KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-FLAG® M2 mouse monoclonal antibody (WB 1:2000) | Millipore Sigma | Cat# F1804; RRID: AB_262044 |
| Anti-HA rabbit monoclonal antibody (WB 1:2000) | Cell Signaling | Cat# 3724; RRID: AB_1549585 |
| Anti-HA mouse monoclonal antibody (WB 1:2000, IP 1:100) | Millipore Sigma | Cat# H3663; RRID: AB_262051 |
| Anti-YTHDF2 rabbit polyclonal antibody (WB 1:2000) | Aviva | Cat# ARP67917; RRID: AB_2861185 |
| Anti-GAPDH rabbit polyclonal antibody (WB 1:5000) | ProteinTech | Cat# 10494-1-AP; RRID: AB_2263076 |
| Anti-IDE rabbit polyclonal antibody (WB 1:1000) | Abcam | Cat# ab32216; RRID: AB_775686 |
| Anti-KI67 rabbit polyclonal antibody (WB 1:1000, IF 1:1000) | Abcam | Cat# ab16667; RRID: AB_302459 |
| Anti-Phospho-Histone H3 (Ser10) rabbit polyclonal antibody (WB 1:1000) | Cell Signaling | Cat# 9701; RRID: AB_331535 |
| Anti-TrkB (NTRK2) rabbit monoclonal antibody (WB 1:1000) | Abcam | Cat# ab134155; RRID: AB_2857962 |
| Anti-SFRP1 rabbit monoclonal antibody (WB 1:500) | Abcam | Cat# ab126613; RRID: AB_11128257 |
| Anti-TLE3/ESG rabbit polyclonal antibody (WB 1:1000) | Abcam | Cat# ab94972; RRID: AB_10860535 |
| Anti-RBM45 rabbit polyclonal antibody (discontinued) (WB 1:1000) | Abcam | Cat# ab123912; RRID: AB_10973537 |
| Anti-Histone H3 rabbit polyclonal antibody (WB 1:5000) | Cell Signaling | Cat# 9715; RRID: AB_331563 |
| Anti-m6A rabbit polyclonal antibody (WB 1:1000) | Abcam | Cat# ab151230; RRID: AB_2753144 |
| Anti-WNT3/WNT3A rabbit monoclonal antibody (WB 1:1000) | Abcam | Cat# ab172612; RRID: AB_2725748 |
| Anti-Rabbit HRP goat polyclonal antibody (WB 1:2500) | Abcam | Cat# ab6721; RRID: AB_955447 |
| Anti-Mouse HRP goat polyclonal antibody (WB 1:5000) | Millipore Sigma | Cat# GENXA-931 |
| Anti-Mouse Alexa 647 goat polyclonal antibody (IF 1:3000) | ThermoFisher | Cat# A-21235; RRID: AB_2535804 |
| Anti-Mouse Alexa 488 goat polyclonal antibody (IF 1:3000) | ThermoFIsher | Cat# A-11029; RRID: AB_138404 |
| Anti-Rabbit Alexa 568 goal polyclonal antibody (IF 1:3000) | ThermoFisher | Cat# A-11036; RRID: AB_10563566 |
| Anti-Rabbit Alexa 488 goal polyclonal antibody (IF 1:3000) | ThermoFisher | Cat# A-11008; RRID: AB_143165 |
| Bacterial and virus strains | ||
| MAX Efficiency™ DH5α Competent Cells | ThermoFisher | Cat# 18258012 |
| Rosetta™ 2(DE3) Competent Cells | Millipore Sigma | Cat# 71397-3 |
| Chemicals, peptides, and recombinant proteins | ||
| Glutathione Sepharose™ 4B Affinity Chromatography Media (GE Healthcare) | GE Healthcare | Cat# 17-0756-01 |
| L(−)-Glutathione (reduced form), ≥98% | VWR | Cat# 97061-574 |
| DAPI (4′,6-Diamidine-2′-phenylindole dihydrochloride) | Roche | Cat# 10236276001 |
| 6xHis-GST-RBM45 | This paper | See STAR Methods |
| Critical commercial assays | ||
| NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) with Sample Purification Beads | NEB | E6350 |
