Imprinted maternally-expressed microRNAs antagonize paternally-driven gene programs in neurons

. Author manuscript; available in PMC: 2021 Apr 2.

Published in final edited form as: Mol Cell. 2020 Feb 6;78(1):85–95.e8. doi: 10.1016/j.molcel.2020.01.020

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit monoclonal anti-Ago2	Cell Signaling Technology	Cat#2897; RRID: AB_2096291
Rat monoclonal anti-HA High Affinity	Roche	Cat#11867423001; RRID: AB_390918
Rabbit polyclonal anti-Enolase-I	Cell Signaling Technology	Cat#3810; RRID: AB_2246524
Rabbit polyclonal anti-Plagl1	Abcam	Cat#ab90472; RRID: AB_2050189
Rabbit polyclonal anti-Peg3	Abcam	Cat#ab99252; RRID: AB_10864541
Rabbit polyclonal anti-Jade-1	Novus	Cat#NBP1-83085; RRID: AB_11024938
Rabbit polyclonal anti-Igf2	Thermo	Cat#PA5-71494; RRID: AB_2717348
Rabbit monoclonal anti-Txnip	Cell Signaling Technology	Cat#14715; RRID: AB_2714178
Rabbit monoclonal anti-NeuroD1	Cell Signaling Technology	Cat#4373; RRID:AB_10549071
Mouse monoclonal anti-Vinculin	Sigma	Cat#V9131; RRID: AB_477629
Sheep anti-mouse IgG-HRP	GE Healthcare	Cat#NA931; RRID: AB_772210
Donkey anti-rabbit IgG-HRP	GE Healthcare	Cat#NA934; RRID: AB_772206
Chemicals, Peptides, and Recombinant Proteins
Doxycycline hyclate	Sigma	Cat#D9891
Critical Commercial Assays
Dual-Glo Luciferase Assay System	Promega	Cat#E2920
Q5 Site-Directed Mutagenesis Kit	NEB	Cat#E0554S
GenElute Mammalian Genomic DNA Miniprep Kit	Sigma	Cat#G1N10
miScript RT Kit	Qiagen	Cat#218160
miScript SYBR Green PCR Kit	Qiagen	Cat#218073
EXPRESS One-Step SuperScript qRT-PCR Kit	Thermo	Cat#11781200
EpiTect Bisulfit Kit	Qiagen	Cat#59104
PyroMark PCR Kit	Qiagen	Cat#978703
QIAseq miRNA Library Kit	Qiagen	Cat#331502
KAPA RNA HyperPrep Kit with RiboErase (HMR)	Kapa Biosystems	Cat#KK8560
Deposited Data
Raw and processed data	This paper	GEO: GSE140838
Unprocessed gel images and additional raw files	This paper	http://dx.doi.org/10.17632/hf4xvtz8t4.1
Mouse reference genome GENCODE release M15 (GRCm38.p5)	The GENCODE Project	https://www.gencodegenes.org/mouse/release_M15.html
miRbase (v21)	Kozomara et al., 2019	ftp://mirbase.org/pub/mirbase/21/; RRID:SCR_003152
TargetScanMouse (v7.2)	Agarwal et al., 2015	http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=mmu_72; RRID:SCR_010845
ENCODE microRNA-seq, mouse tissue (E14.5, P0)	ENCODE Project Consortium	GEO: GSE82739, GSE82730, GSE82822, GSE82532, GSE82490, GSE82478, GSE82749, GSE82708, GSE82864, GSE82558, GSE82982, GSE82633, GSE82873, GSE82585
ENCODE polyA+ RNA-seq, mouse tissue (P0)	ENCODE Project Consortium	GEO: GSE78316, GSE78437, GSE78374, GSE78495, GSE78325, GSE78399, GSE78337
Small RNA-seq, mouse tissue (adult)	Kuchen et al., 2010	GSE21630
RNA-seq, mouse brain cell types	Zhang et al., 2014	GSE52564
Digital gene expression profiling, Neuro-2a cells transfected with Plagl1	Varrault et al., 2017	N/A
RNA-seq, mouse in utero electroporation of Plagl1	Rraklli et al., 2016	N/A
