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. Author manuscript; available in PMC: 2022 Sep 2.
Published in final edited form as: Mol Cell. 2021 Aug 10;81(17):3542–3559.e11. doi: 10.1016/j.molcel.2021.07.010

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Rabbit polyclonal anti-Spt16 T. Formosa N/A
Rabbit polyclonal anti-Pob3 T. Formosa N/A
Mouse monoclonal anti-RNA Polymerase II Rpb3 (1Y26) Neoclone; BioLegend Cat# 665003, RRID:AB_2564529; Cat# 665004, RRID:AB_2565221
Mouse monoclonal anti-Flag (M2) Sigma-Aldrich Cat# F3165, RRID:AB_259529
Mouse monoclonal anti-HA (F7) Santa Cruz Biotechnology Cat# sc-7392, RRID:AB_627809
Rabbit IgG Millipore Cat# 12-370, RRID:AB_145841
Rabbit polyclonal anti-Chd1 A. Lusser N/A
Mouse monoclonal anti-α-tubulin Sigma-Aldrich Cat# T5168, RRID:AB_477579
Mouse monoclonal anti-RNA Polymerase II Rpb1 (8WG16) BioLegend Cat# 664912, RRID:AB_2650945
IRDye800CW Donkey anti-rabbit LI-COR Biosciences Cat# 926-32213 RRID:AB_621848
IRDye680RD Donkey anti-mouse LI-COR Biosciences Cat# 926-68072 RRID:AB_10953628
Chemicals, Peptides, and Recombinant Proteins
1-Naphthyl PP1 (1NAPP1) Tocris Bioscience 3063
Rapamycin Bio Basic R706203
DRB Sigma-Aldrich D1916
RQ1 DNase I Promega M610A
FuGENE HD Promega E2311
37% Formaldehyde Fisher Scientific BP531-500
PMSF Roche 10837091001
Benzamidine Sigma-Aldrich B-6506
Aprotinin Roche 10981532001
Leupeptin Roche 11017101001
Pepstatin Roche 11359053001
Acid washed glass beads (400-600um) Sigma-Aldrich G8772-1KG
Dynabeads Protein G Thermo Fisher Scientific 10004D
Dynabeads M-450 pre-coated with pan anti-mouse IgG Thermo Fisher Scientific 11042
RNaseA Sigma-Aldrich R6513-
Glycogen (20 mg/mL) Roche 10901393001
Proteinase K (20 mg/mL) Thermo Fisher Scientific 25530049
PowerUp SYBR Green Master Mix Thermo Fisher Scientific A25741
NEBuffer 2 New England Biolabs B7002S
T4 DNA polymerase New England Biolabs M0203L
T4 DNA ligase Thermo Fisher Scientific 15224041
ThermoPol Reaction buffer New England Biolabs B9004S
5-(3-aminoallyl)-dUTP (aa-dUTP) Thermo Fisher Scientific AM8439
Taq DNA polymerase Thermo Fisher Scientific 18038240
Pfu DNA polymerase Thermo Fisher Scientific EP0502
Cy3 Mono-Reactive NHS Ester Fluorescent Dye GE Healthcare PA23001
Cy5 Mono-Reactive NHS Ester Fluorescent Dye GE Healthcare PA25001
Salmon Sperm DNA Thermo Fisher Scientific 15632011
Yeast tRNA Thermo Fisher Scientific 15401011
DIG Easy Hyb Roche 11603558001
Klenow Fragment (3’→5’ exo-) New England Biolabs M0212M
T4 polynucleotide kinase New England Biolabs M0201S
Rapid ligation buffer Enzymatics B1010
Rapid T4 DNA ligase Enzymatics L6030-HC-L
phi29 DNA polymerase New England Biolabs M0269S
λ exonuclease New England Biolabs M0262S
KAPA Pure Beads Roche 07983280001
T4 DNA ligase reaction buffer New England Biolabs B0202S
KOD Hot Start DNA polymerase Millipore 71086-3
Zymolyase 100T US Biological Z1004
Spermidine Sigma-Aldrich 85558
MNase (Micrococcal nuclease) Worthington LS004798
Index adapters Roche (SeqCAp Adapter kit A, (07141530001) and SeqCAp Adapter kit B, (07141548001))
Truseq DNA UD Indexes Illumina 20023784
Critical Commercial Assays
QIAquick PCR Purification Kit QIAGEN 28106
RNeasy Mini kit QIAGEN 74134
SuperScript IV Reverse Transcriptase kit Thermo Fisher Scientific 18090050
High Sensitivity DNA Kit Agilent Technologies 5067-4626
NEBNext Library Quant Kit New England Biolabs E7630
Deposited Data
Raw and processed microarray and sequencing data This study GEO: GSE155144
Single-molecule tracking data This study Mendeley Data : DOI: 10.17632/rnf4nc3g6y.1
RNAPII in kin28as and CTD mutants ChIP-chip processed data (Jeronimo and Robert, 2014) GEO: GSE55402
H4 ChIP-chip processed data (Jeronimo et al., 2015) GEO: GSE62880
H2B ChIP-chip processed data (Jeronimo et al., 2019) GEO: GSE113270
Experimental Models: Organisms/Strains
D. melanogaster: S2R+ cells Laboratory of Eric Lécuyer N/A
S. cerevisiae: Strain background W303-1A Laboratory of Rodney Rothstein ATCC:208352
S. cerevisiae: Strain background BY4741 Laboratory of Jef D. Boeke ATCC-201388
S. cerevisiae: Strain background FY4 Laboratory of Fred Winston N/A
See Table S1 for all yeast strains N/A N/A
Oligonucleotides
See Table S2 for all oligonucleotides N/A N/A
Recombinant DNA
pMPY-3xHA (Schneider et al., 1995) N/A
pML104 (Laughery et al., 2015) N/A
pML107 (Laughery et al., 2015) N/A
pKF296 (Kunzelmann et al., 2016) N/A
pRB17 (Bottcher et al., 2014) N/A
pRB14 (Bottcher et al., 2014) N/A
Software and Algorithms
DiaTrack (version 3.04) (Vallotton and Olivier, 2013) http://www.diatrack.org/product.html
Versatile Aggregate Profiler (version 1.1.0) (Brunelle et al., 2015; Coulombe et al., 2014) http://lab-jacques.recherche.usherbrooke.ca/vap/
UCSC Genome Browser (Casper et al., 2018) http://genome.ucsc.edu/
BWA (version 0.7.17) (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/
SAMtools (version 1.8) (Li et al., 2009) http://samtools.sourceforge.net
BEDTools (versions 2.27.1 and 2.28.0) (Quinlan and Hall, 2010) https://bedtools.readthedocs.io/en/latest/
Bowtie 2 (version 2.3.4.3) (Langmead and Salzberg, 2012) http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Java TreeView (Version 1.1.6r4) (Saldanha, 2004) https://sourceforge.net/projects/jtreeview/
Plot2DO (Beati and Chereji, 2020) https://github.com/rchereji/plot2DO
Sojourner R package (Liu et al., 2021) https://rdrr.io/github/sheng-liu/sojourner/
MATLAB MathWorks https://www.mathworks.com/