Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-SRPK2 | BD Biosciences | Cat#BD611118; RRID: AB_398429 |
| Rabbit polyclonal anti-ACLY | Cell Signaling Technology | Cat#4332; RRID: AB_2223744 |
| Rabbit monoclonal anti-FASN | Cell Signaling Technology | Cat#3180; RRID: AB_2100796 |
| Mouse monoclonal anti-S6 | Cell Signaling Technology | Cat#2317; RRID: AB_2238583 |
| Rabbit monoclonal anti-pS6(S240/S244) | Cell Signaling Technology | Cat#5364; RRID: AB_10694233 |
| Rabbit polyclonal anti-SCD1 | Cell Signaling Technology | Cat#2438; RRID: AB_823634 |
| Rabbit polyclonal anti-CHREBP | Novus | Cat# NB400-135;RRID:AB_10002435 |
| Rabbit polyclonal anti-FAM120A | GeneTex | Cat#GTX120824; RRID:AB_10723014 |
| Rabbit polyclonal anti-FAM120A | Thermo Fisher Scientific | Cat# A303-889A; RRID:AB_2620239) |
| Rabbit polyclonal anti-LXR alpha | Thermo Fisher Scientific | Cat#PA1-330;RRID:AB_325600 |
| Mouse monoclonal anti-SREBP2 | BD Biosciences | Cat#557037; RRID:AB_396560 |
| Rabbit polyclonal anti-LXR beta | Thermo Fisher Scientific | Cat#PA1-333;RRID:AB_2154770 |
| Rabbit polyclonal anti-PPAR alpha | Thermo Fisher Scientific | Cat#PA1-822A; RRID:AB_2165595 |
| Rabbit polyclonal anti-PPAR gamma | Abcam | Cat#ab209350; RRID:AB_2890099 |
| Rabbit monoclonal anti-p300 | Cell Signaling Technology | Cat#54062; RRID:AB_2799450 |
| Rabbit monoclonal anti-XBP-1s | Cell Signaling Technology | Cat#12782;RRID:AB_2687943 |
| Mouse monoclonal anti-GAPDH | Sigma-Aldrich | Cat#G8795; RRID: AB_1078991 |
| Rabbit polyclonal anti-ACSS2 | Sigma-Aldrich | Cat#HPA004141; RRID: AB_1078094 |
| Mouse monoclonal anti-V5 | Sigma-Aldrich | Cat#V8012; RRID:AB_261888 |
| Mouse monoclonal anti-Vinculin | Sigma-Aldrich | Cat#V9264; RRID: AB_10603627 |
| Rabbit polyclonal anti-RNA polymerase II | Abcam | Cat#ab26721; RRID:AB_777726 |
| Rabbit monoclonal anti-FDFT1 | Abcam | Cat#ab109723; RRID: AB_10859772 |
| Mouse monoclonal anti-U1–70k | Santa Cruz Biotechnology | Cat#sc-390899; RRID:AB_2801569 |
| Rabbit polyclonal anti-SREBP1 | Santa Cruz Biotechnology | Cat#sc-8984; RRID: AB_2194223 |
| Mouse monoclonal anti-SRSF1 | Santa Cruz Biotechnology | Cat#sc-33652; RRID: AB_628248 |
| Mouse monoclonal anti-T7 | EMD Millipore | Cat#69522; RRID:AB_11211744 |
| Mouse monoclonal anti-Phosphoepitope SR proteins | EMD Millipore | Cat#MABE50;RRID:AB_10807429 |
| Rabbit Normal IgG | Cell Signaling Technology | Cat#2729, RRID:AB_1031062 |
| Mouse Normal IgG | Thermo Scientific |
Cat#10-400-C; RRID:AB_2532980 |
| IRDye 800CW Donkey anti-Rabbit IgG | LI-COR Biosciences | Cat# 926-32213; RRID:AB_621848 |
| IRDye 680RD Donkey anti-Mouse IgG | LI-COR Biosciences | Cat# 926-68072; RRID:AB_10953628 |
| IRDye 680RD Detection Reagent | LI-COR Biosciences | Cat#:926-69100 |
| Bacterial and virus strains | ||
| E. coli BL21 | New England Biolabs | Cat#C2527 |
| Chemicals, peptides, and recombinant proteins | ||
| Rapamycin | Calbiochem | Cat#553210 |
| Torin1 | Tocris Bioscience | Cat#4247 |
| Actinomycin D | Sigma-Aldrich | Cat#A1410 |
| PhosSTOP | Roche | Cat#04906837001 |
| RNase inhibitor | Invitrogen | Cat#10777019 |
| RNase T1 | Thermo Fisher Scientific | Cat#AM2283 |
| RNase A | Thermo Fisher Scientific | Cat#12091-021 |
