Table S1.

NGS summary

Sample	Type of experiment	Total number of reads	Reads with inserts, %	Size of mapped DNA/RNA
Input	IPOUD	9,928,905	99.90	nd
WT no UV rep 1	IPOUD	10,071,017	96.13	136 bp ± 1.38*
WT no UV rep 2	IPOUD	10,529,991	98.37	130.8 bp ± 1.59*
WT UV rep 1	IPOUD	11,518,309	99.66	187.2 bp ± 12*
WT UV rep 2	IPOUD	11,901,736	98.89	150.7 bp ± 2.97*
WT UV rep 3	IPOUD	11,026,009	98.37	153.6 bp ± 1.55*
WT UV rep 4	IPOUD	13,338,184	99.59	138.4 bp ± 2.21*
WT no UV rep 1	Small RNA seq	12,145,652	99.71	15 nt to 45 nt
WT no UV rep 2	Small RNA seq	11,705,035	99.83	15 nt to 45 nt
WT UV rep 1	Small RNA seq	15,395,135	99.80	15 nt to 45 nt
WT UV rep 2	Small RNA seq	11,545,623	99.84	15 nt to 45 nt
WT UV rep 3	Small RNA seq	14,805,788	99.79	15 nt to 45 nt
WT UV rep 4	Small RNA seq	12,812,206	99.51	15 nt to 45 nt
nrpd1 no UV rep 1	Small RNA seq	11,731,877	99.34	15 nt to 45 nt
nrpd1 no UV rep 2	Small RNA seq	15,298,205	99.80	15 nt to 45 nt
nrpd1 UV rep 1	Small RNA seq	14,239,678	99.83	15 nt to 45 nt
nrpd1 UV rep 2	Small RNA seq	15,605,926	99.68	15 nt to 45 nt
Input no UV	Small RNA seq	30,401,033	99.92	15 nt to 45 nt
IP DDB2 no UV	RIP and small RNA seq	25,591,663	99.34	15 nt to 45 nt
IP AGO1 no UV	RIP and small RNA seq	22,389,349	96.52	15 nt to 45 nt
Input UV	Small RNA seq	22,932,956	99.67	15 nt to 45 nt
IP DDB2 UV	RIP and small RNA seq	23,363,408	99.50	15 nt to 45 nt
IP AGO1 UV	RIP and small RNA seq	31,510,294	99.92	15 nt to 45nt

^*Average size in base pair ± SD.