REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
E. coli BL21 star (DE3)	Thermo Fisher Scientific	C601003
E. coli DH5α (DE3)	Thermo Fisher Scientific	18258012
Chemicals, Peptides, and Recombinant Proteins
Insect-XPRESS protein-free insect cell medium with L-glutamine	Lonza	12-730Q
Protease Inhibitor Cocktail	Sigma-Aldrich	11836170001
Desthiobiotin	IBA	2-1000-001
Imidazole	Sigma-Aldrich	I5513
Formamide	Sigma-Aldrich	11814320001
TEMED	Sigma-Aldrich	T9281
Ammonium persulfate (APS)	Sigma-Aldrich	A3678
SYBR Safe DNA Gel Stain	Thermo Fisher Scientific	S33102
SYBR Green II RNA Gel Stain	Thermo Fisher Scientific	S7586
Ni-NTA Agarose	QIAGEN	30210
Glutathione Sepharose 4B	GE Healthcare	17075601
Amicon Ultra Centrifugal Filter Units	Millipore	UFC901096
TWEEN 20	Sigma-Aldrich	P9416
S. pombe Ccr4-Not (WT) protein	Stowell et al., 2016	N/A
S. pombe Ccr4-Not (Ccr4 E387A) protein	Stowell et al., 2016	N/A
S. pombe Ccr4-Not (Caf1 D53A) protein	Stowell et al., 2016	N/A
S. pombe Ccr4-Caf1 (WT) protein	This paper	N/A
S. pombe Ccr4-Caf1 (Ccr4 E387A) protein	This paper	N/A
S. pombe Ccr4-Caf1 (Caf1 D53A) protein	This paper	N/A
S. pombe Ccr4 (EEP domain) protein	This paper	N/A
S. pombe Caf1 protein	This paper	N/A
S. pombe Pab1 protein	This paper	N/A
S. pombe Pab1ΔC protein	This paper	N/A
S. pombe Pab1ΔPC protein	This paper	N/A
S. pombe Pab1 (Y83A) protein	This paper	N/A
S. pombe Pab1 (F171A) protein	This paper	N/A
S. pombe Pab1 (Y264A) protein	This paper	N/A
S. pombe Pab1 (F367A) protein	This paper	N/A
Critical Commercial Assays
Quikchange Lightning Multi Site-Directed Mutagenesis Kit	Agilent Technologies	210513
In-Fusion HD Cloning Kit	Takara Bio	121416
Phusion High-Fidelity DNA Polymerase	New England BioLabs	M0530S
Deposited Data
Sequencing data for mRNA half-life analysis	This paper	GEO: GSE114560
Pab1 RIP-Seq	Costello et al., 2015	13059_2014_559_MOESM2_ESM.xlsx
Poly(A) tail lengths	Subtelny et al., 2014	GSE52809_Cerevisiae_total.txt
Experimental Models: Organisms/Strains
yJC244	Nonet et al., 1987	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1
yJC1257	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1, caf1::HIS3
yJC1347	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1, ccr4::NEO
yJC1892	Presnyak et al., 2015	MATa, ura3, leu2, his3, met15 [pGAL-OPT-pG, URA3]
yJC1893	Presnyak et al., 2015	MATa, ura3, leu2, his3, met15 [pGAL-NON-OPT-pG, URA3]
yJC1961	Presnyak et al., 2015	MATa, ura3, his3, leu2, met15, ccr4:NEO [pGAL-OPT-pG, URA3]
yJC1962	Presnyak et al., 2015	MATa, ura3, leu2, his3, met15, ccr4::NEO [pGAL-NON-OPT-pG, URA3]
yJC1990	This study	MATa, ura3, leu2, his3, met15, dhh1::NEO [pGAL-OPT-pG, URA3]
yJC1991	This study	MATa, ura3, leu2, his3, met15, dhh1::NEO [pGAL-NON-OPT-pG, URA3]
yJC2318	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1, ccr4::NEO [pGAL-OPT-pG, URA3]
yJC2319	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1, ccr4::NEO [pGAL-NON-OPT-pG, URA3]
yJC2320	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1 [pGAL-OPT-pG, URA3]
yJC2321	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1 [pGAL-NON-OPT-pG, URA3]
yJC2324	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1, caf1::HIS3 [pGAL-OPT-pG, URA3]
yJC2325	This study	MATa, ura3-52, his3-200, leu2-3.112, rpb1-1, caf1::HIS3 [pGAL-NON-OPT-pG, URA3]
yJC2364	This study	MATa, ura3, his3, leu2, met15, caf1::NEO [pGAL-OPT-pG, URA3]
yJC2365	This study	MATa, ura3, his3, leu2, met15, caf1::NEO [pGAL-NON-OPT-pG, URA3]
yJC2499	Radhakrishnan et al., 2016	MATa, ura3, leu2, his3, met15 [pGAL-optimal FLAG-0% HIS, URA3]
yJC2504	Radhakrishnan et al., 2016	MATa, ura3, leu2, his3, met15 [pGAL-optimal FLAG-50% HIS, URA3]
yJC2509	Radhakrishnan et al., 2016	MATa, ura3, leu2, his3, met15 [pGAL-optimal FLAG-100% HIS, URA3]
yJC2591	This study	MATa, ura3, leu2, his3, met15 [pGAL-SL-OPT-pG, URA3]
