Table 1. Nuclear body proteins... | Rockefeller University Press

Table 1.

Nuclear body proteins identified by RNase sensitivity screening

Nuclear body and protein	RNA-binding domains	Other domains or motifs	Colocalized markers	Novel	Low-complexity domains	Prion-like domains	Disassembly rate
							%
Paraspeckle
CPSF7	RRM	-	PSPC1	No	Yes	No	12
ELAVL1	3 RRMs	-	PSPC1	Yes	No	No	7
FUS	RRM	ZnF_RanBP2	PSPC1	No	Yes	Yes	19
HNRNPA1	2 RRMs	-	PSPC1	No	Yes	Yes	5
HNRNPUL1	-	SAP, SPRY	PSPC1	No	Yes	Yes	3
PSPC1	2 RRMs	-	PSPC1	No	Yes	Yes	8
RBFOX2	RRM	-	PSPC1	Yes	Yes	No	16
RBM7	RRM	-	PSPC1	No	Yes	No	6
RBM14	2 RRMs	-	PSPC1	No	Yes	Yes	2
	RRM	RS	PSPC1	No	Yes	No	11
TARDBP	2 RRMs	-	PSPC1	No	Yes	Yes	4
Nuclear speckle
FYTTD1	-	UAP56-binding	SRSF2/SC35	No	No	No	4
LSM6	-	-	SRSF2/SC35	Yes	No	No	0
RBM5	2 RRMs	G-patch, ZnF_RanBP2, ZnF_C2H2	SRSF2/SC35	No	Yes	Yes	17
SMNDC1	-	Tudor	SRSF2/SC35	No	Yes	No	2
SNRPE	-	-	SRSF2/SC35	No	Yes	No	18
SRSF1	2 RRMs	RS	SRSF2/SC35	No	Yes	No	3
SRSF7	RRM	RS, ZnF_CCHC	SRSF2/SC35	No	Yes	No	5
YTHDC1	-	YTH, Coiled_coil	SRSF2/SC35	No	Yes	No	9
ZC3H11A	-	Coiled_coil, 3 ZnF_C3H1	SRSF2/SC35	No	Yes	No	18
SNB
CCAR2/DBC1	-	Coiled_coil	KHDRBS1/Sam68	Yes	Yes	No	17
KHDRBS1/Sam68	KH	-	KHDRBS1/Sam68	No	Yes	No	4
HNRNPD	2 RRMs	-	KHDRBS1/Sam68	Yes	Yes	Yes	15
STRBP	2 DSRM	DZF	KHDRBS1/Sam68	Yes	Yes	No	4
ZMAT4	-	4 ZnF_C2H2	KHDRBS1/Sam68	Yes	No	No	13
ZNF346	-	4 ZnF_C2H2	KHDRBS1/Sam68	Yes	No	No	11
ZNF385B	-	4 ZnF_C2H2	KHDRBS1/Sam68	Yes	Yes	No	0
Cajal body
GTF2H1	-	2 BSD	COIL	No	Yes	No	14
SNRPB2	2 RRMs	-	COIL	No	Yes	Yes	10
Centromere
ZNF549	-	15 ZnF_C2H2	CENPB	Yes	No	No	9
Unknown
C1orf147	-	-	-	Yes	No	No	13
PCBP4	3 KH	-	-	Yes	Yes	No	5

Nuclear body and protein	RNA-binding domains	Other domains or motifs	Colocalized markers	Novel	Low-complexity domains	Prion-like domains	Disassembly rate
							%
Paraspeckle
CPSF7	RRM	-	PSPC1	No	Yes	No	12
ELAVL1	3 RRMs	-	PSPC1	Yes	No	No	7
FUS	RRM	ZnF_RanBP2	PSPC1	No	Yes	Yes	19
HNRNPA1	2 RRMs	-	PSPC1	No	Yes	Yes	5
HNRNPUL1	-	SAP, SPRY	PSPC1	No	Yes	Yes	3
PSPC1	2 RRMs	-	PSPC1	No	Yes	Yes	8
RBFOX2	RRM	-	PSPC1	Yes	Yes	No	16
RBM7	RRM	-	PSPC1	No	Yes	No	6
RBM14	2 RRMs	-	PSPC1	No	Yes	Yes	2
	RRM	RS	PSPC1	No	Yes	No	11
TARDBP	2 RRMs	-	PSPC1	No	Yes	Yes	4
Nuclear speckle
FYTTD1	-	UAP56-binding	SRSF2/SC35	No	No	No	4
LSM6	-	-	SRSF2/SC35	Yes	No	No	0
RBM5	2 RRMs	G-patch, ZnF_RanBP2, ZnF_C2H2	SRSF2/SC35	No	Yes	Yes	17
SMNDC1	-	Tudor	SRSF2/SC35	No	Yes	No	2
SNRPE	-	-	SRSF2/SC35	No	Yes	No	18
SRSF1	2 RRMs	RS	SRSF2/SC35	No	Yes	No	3
SRSF7	RRM	RS, ZnF_CCHC	SRSF2/SC35	No	Yes	No	5
YTHDC1	-	YTH, Coiled_coil	SRSF2/SC35	No	Yes	No	9
ZC3H11A	-	Coiled_coil, 3 ZnF_C3H1	SRSF2/SC35	No	Yes	No	18
SNB
CCAR2/DBC1	-	Coiled_coil	KHDRBS1/Sam68	Yes	Yes	No	17
KHDRBS1/Sam68	KH	-	KHDRBS1/Sam68	No	Yes	No	4
HNRNPD	2 RRMs	-	KHDRBS1/Sam68	Yes	Yes	Yes	15
STRBP	2 DSRM	DZF	KHDRBS1/Sam68	Yes	Yes	No	4
ZMAT4	-	4 ZnF_C2H2	KHDRBS1/Sam68	Yes	No	No	13
ZNF346	-	4 ZnF_C2H2	KHDRBS1/Sam68	Yes	No	No	11
ZNF385B	-	4 ZnF_C2H2	KHDRBS1/Sam68	Yes	Yes	No	0
Cajal body
GTF2H1	-	2 BSD	COIL	No	Yes	No	14
SNRPB2	2 RRMs	-	COIL	No	Yes	Yes	10
Centromere
ZNF549	-	15 ZnF_C2H2	CENPB	Yes	No	No	9
Unknown
C1orf147	-	-	-	Yes	No	No	13
PCBP4	3 KH	-	-	Yes	Yes	No	5

The low-complexity region and prion-like domain were judged using Prion-like amino acid composition (http://plaac.wi.mit.edu/) and GlobPlot (http://globplot.embl.de/), respectively. RNase sensitivity (Disassembly rate) was measured by the ratio of the number of nuclear foci–positive cells after RNase treatment relative to the number before RNase treatment (n > 100). RNase sensitivities of C1orf108 and COIL were 103% and 105%, respectively. -, not applicable; RRM, RNA recognition motif; ZnF_RanBP2, zinc finger, RanBP2-type; SAP, SAF-A/B, acinus, and PIAS; SPRY, SPla and the ryanodine receptor; RS, arginine/serine-rich; G-patch, glycine-rich nucleic binding domain; ZnF_C2H2, zinc finger, C2H2-like; ZnF_CCHC, zinc finger, CCHC-type; YTH, YT521-B homology; ZnF_C3H1, zinc finger, C3H1-type; DZF, domain associated with zinc fingers; BSD, BTF2-like transcription factors, Synapse-associated proteins, and DOS2-like proteins.

View Large

This Feature Is Available To Subscribers Only