KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| TET1 | Millipore | Cat. 09-872; RRID: AB_10806199 |
| TET1 | GeneTex | Cat. GTX125888; RRID: AB_11164485 |
| PSPC1 | Santa Cruz | Cat. sc-84577; RRID: AB_2171459 |
| PSPC1 | Bethyl | Cat. A303-206A; RRID: AB_10954256 |
| PSPC1 | Sigma | Cat. SAB4200503; RRID: N/A |
| EZH2 | Cell Signaling | Cat. 5246S; RRID: AB_10694683 |
| SUZ12 | Abcam | Cat. ab12073; RRID: AB_442939 |
| SUZ12 | Active Motif | Cat. 39357; RRID: AB_2614929 |
| V5 | Invitrogen | Cat. R960-25; RRID: AB_2556564 |
| Mouse IgG | Millipore | Cat. 12-371; RRID: AB_145840 |
| Rabbit IgG | Millipore | Cat. PP64; RRID: AB_97852 |
| SIN3A | Abcam | Cat. ab3479; RRID: AB_303839 |
| PELP1 | Bethyl | Cat. A300-180A; RRID: AB_242526 |
| TET2 | Abcam | Cat. ab124297; RRID: AB_2722695 |
| NONO | Bethyl | Cat. A300-587A; RRID: AB_495510 |
| SFPQ | Abcam | Cat. ab38148; RRID: AB_945424 |
| HA | Abcam | Cat. ab9110; RRID: AB_307019 |
| OCT4 | Santa Cruz | Cat. sc-5279; RRID: AB_628051 |
| NANOG | Bethyl | Cat. A300-397A; RRID: AB_386108 |
| ESRRB | R&D Systems | Cat. PP-H6707; RRID: AB_2100411 |
| ACTIN | Sigma | Cat. A5441; RRID: AB_476744 |
| GAPDH | ProteinTech | Cat. 10494-1-AP; RRID: AB_2263076 |
| Histone3 | Abcam | Cat. ab1791; RRID: AB_302613 |
| H3K4me3 | EpiCypher | Cat. 13-0041; RRID: N/A |
| H3K27me3 | Cell Signaling | Cat. 9733S; RRID: AB_2616029 |
| VCL | Abcam | Cat. ab129002; RRID: AB_11144129 |
| Streptavidin-HRP | GE Healthcare | Cat. RPN1231 V; RRID: N/A |
| Mouse IgG HRP | Cell Signaling | Cat. 7076S; RRID: AB_330924 |
| Rabbit IgG HRP | Jackson ImmunoRes | Cat. 715-175-151; RRID: AB_2340820 |
| Trueblot Mouse IgG HRP | Rockland | Cat. 18-8817-31; RRID: AB_2610850 |
| Trueblot Rabbit IgG HRP | Rockland | Cat. 18-8816-31; RRID: AB_2610847 |
| DNA 5mC | Cell Signaling | Cat. 28692; RRID: AB_2798962 |
| DNA 5hmC | Active Motif | Cat. 39769; RRID: AB_10013602 |
| Anti-dsDNA | Abcam | Cat. ab27156; RRID: AB_470907 |
| Chemicals, peptides, and recombinant proteins | ||
| DMEM | GIBCO | Cat. 11965-092 |
| Heat inactivated FBS | GIBCO | Cat. 35-011-CV |
| Penicillin-Streptomycin | GIBCO | Cat. 15140-122 |
| L-Glutamine | GIBCO | Cat. 25030-081 |
| MEM NEAA | GIBCO | Cat. 11140-050 |
| 2-Mercaptoethanol | Sigma | Cat. M6250 |
| Puromycin | Sigma | Cat. P9620-10ML |
| Hygromycin | Omega | Cat. HG-80 |
| N2 | GIBCO | Cat. 17502-048 |
| B27 | GIBCO | Cat. 17504-044 |
| DMEM/F-12 | GIBCO | Cat. 11-330-032 |
| Neurobasal | GIBCO | Cat. 21-103-049 |
| LIF | Lab prep | N/A |
| GSK3i (CHIR99021) | Sigma | Cat. SML1046-25MG |
| MEKi (PD0325901) | Selleckchem | Cat. S1036 |
| Recombinant Fgf2 | R&D System | Cat. 233-FB |
