The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis.

Bruno Di Stefano, En-Ching Luo, Chuck Haggerty, Stefan Aigner, Jocelyn Charlton, Justin Brumbaugh, Fei Ji, Inés Rabano Jiménez, Katie J Clowers, Aaron J Huebner, Kendell Clement, Inna Lipchina, Marit A C de Kort, Anthony Anselmo, John Pulice, Mattia F M Gerli, Hongcang Gu, Steven P Gygi, Ruslan I Sadreyev, Alexander Meissner, Gene W Yeo, Konrad Hochedlinger

Cell stem cell · 2019 · Vol. 25 (5) · pp. 622-638.e13

PubMed DOI PMC Full Text

Abstract

Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells (ESCs) with a differentiation-resistant, "hyper-pluripotent" state, which readily reprograms to a naive state resembling the preimplantation embryo. We further demonstrate that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Mechanistically, DDX6 mediates the translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 activity, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin, and DNA methylation landscapes of undifferentiated cell types. Collectively, our data establish a link between P-body homeostasis, chromatin organization, and stem cell potency.

Publication Types

["Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't"]

Keywords

["P-body", "RNA helicase DDX6", "adult progenitor cells", "chromatin", "differentiation", "embryonic stem cells", "exit from pluripotency", "naive pluripotency", "post-transcriptional regulation", "primed pluripotency", "self-renewal"]

MeSH Terms

["Animals", "Cell Differentiation", "Cell Line", "Cell Plasticity", "Chromatin Assembly and Disassembly", "DEAD-box RNA Helicases", "DNA Methylation", "Embryonic Stem Cells", "Gene Expression Regulation", "Gene Ontology", "Homeostasis", "Humans", "Induced Pluripotent Stem Cells", "Jumonji Domain-Containing Histone Demethylases", "Mice", "Mice, Inbred C57BL", "Nanog Homeobox Protein", "Organoids", "Protein Biosynthesis", "Proteins", "Proto-Oncogene Proteins", "RNA, Messenger", "RNA-Seq", "Ribonucleoproteins", "Ribosomes"]

Funding

P30 DK040561 NIDDK NIH HHS (United States)

P01 GM099117 NIGMS NIH HHS (United States)

P01 GM099134 NIGMS NIH HHS (United States)

R01 GM067945 NIGMS NIH HHS (United States)

R01 HD058013 NICHD NIH HHS (United States)

Linked Datasets (10)

GSE125808 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [polysome RNA-seq]

Homo sapiens

36 data files

File	Type	Size
SRR8501380	RNA-Seq	638.1 MB
SRR8501381	RNA-Seq	280.4 MB
SRR8501382	RNA-Seq	898.5 MB
SRR8501383	RNA-Seq	356.9 MB
SRR8501384	RNA-Seq	309.0 MB
SRR8501385	RNA-Seq	277.9 MB
SRR8501386	RNA-Seq	414.0 MB
SRR8501387	RNA-Seq	523.1 MB
SRR8501388	RNA-Seq	468.4 MB
SRR8501389	RNA-Seq	598.7 MB
SRR8501390	RNA-Seq	541.9 MB
SRR8501391	RNA-Seq	652.8 MB
SRR8501392	RNA-Seq	773.0 MB
SRR8501393	RNA-Seq	479.3 MB
SRR8501394	RNA-Seq	383.9 MB
SRR8501395	RNA-Seq	623.1 MB
SRR8501396	RNA-Seq	457.2 MB
SRR8501397	RNA-Seq	371.1 MB
SRR8501398	RNA-Seq	814.1 MB
SRR8501399	RNA-Seq	489.8 MB
SRR8501400	RNA-Seq	547.1 MB
SRR8501401	RNA-Seq	535.4 MB
SRR8501402	RNA-Seq	598.5 MB
SRR8501403	RNA-Seq	616.0 MB
SRR8501404	RNA-Seq	478.5 MB
SRR8501405	RNA-Seq	560.8 MB
SRR8501406	RNA-Seq	602.5 MB
SRR8501407	RNA-Seq	590.9 MB
SRR8501408	RNA-Seq	429.8 MB
SRR8501409	RNA-Seq	606.9 MB
SRR8501410	RNA-Seq	359.6 MB
SRR8501411	RNA-Seq	716.7 MB
SRR8501412	RNA-Seq	621.7 MB
SRR8501413	RNA-Seq	654.2 MB
SRR8501414	RNA-Seq	754.0 MB
SRR8501415	RNA-Seq	529.2 MB

