REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-H3K9me2	(Kimura et al., 2008)	N/A
anti-FLAG	Sigma	Cat# F3165; RRID: AB_259529
anti-H3K14ac	Abcam	Cat# ab52946; RRID: AB_880442
anti-H3K36me3	Abcam	Cat# ab9050; RRID: AB_306966
anti-H3 (ChIP)	Active Motif	Cat# 61475
anti-H2B	Active Motif	Cat# 39238; RRID: AB_2631110
anti-H2BK119ub	Cell Signaling	Cat# 5546
anti-H3K4me3	Abcam	Cat# ab8580; RRID: AB_306649
anti-H3 (Western)	Abcam	Cat# ab1791; RRID: AB_302613
anti-tubulin	(Woods et al., 1989)	N/A
goat anti-mouse IgG (H + L)-HRP conjugate	Bio-Rad	Cat# 1706516; RRID: AB_11125547
Peroxidase AffiniPure Goat Anti-Mouse IgG (H+L)	Jackson Immunoresearch	Cat# 115-035-146; RRID: AB_2307392
Peroxidase AffiniPure Goat Anti-Rabbit IgG (H+L)	Jackson Immunoresearch	Cat# 111-035-144; RRID: AB_2307391
Acetyl-Lysine Motif Kit	Cell Signaling	Cat# 13416S
Chemicals, Peptides, and Recombinant Proteins
5-Fluoroorotic Acid (FOA)	US biological, Thermo Fisher	Cat# 207291-8-4
nourseothricin dihydrogen sulfate (NAT)	Fisher or WERNER BioAgents GmbH	Cat# 5029426 or Cat# 5.0
G418 sulfate (Geneticin)	Roche or Invitrogen/Life Technologies	Cat# 04727878001-2 or Cat# 10131027
Hygromycin	Sigma or Invitrogen/Life Technologies	Cat# H7772 or Cat# 10687010
PrimeSTAR GXL DNA Polymerase	Clontech	Cat# R050A
Taq DNA Polymerase	NEB	Cat# M0267
Formaldehyde	Sigma or Carl Roth	Cat# F8775 or Cat# 4979
PMSF	Sigma	Cat# P7626
cOmplete Protease Inhibitor Cocktail	Roche	Cat# 11836145001
AEBSF (Pefabloc SC)	Roche	Cat# 11585916001
Dynabeads M-280 Sheep anti-mouse IgG	Thermo Fisher	Cat# 11202D
Dynabeads Protein G	Thermo Fisher/ Life Technologies	Cat# 10009D
Leupeptin hemisulfate	Carl Roth	Cat# CN33
Proteinase K	Roche	Cat# 3115879001
RNase A	Roche	Cat# 10109169001
SuperScript III	Thermo Fisher/ Life Technologies	Cat# 18080085
Acrylamid/BIS solution (30%) 37.5:1	Serva	Cat# 10688
Titriplex III (EDTA)	Merck Millipore	Cat# 108418
SsoAdvanced Universal SYBR Green Supermix	Bio-Rad	Cat# 172-5274
PowerUp SYBR Green Master Mix	Life Technologies	Cat# A25742
Zymolyase	Fischer	Cat# 6064819
Lysing enzyme from Trichoderma harzianum	Sigma	Cat# L1412
DpnI	NEB	Cat# R0176
DpnII	NEB	Cat# R0543
T4 DNA ligase	Roche	Cat# 10481220001
Lys-C	Wako Chemicals	Cat# 125-05061
Trypsin	Thermo Fisher	Cat# 20233
SEP-PAK	Waters	Cat# WAT036790
YMC Triart C18 0.5 × 250 mm column	YMC Europe GmBH	Cat# TA12S0325J0AU
PepMap 100 C18 2 cm trap	Thermo Fisher	Cat# 164946
EASY-Spray C18 column	Thermo Fisher	Cat# ES801
Bolt 4-12% Bis-Tris Plus Gels	Thermo Fisher	Cat# NW04127BOX
Immobilon Western Chemiluminescent HRP Substrate	Millipore	Cat# WBKLS0500
Immobilon-P Membran, PVDF, 0,45 μm	Merck Millipore	Cat# IPVH00010
Critical Commercial Assays
MasterPure Yeast RNA Purification Kit	Epicenter	Cat# MPY03100
Bio-Rad Protein Assay Dye Reagent Concentrate	Bio-Rad	Cat# 500-0006
TruSeq Small RNA library preparation kit	Illumina	Cat# RS-200-0012
TruSeq Stranded mRNA library preparation kit	Illumina	Cat# RS-122-2101
DNeasy Blood and Tissue Kit	QIAGEN	Cat# 69506
RNeasy Midi Kit	QIAGEN	Cat# 75144
GeneChip Hybridization, Wash, and Stain Kit	Affymetrix	Cat# 900720
Turbo DNA free	Thermo Fisher/ Life Technologies	Cat# AM1907
ChIP DNA Clean & Concentrator	Zymo Research	Cat# D5201
Deposited Data
smallRNA and poly(A) mRNA sequencing data	This study	GEO: GSE93434
DamID data	This study	GEO: GSE93434
Mendeley Data dataset (original unprocessed Western Blot images)	This study	http://dx.doi.org/10.17632/98ywc24xv7.1
Mass spectrometry raw data	This study	ProteomeXchange: PXD005714
H3K36me3 ChIP-chip data	(Wilhelm et al., 2011)	ArrayExpress: E-TABM-946
Experimental Models: Organisms/Strains
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX	(Kowalik et al., 2015)	spb464
h+leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX	(Kowalik et al., 2015)	spb1788
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2	(Kowalik et al., 2015)	spb2047
h+leu1-32 ura4-D18 ade6-704 or 210 trp1+::ade6+nmt1+::ade6-hp+::natMX Paf1-SMS8::kanMX	(Kowalik et al., 2015)	spb2076
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 mst2Δ::kanMX	This study	spb2151
