KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-ACTB antibody produced in rabbit | Sigma-Aldrich | Cat# AV40173, RRID:AB_1844540 |
| CTCF Antibody | Cell Signaling Technology | Cat# 2899, RRID:AB_2086794 |
| Anti-DNMT1 antibody produced in rabbit | Sigma-Aldrich | Cat# D4692, RRID:AB_262096 |
| Anti-HEATR2 antibody produced in rabbit | Proteintech | Cat# 24578-1-AP RRID: AB_2827668 |
| Anti-NFYA antibody produced in rabbit | Abcam | Cat# ab139402 RRID: AB_2827669 |
| Anti-RAD21 antibody produced in rabbit | Abcam | Cat# ab996 RRID: AB_2176601 |
| RNA pol II antibody | Active motif | Cat# 39097, RRID:AB_2732926 |
| Anti-NUDT21 antibody | Abcam | Cat# 183660 RRID: AB_2827670 |
| Bacterial and Virus Strains | ||
| CTD-2028A10_BAC clone | BACPAC_CHORI | N/A |
| RP11-439P13_BAC clone | BACPAC_CHORI | N/A |
| Biological Samples | ||
| N/A | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| 5-Aza-2′-deoxycytidine | Sigma Aldrich | Cat# A3656 RRID: Not Available |
| 3-indoleacetic acid | Sigma Aldrich | Cat# 45533 RRID: Not Available |
| 4-Thiouridine | Sigma Aldrich | Cat# 13957-31-8 |
| EZ-link HPDP-Biotin | Thermo Fisher Scientific | Cat# A35390 |
| oligo(dT)25 Dynabeads | Thermo Fisher Scientific | Cat# 61002 |
| Critical Commercial Assays | ||
| Gibson Assembly | NEB | Cat# E5510S |
| Topo TA Cloning Kit for Sequencing with One Shot Top10 Chemically Competent E. Coli | Thermofisher | Cat# K457540 |
| AllPrep DNA/RNA Mini Kit | Qiagen | Cat# 80204 |
| Deposited Data | ||
| Raw and analyzed data (Poly(A)-seq) | This paper | GEO: GSE86178 |
| Raw and analyzed data (ChIP-Seq) | This paper | GEO: GSE131606 |
| Raw western blots and Agarose gel images | This paper, Mendeley data | http://dx.doi.org/10.17632/6tstd7xkg8.1 |
| Experimental Models: Cell Lines | ||
| HCT116 | ATCC | CCL247 |
| DKO (clone #2) | Laboratory of Dr. Bert Vogelstein | Rhee et al., 2002 |
| HCT116-mAID-RAD21 | Laboratory of Dr. Masatao T. Kanemaki | Natsume et al., 2016 |
| HCT116- NFYA−/−ΔCTCF | This paper | N/A |
| HCT116- NFYA−/+ΔCTCF | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| N/A | ||
| Oligonucleotides | ||
| Primers for Bisulfite sequencing, methylation specific PCR, ChIP-qPCR, Northern probe, qRTPCR, 3C-qPCR, & CRISPR gRNA, see Table S7 | This paper | N/A |
| Recombinant DNA | ||
| pSC-A-amp/kan | Strataclone PCR Cloning Kit; Agilent | Cat# 240205 |
| lentiCRISPR_V2_D10A | This paper | N/A |
| pGL4.74 | Promega | Cat# E692A |
| Software and Algorithms | ||
| GraphPad Prism 7 for windows for statistical analysis | GraphPad Software | https://www.graphpad.com/ |
| DEXSeq | Anders et al., 2012 | https://bioconductor.org/packages/release/bioc/html/DEXSeq.html |
| ChIP-seq data processing | ENCODE pipeline | https://github.com/kundajelab/chipseq_pipeline |
| MANorm | Shao et al., 2012 | http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm |
| bowtie | Langmead and Salzberg., 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Other | ||
| Analysis codes | This paper | https://github.com/hwanglab/apa_atingLab2019. |