| Anti-V5 agarose affinity gel | Sigma-Aldrich | Cat#A7345 |
| Anti-Flag agarose affinity gel | Sigma-Aldrich | Cat# A2220 |
| Lipofectamine™ RNAiMAX Transfection Reagent | Invitrogen | Cat#13778075 |
| DNase I | Sigma-Aldrich | Cat#AMPD1 |
| TRIzol | Invitrogen | Cat#15596018 |
| Protein A/G magnetic beads | Thermo Fisher Scientific | Cat#88802 |
| Protein A/G PLUS-Agarose | Santa Cruz Biotechnology | Cat#sc-2003 |
| Proteinase K | New England Biolabs | Cat#P8107 |
| Lipofectamine 2000 reagent | Invitrogen | Cat#11668500 |
| Phenol:Chloroform:IAA, 25:24:1, pH 6.6 | Thermo Fisher Scientific | Cat#AM9730 |
| Insulin solution human | Sigma-Aldrich | Cat#I9278 |
| Crystal Violet | Sigma-Aldrich | Cat#C3886 |
| SRPIN340 | Selleck Chemicals | Cat#S7270 |
| SRPKIN-1 | MedChem Express | Cat#HY-116856 |
| Lipoprotein, low density from human plasma | Sigma-Aldrich | Cat#L7914 |
| Oleic acid-albumin | Sigma-Aldrich | Cat#O3008 |
| Fatty acid-free albumin | Sigma-Aldrich | Cat#A8806 |
| Lipoprotein-deficient serum | Alfa Aesar | Cat#BT-907 |
| Sodium palmitate | Sigma-Aldrich | Cat#P9767 |
| Methanol-free 10% formaldehyde | Polysciences | Cat#04018-1 |
| 25-Hydroxycholesterol | MedChem Express | Cat#HY-113134 |
| Critical commercial assays | ||
| PureLink RNA Mini kit | Ambion | Cat#12183018A |
| iScript cDNA synthesis kit | Bio-rad | Cat#170–8891BUN |
| Illumina® Stranded mRNA Prep Kit | Illumina | Cat#20040534 |
| Gateway LR clonase II enzyme mix | Invitrogen | Cat#11791 |
| QuickChange site-directed mutagenesis kit | Strategene | Cat#200521 |
| RNA Clean & Concentrator | Zymo Research | Cat#R1016 |
| Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus | Illumina | Cat#20040529 |
| LightSwitch dual assay kit (promoter assay) | Active Motif | Cat#32035 |
| Chromatin IP DNA purification kit | Active Motif | Cat#58002 |
| SYBR Green PCR Master Mix | Life Technologies | Cat#4312704 |
| QuikChange II XL Site-Directed Mutagenesis Kit | Strategene | Cat#200521 |
| ChIP-IT Express Kit | Active Motif | Cat#53009 |
| Deposited data | ||
| Raw RNAseq data (siNTC and siFAM120A) | This paper | GSE207172 |
| Raw RNAseq data (siNTC, siFAM120, and siSRSF1) | This paper | GSE229657 |
| Raw data of Images and WB | This paper, Mendeley Data | DOI: 10.17632/rgfgx9xb8w.1 |
| Experimental models: Cell lines | ||
| Human: Renal angiomyolipoma-derived LAM 621–101 (TSC2−/−) | Drs. Jane Yu and Elizabeth Henske | Yu et al., 2004; RRID: CVCL_S879 |
| Human: HEK293E | ATCC | Cat#293 c18; RRID: CVCL_6974 |
| Human: HEK293T | GenHunter | Cat#Q401; RRID: CVCL_0063 |
| Human: MCF7 | ATCC | Cat#HTB-22; RRID: CVCL_0031 |
| Human: DLD1 | ATCC | Cat#CCL-221; RRID: CVCL_0248 |
| Human: NCI-H1299 | ATCC | Cat#CRL-5803; RRID: CVCL_0060 |
| Human: LNCaP | ATCC | Cat#CRL-1740; RRID:CVCL_1379 |
| Experimental models: Organisms/strains | ||
| nu/nu athymic mice | Envigo | Cat#069 |
| Oligonucleotides | ||
| siRNA negative control-#1(siNTC) | Sigma-Aldrich | SIC001 |
| siRNA negative control-#2(siNTC) | Sigma-Aldrich | SIC002 |
| siRNA (Human SRSF1) | Sigma-Aldrich | SASI_Hs01_00115059 |
| siRNA (Human SRSF1) | Sigma-Aldrich | SASI_Hs02_00342609 |
| siRNA (Human UPF1) | Sigma-Aldrich | SASI_Hs01_00101017 |
| siRNA (Human UPF1) | Sigma-Aldrich | SASI_Hs01_00101018 |
