REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
TAP Tag Polyclonal Antibody	ThermoFisher	Cat#CAB1001
Chemicals, peptides, and recombinant proteins
-Trp synthetic dropout mix	Formedium	Cat#DCS0149
Guanidine hydrochloride	Sigma	Cat#G4505-1 KG
HaloTEV Protease	Promega	Cat#G6601
Critical commercial assays
cOmplete EDTA-free protease inhibitor cocktail tablets	Roche	Cat#11873580001
Ni-NTA Superflow	QIAGEN	Cat#30410
Calmodulin Affinity resin	Agilent	Cat#214303-52
Pierce spin columns snap cap	Thermo Scientific	Cat#69725
Slide-A-lyzer cassette 2000MWCO	Thermo Scientific	Cat#66205
RNace-It Ribonuclease cocktail	Agilent	Cat#400720
RNasin Ribonuclease Inhibitor	Promega	Cat#N21150
Recombinant RNasin Ribonuclease Inhibitor	Promega	Cat#N2511
DNase RQ1	Promega	Cat#M6101
T4 RNA Ligase 2, truncated K227Q	NEB	Cat#M0351
T4 RNA Ligase 1	NEB	Cat#M0204L
T4 PNK	NEB	Cat#M0201L
Nitrocellulose membranes	GE Healthcare	Cat#10 439 196
MetaPhor agarose	Lonza	Cat#50180
NuPAGE 4–12% polyacrylamide Bis-Tris Gels	Life Technologies	Cat#NP0335
NuPAGE LDS 4x sample buffer	Life Technologies	Cat#NP0007
NuPAGE SDS-MOPS running buffer	Life Technologies	Cat#NP0001
NuPAGE Transfer Buffer	Life Technologies	Cat#NP00061
MinElute Gel Extraction kit	QIAGEN	Cat#28604
Proteinase K	Roche	Cat#03115836001
RNase H	NEB	Cat#M0297L
LA Taq	Takara	Cat#RR002M
Deposited data
Raw data files from CRAC	NCBI Gene expression omnibus	GSE136056
Raw image files	Mendeley	https://doi.org/10.17632/m253kk9sm6.1
Experimental models: Organisms/strains
S. cerevisiae Strain background: BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)	Longtine et al.72	yTWT001
S. cerevisiae Strain Rpa190HTP a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 RPA190-HTP::URA3MX	Turowski et al.7	yTWT046
S. cerevisiae Strain Rpa135 HTP a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 RPA135-HTP::URA3MX	Turowski et al.7	yTWT051
S. cerevisiae Strain Rpa135 HTP Rpa12ΔC a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 RPA12(1-74aa only) RPA135-HTP::URA3MX	This study	yTWT232
S. cerevisiae Strain nsi1Δ Rpa135 HTP a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 RPA135-HTP::URA3MX nsilΔHIS	This study	D1436
S. cerevisiae Strain nsi1Δ Rpa135 HTP Rpa12ΔC a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 RPA12(1-74aa only) RPA135-HTP::URA3MX nsi1ΔHIS	This study	D1433
S.cerevisiae strain Rat1-TAP::HIS a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Rat1-TAP::HIS	Open biosystems	N/A
S.cerevisiae strain Rai1-TAP::URA a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Rai1-TAP::URA	This study	D1375
S cerevisiae strain Trf4-TAP a his3D1 leu2Δ0 met15Δ0 ura3Δ0 TRF4-TAP-his	Open biosystems	N/A
S cerevisiae strain rat1-1 ura3-52, leu2Δ1,his3-200 rat1-1	Henry et al.73	DAH18
S cerevisiae strain rat1-1 ura3-52, leu2Δ1,his3-200 rat1-1, Rpa190-HTP	This study	D1464
S cerevisiae strain trf4ts-gfp-kan trf5Δnat his3D1 leu2D0 met15Δ0 ura3D0	Houseley and Tollervey74	JH385
S cerevisiae strain trf4ts-gfp-kan trf5Δnat his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Rpa190-HTP	This study	D1457
S cerevisiae strain air1Δnat, air2Δkan MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 air1Δ:nat air2Δ:kanMATa	LaCava et al.75	JH696
S cerevisiae strain air1Δnat, air2Δkan MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 air1Δ:nat air2Δ:kanMATa Rpa190-HTP	This study	D1474
S cerevisiae strain trf4ts-gfp-kan trf5Δnat his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Rpa190-HTP	This study	D1457
S cerevisiae strain AID-RNT1 RPA190-HTP a leu2Δ0 ura3Δ0 his3Δ1:OsTIR:NatMX HygMX:pMET::AID-6xFLAG-RNT1 RPA190-HTP::URA3MX	This study	yTWT195
S cerevisiae strain A190-HTP Rrp44-D551N a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 RPA190-HTP::URA3MX, Rrp44 D551N	This study	yTWT298
S cerevisiae strain Rpa135-HTP Rpa12DC Rrp44-D551N a his3D1 leu2D0 met15D0 ura300 RPA12(1-74aa only) RPA135-HTP::URA3MX, Rrp44 D551N	This study	yTWT300
S cerevisiae strain A135-HTP Rrp44-D551N a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 RPA135-HTP::URA3MX Rrp44 D551N	This study	yTWT302
Software and algorithms
PyCRAC	Webb et al.76	https://bitbucket.org/sgrann/pycrac
SAMtools v1.3.1	Li et al.77	http://www.htslib.org/
Bedtools v2.25	Quinlan and Hall78	https://github.com/arq5x/bedtools2
Prism 7	Graphpad	http://www.graphpad.com
Integrative Genomics Viewer	Broad Institute	http://software.broadinstitute.org/software/igv/
STAR v2.7.10a	Dobin et al.79	N/A
trxtools 0.2.1	This study	https://github.com/TurowskiLab/trxtools
MATLAB code for mathematical model: git repository	This study	https://github.com/tturowski/RNAPI-model-v2 https://doi.org/10.5281/zenodo.14587255
Analysis steps code for mathematical model: git repository	This study	https://github.com/tturowski/Pol1_termination_MS https://doi.org/10.5281/zenodo.14592083