DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells.
DAP5
RNA-seq
noncanonical protein translation
pluripotent embryonic stem cells
ribosome profiling
uORF
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
10 2022
10 2022
Historique:
received:
05
04
2022
accepted:
26
07
2022
pubmed:
13
8
2022
medline:
21
9
2022
entrez:
12
8
2022
Statut:
ppublish
Résumé
Death associated protein 5 (DAP5/eIF4G2/NAT1) is a member of the eIF4G translation initiation factors that has been shown to mediate noncanonical and/or cap-independent translation. It is essential for embryonic development and for differentiation of embryonic stem cells (ESCs), specifically its ability to drive translation of specific target mRNAs. In order to expand the repertoire of DAP5 target mRNAs, we compared ribosome profiles in control and DAP5 knockdown (KD) human ESCs (hESCs) to identify mRNAs with decreased ribosomal occupancy upon DAP5 silencing. A cohort of 68 genes showed decreased translation efficiency in DAP5 KD cells. Mass spectrometry confirmed decreased protein abundance of a significant portion of these targets. Among these was KMT2D, a histone methylase previously shown to be essential for ESC differentiation and embryonic development. We found that nearly half of the cohort of DAP5 target mRNAs displaying reduced translation efficiency of their main coding sequences upon DAP5 KD contained upstream open reading frames (uORFs) that are actively translated independently of DAP5. This is consistent with previously suggested mechanisms by which DAP5 mediates leaky scanning through uORFs and/or reinitiation at the main coding sequence. Crosslinking protein-RNA immunoprecipitation experiments indicated that a significant subset of DAP5 mRNA targets bound DAP5, indicating that direct binding between DAP5 protein and its target mRNAs is a frequent but not absolute requirement for DAP5-dependent translation of the main coding sequence. Thus, we have extended DAP5's function in translation of specific mRNAs in hESCs by a mechanism allowing translation of the main coding sequence following upstream translation of short ORFs.
Identifiants
pubmed: 35961752
pii: rna.079194.122
doi: 10.1261/rna.079194.122
pmc: PMC9479741
doi:
Substances chimiques
EIF4G2 protein, human
0
Eukaryotic Initiation Factor-4G
0
Proteins
0
RNA, Messenger
0
Histone Methyltransferases
EC 2.1.1.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1325-1336Informations de copyright
© 2022 David et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Références
Mol Cell Biol. 1997 Mar;17(3):1615-25
pubmed: 9032289
Genome Biol. 2014;15(12):550
pubmed: 25516281
Nature. 2021 Jun;594(7862):240-245
pubmed: 33979833
RNA. 2007 Mar;13(3):374-84
pubmed: 17237356
Methods. 2017 Aug 15;126:112-129
pubmed: 28579404
Mol Cell. 2012 Jun 8;46(5):674-90
pubmed: 22681889
Genes Dev. 2016 Sep 1;30(17):1991-2004
pubmed: 27664238
J Biol Chem. 2004 Apr 23;279(17):17148-57
pubmed: 14960583
Nucleic Acids Res. 2022 Jan 25;50(2):1111-1127
pubmed: 35018467
Nat Methods. 2018 May;15(5):363-366
pubmed: 29529017
Mol Cell. 2008 May 23;30(4):447-59
pubmed: 18450493
Nat Rev Genet. 2020 Oct;21(10):630-644
pubmed: 32709985
Nucleic Acids Res. 2015 Apr 20;43(7):3764-75
pubmed: 25779044
Oncogene. 2014 Jan 30;33(5):611-8
pubmed: 23318444
Sci Adv. 2018 Jan 31;4(1):eaap8747
pubmed: 29404406
RNA Biol. 2019 Oct;16(10):1327-1338
pubmed: 31234713
Mol Cell. 2016 Mar 3;61(5):760-773
pubmed: 26942679
Nat Struct Mol Biol. 2013 Sep;20(9):1122-30
pubmed: 23912277
Genomics. 1997 Jan 15;39(2):192-7
pubmed: 9027506
EMBO J. 2000 Oct 16;19(20):5533-41
pubmed: 11032820
Mol Syst Biol. 2019 Feb 18;15(2):e8503
pubmed: 30777892
J Biol Chem. 2016 Aug 12;291(33):16927-35
pubmed: 27358398
Nucleic Acids Res. 2008 Jan;36(1):168-78
pubmed: 18003655
Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11871-11876
pubmed: 27698142
Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):340-345
pubmed: 28003464
J Biol Chem. 2020 Aug 14;295(33):11693-11706
pubmed: 32571876
Science. 2009 Apr 10;324(5924):218-23
pubmed: 19213877
Genes Dev. 1997 Feb 1;11(3):321-33
pubmed: 9030685
Tissue Eng Part A. 2014 Jan;20(1-2):54-66
pubmed: 23848515
RNA. 2022 Feb;28(2):123-138
pubmed: 34848561
Nat Commun. 2018 Aug 3;9(1):3068
pubmed: 30076308
PLoS One. 2015 Sep 25;10(9):e0139076
pubmed: 26406898
J Biol Chem. 2003 Feb 7;278(6):3572-9
pubmed: 12458215
Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5400-5
pubmed: 11943866
Cell Res. 2017 May;27(5):626-641
pubmed: 28281539
Cell Stem Cell. 2008 May 8;2(5):448-60
pubmed: 18462695
Nat Commun. 2021 Nov 30;12(1):6979
pubmed: 34848685
Nature. 2021 Jan;589(7840):125-130
pubmed: 32906143
Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450
pubmed: 30395289
Biochem Insights. 2015 Sep 28;8(Suppl 2):15-21
pubmed: 26462244
EMBO J. 1997 Feb 17;16(4):817-25
pubmed: 9049310
Cell. 2012 Jun 8;149(6):1393-406
pubmed: 22658674
Dev Growth Differ. 2007 Sep;49(7):623-34
pubmed: 17716306
Nature. 2016 Aug 4;536(7614):96-9
pubmed: 27462815