KEY RESOURCES TABLE
| REAGENT or RESOURCESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-γH2A.X (Ser139) conjugated to phycoerythrin | Cell Signaling Technology | Cat#5763S; RRID: AB_10706778 |
| Rabbit anti-γH2A.X(Ser139) | Cell Signaling Technology | Cat#9718S; RRID: AB_2118009 |
| Mouse S9.6 antibody | Kerafast | Cat#ENH001; RRID:AB_2687463 |
| Chicken anti-Lamin A+C | Novus Biologicals | Cat#NBP2–25152; RRID: N/A |
| anti-nucleolin | Abcam | Cat#ab22758; RRID: AB_776878 |
| Mouse anti-ATR | Santa Cruz Biotechnology | Cat#sc-516173; RRID: N/A |
| Rabbit anti-ATM | Abcam | Cat#ab32420; RRID: AB_725574 |
| Mouse anti-Chk1 | Santa Cruz Biotechnology | Cat#sc-8408; RRID: AB_627257 |
| Mouse anti-RPA2 | Abcam | Cat#ab2175; RRID: AB_302873 |
| Mouse anti-H2A.X | Santa Cruz Biotechnology | Cat#sc-517336; RRID: N/A |
| Rabbit anti-phospho-ATR (Ser428) | Cell Signaling Technology | Cat#2853S; RRID: AB_2290281 |
| Rabbit anti-phospho-ATM (Ser1981) | Abcam | Cat#ab81292; RRID: AB_1640207 |
| Rabbit anti-phospho-Chk1 (Ser345) | Thermo Fisher Scientific | Cat#MA5–15145; RRID: AB_10979221 |
| Rabbit anti-phospho-RPA2 (Thr21) | Abcam | Cat#ab109394; RRID: AB_10860648 |
| Mouse anti-GAPDH | Santa Cruz Biotechnology | Cat#sc-47724; RRID: AB_627678 |
| Mouse anti-FMRP | Biolegend | Cat#834601; RRID: AB_2564992 |
| Mouse anti-FLAG-M2-Peroxidase (HRP) | Sigma-Aldrich | Cat#A8592-.2MG; RRID: AB_439702 |
| Mouse anti-actin | MP Biomedical | Cat#691001; RRID: N/A |
| Donkey anti-Rabbit Secondary Antibody, Alexa fluor 488 | Invitrogen | Cat#A-21206; RRID:AB_2535792 |
| Donkey anti-Mouse Secondary Antibody, Alexa Fluor 568 | Invitrogen | Cat#A10037; RRID:AB_2534013 |
| Goat anti-Chicken Secondary Antibody, Alexa Fluor 647 | Invitrogen | Cat#A-21449; RRID:AB_2535866 |
| Goat anti-Rabbit Secondary Antibody, Alexa Fluor 647 | Invitrogen | Cat#A-21244; RRID:AB_2535812 |
| Bacterial and Virus Strains | ||
| Turbo competent E. coli cells | NEB | Cat#C2984H |
| Chemicals, Peptides, and Recombinant Proteins | ||
| TransIT-2020 transfection reagent | Mirus Bio | Cat#MIR 6003 |
| poly-D-lysine | Sigma Aldrich | Cat#P6407 |
| RNase H | NEB | Cat#M0297L |
| β-Agarase I | NEB | Cat#M0392L |
| Aphidicolin | AG Scientific | Cat#A-1026-1 mg |
| Propidium Iodide | Acros Organics | Cat#AC440300250 |
| Prolong Diamond antifade mountant plus DAPI | Invitrogen | Cat#P36962 |
| Halt protease and phosphatase inhibitor | Thermo Scientific | Cat#1861280 |
| Biotin-14-dTAP | Invitrogen | Cat#19524016 |
| Dynabeads M-270 Streptavidin | Invitrogen | Cat#65305 |
| DMEM | GIBCO | Cat#11965-092 |
| RPMI1640 | Corning | Cat#15-040-CV |
| MEM | GIBCO | Cat#10370-021 |
| BenchMark FBS heat inactivated | Gemini Bioproducts | Cat#100-106 |
| FBS | Corning | Cat#350-010-CV |
| HEPES buffer | Corning | Cat#25-060-CI |
| Sodium pyruvate | Corning | Cat#25-000-CI |
| MEM nonessential amino acids | Corning | Cat#25-025-CI |
| GlutaMAX | GIBCO | Cat#35050-061 |
| Penicillin streptomycin solution | Corning | Cat#30-002-CI |
| KAPA HiFi HotStart Ready mix | Kapabiosystems/Roche | Cat#07958927001 |
| AMPure XP beads | Beckman Coulter | Cat#A63880 |
| Critical Commercial Assays | ||
| CometAssay Kit | Trevigen | Cat#4250-050-K |
| Zombie Aqua Fixable Viability Kit | Biolegend | Cat#423101 |
| End-It Kit | Epicenter/Lucigen | Cat#ER81050 |
| A-tailing Kit | NEB | Cat#E6053L |
| Deposited Data | ||
| Break-seq and DNA-seq sequencing data | This paper | GEO:GSE124403 |
| GRCh37/hg19 | UCSC human genome assembly | http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/ |
| Replication timing series in GM06990 | Hansenetal., 2010 | https://www.encodeproject.org/replication-timing-series/ENCSR595CLF/ |
