| Antibodies |
| Mouse anti-PCF11 |
Santa Cruz Biotechnology |
Cat# sc-514158 |
| Mouse anti-Myogenin |
Santa Cruz Biotechnology |
Cat# sc-12732; RRID: AB_627980 |
| Mouse anti-GAPDH |
Santa Cruz Biotechnology |
Cat# sc-47724; RRID: AB_627678 |
| Mouse anti-β-tubulin |
Developmental Studies Hybridoma Bank (DSHB) |
Cat# E7; RRID: AB_528499 |
| m-IgGκ BP-HRP |
Santa Cruz Biotechnology |
Cat# sc-516102; RRID: AB_2687626 |
| Chemicals, Peptides, and Recombinant Proteins |
| Phosphate buffered saline (PBS) |
Lab made |
N/A |
| Dulbecco’s Modified Eagle Medium (DMEM) |
Lab made |
N/A |
| RPMI-1640 |
Lab made |
N/A |
| Bovine Calf Serum (CS) |
Sigma-Aldrich |
Cat# 12133C-500ML |
| Fetal Bovine Serum (FBS) |
Atlanta biologicals |
Cat# S11550 |
| Horse serum |
Sigma-Aldrich |
Cat# H1138–500ML |
| Penicillin/Streptomycin |
GIBCO |
Cat# 15140–122 |
| Lipofectamine 3000 |
Thermo Fisher Scientific |
Cat# L3000015 |
| TRIzol Reagent |
Thermo Fisher Scientific |
Cat# 15596018 |
| Oligo d(T)25 Magnetic Beads |
NEB |
Cat# S1419S |
| Adenosine 5′-Triphosphate (ATP) |
NEB |
Cat# P0756S |
| SUPERase● In RNase Inhibitor (20 U/μL) |
Thermo Fisher Scientific |
Cat# AM2694 |
| NEBNext RNase III RNA Fragmentation Module |
NEB |
Cat# E6146 |
| T4 RNA Ligase 1 |
NEB |
Cat# M0204S |
| T4 RNA Ligase 2, truncated KQ |
NEB |
Cat# M0373S |
| TURBO DNA-free Kit |
Thermo Fisher Scientific |
Cat# AM1907 |
| M-MLV Reverse transcriptase |
Promega |
Cat# M1705 |
| Phusion High-Fidelity DNA Polymerase |
NEB |
Cat# M0530S |
| Q5 High-Fidelity DNA Polymerase |
NEB |
Cat# M0491S |
| Dynabeads MyOne Streptavidin C1 |
Thermo Fisher Scientific |
Cat# 65001 |
| RNase H |
Epicenter |
Cat# R52250
|
| T4 Polynucleotide Kinase |
NEB |
Cat# M0201S |
| Shrimp Alkaline Phosphatase (rSAP) |
NEB |
Cat# M0371S |
| 5′ adaptor: 5′-CCUUGGCACCCGAGAAU UCCANNNN |
Sigma-Aldrich |
N/A |
| DNA/LNA oligo: biotin-TTTTTTTTTTTTTTT+ TT+TT+TT+TT+TT, where “+T” denotes LNA |
Exiqon |
N/A |
| 5′ adenylated 3′ blocked 3′ adaptor with degenerated nucleotides: 5′-rApp/NNNNGATCGTCGGACTGTA GAACTCTGAAC/3ddC |
Bioo Scientific |
N/A |
| Reverse transcription primer: 5′-GTTCAGA GTTCTACAGTCCGACGATC |
Sigma-Aldrich |
N/A |
| Reverse PCR primer (GX3): 5′-AATGATACGGCGACC ACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA |
Sigma-Aldrich |
N/A |
| Indexed forward PCR primers (index region in bracket): 5′-CAAGCAGAAGA CGGCATACGAGAT[NNNNNN] GTGACTGGAGTT CCTTGGCACCCGAGAATTCCA |
Sigma-Aldrich |
N/A |
| AMPure XP beads |
Beckman Coulter |
Cat# A63881 |
| Agilent RNA 6000 Pico Kit |
Agilent Technologies |
Cat# 5067–1513 |
| Critical Commercial Assays |