| High Sensitivity DNA Kit, for Bioanalyzer 2100 platform | Agilent | 5067-4626 |
| RNA 6000 Pico Kit, for Bioanalyzer 2100 platform | Agilent | 5067-1513 |
| Invitrogen™ Dynabeads™ Oligo(dT)25 mRNA isolation beads | ThermoFisher | 61005 |
| Invitrogen™ RiboMinus™ Transcriptome Isolation Kit, human/mouse | ThermoFisher | K155002 |
| NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® | NEB | E7770 |
| SMARTer® Stranded Total RNA-Seq Kit v3 | Takara Bio | 634485 |
| LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit | ThermoFisher | L34975 |
| RNeasy Micro Kit | QIAGEN | 74004 |
| Qproteome Bacterial Protein Prep Kit | QIAGEN | 37900 |
| QIAEX II Gel Extraction Kit | QIAGEN | 20021 |
| QIAGEN Plasmid Plus Midiprep Kit | QIAGEN | 12943 |
| QIAprep Spin Miniprep Kit | QIAGEN | 27106 |
| QIAquick Gel Extraction Kit | QIAGEN | 28704 |
| QuickLyse Miniprep Kit | QIAGEN | 27406 |
| Deposited data | ||
| RNA-pulldown LC-MS/MS in mHippoE-2 cell lysate | This paper, PRIDE | PXD034161 |
| RNA-pulldown LC-MS/MS in adult mouse (C57BLK6/J) brain lysate | This paper, PRIDE | PXD034159 |
| HA-tagged RBM45 CLIP-seq in mHippoE-2 cells | This paper, GEO | GSE190292 |
| HA-tagged RBM45 CLIP-seq in HEK293T cells | This paper, GEO | GSE190287 |
| HA-tagged RBM45 CLIP-seq in DMSO-/RA-treated SH-SY5Y cells | This paper, GEO | GSE205625 |
| in vitro subcellular fractionation DART-seq in mHippoE-2 cells | This paper, GEO | GSE190311 |
| in vitro subcellular fractionation DART-seq in HEK293T cells | This paper, GEO | GSE190303 |
| Ribo-depleted RNA-seq data in mHippoE-2 cells | This paper, GEO | GSE190322 |
| Ribo-depleted RNA-seq data in DMSO-/RA-treated SH-SY5Y cells | This paper, GEO | GSE190316 |
| SRSF7 eCLIP in HepG2 cells | Gene Yeo, UCSD ENCODE | ENCSR513NDD |
| SRSF7 eCLIP in K562 cells | Gene Yeo, UCSD ENCODE | ENCSR468FSW |
| poly(A) RNA-seq, embryonic mouse (B6NCrl) forebrain timecourse | Barbara Wold, CalTech ENCODE | ENCSR443OEA |
| poly(A) RNA-seq, embryonic mouse (B6NCrl) midbrain timecourse | Barbara Wold, CalTech ENCODE | ENCSR505AHT |
| poly(A) RNA-seq, embryonic mouse (B6NCrl) hindbrain timecourse | Barbara Wold, CalTech ENCODE | ENCSR328UYN |
| Experimental models: Cell lines | ||
| Immortalized mouse hippocampal cell line (mHippoE-2) | Cedarlane Labs | CVCL_D377 |
| Human embryonic kidney (HEK) cell line (HEK293T) | ATCC | CVCL_0063 |
| Human neuroblastoma cell line (SH-SY5Y) | ATCC | CVCL_0019 |
| Experimental models: Organisms/strains | ||
| C57BL/6J, mus musculus | Jackson Labs | IMSR_JAX:000664 |
| Oligonucleotides | ||
| Biotin-labeled non-m6A Dlg4 RNA oligo: 5′-Biotin-GGGCCCUUGGUCUGGACU GAAUAGCCCAAGCCC-3′ | This paper | N/A |
| Biotin-labeled m6A Dlg4 RNA oligo: 5′-Biotin-GGGCCCUUGGUCUGGm6A CUGAAUAGCCCAAGCCC-3′ | This paper | N/A |
