PMID- 35961752
OWN - NLM
STAT- MEDLINE
DCOM- 20220920
LR  - 20221104
IS  - 1469-9001 (Electronic)
IS  - 1355-8382 (Print)
IS  - 1355-8382 (Linking)
VI  - 28
IP  - 10
DP  - 2022 Oct
TI  - DAP5 drives translation of specific mRNA targets with upstream ORFs in human 
      embryonic stem cells.
PG  - 1325-1336
LID - 10.1261/rna.079194.122 [doi]
AB  - 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.
CI  - (c) 2022 David et al.; Published by Cold Spring Harbor Laboratory Press for the RNA 
      Society.
FAU - David, Maya
AU  - David M
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Olender, Tsviya
AU  - Olender T
AUID- ORCID: 0000-0002-4194-6420
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Mizrahi, Orel
AU  - Mizrahi O
AUID- ORCID: 0000-0003-2189-5731
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Weingarten-Gabbay, Shira
AU  - Weingarten-Gabbay S
AUID- ORCID: 0000-0001-7579-0236
AD  - The Broad Institute, Cambridge, Massachusetts 02141, USA.
FAU - Friedlander, Gilgi
AU  - Friedlander G
AUID- ORCID: 0000-0001-8513-1998
AD  - The Mantoux Bioinformatics Institute, Weizmann Institute of Science, Rehovot 
      7610001, Israel.
FAU - Meril, Sara
AU  - Meril S
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Goldberg, Nadav
AU  - Goldberg N
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Savidor, Alon
AU  - Savidor A
AUID- ORCID: 0000-0001-8884-6948
AD  - The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand 
      Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of 
      Science, Rehovot 7610001, Israel.
FAU - Levin, Yishai
AU  - Levin Y
AUID- ORCID: 0000-0002-7279-0246
AD  - The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand 
      Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of 
      Science, Rehovot 7610001, Israel.
FAU - Salomon, Vered
AU  - Salomon V
AUID- ORCID: 0000-0002-0701-7521
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Stern-Ginossar, Noam
AU  - Stern-Ginossar N
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Bialik, Shani
AU  - Bialik S
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
FAU - Kimchi, Adi
AU  - Kimchi A
AUID- ORCID: 0000-0002-8236-8989
AD  - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, 
      Israel.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20220812
PL  - United States
TA  - RNA
JT  - RNA (New York, N.Y.)
JID - 9509184
RN  - 0 (EIF4G2 protein, human)
RN  - 0 (Eukaryotic Initiation Factor-4G)
RN  - 0 (Proteins)
RN  - 0 (RNA, Messenger)
RN  - EC 2.1.1.- (Histone Methyltransferases)
SB  - IM
MH  - Eukaryotic Initiation Factor-4G/*metabolism
MH  - Histone Methyltransferases/genetics/metabolism
MH  - *Human Embryonic Stem Cells/metabolism
MH  - Humans
MH  - Open Reading Frames/genetics
MH  - Protein Biosynthesis
MH  - Proteins/genetics
MH  - RNA, Messenger/genetics/metabolism
PMC - PMC9479741
OTO - NOTNLM
OT  - DAP5
OT  - RNA-seq
OT  - noncanonical protein translation
OT  - pluripotent embryonic stem cells
OT  - ribosome profiling
OT  - uORF
EDAT- 2022/08/13 06:00
MHDA- 2022/09/21 06:00
PMCR- 2022/10/01
CRDT- 2022/08/12 21:06
PHST- 2022/04/05 00:00 [received]
PHST- 2022/07/26 00:00 [accepted]
PHST- 2022/08/13 06:00 [pubmed]
PHST- 2022/09/21 06:00 [medline]
PHST- 2022/08/12 21:06 [entrez]
PHST- 2022/10/01 00:00 [pmc-release]
AID - rna.079194.122 [pii]
AID - RA [pii]
AID - 10.1261/rna.079194.122 [doi]
PST - ppublish
SO  - RNA. 2022 Oct;28(10):1325-1336. doi: 10.1261/rna.079194.122. Epub 2022 Aug 12.