GSE124072 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-Seq]

Homo sapiens

10 data files

File	Type	Size
Myoblast.shCTRL_1.R1.fastq.gz	RNA-Seq	1.3 GB
Myoblast.shCTRL_2.R1.fastq.gz	RNA-Seq	1.7 GB
Myoblast.shDDX6_1.R1.fastq.gz	RNA-Seq	1.5 GB
Myoblast.shDDX6_2.R1.fastq.gz	RNA-Seq	1.6 GB
Myoblast.shDDX6_2.R2.fastq.gz	RNA-Seq	1.6 GB
NPC.shCTRL_1.R1.fastq.gz	RNA-Seq	1.7 GB
NPC.shCTRL_2.R1.fastq.gz	RNA-Seq	996.9 MB
NPC.shDDX6_1.R1.fastq.gz	RNA-Seq	1.6 GB
NPC.shDDX6_2.R1.fastq.gz	RNA-Seq	2.2 GB
SRR8351040	RNA-Seq	1.7 GB

GSE134164 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq2]

Homo sapiens

8 data files

File	Type	Size
CTRL-TESR-1_R1.fastq.gz	RNA-Seq	1.2 GB
CTRL-TESR-2_R1.fastq.gz	RNA-Seq	1.1 GB
CTRL-TGFBI-1_R1.fastq.gz	RNA-Seq	1.1 GB
CTRL-TGFBI-2_R1.fastq.gz	RNA-Seq	1.3 GB
DDXOE-TESR-1_R1.fastq.gz	RNA-Seq	1.4 GB
DDXOE-TESR-2_R1.fastq.gz	RNA-Seq	1.0 GB
DDXOE-TGFBI-1_R1.fastq.gz	RNA-Seq	1.2 GB
DDXOE-TGFBI-2_R1.fastq.gz	RNA-Seq	1.4 GB

GSE125809 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

Homo sapiens

4 data files

File	Type	Size
SRR8501416	RIP-Seq	422.7 MB
SRR8501417	RIP-Seq	532.8 MB
SRR8501418	RIP-Seq	727.0 MB
SRR8501419	RIP-Seq	700.6 MB

GSE124071 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ATAC-Seq]

Homo sapiens

10 data files

File	Type	Size
iPSC.CTRL.1.R1.fastq.gz	ATAC-seq	2.5 GB
iPSC.CTRL.2.R1.fastq.gz	ATAC-seq	2.4 GB
iPSC.DDX6.1.R1.fastq.gz	ATAC-seq	2.2 GB
iPSC.DDX6.2.R1.fastq.gz	ATAC-seq	2.3 GB
Myoblast.CTRL.1.R1.fastq.gz	ATAC-seq	2.4 GB
Myoblast.CTRL.1.R2.fastq.gz	ATAC-seq	2.4 GB
Myoblast.CTRL.2.R1.fastq.gz	ATAC-seq	2.0 GB
Myoblast.DDX6.1.R1.fastq.gz	ATAC-seq	2.0 GB
Myoblast.DDX6.2.R1.fastq.gz	ATAC-seq	2.3 GB
Myoblast.DDX6.2.R2.fastq.gz	ATAC-seq	2.3 GB

GSE112479 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells

Homo sapiens

GSE125954 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [ChIP-Seq]

Homo sapiens

15 data files

File	Type	Size
CTRL_H3K27ac_rep1.bam	ChIP-Seq	162.8 MB
CTRL_H3K27ac_rep2.bam	ChIP-Seq	177.2 MB
CTRL_H3K4me3_rep1.bam	ChIP-Seq	99.1 MB
CTRL_H3K4me3_rep2.bam	ChIP-Seq	172.6 MB
CTRL_H3K9me3_rep1.bam	ChIP-Seq	92.0 MB
CTRL_H3K9me3_rep2.bam	ChIP-Seq	257.7 MB
DDX6_H3K27ac_rep1.bam	ChIP-Seq	136.4 MB
DDX6_H3K27ac_rep2.bam	ChIP-Seq	223.0 MB
DDX6_H3K4me3_rep1.bam	ChIP-Seq	113.2 MB
DDX6_H3K4me3_rep2.bam	ChIP-Seq	150.6 MB
DDX6_H3K9me3_rep1.bam	ChIP-Seq	87.4 MB
DDX6_H3K9me3_rep2.bam	ChIP-Seq	244.5 MB
SRR8511935	ChIP-Seq	99.1 MB
SRR8511938	ChIP-Seq	177.2 MB
SRR8511940	ChIP-Seq	257.7 MB