h+leu1-32 ura4-D18 ade6-M210 or 704 trp1+::ade6+nmt1+::ade6-hp+::natMX mst2Δ::kanMX paf1-sms8::LEU2	This study	spb2630
h+leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX mst2Δ::kanMX	This study	spb2094
h+leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX clr4Δ::hphMX	(Kowalik et al., 2015)	spb1950
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX	(Keller et al., 2013)	spb1591
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA (C. albicans) mst2Δ::hphMX	This study	spb1719
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX clr4Δ::kanMX	This study	spb1754
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 or M216 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX dcr1Δ::kanMX	This study	spb1776
h? mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 or 216 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX ago1Δ::kanMX	This study	spb1755
h+otr1R(SphI)::ura4+ura4-DS/E ade6-M210 leu1Δ::nmt1(81x)-dam-myc::kanMX	(Woolcock et al., 2011)	spb492
h+otr1R(SphI)::ura4+ura4-DS/E leu1-32 ade6-M210 leu1Δ::nmt1(81x)-dam-myc-mst2::kanMX	This study	spb2104
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+	(Kowalik et al., 2015)	spb426 (PSB1782)
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+mst2-CBP-2xFLAG::natMX	This study	PSB1855
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+mst2-FLAG::natMX set2Δ::kanMX	This study	PSB1870
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+mst2-FLAG::natMX pdp3D::kanMX	This study	PSB1871
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+mst2-FLAG::natMX set2-SRIΔ::kanMX	This study	PSB1882
h+imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210	(Ekwall et al., 1999)	PSB65
h+imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210 natMX::CBP-2xFLAG-pdp3	This study	PSB1696
h+imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210 pdp3Δ::natMX::CBP-2xFLAG-pdp3_F109A	This study	PSB1698
h+otr1R(SphI)::ura4+ura4-DS/E leu1-32 ade6-M210 leu1Δ::nmt1(81x)-dam-myc-mst2::kanMX pdp3Δ::natMX	This study	spb2212
h? leu1-32 ura4-D18 ade6-704 or ade6M210 trp1+::ade6+ nmt1+::ade6-hp::natMX paf1-sms8::LEU2 pdp3Δ::kanMX	This study	spb2647
h? leu1-32 ura4-D18 ade6-704 or ade6M210 trp1+::ade6+ nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 set2Δ::kanMX	This study	spb2646
h+otr1R(SphI)::ura4+ura4-DS/E leu1-32 ade6-M210 leu1Δ::nmt1(81x)-dam-myc-mst2::kanMX set2Δ::natMX	This study	spb2220
h+otr1R(SphI)::ura4+ura4-DS/E leu1-32 ade6-M210 leu1Δ::nmt1(81x)-dam-myc-mst2::kanMX set1Δ::natMX	This study	spb2239
h+leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX pdp3Δ::kanMX	This study	spb2319
h-SPSQ (cyhR) SPL42 (cyhS) hphMX::cen1 imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210	(Barrales et al., 2016)	PSB582
h-SPSQ (cyhR) SPL42 (cyhS) hphMX::cen1 imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210 pdp3Δ::natMX	This study	PSB689
h-SPSQ (cyhR) SPL42 (cyhS) hphMX::cen1 imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210 mst2Δ::natMX	This study	PSB1122
h-SPSQ (cyhR) SPL42 (cyhS) hphMX::cen1 imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210 pdp3D::natMX mst2Δ::kanMX	This study	PSB2099
h? otr1R(SphI)::ade6-4LexAb.s. (binding site) leu1-32 ura4-D18 or DS/E ade6-M210	This study	spb2835
h+ otr1R(SphI)::ade6-4LexAb.s. leu1-32 ura4-D18 or DS/E ade6-M210 LexA-mst2	This study	spb2821
h+ otr1R(SphI)::ade6-4LexAb.s. leu1-32 ura4-D18 or DS/E ade6-M210 LexA-mst2(E274Q) cat.dead	This study	spb2822
h? otr1R(SphI)::ade6-4LexAb.s. leu1-32 ura4-D18 or DS/E ade6-M210 pdp3Δ::kanMX	This study	spb2836
h+ otr1R(SphI)::ade6-4LexAb.s. leu1-32 ura4-D18 or DS/E ade6-M210 LexA-Mst2 pdp3Δ::kanMX	This study	spb2804
h+ otr1R(SphI)::ade6-4LexAb.s. leu1-32 ura4-D18 or DS/E ade6-M210 LexA-mst2(E274Q) cat.dead pdp3Δ::kanMX	This study	spb2852
h- leu1-32 ura4-D18 or DS/E otr1R(SphI)::ade6-4LexAb.s. ade6-M210 set2Δ::kanMX	This study	spb2881
h+ otr1R(SphI)::ade6-4LexAb.s. leu1-32 ura4-D18 or DS/E ade6-M210 set2Δ::kanMX LexA-mst2	This study	spb2885
h? otr1R(SphI)::ade6-4LexAb.s. leu1-32 ura4-D18 or DS/E ade6-M210 set2Δ::kanMX LexA-mst2(E274Q) cat.dead	This study	spb2894
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) gcn5Δ::kanMX	This study	spb2101
