Critical contribution of 3′ non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA

. Author manuscript; available in PMC: 2022 Jun 2.

Published in final edited form as: Cell Rep. 2022 Apr 26;39(4):110745. doi: 10.1016/j.celrep.2022.110745

KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
E.coli HB101	N/A	N/A
E.coli HT115 RNAi clones	Kamath et al., 2003	N/A
Chemicals, peptides, and recombinant proteins
1X duplex buffer	IDT	Cat#11010301
QIAzol Lysis Reagent	Qiagen	Cat#79306
GlycoBlue	Invitrogen	Cat#AM9516
Protease Inhibitor Cocktail	Sigma-Aldrich	Cat#P2714
Turbo DNase	Invitrogen	Cat#AM2238
400 μm silica beads	OPS Diagnostic	Cat#PFAW-400-100-04
RNase I	Invitrogen	Cat#AM2294
SUPERase.In RNase Inhibitor	Invitrogen	Cat#AM2694
SYBR Gold Nucleic Acid Gel Stain	Invitrogen	Cat#S11494
T4 PNK	NEB	Cat#M0201S
RNase Inhibitor, Murine	NEB	Cat#M0314S
Thermostable RNase H	MCLAB	Cat#HTRH-100
Critical commercial cssays
Q5 site-directed mutagenesis kit	NEB	Cat#E0552S
QIAseq miRNA Library kit	Qiagen	Cat#331505
QIAseq miRNA NGS 96 Index IL	Qiagen	Cat#331565
KAPA Library Quantification Kit	KAPA Biosystems	Cat#KK4824
RNA Clean & Concentrator-5 Kit	Zymo	Cat#R1015
NEBNext Multiplex Small RNA Library Prep Set	NEB	Cat#E7300
NEBNext Ultra II RNA Library Prep kit	NEB	Cat#E7775
NEBNext Multiplex oligo for Illumina	NEB	Cat#E7500 E7335 E7710 E7730
HiFiScript gDNA Removal cDNA Synthesis Kit	CWBIO	CW2020M
UltraSYBR Mixture (Low ROX)	CWBIO	CW2601L
Deposited data
Raw and processed data of ribosome profiling	This paper	GEO: GSE171726
Raw and processed data of RNA-seq	This paper	GEO: GSE171733
Raw and processed data of small RNA seq	This paper	GEO: GSE171747
Code of target prediction algorithm	This paper	GitHub: https://github.com/IsanaVekslerLublinsky/Let7_Proj_code.git; Zenodo DOI: 6465945
C.elegans Reference Genome WBCel235	Ensemble/iGenome (Illumina)	https://support.illumina.com/sequencing/sequencing_software/igenome.html
miRBase release 22.1	miRBase	http://www.mirbase.org/ftp.shtml
Experimental models: Organisms/strains
C.elegans: Strain N2	Caenorhabditis Genetics Center	WormBase Strain: N2
C.elegans: Strain VT1313 (maIs105 V; mir-84(n4037) X)	This paper	VT1313
C.elegans: Strain VT1367 (maIs105 V)	This paper	VT1367
C.elegans: Strain VT2692 (maIs105 V; let-7(n2853) X)	This paper	VT2692
C.elegans: Strain VT3439 (maIs105 V; let-7(ma341) X)	This paper	VT3439
C.elegans: Strain VT3455 (wIs51 V)	This paper	VT3455
C.elegans: Strain VT3460 (wIs51 V; let-7a(ma341) X)	This paper	VT3460
C.elegans: Strain VT3479 (maIs105 V; let-7(ma341); mir-84(n4037) X)	This paper	VT3479
C.elegans: Strain VT3585 (lin-41(ma378) I; maIs105 V; let-7(ma341) X)	This paper	VT3585
C.elegans: Strain VT3639 (lin-41(ma378) I; maIs105 V)	This paper	VT3639
C.elegans: Strain VT3645 (mnDp1(umnIs25) (X;V),+/+, maIs105 V; let-7(ma393) X)	Duan et al., 2020a; 2020b	VT3645
C.elegans: Strain VT3648 (mnDp1(umnIs25) (X;V),+/+, maIs105 V; let-7(ma341) X)	This paper	VT3648
C.elegans: Strain VT3729 (mnDp1(umnIs25) (X;V),+/+, maIs105 V; let-7(ma432ma435) X)	This paper	VT3729 ma432ma435 is also labeled as ma428
C.elegans: Strain VT3742 (oxSi1091(Pmex-5::Cas-9(smu-2 introns) unc-119+) II; mnDp1(umnIs25) (X;V)/+ V; let-7(ma393) X)	This paper	VT3742
C.elegans: Strain VT3793 (mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma431) X)	This paper	VT3793
