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/
|