KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
BL21(DE3) competent cells	Agilent	Cat#200131
BL21-CodonPlus (DE3)-RIPL competent cells	Agilent	Cat#230280
Chemicals, Peptides and Recombinant Proteins
SNAP-hPUM2	This paper	N/A
hPUM1-SNAP	This paper	N/A
hPUM1 MUT3–1-SNAP	This paper	N/A
His-TEV Protease	This paper	N/A
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail	Sigma-Aldrich	Cat#11836153001
Cy3B NHS ester	GE Healthcare	Cat#PA63100
BG-NH2	New England Biolabs (NEB)	Cat#S9148S
Agencourt AMPure XP beads	Beckman Coulter	Cat#A63881
SYBR Green I Nucleic Acid Stain	Lonza	Cat#50513
SYBR Gold Nucleic Acid Gel Stain	Invitrogen	Cat#S11494
Phusion High-Fidelity DNA Polymerase	Thermo Fisher Scientific	Cat#F530S
Phusion Hot Start II DNA Polymerase	Thermo Fisher Scientific	Cat#F549
Klenow fragment (3’−5’ exo(−))	NEB	Cat#M0212L
Streptavidin	PROzyme	Cat#SA10
D-Biotin	Thermo Fisher Scientific	Cat#B20656
E. coli RNA polymerase holoenzyme	NEB	Cat#M0551S
Low Molecular Weight DNA Ladder	NEB	Cat#N3233S
T4 Polynucleotide Kinase	Thermo Fisher Scientific	Cat#EK0031
Gamma-32P ATP	Perkin Elmer	Cat#NEG035C
Bovine Serum Albumin	NEB	Cat#B9000S
Critical Commercial Assays
MiSeq Reagent Kit v3 (150-cycle)	Illumina	Cat#MS-102–3001
PhiX Control V3	Illumina	Cat#FC-110–3001
QIAquick Gel Extraction Kit	QIAGEN	Cat#28704
MinElute PCR Purification Kit	QIAGEN	Cat#28004
QIAquick PCR Purification Kit	QIAGEN	Cat#28106
Zeba Spin Desalting Columns 7K MWCO, 5 mL	Thermo Fisher Scientific	Cat#89892
Amicon Ultra-4 Centrifugal Filter Unit, 3KDa	Millipore Sigma	Cat#UFC800324
Amicon Ultra-0.5 Centrifugal Filter Unit, 10KDa	Millipore Sigma	Cat#UFC501024
Oligonucleotides
DNA oligonucleotide library, see Table S5	CustomArray, this Study	N/A
DNA oligonucleotides used for library assembly and RNA array preparation, see Table S7	IDT	N/A
RNA oligonucleotides used in gel-shift measurements, see STAR Methods	IDT	N/A
Deposited data
RNA-seq expression data for K562 cell lines	ENCODE project (Consortium, 2012)	https://www.encodeproject.org/files/ENCFF272HJP/@@download/ENCFF272HJP.tsv,https://www.encodeproject.org/files/ENCFF471SEN/@@download/ENCFF471SEN.tsv
eCLIP data for PUM2 protein in human K562 cells	(Consortium, 2012; Van Nostrand et al., 2016)	https://www.encodeproject.org/files/ENCFF786ZZB/@@download/ENCFF786ZZB.bam,https://www.encodeproject.org/files/ENCFF732EQX/@@download/ENCFF732EQX.bam,https://www.encodeproject.org/files/ENCFF231WHF/@@download/ENCFF231WHF.bamhttps://www.encodeproject.org/files/ENCFF141SVY/@@download/ENCFF141SVY.bed.gzhttps://www.encodeproject.org/files/ENCFF141SVY/@@download/ENCFF141SVY.bed.gz
Refseq annotations for human genome assembly GRCh38 (hg38)	(O’Leary et al., 2016)	https://www.ncbi.nlm.nih.gov/refseq/
Protein-coding transcript sequences, genome release GRCh38.p12	(Harrow et al., 2012)	https://www.gencodegenes.org/human/release_28.html
RNA Bind-N-Seq data for PUM1	(Consortium, 2012; Dominguez et al., 2018)	https://www.encodeproject.org/files/ENCFF894MLG/ https://www.encodeproject.org/files/ENCFF761JAF/ (input)
Software and Algorithms
RNAfold, v2.1.8, v2.1.9	(Lorenz et al., 2011)	https://www.tbi.univie.ac.at/RNA/RNAfold.1.html
Bedtools		https://bedtools.readthedocs.io/en/latest/
HOMER (v4.8.3)	(Heinz et al., 2010)	http://homer.ucsd.edu/homer/
Ensembl Biomart	(Zerbino et al., 2018)	http://ensembl.org
Samtools (v0.1.19–96b5f2294a)		http://www.htslib.org/
pyatac ins		https://nucleoatac.readthedocs.io/en/latest/pyatac/
Global fitting scripts to determine PUM2 thermodynamic model parameters	This paper	https://github.com/pufmodel/PUM2_global_fitting
Pipeline for comparing in vivo to in vitro occupancy across genomic sites	This paper	https://github.com/GreenleafLab/puflibs/blob/master/analyze_clip_data.py
Pipeline for fitting thermodynamic constants from fluorescence data	This paper	https://github.com/GreenleafLab/array_fitting_tools/