C.elegans: Strain VT3794 (mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma432) X)	This paper	VT3794
C.elegans: Strain VT3795 (mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma433) X)	This paper	VT3795
C.elegans: Strain VT3796 (mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma434) X)	This paper	VT3796
C.elegans: Strain VT3797 (maIs105 V; let-7(ma435) X)	This paper	VT3797
C.elegans: Strain VT3798 (maIs105 V; let-7(ma436) X)	This paper	VT3798
C.elegans: Strain VT3799 (maIs105 V; let-7(ma437) X)	This paper	VT3799
C.elegans: Strain VT3825 (mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma448) X)	This paper	VT3825
C.elegans: Strain VT3826 (mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma449) X)	This paper	VT3826
C.elegans: Strain VT3827 (maIs105 V; let-7(ma450) X)	This paper	VT3827
C.elegans: Strain VT3828 (maIs105 V; let-7(ma451) X)	This paper	VT3828
C.elegans: Strain VT3829 (maIs105 V; let-7(ma452) X)	This paper	VT3829
C.elegans: Strain VT3835 (maIs105 V; let-7(ma453) X)	This paper	VT3835
C.elegans: Strain VT3836 (maIs105 V; let-7(ma454) X)	This paper	VT3836
C.elegans: Strain VT3843 (maIs105 V; let-7(ma455) X)	This paper	VT3843
C.elegans: Strain VT3844 (maIs105 V; let-7(ma456) X)	This paper	VT3844
C.elegans: Strain VT3867 (lin-41(tn1541) I; oxSi1091 II; mnDp1(umnIs25) (X;V)/+ V; let-7(ma432) X)	This paper	VT3867
C.elegans: Strain VT3868 (lin-41(tn1541) I; mnDp1(umnIs25) (X;V)/+ V; let-7(ma432) X)	This paper	VT3868
C.elegans: Strain VT3873 (oxSi1091 II; mnDp1(umnIs25) (X;V)/+ V; let-7(ma432) X)	This paper	VT3873
C.elegans: Strain VT3874 (maIs105 V; let-7(ma476) X)	This paper	VT3874
C.elegans: Strain VT3875 (maIs105 V; let-7(ma477) X)	This paper	VT3875
C.elegans: Strain VT3876 (maIs105 V; let-7a(ma478) X)	This paper	VT3876
C.elegans: Strain VT3877 (mnDp1(umnIs25) (X;V),+/+, maIs105 V; let-7(ma449ma435) X)	This paper	VT3877 ma449ma435 is also labeled as ma479
C.elegans: Strain VT3878 (lin-41(tn1541ma480) I; let-7(ma432) X)	This paper	VT3878
C.elegans: Strain VT3879 (lin-41(tn1541ma480) I; maIs105 V; let-7(ma432) X)	This paper	VT3879
C.elegans: Strain VT3945 (lin-41(tn1541ma501) I; maIs105 V)	This paper	VT3945
C.elegans: Strain VT3949 (lin-41(tn1541ma480) I)	This paper	VT3949
C.elegans: Strain VT3950 (lin-41(tn1541ma480) I; maIs105 V)	This paper	VT3950
C.elegans: Strain VT3954 (lin-41(tn1541ma501) I; mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma393) X)	This paper	VT3954
C.elegans: Strain VT3959 (lin-41(tn1541) I; mnDp1(umnIs25) (X;V),+/+,maIs105 V; let-7(ma393) X)	This paper	VT3959
C.elegans: Strain VT3974 (lin-41(ma501ma545) I; maIs105 V)	This paper	VT3974 ma501ma545 is also labeled as ma511
C.elegans: Strain VT3975 (lin-41(xe11) I; maIs105 V)	This paper	VT3975
C.elegans: Strain VT4009 (lin-41(ma501ma572) I; maIs105 V)	This paper	VT4009 ma501ma572 is also labeled as ma554
C.elegans: Strain VT4058 (lin-41(ma501ma480) I; maIs105 V)	This paper	VT4058 ma501ma480 is also labeled as ma504
C.elegans: Strain VT4060 (lin-41(ma480) I; maIs105 V)	This paper	VT4060
C.elegans: Strain VT4091 (lin-41(ma501ma555) I; maIs105 V)	This paper	VT4091 ma501ma555 is also labeled as ma552
C.elegans: Strain VT4092 (lin-41(ma501ma556) I; maIs105 V)	This paper	VT4092 ma501ma556 is also labeled as ma553