RNA-seq, ectopic NeuroD1 induction for 48 hours in ESCs	Pataskar et al., 2016	GSE65072
Experimental Models: Cell Lines
Mouse: F_1.2-3 ESC: 129/Sv x M. cast	Eggan et al., 2001	N/A
Mouse: ESC: F_1.2-3;M2rtTA;TetO-Ngn2-mCherry;Tubb3-GFP	This paper	N/A
Mouse: Mirg^fl/+: F_1.2-3;M2rtTA;TetO-Ngn2-mCherry;Tubb3-GFP;Mirg^fl/+	This paper	N/A
Mouse: Mirg^Δ/+: F_1.2-3;M2rtTA;TetO-Ngn2-mCherry;Tubb3-GFP;Mirg^Δ/+	This paper	N/A
Mouse: Mirg^fl/+;untag-Ago2: F_1.2-3;M2rtTA;TetO-Ngn2-mCherry;Tubb3-GFP;Mirg^fl/+;untag-Ago2	This paper	N/A
Mouse: Mirg^fl/+;HA-Ago2: F_1.2-3;M2rtTA;TetO-Ngn2-mCherry;Tubb3-GFP;Mirg^fl/+;HA-Ago2	This paper	N/A
Mouse: Mirg^Δ/+;miR-369: F_1.2-3;M2rtTA;TetO-Ngn2-mCherry;Tubb3-GFP;Mirg^Δ/+;miR-369	This paper	N/A
Mouse: primary astrocytes	ScienCell	Cat#M1800
Oligonucleotides
See Table S3	This paper	N/A
Recombinant DNA
Plasmid: pSpCas9(BB)-2A-GFP (pX458)	Ran et al., 2013	Cat#48138 Addgene
Plasmid: PB-EF1α-M2rtTA (pAC4)	A.W. Cheng	N/A
Plasmid: PB transposase (mPBase)	A.W. Cheng	N/A
Plasmid: pcDNA3.1 FH-NLS-hAgo2	T. Kelly	N/A
Plasmid: pTetO-Ngn2-Puro	Zhang et al., 2013	Cat#52047 Addgene
Plasmid: pTetO-Ngn2-mCherry	This paper	N/A
Plasmid: pCMV-dR8.2	Stewart et al., 2003	Cat#8455 Addgene
Plasmid: pCMV-VSV-G	Stewart et al., 2003	Cat#8454 Addgene
Plasmid: pCAG-Cre:GFP	Matsuda et al., 2007	Cat#13776 Addgene
Plasmid: PB-EF1α-MCS-IRES-Neo	System Biosciences	Cat#PB533A-2
Plasmid: pmirGLO	Promega	Cat#E1330
Plasmid: pmirGLO-miR.target.site	This paper	N/A
Plasmid: pmirGLO-Plagl1.3’UTR	This paper	N/A
Plasmid: pmirGLO-Plagl1.3’UTR.Del	This paper	N/A
Plasmid: pmirGLO-Neurod1.3’UTR	This paper	N/A
Plasmid: pmirGLO-Neurod1.3’UTR.Del	This paper	N/A
Software and Algorithms
BD FACSDiva Software (v8.0)	BD Biosciences	RRID:SCR_001456
FlowJo (v9)	FlowJo	RRID:SCR_008520
NEBaseChanger (v1.2.9)	NEB	https://nebasechanger.neb.com/
pCLAMP10 with Clampfit (v10.7) Software	Molecular Devices	RRID:SCR_011323
MATLAB (vR2018b)	MathWorks	RRID:SCR_001622
R (v3.5.1)	R Project	https://www.r-project.org/; RRID:SCR_001905
ComplexHeatmap (v1.20.0) R package	Gu et al., 2016	https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html; RRID:SCR_017270
Metagene (v2.14.0) R package	Beauparlant et al., 2019	https://bioconductor.org/packages/release/bioc/html/metagene.html
STAR (v2.4.1)	Dobin et al., 2013	https://github.com/alexdobin/STAR; RRID:SCR_015899
RSEM (v1.2.30)	Li et al., 2011	https://github.com/deweylab/RSEM; RRID:SCR_013027
DESeq2	https://www.bioconductor.org	RRID:SCR_015687
Samtools	Li et al., 2009	http://samtools.sourceforge.net/; RRID:SCR_002105
Cutadapt (v1.4.2)	Martin M. 2011	https://cutadapt.readthedocs.io/en/stable/; RRID:SCR_011841
Fastxtoolkit (v0.0.13)	N/A	http://hannonlab.cshl.edu/fastx_toolkit/
CLIPper	Lovci et al., 2013	https://github.com/YeoLab/clipper
GSEA	Subramanian et al., 2005; Mootha et al., 2003	RRID:SCR_003199
Cytoscape (v3.7.1)	Shannon et al., 2003	RRID:SCR_003032