Table 1.

Stable RNPs Identified by DIF-FRAC

Gene Names	Complex Name	Function	Soluble without RNA?a	Disease Links	CORUM/hu.MAPb	rna.MAP ID	DIF-FRAC Plot	RNP Classc	References
CLASP1	N/A	microtubule binding	yes	N/A	no/yes	3807		apo-stable	Efimov et al., 2007
CLASP2		microtubule dynamics
DAXX	DAXX-TP53 complex	transcription repression	yes	pancreatic neuroendocrine tumors	yes/no	4518		apo-stable	Zhao et al., 2004
TP53				glioblastoma multiforme					Dyer et al., 2017
				adrenocortical tumors
DRG1	Drg1/Dfrp1 complex	microtubule binding	yes	lung adenocarcinoma	no/no	4096		apo-stable	Lu et al., 2016
ZC3H15		microtubule polymerase							Schellhaus et al., 2017
		GTPase							Ishikawa et al., 2009
BOD1L1	SET1A/SET1B complexes	histone methyltransferase	yes	Fanconi anemia	yes/yes	2005, 3307		apo-stable	Vedadi et al., 2017
SETD1A		transcription regulation		mixed-lineage leukemia					Higgs et al., 2015
CXXC1*,d									Brown et al., 2017
ASH2L
RBBP5
WDR5
NIPSNAP1*	N/A	vesicular transport	no	inflammatory pain	no/yes	5822		apo-stable	Okuda-Ashitaka et al., 2012
NIPSNAP2*									Yamamoto et al., 2017
RPA1	replication protein A complex	single-stranded DNA binding	yes	Werner syndrome	yes/yes	3204		apo-stable	Machwe et al., 2011
RPA2*		DNA metabolism							Fan and Pavletich, 2012
RPA3*,d
FLII	FLII-LRRFIP1 complex	transcriptional activation	yes	prostate cancer	no/yes	3626		apo-stable	Wilson et al., 1998
LRRFIP1		actin binding							Wang et al., 2016
BAZ1A*	WCRF complex	chromatin remodeling	No	intellectual disability	yes/no	2105		compositional	Bochar et al., 2000
SMARCA5									Zaghlool et al., 2016
MICU1*,d	MICU1-MICU2 heterodimer	calcium ion transport	yes	myopathy with extrapyramidal signs	yes/yes	4318		structural	Logan et al., 2014
MICU2*,d
NOC4L	N/A	ribosome processing and biogenesis	no	recurrent pregnancy loss	no/yes	4220		structural	Suzuki et al., 2018
NOP14
SFPQ	PSF-p54(nrb) complex	splicing factor	yes	intellectual disability	yes/yes	327		apo-stable	Bladen et al., 2005
NONO		DNA recombination							Mircsof et al., 2015
RRP12	N/A	rRNA processing	no	N/A	no/yes	5795		structural	Zemp et al., 2009
RIOK2
H1FX
SAP18	N/A	SAP18 is involved in RNA processing and splicing	no	N/A	no/yes	6027		structural	Davis et al., 2010
NKTR
CCDC9		NKTR is involved in protein peptidyl-prolyl isomerization
LARP4	N/A	translation regulation	yes	N/A	no/yes	3327		apo-stable	Yang et al., 2011
LARP4B									Schäffler et al., 2010
XRCC5	Ku antigen complex	DNA damage and repair	yes	systemic lupus erythematosus	yes/no	2930		apo-stable	Spagnolo et al., 2006
XRCC6
SAMM50*,d	N/A	protein transport	yes	N/A	no/yes	1450		apo-stable
MTX3*,d
MTX2*
SLC25A5	prohibitin	apoptosis	yes	N/A	yes/no	204		apo-stable	Kasashima et al., 2006
VDAC2
PHB
HAX1*
PHB2*
TPP2	tripeptidyl-peptidase II	serine protease	yes	muscle wasting	yes/no			apo-stable	Schönegge et al., 2012
				obesity					Rockel et al., 2012
				cancer

^*Previously unreported RNA-associated proteins identified by DIF-FRAC (see Table S1).

^aInsolubility in the absence of RNA is inferred by an increase in apparent molecular weight of the complex upon RNA digestion or a complete disappearance of signal. This is consistent with the RNP’s being solubilized by RNA, as suggested by Maharana et al. (2018).

^bEvidence for all or some protein complex subunits interacting in CORUM or hu.MAP.

^cRNP classes apo-stable, structural, and compositional, as described in Figure 4.

^dPreviously unreported RNA-associated proteins that are above the 5% FDR cutoff.