C.elegans: Strain VT4093 (lin-41(ma501ma571) I; maIs105 V)	This paper	VT4093 ma501ma571 is also labeled as ma554
C.elegans: Strain VT4094 (lin-41(ma555) I; maIs105 V)	This paper	VT4094
C.elegans: Strain VT4095 (lin-41(ma556) I; maIs105 V)	This paper	VT4095
C.elegans: Strain VT4123 (lin-41(ma564) I; maIs105 V)	This paper	VT4123
C.elegans: Strain VT4124 (lin-41(ma565) I; maIs105 V)	This paper	VT4124
C.elegans: Strain VT4125 (lin-41(ma566) I; maIs105V)	This paper	VT4125
C.elegans: Strain VT4126 (oxSi1091 II; maIs105 V; daf-12(ma498ma567) X)	This paper	VT4126
C.elegans: Strain VT4128 (lin-41(tn1541) I; maIs105 V; daf-12(ma498ma568) X)	This paper	VT4128
C.elegans: Strain VT4129 (lin-41(tn1541) I; maIs105 V; daf-12(ma498) X)	This paper	VT4129
C.elegans: Strain DG3913 (lin-41(tn1541) I)	Caenorhabditis Genetics Center	WormBase: DG3913
Oligonucleotides
see Table S6	N/A	N/A
Recombinant DNA
Plasmid: pBlueScript SK(+) let-7a(mir-84 swap)	This paper	pBS-09
Plasmid: pCR2.1-TOPO let-7a(U9G)	This paper	pCR-32
Plasmid: pCR2.1-TOPO let-7a(A10U)	This paper	pCR-33
Plasmid: pCR2.1-TOPO let-7a(G11U)	This paper	pCR-12
Plasmid: pCR2.1-TOPO let-7a(G12U)	This paper	pCR-34
Plasmid: pCR2.1-TOPO let-7a(U13A)	This paper	pCR-25
Plasmid: pCR2.1-TOPO let-7a(U14A)	This paper	pCR-13
Plasmid: pCR2.1-TOPO let-7a(G15A)	This paper	pCR-14
Plasmid: pCR2.1-TOPO let-7a(U16G)	This paper	pCR-35
Plasmid: pCR2.1-TOPO let-7a(A17U)	This paper	pCR-36
Plasmid: pCR2.1-TOPO let-7a(U18A)	This paper	pCR-26
Plasmid: pCR2.1-TOPO let-7a(A19U)	This paper	pCR-15
Plasmid: pCR2.1-TOPO let-7a(G20C)	This paper	pCR-39
Plasmid: pCR2.1-TOPO let-7a(U21A)	This paper	pCR-40
Plasmid: pCR2.1-TOPO let-7a(U22A)	This paper	pCR-16
Plasmid: pCR2.1-TOPO let-7a(U18C)	This paper	pCR-37
Plasmid: pCR2.1-TOPO let-7a(U18G)	This paper	pCR-38
Plasmid: pCR2.1-TOPO let-7a(U16G + U18A)	This paper	pCR-41
Plasmid: pCR2.1-TOPO let-7a(17–22)	This paper	pCR-42
Plasmid: pCR2.1-TOPO let-7a(A17U + U18A + A19U)	This paper	pCR-43
Plasmid: pCR2.1-TOPO let-7a(G20C + U21A + U22A)	This paper	pCR-44
Plasmid: pCR2.1-TOPO let-7(INPP4A, Jump Board, null)	This paper	pCR-07
Software and algorithms
let-7a target prediction algorithm	This paper	https://github.com/IsanaVekslerLublinsky/Let7_Proj_code.git Zenodo DOI: 6465945
ImageJ-FIJI	Schindelin et al., 2012	https://imagej.net/Fiji
Prism 8	GraphPad	https://www.graphpad.com/scientific-software/prism/
SnapGene Viewer	SnapGene	https://www.snapgene.com/snapgene-viewer/
Jalview2	Waterhouse et al., 2009	https://www.jalview.org/
Adobe Illustrator CS5	Adobe Inc.	https://www.adobe.com/products/illustrator.html
Cutadapt/1.9	Martin, 2011	https://cutadapt.readthedocs.io/en/stable/
Bowtie2/2.3.4.3	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
STAR/2.7.6a	Dobin et al., 2013	https://github.com/alexdobin/STAR
featureCounts (Subread/1.6.2)	Liao et al., 2014	http://subread.sourceforge.net/
plastid/0.4.8	Dunn and Weissman, 2016	https://plastid.readthedocs.io/en/latest/index.html
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
RStudio(2019)	RStudio	https://rstudio.com/
ggplot2	Hadley, 2016	https://ggplot2.tidyverse.org/
Other
SW 41 Ti swinging-bucket rotor	Beckman-Coulter	Cat#331362
Spin-X centrifuge tube filter	Millipore	Cat#CLS8160
Fisherbrand™ RNase-Free Disposable Pellet Pestles	Fisher Scientific	Cat#12-141-364