Table S1 . Fly Stocks Used, Related to Experimental Procedures

 S1 For the HMG rescue construct, the first 240 nucleotides of maelstrom were deleted from the original FLAG-eGFP-Mael construct.flamencorestrictive and permissive flies(Sarot et al, 2004)All flies were aged 5 days at 25°C before analysis. 


	tj-GAL4 (DGRC # 104055);						
	tj-Gal4; gypsy-lacZ (Olivieri et al, 2010)					
	MTD-GAL4 (Ni et al., 2011);						
	armi RNAi (VDRC # 16205);						
	mael RNAi (VDRC # 100907 (KK));						
	mael RNAi (VDRC # 18198 (GD));; mael M391 /mael Df (Findley et al, 2003) mael Df (DGRC: 150235) (rescue experiments)				
	Short hairpin RNAi lines were cloned into the Valium-22 vector (Ni et al, 2011) modified
	with a white selection marker and integrated into the attp2 landing site reported in
	Markstein	et	al	(2008).	The	hairpin	sequence	for	mael	was
	CCGAAGCTTGTTCGCTTTCTA						
	y,w,hsFlp122;;act<CD2>GAL4, UAS-GFP (Olivieri et al, 2010)			
	FLAG-eGFP-Mael was cloned by inserting an N-terminal FLAG-eGFP cassette via	
	bacterial recombineering into a genomic rescue construct (3L : 22712955 -22721349)	
	which was integrated into the attp40 landing site.				

Table S2 . Primers for qPCR Analysis, Related to Experimental Procedures

 S2 
	GENE	Primer	Sequence
	rp49	rp49_fwd	CCGCTTCAAGGGACAGTATCTG
		rp49_rev	ATCTCGCCGCAGTAAACGC
	ZAM	ZAM_fwd	ACTTGACCTGGATACACTCACAAC
		ZAM_rev	GAGTATTACGGCGACTAGGGATAC
	HeT-A	HeT-A_fwd CGCGCGGAACCCATCTTCAGA
		HeT-A_rev	CGCCGCAGTCGTTTGGTGAGT
	DM412	412_fwd	AAAGTACGGTCCAATGAAGACG
		412_rev	GTGGTGATGAGCTGTTGATGTT
	actin5C	Act5C_fwd	AAGTTGCTGCTCTGGTTGTCG
		Act5C_rev	GCCACACGCAGCTCATTGTAG
	mdg1	Mdg1_fwd	AAACTCCAACTCCCAATCCG
		Mdg1_rev	AGTGGTCCCTCGCAGTCGTT
	gypsy	Gypsy_fwd	CAACAATCTGAACCCACCAATCT
		Gypsy_rev	TATGAACATCATGAGGGTGAACG
	piwi locus	Piwi_fwd	TTACCCGTACTTCGTCCTGATG
		Piwi_rev	TTGGGCACCGAAATAACTCA
	mael locus	Mael_fwd	AGACCACACTTCCTTTGCC
		Mael_rev	GTGCGTCGGTAAGTTCCTAG
	reporter_1	1_fwd	CGTTAGGTCCTGTTCATTGTTTA
		1_rev	CGTCAGCATTGTTCATACAAAG
	reporter_2	2_fwd	CTCGGCAACAGTATATTTGTGGT
		2_rev	AGGCGATTAAGTTGGGTAACG

Table S3 . Probes Used for Northern Blots, Related to Experimental Procedures

 S3 
	Probe	Sequence
	mir-310	AAAGGCCGGGAAGTGTGCAATA
	tj-piRNAs	GGTAATGGGAATGCACTTCTCTTGAA
	Idefix-piRNA	AAACTACTGGCAATCGTTTGGGAA

Table S4 . siRNAs Used for RNAi in OSCs, Related to Experimental Procedures

 S4 
	GENE	siRNA	Sequence
	eGFP	eGFP_guide	ACUUCAGGGUCAGCUUGCCTT
		eGFP_passenger	GGCAAGCUGACCCUGAAGUTT
	armi	Armi_guide	UAAACUUAGCUUGACAGCGTT
		Armi_passenger	CGCUGUCAAGCUAAGUUUATT
	mael	Mael1_guide	UUCUUCGAACAAGCGAAAGUU
		Mael1_passenger	GAAGCUUGUUCGCUUUCUAUU
		Mael2_guide	UUCCAAAUACUACAAGCAUU
		Mael2_passenger	GGUUUAUGAUGUUCGUAAAUU
	piwi	Piwi_guide	CACCUUCACGCCUGGGAGCTT
		Piwi_passenger	GCUCCCAGGCGUGAAGGUGTT

Table S5 . Sequencing Data Used in This Study, Related to Experimental Procedures

 S5 
	cells methods	Genotype
	OSC RNA-seq	ctrl-KD
			piwi-KD
			armi-KD
			mael-KD
		GRO-seq	wild-type
			piwi-KD
		Rpb3 ChIP-seq	ctrl-KD
			ctrl-KD
			piwi-KD
			piwi-KD
			mael-KD
			mael-KD
		H3K9me3 ChIP-seq ctrl-KD
			ctrl-KD
			piwi-KD
			piwi-KD
			mael-KD
			mael-KD
		input ChIP-seq	ctrl-KD
			ctrl-KD
			piwi-KD
			piwi-KD
			mael-KD
			mael-KD
		DNA-seq	wild-type
		small RNA-seq	wild-type
	fly	Rpb3 ChIP-seq	tj-GAL4>tej RNAi
			tj-GAL4>tej RNAi
			tj-GAL4>armi RNAi
			tj-GAL4>armi RNAi
		small RNA-seq	flam(permissive)
		small RNA-seq	flam(reactive)

Table S6 . Coordinates of Heterochromatin Used in This Study, Related to Figure 5

 S6 
	chromosome start	end
	chr2L	20100000 23011544
	chr2LHet	1	368872
	chr2R	1	2400000
	chr2RHet	1	3288761
	chr3L	22500000 24543557
	chr3LHet	1	2555491
	chr3RHet	1	2517507
	chrU	1	10049037
	chrX	21300000 22422827
	chrXHet	1	204112
	chrYHet	1	347038