Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (murine herpesvirus 68) |
MHV68 | PMID: 10888635 | NCBI_refseq ID: NC_001826.2 |
Koszinowski Lab |
| Strain, strain background (murine herpesvirus 68) |
R443I MHV68 | PMID: 21811408 | Glaunsinger Lab |
|
| Cell line (Homo sapiens) |
HEK293T | American Type Culture Collection |
Cat# CRL-11268; RRID: CVCL_1926 |
|
| Cell line (Mus musculus) |
NIH3T3 | American Type Culture Collection |
Cat# CRL-1658; RRID: CVCL_0594 |
|
| Transfected construct (synthesized) |
Xrn1 knockout (KO) cells |
This paper | HEK293T clone stably expressing Cas9 and Xrn1 single-guide RNA. |
|
| Transfected construct (synthesized) |
Cas9-expressing WT cells |
This paper | HEK293T clone stably expressing Cas9 alone with no guide RNA. |
|
| Recombinant DNA reagent |
GFP-muSOX (plasmid) |
This paper | Progenitors: pcDNA3-HA-muSOX ( Covarrubias et al., 2009); Gateway vector peGFP-C1 |
|
| Recombinant D NA reagent |
Thy1.1-muSOX (plasmid) |
This paper | Progenitors: GFP-muSOX |
|
| Recombinant DNA reagent |
Thy1.1-muSOX D219A (plasmid) |
This paper | Progenitors: Thy1.1-muSOX |
|
| Recombinant DNA reagent |
Thy1.1-GFP (plasmid) | This paper | Progenitors: Thy1.1-muSOX |
|
| Recombinant DNA reagent |
pCDEF3-FLAG-PABPC1 (plasmid) |
PMID: 20823266 | Glaunsinger Lab | |
| Recombinant DNA reagent |
lentiCas9-Blast (lentiviral vector) |
Addgene; PMID: 25075903; PMID: 24336571 |
52962 | |
| Recombinant DNA reagent |
lentiGuide-Puro (lentiviral vector) |
Addgene; PMID: 25075903; PMID: 24336571 |
52963 | |
| Antibody | Mouse monoclonal anti-PABPC |
Santa Cruz Biotechnologies |
Clone 10 E 10; SC32318 | IFA (1:25) |
| Antibody | Rabbit polyclonal anti-LARP4 |
Thermofisher | PA5-58727 | IFA (1:200); Western (1:1000) |
| Antibody | Rabbit polyclonal anti-PABPC |
Cell Signaling Technology |
4992S | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-PABPC4 |
Bethyl | A301-466A-M | Western (1:1000) |
| Antibody | Mouse monoclonal anti-Gapdh |
Abcam | Clone 6C5; ab8245 | Western (1:5000) |
| Antibody | Rabbit monoclonal anti-Histone H3 |
Cell Signaling Technology |
Clone D1H2; 4499S | Western (1:2000) |
| Antibody | Rabbit polyclonal anti-LYRIC |
Abcam | ab124789 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-RRBP1 |
Bethyl | A303-996A-T | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-MSI1 |
Abcam | ab52865 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-LIN28B |
Abcam | ab71415 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-RPP20 |
Novus Biologicals | NBP15707220 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-CHD3 |
Cell Signaling Technology |
4241T | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-THOC6 |
Life Technologies | PA543172 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-PNN |
Life Technologies | PA535053 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-EXO4 |
This paper | Western (1:1000) | |
| Antibody | Rabbit polyclonal anti-NPM |
Abcam | ab10530 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-TRIM32 |
Abcam | ab131223 | Western (1:1000) |
| Antibody | Mouse monoclonal anti-GW182 |
Abcam | Clone 4B6; ab70522 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-DDX6 |
Bethyl | A300-460 | Western (1:1000) |
| Antibody | Rabbit polyclonal anti-DCP2 |
Bethyl | A302-597A-M | Western (1:1000) |
| Antibody | Mouse monoclonal anti-RNAPII Rpb1 |
BioLegend | 8WG16 | Western (1:2000); ChIP (10 mg) |
| Antibody | Rabbit polyclonal anti-TBP |
Abcam | ab28175 | Western (1:2000); ChIP (10 mg) |
| Antibody | Rabbit polyclonal anti-RNAPII phospho S5 |
Abcam | ab5131 | ChIP (10 mg) |
| Antibody | Rabbit polyclonal anti-RNAPII phospho S2 |
Abcam | ab5095 | ChIP (10 mg) |
| Antibody | Rabbit polyclonal anti-POLR3A |
Abcam | ab96328 | ChIP (10 mg) |
| Sequence-based reagent (H. sapiens) |
siPABPC1 | PMID: 20823266 | Custom siRNA; see Table S5 for sequence |
|
| Sequence-based reagent (H. sapiens) |
siPABPC4 | PMID: 20823266 | Custom siRNA; see Table S5 for sequence |
|
| Sequence-based reagent (H. sapiens) |
siLARP4 | Dharmacon | M-016523-00-0020 | |
| Sequence-based reagent (H. sapiens) |
siCHD3 | Dharmacon | M-023015-01-0020 | |
| Sequence-based reagent (H. sapiens) |
siMSI1 | Dharmacon | M-011338-01-0010 | |
| Sequence-based reagent (H. sapiens) |
siTRIM32 | Dharmacon | M-006950-01-0010 | |
| Commercial assay or kit | Protein G dynabeads | Thermofisher | 10004D | |
| Commercial assay or kit | Protein A dynabeads | Thermofisher | 10002D | |
| Commercial assay or kit | 10-plex TMT kit | Thermofisher | 90113 | |
| Chemical compound, drug | Alexa Fluor 594, goat anti-rabbit |
Thermofisher | A-11072 | |
| Chemical compound, drug | Alexa Fluor 594, goat anti-mouse |
Thermofisher | A-11020 | |
| Software, algorithm | Proteome Discoverer |
Thermofisher | v2.2.0.388 |