DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state

. Author manuscript; available in PMC: 2021 Apr 26.

Published in final edited form as: Cell Stem Cell. 2020 Feb 6;26(2):234–250.e7. doi: 10.1016/j.stem.2020.01.004

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-β-Actin, Clone AC-15 (human/mouse)	Sigma-Aldrich	Cat. A5441; RRID:AB_476744
Anti-mouse-ZMYM2 antibody, clone F4	Abcam	Cat. ab30783 (AP: 228894); RRID:AB_874057
Anti-mouse/human LSD1,	Abcam	Cat. ab129195; RRID:AB_11145494
Anti-mouse ZSCAN4	Millipore	Cat. AB4340
Anti-mouse/human CHD4	Abcam	Cat. ab70469; RRID:AB_2229454
Anti-mouse/human HDAC1	Bethyl	Cat. A300-713A; RRID:AB_533395
Anti-mouse/human HDAC2	Bethyl	Cat. A300-705A; RRID:AB_533399
Anti-Histone H3, monomethyl (Lys4)	Abcam	Cat. ab8895; RRID:AB_306847
Anti-Histone H3, trimethyl (Lys4)	Abcam	Cat. ab8580; RRID:AB_306649
Anti-Histone H3	Abcam	Cat. ab1791; RRID:AB_302613
Anti-FLAG	Sigma-Aldrich	Cat. A8592; RRID:AB_439702
Anti-PROLIFERIN	Santa Cruz	Cat. Sc-271891; RRID: AB 10710396
Anti-TPBPA	Abcam	Cat: ab104401; RRID: AB 10901888
Anti-GFP	Proteintech Group	Cat. 50430-2-AP; RRID:AB_11042881
Experimental Models: Cell & mouse Lines
C57BL/6(C57) mice	Beijing Vital River Laboratory Animal Technology	Stock No.: 213
DBA2 mice	Beijing Vital River Laboratory Animal Technology	Stock No.: 214
Mouse embryonic stem cell line J1	ATCC	SCRC-1010
Zmym2^GT/GT mESCs	This study	N/A
Zmym2^3Flag mESCs	This study	N/A
Zmym2^−/− Knock out mESCs	This study	N/A
Chemicals, Peptides, and Recombinant Proteins
DMEM	GIBCO	Cat. 11965-092
Heat inactivated FBS	GIBCO	Cat. 35-010-cv
Penicillin-Streptomycin (5,000 U/mL)	GIBCO	Cat. 15070-063
Glutamine	GIBCO	Cat. 25030-081
Non-essential NEAA	GIBCO	Cat. 1140-050
2-Mercaptoethanol	Sigma-Aldrich	Cat. M6250
Puromycin	Sigma-Aldrich	Cat. P9620-10ML
Blasticidin S HCl	Life Technologies	Cat. A11139-03
Zeocin	Fisher Scientific	Cat. Z22100-0.25
Oligonucleotides
mmu-miR-344-3p mimics and Zmym2 siRNAs	GenePharma (Shanghai, China)	Table S7
Recombinant DNA
lenti sgRNA(MS2)_zeo backbone	Konermann et al., 2015	RRID:Addgene_61427
lenti MS2-P65-HSF1_Hygro	Konermann et al., 2015	RRID:Addgene_61426
lenti dCAS-VP64_Blast	Konermann et al., 2015	RRID:Addgene_61425
phH1-gRNA	Kabadi et al., 2014	RRID:Addgene_53186
pmU6-gRNA	Kabadi et al., 2014	RRID:Addgene_53187
phU6-gRNA	Kabadi et al., 2014	RRID:Addgene_53188
ph7SK-gRNA	Kabadi et al., 2014	RRID:Addgene_53189
pLV hUbC-dCas9-T2A-GFP	Kabadi et al., 2014	RRID:Addgene_53191
2C::tdTomato Reporter	Macfarlan et al., 2012	RRID:Addgene_40281
pZscan4c-EGFP	Dan et al., 2013	N/A
Critical Commercial Assays
Dual-Glo Luciferase Assay	Promega	Cat. E2920
SimpleChIP Plus Enzymatic Chromatin IP Kit	Cell Signaling Tech.	Cat. #9005
Deposited Data
RNA-seq on control (EV) and MERVL or miR-344-2 activated cells, raw and processed data	This study	NCBI GEO: GSE119819
RNA-Seq on WT and Zmym2 deficient mESCs, raw and processed data	This study	NCBI GEO: GSE119819
RNA-seq on 8-cell and blastocyst injected with NC, raw data and processed data	This study	NCBI GEO: GSE119819
RNA-seq on 8-cell and blastocyst injected with siRNA against Zmym2, raw data and processed data	This study	NCBI GEO: GSE119819
RNA-seq on 8-cell and blastocyst injected with miR-344 mimics, raw data and processed data	This study	NCBI GEO: GSE119819
RNA-seq on control and MERVL or miR-344-2 activated cells after sorting of DR+/+ population, raw and processed data.	This study	NCBI GEO: GSE119819
RNA-seq of 2-cell embryos.	This study	NCBI GEO: GSE119819
ChIP-seq on 3Flag-Zmym2 in mESCs, raw and processed data	This study	NCBI GEO: GSE119819
ChIP-seq of LSD1 in WT and Zmym2KO ESCs	This study	NCBI GEO: GSE119819
ATAC-seq on DR+/+ and DR−/− mESCs population	This study	NCBI GEO: GSE119817
Other Data
RNA-seq on WT and Chd4 deficient mESCs, raw data and processed data	Stevens et al., 2017	NCBI GEO: GSE80280
RNA-seq on DR−/− and DR+/+ mESCs, raw data and processed data	Macfarlan et al., 2012	E-MTAB-5058
RNA-seq on miR34a and miR34a deficient mESCs, raw data and processed data	Choi et al., 2017	NCBI GEO: GSE69484
RNA-seq on WT and DUX deficient mESCs, raw data and processed data	Hendrickson et al., 2017	NCBI GEO: GSE85632
RNA-seq on untreated 8-cell and blastocyst, raw data and processed data	Liu et al., 2016	NCBI GEO: GSE70608
ChIP-seq on LSD1 in mESCs	Whyte et al., 2012	NCBI GEO: GSE27844
ChIP-seq on DUX/DXU4 in mESCs	Whiddon et al., 2017	NCBI GEO: GSE87279
Software and Algorithms	Version	Source
FlowJo	7.6.1	https://www.flowjo.com/
STAR	2.5.3	https://github.com/alexdobin/STAR
Tophat	2.1.1	http://ccb.jhu.edu/software/tophat/index.shtml
Cufflinks	2.1.1	http://cole-trapnell-lab.github.io/cufflinks/
Diffbind	1.16.3	https://bioconductor.org/packages/release/bioc/html/DiffBind.html