| Biotin-labeled non-m6A ssRNA oligo: 5′-Biotin-UUCUUCUGUGGACUGUG-3′ | This paper | N/A |
| Biotin-labeled m6A ssRNA oligo: 5′-Biotin-UUCUUCUGUGGm6ACUGUG-3′ | This paper | N/A |
| Biotin-labeled non-m6A randomer RNA oligo: 5′-Biotin-GGGGAGUUCUACAGUCCGA CNNNNNNNNNNNRACNNNNNNNNN NNGGAAUUCUCGGGUGUCAAGG-3′ | This paper | N/A |
| Biotin-labeled m6A randomer RNA oligo: 5′-Biotin-GGGGAGUUCUACAGUCCG ACNNNNNNNNNNNRm6ACNNNNNN NNNNNGGAAUUCUCGGGUGUCAAGG-3′ | This paper | N/A |
| Fluorescein-labeled (FAM) non-m6A ssRNA oligo: 5′-FAM-UUCUUCUGUGGACUGUG-3′ | This paper | N/A |
| Fluorescein-labeled (FAM) m6A ssRNA oligo: 5′-FAM-UUCUUCUGUGGm6ACUGUG-3′ | This paper | N/A |
| For DNA oligonucleotides used in this study, see Table S1 | This paper | Table S1 |
| Recombinant DNA | ||
| pcDNA™3.1 (+) Mammalian Expression Vector | Invitrogen | Cat# V79020 |
| pcDNA™4/TO Mammalian Expression Vector | Invitrogen | Cat# V102020 |
| pET-GST | Addgene | Plasmid #42049 |
| pCMV-VSV-G | Addgene | Plasmid #8454 |
| psPAX2 | Addgene | Plasmid #12260 |
| lentiCRISPR v2 | Addgene | Plasmid #52961 |
| pLenti-puro | Addgene | Plasmid #39481 |
| Software and algorithms | ||
| Prism 8 (v8.2.1) | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| ImageJ (v1.53a) | NIH | https://imagej.nih.gov/ij/ |
| NeuronJ (v1.4.3) | E. Meijering et al., 2004 | https://imagescience.org/meijering/software/neuronj/ |
| IGV (v2.8.9, v2.9.4) | J.T. Robinson et al., 2011 | https://igv.org |
| SeqAn (v2.3.2), FLEXBAR (v3.0.3) | M. Dodt et al., 2012 | https://github.com/seqan/flexbar |
| Novoalign (v3.09.00) | Novocraft | http://www.novocraft.com/products/novoalign/ |
| Python (v2.7.11) | Python | https://www.python.org |
| homer (v4.11.1) | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| MEME (v5.0.5) | Bailey and Elkan, 1994 | https://meme-suite.org/meme/index.html |
| R (v3.6.0) | R | https://www.r-project.org |
| DESeq2 (v1.32.0) | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Picard (v2.18.2) | “Picard Toolkit.” 2019. Broad Institute | https://broadinstitute.github.io/picard/ |
| rMATS (v4.0.2) | Shen et al., 2014 | http://rnaseq-mats.sourceforge.net |
| DEXSeq (v1.38.0) | Anders et al., 2012 | https://bioconductor.org/packages/release/bioc/html/DEXSeq.html |
| Subread (v1.6.3) | Liao et al., 2014 | http://subread.sourceforge.net |
| deeptools (v3.2.1) | Ramírez et al., 2016 | https://deeptools.readthedocs.io/en/develop/ |
| HiSAT2 (v2.1.0) | Kim et al., 2019 | http://daehwankimlab.github.io/hisat2/ |
| Bedtools (v2.25.0) | Quinlan Lab, Univ. of Utah | https://bedtools.readthedocs.io/en/latest/ |
| Trimmomatic (v0.38) | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| MACS2 (v2.1.1.20160309) | Y. Zhang et al., 2008 | https://github.com/macs3-project/MACS |
| Bullseye (unreleased) | Tegowski et al., 2022 | https://github.com/mflamand/Bullseye |