GSE112383 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-seq]

Homo sapiens

18 data files

File	Type	Size
GEN1C_sgCTRL_rep1.fastq.gz	RNA-Seq	1.4 GB
GEN1C_sgCTRL_rep2.fastq.gz	RNA-Seq	2.2 GB
GEN1C_sgCTRL_TGFBi_rep1.fastq.gz	RNA-Seq	1.5 GB
GEN1C_sgCTRL_TGFBi_rep2.fastq.gz	RNA-Seq	1.4 GB
GEN1C_sgDDX6_rep1.fastq.gz	RNA-Seq	1.6 GB
GEN1C_sgDDX6_rep2.fastq.gz	RNA-Seq	1.4 GB
GEN1C_sgDDX6_TGFBi_rep1.fastq.gz	RNA-Seq	1.4 GB
GEN1C_sgDDX6_TGFBi_rep2.fastq.gz	RNA-Seq	1.4 GB
WIBR3_Naive_rep1.fastq.gz	RNA-Seq	895.0 MB
WIBR3_Naive_rep2.fastq.gz	RNA-Seq	823.3 MB
WIBR3_shCTRL_rep1.fastq.gz	RNA-Seq	1.3 GB
WIBR3_shCTRL_rep2.fastq.gz	RNA-Seq	1.5 GB
WIBR3_shCTRL_TGFBi_rep1.fastq.gz	RNA-Seq	1.7 GB
WIBR3_shCTRL_TGFBi_rep2.fastq.gz	RNA-Seq	1.4 GB
WIBR3_shDDX6_rep1.fastq.gz	RNA-Seq	1.5 GB
WIBR3_shDDX6_rep2.fastq.gz	RNA-Seq	1.4 GB
WIBR3_shDDX6_TGFBi_rep1.fastq.gz	RNA-Seq	1.6 GB
WIBR3_shDDX6_TGFBi_rep2.fastq.gz	RNA-Seq	1.4 GB

GSE112782 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [CLIP-Seq]

Homo sapiens

12 data files

File	Type	Size
EY_INPUT_DCP1B_H1_S2_L006_R1_001.fastq.gz	RIP-Seq	673.2 MB
EY_INPUT_FUS_H1_S1_L006_R1_001.fastq.gz	RIP-Seq	477.5 MB
EY_INPUT_ILF2_H1_S3_L006_R1_001.fastq.gz	RIP-Seq	618.7 MB
EY_IP_DCP1B_H1_S5_L006_R1_001.fastq.gz	RIP-Seq	588.3 MB
EY_IP_FUS_H1_S4_L006_R1_001.fastq.gz	RIP-Seq	567.4 MB
EY_IP_ILF2_H1_S6_L006_R1_001.fastq.gz	RIP-Seq	455.5 MB
SA_DX6Ai_S97_L007_R1_001.fastq.gz	RIP-Seq	2.1 GB
SA_DX6A_S98_L007_R1_001.fastq.gz	RIP-Seq	1.6 GB
SA_DX6Bi_S99_L007_R1_001.fastq.gz	RIP-Seq	1.7 GB
SA_DX6B_S100_L007_R1_001.fastq.gz	RIP-Seq	900.5 MB
SRR6950639	RIP-Seq	900.5 MB
SRR6950641	RIP-Seq	477.5 MB

GSE112439 GSE via ncbi_elink

GEO

The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RRBS]

Homo sapiens

8 data files

File	Type	Size
ESC_sgCTRL.1.R1.fq.gz	Bisulfite-Seq	661.0 MB
ESC_sgCTRL.2.R1.fq.gz	Bisulfite-Seq	631.9 MB
ESC_sgCTRL.3.R1.fq.gz	Bisulfite-Seq	629.7 MB
ESC_sgCTRL.4.R1.fq.gz	Bisulfite-Seq	614.6 MB
ESC_sgDDX6.1.R1.fq.gz	Bisulfite-Seq	461.4 MB
ESC_sgDDX6.2.R1.fq.gz	Bisulfite-Seq	440.9 MB
ESC_sgDDX6.3.R1.fq.gz	Bisulfite-Seq	447.1 MB
ESC_sgDDX6.4.R1.fq.gz	Bisulfite-Seq	436.4 MB