| siRNA (Human U1–70k/SNRNP70) | Sigma-Aldrich | SASI_Hs02_00335028 |
| siRNA (Human U1–70k/SNRNP70) | Sigma-Aldrich | SASI_Hs01_00165101 |
| siRNA (Human FAM120A) | Sigma-Aldrich | SASI_Hs01_00149752 |
| siRNA (Human FAM120A) | Sigma-Aldrich | SASI_Hs02_00345898 |
| siRNA (Human FAM120A) | Sigma-Aldrich | SASI_Hs02_00345899 |
| siRNA (Human SREBP1) | Sigma-Aldrich | SASI_Hs01_00051828 |
| siRNA (Human SREBP1) | Sigma-Aldrich | SASI_Hs01_00051829 |
| siRNA (Human SREBP1) | Sigma-Aldrich | SASI_Hs01_00051830 |
| siRNA (Human SREBP2) | Sigma-Aldrich | SASI_Hs01_00075424 |
| siRNA (Human SREBP2) | Sigma-Aldrich | SASI_Hs01_00075425 |
| siRNA (Human SREBP2) | Sigma-Aldrich | SASI_Hs01_00075426 |
| Primers for qPCR analysis, see Table S2 | This paper | N/A |
| Recombinant DNA | ||
| ACSS2 promoter construct | SwitchGear Genomics | Cat#S715263 |
| SCD1 promoter construct | SwitchGear Genomics | Cat#S714484 |
| pLX304-SRSF1-V5 | Harvard plasmid | Cat#HsCD00420441 |
| Lentiviral packaging and envelope plasmids | Dr. David Baltimore | N/A |
| pcDNA3-EGFP | Addgene | Cat#13031 |
| pKH3-HA-SRPK2-WT, K110M | Dr. John Blenis | Lee et al., 2007 |
| pLNCX-HA-SRPK2-S494A/S497A | Dr. John Blenis | Lee et al., 2007 |
| pLX304-FAM120A-V5 | Harvard plasmid | HsCD00440255 |
| pENTR1A-Flag-FAM120A(WT) | This paper | N/A |
| pENTR1A-Flag-FAM120A(∆RBD) | This paper | N/A |
| pLenti-CMV-Puro-DEST | Addgene | Cat#17452 |
| pENTR223-SRSF1 | Harvard plasmid | Cat#HsCD00367645 |
| pLenti-CMV-Puro-SRSF1 | This paper | N/A |
| pLenti-CMV-Puro-FAM120A | This paper | N/A |
| pLenti-CMV-Puro-Flag-FAM120A(WT) | This paper | N/A |
| pLenti-CMV-Puro-Flag-FAM120A(∆RBD) | This paper | N/A |
| pENTR223-FAM120A | Harvard plasmid | Cat#HsCD00438604 |
| T7-SRSF1(WT) | Dr. Adrian Krainer | Fregoso et al., 2013 |
| T7-SRSF1(∆RRM1) | Dr. Adrian Krainer | Fregoso et al., 2013 |
| T7-SRSF1(∆RRM2) | Dr. Adrian Krainer | Fregoso et al., 2013 |
| T7-SRSF1(∆RS) | Dr. Adrian Krainer | Fregoso et al., 2013 |
| pLKO.1-puro-Non-Mammalian shRNA Control | Sigma-Aldrich | SHC002 |
| pLKO.1-puro-shSRPK2 | Sigma-Aldrich | TRCN0000006274 |
| pLKO.1-puro-shFAM120A | Sigma-Aldrich | TRCN0000074918 |
| pLKO.1-puro-shSREBP1 | Sigma-Aldrich | TRCN0000055325 |
| pLKO.1-puro-shSREBP2 | Sigma-Aldrich | TRCN0000020667 |
| Software and algorithms | ||
| IRFinder-S | Lorenzi et. al., 2021 | https://europepmc.org/article/med/34749764 |
| HISAT2 v2.2.1 | Kim et. al., 2019 | https://www.nature.com/articles/s41587-019-0201-4 |
| StringTie2 v2.1.4 | Kovaka et. al., 2019 | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1910-1 |
| DESeq2 (v1.30.1) | Love et. al., 2014 | https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8 |
| Enhanced Volcano v1.8.0 R package | Blighe, 2022 | https://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html |
| Adobe Photoshop | Adobe | Adobe |
| Odyssey imaging system | LI-COR Biosciences | LI-COR Biosciences |
| enrichR v3.0 package | Webb et al., 2014 | https://git.ecdf.ed.ac.uk/sgrannem/pycrac |
| EI-MAVEN, Version 0.12.0 | Agrawal et al, 2019 | Elucidata |
| VAST-tools | Irimia et. al., 2014 | https://www.sciencedirect.com/science/article/pii/S0092867414015128?via%3Dihub |
| BioRender | BioRender | https://www.biorender.com/ |