| High Sensitivity DNA analysis kit |
Agilent Technologies |
Cat# 5067–4626 |
| Luna Universal qPCR master mix |
NEB |
Cat# M3003 |
| NEBNext Magnesium RNA Fragmentation Module |
NEB |
Cat# E6150S |
| CellTrace CFSE Cell Proliferation Kit, for flow cytometry |
Thermo Fisher Scientific |
Cat# C34554
|
| Deposited Data |
| 3′READS data |
This study |
GEO: GSE115232
|
| RNA-seq data |
This study |
GEO: GSE115232
|
| Experimental Models: Cell Lines |
| Mouse: NIH 3T3 cells |
ATCC |
Cat# CRL-1658; RRID: CVCL_0594 |
| Mouse: C2C12 cells |
ATCC |
Cat# CRL-1772; RRID: CVCL_0188 |
| Mouse: 3T3-L1 cells |
ATCC |
Cat# CL-173; RRID: CVCL_0123 |
| Mouse: 4T1-luc2-GFP |
Perkin Elmer |
Cat# 128090; RRID: CVCL_5J28 |
| Mouse: 4T1-IPAPcf11-KO |
Generated in this study |
N/A |
| Recombinant DNA |
| Plasmid: PX459 |
Addgene |
Cat# 62988; RRID: Addgene_62988 |
| Plasmid: PX459-mPcf11-IPA-g1 |
Cloned in this study |
N/A |
| Plasmid: PX459-mPcf11-IPA-g2 |
Cloned in this study |
N/A |
| Plasmid: pRiG |
Cloned and stored in lab |
N/A |
| Plasmid: pRiG-AD |
Cloned and stored in lab |
N/A |
| Plasmid: pRiG-Pcf11 Ctrl-seq |
Cloned in this study |
N/A |
| Plasmid: pRiG- Pcf11 IPA site |
Cloned in this study |
N/A |
| Plasmid: pRiG- Pcf11 pPAS |
Cloned in this study |
N/A |
| Plasmid: pRiG- Pcf11 dPAS |
Cloned in this study |
N/A |
| Oligonucleotides (See Tables S2 and S3) |
| Software and Algorithms |
| FIJI |
Schindelin et al., 2012 |
https://imagej.net/Fiji |
| Primer-BLAST |
Ye et al., 2012 |
https://www.ncbi.nlm.nih.gov/tools/primer-blast/ |
| Prism version 7.0a for Mac |
GraphPad Software |
N/A |
| Cutadapt |
Martin, 2011 |
http://cutadapt.readthedocs.io/en/stable/guide.html |
| Bowtie2 |
Langmead and Salzberg, 2012 |
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| DESeq & DEXSeq |
Anders and Huber, 2010 |
https://bioconductor.org/packages/devel/bioc/html/DESeq.html |
| STAR (v2.5.2) |
Dobin et al., 2013 |
https://github.com/alexdobin/STAR |
| Scikit-learn |
Pedregosa et al., 2011 |
http://scikit-learn.org/stable/index.html |
| MaxEntScan |
Yeo and Burge, 2004 |
http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html |
| Other data sets |
| KD of core CPA and splicing factors (3′READS) |
Li et al., 2015 |
GEO: GSE11415
|
| Transcriptional profiling of longitudinal changes during neurogenesis (RNA-seq) |
Hubbard et al., 2013 |
SRA: SRP017778 |
| Genotype-Tissue Expression Project (GTEx) |
GTEx Consortium, 2017 |
dbGaP: phs000424.v7 |
| Early stages of C2C12 differentiation (RNA-seq) |
Hamed et al., 2017 |
GEO: GSE94560
|
| Pan-readthrough genes induced by stress (gene set) |
Vilborg et al., 2017 |
GEO: GSE98906
|
