KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
IntS1	Ezzeddine et al., 2011
IntS9	Ezzeddine et al., 2011
IntS11	Ezzeddine et al., 2011
alpha-tubulin	abcam ab15246	AB_301787
H3K4me3	EpiCypher 13-0028
Normal Rabbit serum	Invitrogen 01-610-1
Chemicals, Peptides, and Recombinant Proteins
AzNTPs	TriLink Technologies	Cat# K-1005
Biotin-11-NTPs	Perkin Elmer	Cat# NEL54(2/3/4/5)001
Critical Commercial Assays
NEBNext Ultra II DNA library kit	NEB	Cat# E7103S
Deposited Data
Raw and analyzed data	This paper	GEO: GSE114467
Start-seq from Triptolide-treated S2 cells	Krebs et al., 2017	GEO: GSE77369
H3K4me1, H3K4me3 and H3K36me3 ChIP-seq from S2 cells	Henriques et al., 2018	GEO: GSE85191
Start-seq from Control and Rrp40-depleted S2 cells	Henriques et al., 2013	GEO: GSE49078
Chromatin RNA-seq from IntS11-depleted HeLa cells	Lai et al., 2015	GEO: GSE68401
H3K4me1, H3K4me3 and H3K36me3 ChIP-seq from HeLa cells	Gerstein et al., 2012	GEO: GSE29611
PRO-seq from DMSO-treated HeLa cells	Nilson et al. 2017	GEO: GSE100742
Chromatin RNA-seq from Xrn2 or CPS73-depleted HeLa cells	Nojima et al., 2015	GEO: GSE60358
Experimental Models: Cell Lines
DL1 cells	Dr. Sara Cherry, UPenn
S2-DGRC clone 6	DGRC	Stock number 6
DL1 FLAG-eGFP	This paper
DL1 FLAG-IntS11WT	This paper
DL1 FLAG-IntS11E203Q	This paper
Oligonucleotides
Table S3	This paper
Recombinant DNA
pUB-3xFLAG vector	Chen et al., 2012
pMT-puro	David Sabatini lab	Addgene #17923
pMT-FLAG-dIntS11-WT-puro	This paper
pMT-FLAG-dIntS11-E203Q-puro	This paper
pMT-FLAG-eGFP-puro	This paper
Software and Algorithms
bowtie 1.2.2	Langmead et al., 2009
R v3.3.1	www.r-project.org
Rstudio v1.0.136	www.rstudio.com
featureCounts	Liao et al., 2014
DESeq2	Love et al., 2014
MISO	Katz et al., 2010
Prism v8.1.2	GraphPad
Partek Genomics Suite v6.15.0127	www.partek.com