| APH_breakome | Crosetto et al., 2013 | http://breakome.utmb.edu/supplementary_database/Downloads.html |
| NT2 and K562 cells_DRIP-seq | Sanzet al., 2016 | GEO: GSE70189 (GSM1720615, GSM1720616,GSM1720617, GSM1720618,GSM1720619) |
| RLFS computationally predicted sequences | Wongsurawat et al., 2012 | http://rloop.bii.a-star.edu.sg/ |
| Experimental Models: Cell Lines | ||
| Human EBV transformed lymphoblastoid cell lines GM06990 (control) | Coriell Institute | GM06990; RRID:CVCL_9587 |
| Human EBV transformed lymphoblastoid cell line: GM03200 (Fragile X) | Coriell Institute | GM03200; RRID:CVCL_AX76 |
| Human fibroblast cell line: GM00357 (control) | Coriell Institute | GM00357; RRID:CVCL_6B36 |
| Human fibroblast cell line: GM05848 (Fragile X) | Coriell Institute | GM05848; RRID:CVCL_AX83 |
| Phoenix-AMPHO producer cells (ATCC) | ATCC | ATCC® CRL-3213; RRID:CVCL_H716 |
| Experimental Models: Organisms/Strains | ||
| S. cerevisiae: BY4741 (MATa his3Δ1 leu2Δ0 met15Δ ura3Δ0) | Charlie Boone lab | N/A |
| S. cerevisiae: rnh1Δ (MATa rnh1Δ::KAN leu2Δ0 his3Δ 1met15Δ0 ura3Δ0) | Charlie Boone lab | N/A |
| Oligonucleotides | ||
| See Table S6 for the list of Oligonucleotides. | N/A | |
| Recombinant DNA | ||
| pcDNA3-EGFP | Addgene | Cat#13031, RRID:Addgene_13031 |
| pMSCVpuro | Addgene | Cat#K1062–1, RRID: N/A |
| pFRT-TODestFLAGHAhFMRPiso1 | Addgene | Cat#48690, RRID:Addgene_48690 |
| pMSCVpuro-EGFP | This paper | N/A |
| pMSCVpuro-EGFP-FMRP | This paper | N/A |
| pARS-GLB-OUT | Prado and Aguilera, 2005 | N/A |
| pARS-GLB-IN | Prado and Aguilera, 2005 | N/A |
| pARS-GLB-OUT-Control-1 | This paper | N/A |
| pARS-GLB-OUT-Control-2 | This paper | N/A |
| pARS-GLB-IN-Control-1 | This paper | N/A |
| pARS-GLB-IN-Control-2 | This paper | N/A |
| pARS-GLB-OUT-RLFS1 | This paper | N/A |
| pARS-GLB-OUT-RLFS2 | This paper | N/A |
| pARS-GLB-IN-RLFS1 | This paper | N/A |
| pARS-GLB-IN-RLFS2 | This paper | N/A |
| pFRT-TODestFLAGHAhFMRPiso1I304N | Addgene | Cat#48692, RRID:Addgene_48692 |
| pRS313 | ATCC | Cat#ATCC® 77142 |
| pRS316 | ATCC | Ca#tUATCC® 77145 |
| pRS313-CMV-FMRPiso1 | This paper | N/A |
| pRS313-CMV-FMRPiso1I304N | This paper | N/A |
| pRS313-CMV-RNH1 | This paper | N/A |
| pRS313-CMV-SHE2 | This paper | N/A |
| Software and Algorithms | ||
| DAVID Bioinformatics tools | Huang et al., 2009 | https://david.ncifcrf.gov/ |
| Bowtie 2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Picard MarkDuplicates | Broad Institute/ Github | http://broadinstitute.github.io/picard |
| Samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| BEDtools | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| Preseq | Daley and Smith, 2013 | https://github.com/smithlabcode/preseq |
| DiffBind | Ross-Innes et al., 2012 | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| ChIPpeakAnno R package (binOverFeature and annotatePeakInBatch functions) | Zhuetal., 2010 | https://www.rdocumentation.org/packages/ChIPpeakAnno/versions/ure and https://www.rdocumentation.org/packages/ChIPpeakAnno/versions/3.6.5/topics/annotatePeakInBatch |
| Model-based Analysis for ChIP-seq (MACS version 2.1.1) | Zhang et al., 2008 | https://pypi.org/project/MACS2/ |
| Genomic Association Test | Heger et al., 2013 | https://github.com/AndreasHeger/gat |
| WebGestalt | Wang etal., 2017 | http://webgestalt.org |
| Fiji | Schindelin et al., 2012 | https://fiji.sc/ |
| Graphpad Prism | https://www.graphpad.com/scientific-software/prism/ | |
| OpenComet v1.3.1 | Gyoriet al., 2014 | https://www.cometbio.org |
| Kaleidagraph | Hoover, 2000 | https://www.synergy.com |
| Flowjo | Ashland, OR: Becton, Dickinson and Company | https://www.flowjo.com |
| SeqMonkv1.43.0 | Babraham Bioinformatics | https://www.bioinformatics.babraham.ac.uk/ |