Table 3. Validations of our predicted RLR candidates by independent studies.

Gene symbol	Gene description	RLR rank	Described function	References	Type of regulation (literature) a	Type of regulation (our RNAi screens) b
CSNK2A1	Casein kinase II subunit alpha	45	The casein kinase II complex inhibits the RIG-I-mediated antiviral response through phosphorylation of RIG-I	[93]	-	0c
TRIM38	Tripartite motif-containing protein 38	56	Negative regulator of RIG-I-mediated IFNβ production by targeting AZI2 (NAP1) for degradation	[94]	-	-
RNF11	RING finger protein 11	78	Interacts with TBK1 and IKBKE (IKKε) to block TRAF3 interaction and restrict IRF3 activation	[95]	-
SMAD3	SMAD family member 3	100	Regulates dsRNA-induced transcriptional activation of IRF7 at the IFNβ promoter	[96]	+	0
UBE2D1	Ubiquitin-conjugating enzyme E2 D1	139	This Ubc5 E2 ligase is required for viral activation of IRF3 and MAVS by RIG-I	[97]	+	0
CDC37	Hsp90 co-chaperone Cdc37 (cell division cycle 37)	165	Regulates stability of TBK1 via Hsp90, allowing for induction of IFNβ in response to DNA viral and retroviral infections	[13]	+	+
RNF114	RING finger protein 114	181	Enhancer of dsRNA-induced production of type I IFN through positive feedback regulation	[45]	+	-
SRPK1	Serine/threonine-protein kinase SRPK1	235	Enhancer of RIG-I-dependent IFNβ and IFNλ1 promoter activation during Sendai virus infection, possibly via IRF3/7 phosphorylation	[98]	+	-
CSNK2A2	Casein kinase II subunit alpha prime	249	The casein kinase II complex inhibits the RIG-I-mediated antiviral response through phosphorylation of RIG-I	[93]	-	0c
G3BP1	GTPase-activating protein-binding protein 1	282	Functions in the formation of stress granules, which act as RLR signaling platforms that in some cases enhance IFN induction	[44]	+	+
UBE2I	SUMO-conjugating enzyme UBC9	284	Enhances RIG-I and MDA5 SUMOylation, which correlates with increased IFNβ expression and repressed virus replication	[99,100]	+
SUMO1	Small ubiquitin-related modifier 1	326	IRF3/7 SUMOylation down-regulates IFN production; RIG-I/MDA5 SUMOylation correlates with increased IFNβ expression	[99–101]	- / +
PPP1R15A	Protein phosphatase 1 regulatory subunit 15A	389	Required for IFNβ production induced by dsRNA and chikungunya virus in mouse; expression depends on PKR activation	[102]	+	+
TRIM14	Tripartite motif-containing protein 14	491	Interacts with MAVS upon viral infection, thereby recruiting IKKγ (NEMO), which leads to activation of IRF3 and NFκB	[43]	+	+
DDX60	DEAD box protein 60	616	Promotes virus-induced, RLR-mediated type I IFN expression and increases binding of RIG-I to dsRNA	[103]	+
				Total:	15	7 hits (out of 11)

^a '+': positive regulator (expected decrease in IFNβ induction upon knockdown). '-': negative regulator (expected increase in IFNβ induction upon knockdown).

^b Annotated cells (‘+’, ‘-’, ‘0’) indicate 11 candidate RLR genes that were tested in RNAi screen 1. ‘+’: down-hits from RNAi screen 1 (decreased RIG-I-mediated IFNβ induction upon knockdown, Z-score <-1.25). ‘-’: up-hits from RNAi screen 1 (increased RIG-I-mediated IFNβ induction upon knockdown, Z-score >1.25). ‘0’: no hit in RNAi screen 1, or inconsistent effect across RNAi screens 1 and 2 (CSNK2A1 and CSNK2A2, ^c).