| Recombinant Activin A | R&D System | Cat. 338-AC |
| 13C615N4 L-arginine | Cambridge Isotope | Cat. CNLM-539-H |
| 13C615N2 L-lysine | Cambridge Isotope | Cat. CNLM-291-H |
| 13C6 L-lysine | Cambridge Isotope | Cat. CLM-2247-H |
| dTAG-13 | Tocris | Cat. 6605 |
| Deposited data | ||
| PSPC1 ChIP-seq in ESC | This paper | NCBI GEO: GSE182443 |
| SUZ12 ChIP-seq in ESC | This paper | NCBI GEO: GSE182443 |
| SUZ12 ChIP-seq in EpiLC upon Pspc1 KO, Neat1 KO, and Tet1-degron treatments | This paper | NCBI GEO: GSE182443 |
| H3K27me3 ChIP-seq in ESC and EpiLC upon Pspc1 KO, Neat1 KO, and Tet1-degron treatments | This paper | NCBI GEO: GSE182443 |
| H3K4me3 ChIP-seq in ESC and EpiLC upon Pspc1 KO and Neat1 KO | This paper | NCBI GEO: GSE182443 |
| Neat1 ChIRP-seq in WT and Neat1 KO ESC and EpiLC | This paper | NCBI GEO: GSE182443 |
| Pspc1 WT/KO RNA-seq in ESC and EpiLC | This paper | NCBI GEO: GSE182443 |
| Neat1 WT/KO RNA-seq in ESC and EpiLC | This paper | NCBI GEO: GSE182443 |
| TET1 affinity purification followed by mass spectrometry data in ESC | This paper | ProteomeXchange PRIDE: PXD033587 |
| TET1 ChIP-seq in ESC | Wu et al., 2011 | NCBI GEO: GSE26833 |
| PSPC1 CLIP-seq in ESC | Guallar et al., 2018 | NCBI GEO: GSE103269 |
| H3K4me3 and H3K27ac in ESC | Hon et al., 2014 | NCBI GEO: GSE48519 |
| 5mC and 5hmC meDIP-seq in ESC | Xiong et al., 2016 | NCBI GEO: GSE57700 |
| Experimental models: Cell lines | ||
| Mouse ESC CCE | This paper | N/A |
| Pspc1 KO ESC | Guallar et al., 2018 | N/A |
| Pspc1 KO ESC rescued with WT or RRMmut PSPC1 protein | Guallar et al., 2018 | N/A |
| Tet1-degron ESC | This paper | N/A |
| Mouse ESC 46C | This paper | N/A |
| Neat1 KO ESC | This paper | N/A |
| Ezh2 KO ESC | Shen et al., 2008 | N/A |
| Mouse ESC V6.5 | Laboratory of R. Jaenisch | N/A |
| Tet1 KO ESCs | Laboratory of R. Jaenisch | N/A |
| Tet1/2/3 KO ESCs | Laboratory of R. Jaenisch | N/A |
| Dnmt1/3a/3b KO ESC | Laboratory of T. Chen | N/A |
| Nono KO ESC | Laboratory of F. Lan | N/A |
| Oligonucleotides | ||
| Oligonucleotides (see Table S4) | This paper | N/A |
| Software and algorithms | ||
| STAR | 2.7.6a | https://github.com/alexdobin/STAR |
| Cufflinks | 2.2.1 | http://cole-trapnell-lab.github.io/cufflinks/ |
| Bowtie2 | 2.3.5 | http://bowtie-bio.sourceforge.net/bowtie2/ |
| IGV | 2.10.2 | https://software.broadinstitute.org/software/igv |
| samtools | 1.10 | http://www.htslib.org/ |
| PICARD | 2.18.5 | https://broadinstitute.github.io/picard/ |
| HOMER | 4.11.1 | http://homer.ucsd.edu/homer/ |
| MACS2 | 2.2.7 | https://github.com/macs3-project/MACS |
| NGSplot | 2.61 | https://github.com/shenlab-sinai/ngsplot |