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) pdp3Δ::kanMX	This study	spb2153
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX pdp3Δ::kanMX	This study	spb2115
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX brl1-K242R	This study	spb2982
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX brl1-K242Q	This study	spb2983
h+leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX mst2Δ::kanMX brl1-K242Q	This study	spb2984
h+leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX mst2Δ::kanMX brl1-K242R	This study	spb3023
h-leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX mst2Δ::kanMX paf1SMS8::LEU2 brl1-K242R	This study	spb3024
h-leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 mst2Δ::kanMX brl1-K242Q	This study	spb2996
h+leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX mst2Δ::kanMX dcr1Δ::hphMX	This study	spb2364
h+leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX dcr1Δ::hphMX paf1sms8::LEU2 mst2Δ::kanMX	This study	spb2661
h-leu1-32 ura4-D18 ade6-M210 trp1+::ade6+nmt1+::ade6-hp+::natMX dcr1Δ::hphMX paf1sms8::LEU2 mst2Δ::kanMX	This study	spb2662
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX arb2Δ::kanMX	This study	spb1739
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX arb1Δ::kanMX	This study	spb1740
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX cid12Δ::kanMX	This study	spb1741
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX ers1Δ::kanMX	This study	spb1745
h90mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX stc1Δ::kanMX	This study	spb1747
h? mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-? ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX tas3Δ::kanMX	This study	spb1753
h? mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-? ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX chp1Δ::kanMX	This study	spb1756
h? mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-? ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX rik1Δ::kanMX	This study	spb1757
h? mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-? ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMXD hrr1Δ::kanMX	This study	spb1772
h90 mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-M210 ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX rdp1Δ::kanMX	This study	spb1774
h? mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-? ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX raf1Δ::kanMX	This study	spb1802
h? mat3::GFP-natMX (ura4 promoter and adh1 terminator) ura4-DS/E leu1-32 ade6-? ncRNA.95Δ::URA3 (C. albicans) mst2Δ::hphMX raf2Δ::kanMX	This study	spb1803
h+SPSQ (cyhR) hphMX::cen1 imr1L(NcoI)::ura4+otr1R(SphI)::ade6+leu1-32 ura4-DS/E ade6-M210 clr3Δ::kanMX	This study	PSB1524
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX gcn5Δ::kanMX	This study	spb2404
h-leu1-32 ura4-D18 ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX gcn5Δ::kanMX paf1SMS8::LEU	This study	spb2443
h+leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 mst2Δ::kanMX brl1-K242Q	This study	spb3115
h+leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 mst2Δ::kanMX brl1-K242Q	This study	spb3116
h+leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 mst2Δ::kanMX brl1-K242Q	This study	spb3117
h+leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 mst2Δ::kanMX brl1-K242R	This study	spb3118
h+leu1-32 ura4-D18 ade6-M210 or ade6-704 trp1+::ade6+nmt1+::ade6-hp+::natMX paf1-sms8::LEU2 mst2Δ::kanMX brl1-K242R	This study	spb3119
Oligonucleotides
Primers	This study	Table S2
Recombinant DNA
pFa6a 81xnmt1 - Dam - mst2	This study	pMB1436
pJR1 - 3xL - LexA - Mst2 gDNA	This study	pMB1636
pJR1 - 3xL - LexA - Mst2 mut (E274Q)-gDNA	This study	pMB1639
Software and Algorithms
ImageJ 1.47v	(Schneider et al., 2012)	N/A
R	(Team, 2014)	https://www.r-project.org/
QuasR	(Gaidatzis et al., 2015)	N/A
Proteome Discoverer 2.1 software	Thermo Fisher	Cat# IQLAAEGAB SFAKJMAUH
Other
Illumina HiSeq2500	Illumina	N/A
GeneChip Scanner 3000 7G System	Affymetrix	Cat# 00-0213
Agilent 1100 system	Agilent	Cat# DE33201061
Orbitrap Fusion Tribrid	Thermo Fisher	Cat# IQLAAEGA APFADBMBCX
Easy nLC 1000 system	Thermo Fisher	Cat# LC-010190