REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
α-H3K4me3	Millipore	07-473
α-H3K4me2	Millipore	07-030
α-H3K4me1	Millipore	07-436
α-H3	Abcam	Ab1791
α-Rpb3	Neoclone	W0012
α-Rpb4	Neoclone	W0013
α-CTD-Ser5P	Custom, Warren et al. (1992) J. Cell Sci.	H14
α-CTD-Ser2P	Custom, Warren et al. (1992) J. Cell Sci.	H5
Critical Commercial Assays
Qubit dsDNA HS Assay kit	ThermoFisher Scientific	Q32851
QIAquick PCR Purification Kit	Qiagen	ID:28104
QIAquick Gel Extraction Kit	Qiagen	ID:28704
MinElute PCR Purification Kit	Qiagen	ID:28004
T4 Polynucleotide Kinase	NEB	M0201S
T4 DNA Polymerase	NEB	M0203S
DNA Polymerase I, Large (Klenow) Fragment	NEB	M0210S
Klenow Fragment (3′->5′ exo-)	NEB	M0212S
Quick Ligation Kit	NEB	M2200S
Bioanalyzer High Sensitivity DNA kit	Agilent	5067-4626
Deposited Data
Raw and analyzed data	This Study	GEO: GSE95356
SAGA versus TFIID dominated gene classification	Huisinga and Pugh (2004)	N/A
Transcriptional unit coordinates	Pelechano et al. (2014)	N/A
RNA levels	Xu et al. (2009)	http://steinmetzlab.embl.de/NFRsharing/
S.cerevisiae Reference Genome version R64-1-1	Engel et al., (2013)	https://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases
S.pombe Reference Genome version ASM294v2	Wood et al., (2002)	ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Chromosome_Dumps/
Experimental Models: Organisms/Strains
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, his3Δ1, met15Δ0	http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html/ OpenBiosystems (now Dharmacon)	BY4741
S.cerevisiae Strain: MATa, ura3-52, leu2Δ1, trp1Δ63, his4-912∂, lys2-128δ	Fred Winston	FY118
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, his3Δ1, met15Δ0, spp1Δ::KanMX	http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html/ OpenBiosystems (now Dharmacon)	YF523
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, his3Δ1, met15Δ0, jhd2Δ::KanMX	http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html/ OpenBiosystems (now Dharmacon)	YF1474
S.pombe strain: h+ N	Fred Winston	975, FWP9
S.cerevisiae Strain: MATa, URA3::CMV-tTA, leu2Δ, trp1Δ::hisG, his3Δ, met15Δ, lys2Δ	Malagon et al., (2006)	GRY3020
S.cerevisiae Strain: MATa, URA3::CMV-tTA, leu2Δ, trp1Δ::hisG, his3Δ, met15Δ, lys2Δ, rpb1-E1103G	Malagon et al., (2006)	GRY3028
S.cerevisiae Strain: MATa, URA3::CMV-tTA, leu2Δ, trp1Δ::hisG, his3Δ, met15Δ, lys2Δ, rpb1-N488D	Malagon et al., (2006)	GRY3027
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, his3Δ1, met15Δ0, FLAG-Set1(Δ700)	Soares et al., (2014)	YSB3119
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX [pRS414]	This study	YSB3342
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, rpb4Δ::NatMX [pRS314-RPB4NheI]	This study	YSB2827
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, rpb4Δ::NatMX [pRS414-SET1 (1-1080)]	This study	YSB2826
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, rpb4Δ::NatMX [pRS414-RPB4-SET1]	This study	YSB2828
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, rpb4Δ::NatMX [pRS414]	This study	YSB3343
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, rpb4Δ::NatMX [pRS414-SET1 Δ500]	This study	YSB3344
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX [pRS414-SET1 (1-1080)]	This study	YSB3345
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX [pRS414-SET1 Δ500]	This study	YSB3346
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, rpb4Δ::NatMX [pRS314-RPB4-SET1ΔN500]	This study	YSB3347
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, bre1Δ::URA3MX [pRS414-SET1 (1-1080)]	This study	YSB3318
S.cerevisiae Strain: MATa, ura3Δ0, leu2Δ0, trp1Δ::LEU2/KanR, his3Δ1, met15Δ0, set1Δ::KanMX, rpb4Δ::NatMX, bre1Δ::URA3MX [pRS314-RPB4-SET1ΔN500]	This study	YSB3319
Oligonucleotides
Barcoded adapter oligo 1 (BA1): 5′ ACACTCTTTCCCTACACGACGCTCTTCCGATCT-barcode-T 3′	Wong et al., (2013)	Reference table 7.11.2
Barcoded adapter oligo 2 (BA2): 5 p-barcode(reverse complement)-AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG 3a	Wong et al., (2013)	Reference table 7.11.2
Library amplification PCR primer forward (PCR1): CAAGCAGAAGACGGCATACGAGATCGGTCTCGG CATTCCTGCTGAACCGCTCTTCCGATC*T * Indicates phosphorothioate bond	Wong et al., (2013)	N/A
Library amplification PCR primer reverse (PCR2): AATGATACGGCGACCACCGAGATCTACACTCTT TCCCTACACGACGCTCTTCCGATC*T * Indicates phosphorothioate bond	Wong et al., (2013)	N/A
Recombinant DNA
Plasmid: pRS414-SET1(1-1080) (ADH1 promoter driving SET1 (1-1080) with N-terminal FLAG tag, TRP1, CEN/ARS, f1+ ori, AmpR)	Fingerman et al., (2005)	N/A
Plasmid: pRS414-SET1Δ500 (ADH1 promoter driving SET1 Δ500 with N-terminal FLAG tag, TRP1, CEN/ARS, f1+ ori, AmpR)	This study	N/A
Plasmid: pRS314-RPB4NheI (RPB4 with NheI site inserted in front of stop codon, TRP1, CEN/ARS, f1+ ori, AmpR)	Suh et al., (2013)	N/A
Plasmid: pRS314-RPB4-SET1 (RPB4-SET1 fusion, 3 glycine residues link the RPB4 and SET1 ORFs, TRP1, CEN/ARS, f1+ori, AmpR)	This study	N/A
Plasmid: pRS314-RPB4-SET1ΔN500 (RPB4-SET1ΔN500 fusion, 3 glycine residues link the RPB4 and SET1ΔN500 ORFs, TRP1, CEN/ARS, f1+ori, AmpR)	This study	N/A
Software and Algorithms
Sabre	N/A	https://github.com/najoshi/sabre
Bowtie 1.1.1	Langmead et al., (2009)	http://bowtie-bio.sourceforge.net/index.shtml
Samtools 1.2	Li et al., (2009)	http://samtools.sourceforge.net/
MACS 2.1.0	Zhang et al., (2008)	https://pypi.python.org/pypi/MACS2
Python 3.4	N/A	https://www.python.org/download/releases/3.4.0/
Python Scripts	This study	https://github.com/LuisSoares/Manuscript