sep;5(9):1431-42
pubmed: 24000153
RNA. 2004 Apr;10(4):565-73
pubmed: 15037765
Nat Protoc. 2014;9(6):1428-50
pubmed: 24853928
J Biol Chem. 2009 Aug 21;284(34):22803-14
pubmed: 19509282
Curr Opin Cell Biol. 2004 Jun;16(3):272-8
pubmed: 15145351
Genome Res. 2002 Aug;12(8):1231-45
pubmed: 12176931
Curr Protoc Mol Biol. 2006 Aug;Chapter 27:Unit 27.4
pubmed: 18265380
Nucleic Acids Res. 1996 Aug 1;24(15):2990-7
pubmed: 8760884
Oncogene. 2010 Jan 14;29(2):305-12
pubmed: 19881542
Biol Open. 2019 Nov 6;8(11):
pubmed: 31649118
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Curr Opin Virol. 2019 Dec;39:23-32
pubmed: 31408800
Nucleic Acids Res. 2011 Oct;39(18):7961-73
pubmed: 21729869
Nature. 2006 Dec 14;444(7121):953-6
pubmed: 17128255
Nat Methods. 2013 Feb;10(2):133-9
pubmed: 23241633
Nucleic Acids Res. 1998 Jul 1;26(13):3119-26
pubmed: 9628908
Nature. 2008 Feb 21;451(7181):1013-7
pubmed: 18288197
Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1419-E1428
pubmed: 29208711
Bioinformatics. 2017 Feb 15;33(4):566-567
pubmed: 27797762
Cell. 2001 Nov 16;107(4):451-64
pubmed: 11719186
PLoS One. 2013 Jul 18;8(7):e69630
pubmed: 23874977
RNA. 2006 Aug;12(8):1494-504
pubmed: 16790842
Nucleic Acids Res. 2017 Jun 2;45(10):6064-6073
pubmed: 28334781
Nat Rev Mol Cell Biol. 2017 Jan;18(1):18-30
pubmed: 27677860
J Cell Biochem. 2005 Jan 1;94(1):5-24
pubmed: 15514923
Microbiol Mol Biol Rev. 1999 Jun;63(2):405-45
pubmed: 10357856
Genes Dev. 2014 Nov 1;28(21):2381-93
pubmed: 25301781
Cell Rep. 2018 Sep 25;24(13):3539-3553
pubmed: 30257214
Mol Cell. 2004 May 21;14(4):457-64
pubmed: 15149595
Wiley Interdiscip Rev RNA. 2011 Jan-Feb;2(1):42-57
pubmed: 21278925
Genes Dev. 2014 Nov 1;28(21):2370-80
pubmed: 25301780
FEBS Lett. 2014 Jun 27;588(14):2185-97
pubmed: 24873880
Cell Mol Life Sci. 2008 Apr;65(7-8):1099-122
pubmed: 18158581
Nucleic Acids Res. 2016 Apr 7;44(6):2873-87
pubmed: 26809675
Cell. 1999 Sep 17;98(6):835-45
pubmed: 10499800
Nat Struct Mol Biol. 2018 Feb;25(2):135-138
pubmed: 29358758
Genes Dev. 2015 Aug 1;29(15):1599-604
pubmed: 26253535
Mol Cell Biol. 2018 Feb 12;38(5):
pubmed: 29203642
Mol Cell. 2004 Jun 4;14(5):571-83
pubmed: 15175153
Nucleic Acids Res. 2015 Aug 18;43(14):7005-20
pubmed: 26138484
Biochim Biophys Acta. 2004 May 25;1678(2-3):67-84
pubmed: 15157733
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Cell Death Dis. 2017 Feb 2;8(2):e2582
pubmed: 28151486
Nucleic Acids Res. 2019 Nov 18;47(20):10771-10787
pubmed: 31598705
Trends Biochem Sci. 1996 Jul;21(7):247-50
pubmed: 8755245
Biol Cell. 2013 Apr;105(4):162-74
pubmed: 23294349
Nat Rev Genet. 2007 Jul;8(7):533-43
pubmed: 17572691
Nucleic Acids Res. 2001 May 1;29(9):e45
pubmed: 11328886
Am J Med Genet A. 2011 Oct;155A(10):2516-20
pubmed: 21910224
Mol Cell Biol. 2001 Aug;21(16):5614-23
pubmed: 11463842
Methods. 2005 Dec;37(4):376-86
pubmed: 16314267
Nucleic Acids Res. 2012 Mar;40(6):2639-52
pubmed: 22110043
Mol Cell. 2012 Jan 13;45(1):25-37
pubmed: 22244330
Mol Cell Biol. 1997 Jul;17(7):3907-14
pubmed: 9199325
Mol Cell Biol. 2011 Jul;31(13):2667-82
pubmed: 21536652
Nat Struct Mol Biol. 2013 Jun;20(6):735-9
pubmed: 23644599
Mol Cell. 2009 Feb 13;33(3):365-76
pubmed: 19217410
Cell. 2012 Sep 14;150(6):1107-20
pubmed: 22980975
Trends Biochem Sci. 1999 Sep;24(9):342-4
pubmed: 10470032
Nucleic Acids Res. 2013 Feb 1;41(4):2644-58
pubmed: 23303783
Nucleic Acids Res. 2016 Jan 29;44(2):811-23
pubmed: 26496945
EMBO J. 2010 Dec 15;29(24):4132-45
pubmed: 21102410
Nat Commun. 2017 Jun 07;8:15788
pubmed: 28589955
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
J Mol Biol. 2011 Mar 25;407(2):273-83
pubmed: 21256132
Brief Bioinform. 2013 Mar;14(2):178-92
pubmed: 22517427
FEBS Lett. 2008 Jun 18;582(14):1977-86
pubmed: 18342629
Cold Spring Harb Protoc. 2009 Jun;2009(6):pdb.prot5234
pubmed: 20147192