yJC2592	This study	MATa, ura3, leu2, his3, met15 [pGAL-SL-NON-OPT-pG, URA3]
yJC2658	This study	MATa, ura3, his3, leu2, met15, ccr4::NEO [pGAL-SL-OPT-pG, URA3]
yJC2659	This study	MATa, ura3, his3, leu2, met15, ccr4::NEO [pGAL-SL-NON-OPT-pG, URA3]
yJC2660	This study	MATa, ura3, his3, leu2, met15, caf1::NEO [pGAL-SL-OPT-pG, URA3]
yJC2661	This study	MATa, ura3, his3, leu2, met15, caf1::NEO [pGAL-SL-NON-OPT-pG, URA3]
yJC2666	This study	MATa, ura3, leu2, his3, met15, dhh1::NEO [pGAL-SL-OPT-pG, URA3]
yJC2667	This study	MATa, ura3, leu2, his3, met15, dhh1::NEO [pGAL-SL-NON-OPT-pG, URA3]
yJC2709	This study	MATa, ura3, his3, leu2, met15, caf1::NEO [pGAL-optimal FLAG-0% HIS, URA3]
yJC2710	This study	MATa, ura3, his3, leu2, met15, caf1::NEO [pGAL-optimal FLAG-50% HIS, URA3]
yJC2711	This study	MATa, ura3, his3, leu2, met15, caf1::NEO [pGAL-optimal FLAG-100% HIS, URA3]
yJC2724	This study	MATa, ura3, his3, leu2, met15, ccr4::NEO [pGAL-optimal FLAG-0% HIS, URA3]
yJC2725	This study	MATa, ura3, his3, leu2, met15, ccr4::NEO [pGAL-optimal FLAG-50% HIS, URA3]
yJC2726	This study	MATa, ura3, his3, leu2, met15, ccr4::NEO [pGAL-optimal FLAG-100% HIS, URA3]
Oligonucleotides
DNA and RNA sequences	This paper	See Table S2
Recombinant DNA
pJC134	This study	PGK1pG with stem loop at 5′ UTR (under control of GAL1 UAS)
pJC672	Presnyak et al., 2015	PGK1pG reporter with OPT ORF (under control of GAL1 UAS)
pJC673	Presnyak et al., 2015	PGK1pG reporter with NON-OPT ORF (under control of GAL1 UAS)
pJC857	Radhakrishnan et al., 2016	0% optimal HIS3 with N-terminal FLAG tag (GAL1 promoter)
pJC862	Radhakrishnan et al., 2016	50% optimal HIS3 with N-terminal FLAG tag (GAL1 promoter)
pJC867	Radhakrishnan et al., 2016	100% optimal HIS3 with N-terminal FLAG tag (GAL1 promoter)
pJC929	This study	pJC134 with SpeI before start codon and XhoI sites after stop codon of PGK1 ORF
pJC930	This study	PGK1pG reporter with stem loop at 5′ of OPT ORF (under control of GAL1 UAS)
pJC931	This study	PGK1pG reporter with stem loop at 5′ of NON-OPT ORF (under control of GAL1 UAS)
LP_P24-1	Stowell et al., 2016	MultiBac expression vector for S. pombe Ccr4-Not
LP_P24-2	Stowell et al., 2016	MultiBac expression vector for S. pombe Ccr4-Not (Ccr4 E387A)
LP_P24-3	Stowell et al., 2016	MultiBac expression vector for S. pombe Ccr4-Not (Caf1 D53A)
LP_P24-4	Stowell et al., 2016	MultiBac expression vector for S. pombe Ccr4-Not (Ccr4 E387A, Caf1 D53A)
LP_P22-9	This study	pGEX6P-2 expression vector for S. pombe Ccr4(EEP) (res 331-621)
LP_P24-5	This study	pET28a expression vector for S. pombe Caf1(FL) (res 1-335)
LP_P22-10	This study	pGEX6P-2 expression vector for S. pombe Pab1(FL) (res1-653)
LP_P22-11	This study	pGEX6P-2 expression vector for S. pombe Pab1 (res80-653)
LP_P22-12	This study	pGEX6P-2 expression vector for S. pombe Pab1ΔC (res80-576)
LP_P22-13	This study	pGEX6P-2 expression vector for S. pombe Pab1ΔPC (res80-441)
LP_P22-14	This study	pGEX6P-2 expression vector for S. pombe Pab1(RRM1mut) (res80-653; Y83A)
LP_P22-15	This study	pGEX6P-2 expression vector for S. pombe Pab1(RRM2mut) (res80-653; F171A)
LP_P22-16	This study	pGEX6P-2 expression vector for S. pombe Pab1(RRM3mut) (res80-653; Y264A)
LP_P22-17	This study	pGEX6P-2 expression vector for S. pombe Pab1(RRM4mut) (res80-653; F367A)
Software and Algorithms
ImageJ	NIH	https://imagej.nih.gov/ij/
GraphPad Prism 6	GraphPad	https://www.graphpad.com/scientific-software/prism/
switchANALYSIS	Dynamic Biosensors	https://www.dynamic-biosensors.com/software/
ImageQuant	GE Healthcare	TL 5.2
Bowtie	Langmead et al., 2009	http://bowtie-bio.sourceforge.net
Samtools	Li et al., 2009	http://samtools.sourceforge.net/
Cufflinks	Trapnell et al., 2010	http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
R v.3.3.2	The R Foundation for Statistical Computing	https://www.r-project.org/
RStudio Desktop v.1.1.383	RStudio	https://www.rstudio.com/products/rstudio/