REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-V5	Invitrogen	Cat # 46-0705
Anti-FLAG M2 Magnetic Beads	Sigma-Aldrich	Cat # M8823
Rabbit polyclonal anti-Taf1	Hahn lab	Rabbit # 3506
Rabbit polyclonal anti-Taf4	Hahn lab	Rabbit # 4022
Rabbit polyclonal anti-Taf12	Hahn lab	Rabbit # 3434
Rabbit polyclonal anti-Taf3	Hahn lab	Rabbit # 4045
Rabbit polyclonal anti-TBP	Hahn lab	Rabbit # 7370
Rabbit polyclonal anti-H3	Abcam	Cat # ab1791
Rabbit polyclonal anti-Taf4	P. Anthony Weil	N/A
Rabbit polyclonal anti-Taf5	P. Anthony Weil	N/A
Rabbit polyclonal anti-Taf11	P. Anthony Weil	N/A
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
3-Indoleacetic acid (3-IAA)	Sigma-Aldrich	I3750; CAS: 87-51-4
Micrococcal Nuclease (MNase)	Worthington Biochemical Corporation	Cat # NFCB
cOmplete Mini, EDTA-free Protease inhibitor cocktail tablets	Roche	Cat # 11836170001
4-thiouracil	Sigma-Aldrich	Cat # 440736; CAS: 591-28-6
MTSEA biotin-XX	Biotium	Cat # 90066
Dynabeads MyOne Streptavidin C1	Invitrogen, ThermoFisher	Cat # 65001
AMPureXP beads	Beckman Coulter	Cat # A63881
EZ-Link HPDP Biotin	ThermoFisher	Cat # 21341
Rapamycin	Euromedex	Cat # SYN-1185
Dyanabeads Protein G	Thermo Fisher Scientific	Cat # 10004D
0.5 mm zirconia disruption beads	Research Products International	Cat # 9834
Critical Commercial Assays
RiboPure yeast kit	Ambion, Life Technologies	Cat # AM1926
RNeasy MinElute Cleanup Kit	Qiagen	Cat # 742040
μMACS Streptavidin Kit	Miltenyi Biotec	Cat# 130-074-101
Deposited Data
All sequencing datasets have been uploaded in GEO under accession GSE97081
Western blot original images	Mendeley Data file	http://dx.doi.org/10.17632/gwtwc4ndpj.1
Experimental Models: Cell Lines
Experimental Models: Organisms/Strains
S. pombe: Strain background: 972h	Laboratory of Gerald Smith	ATCC: 24843
S. cerevisiae: Strain background: BY4705	Laboratory of Dan Gottschling	ATCC: 200869
Yeast strains, see Table S2	This paper	N/A
Recombinant DNA
Sequence-Based Reagents
Primers for RT-qPCR, see Table S1	This paper	N/A
Software and Algorithms
Bowtie2	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml	N/A
Shell Scripts for Sequence Alignment	This paper
Perl Scripts for analysis	This paper
R Scripts for analysis	This paper
Other