ExoCarta: Gene summary

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Gene description for EXOSC4
Gene name	exosome component 4
Gene symbol	EXOSC4
Other names/aliases	RRP41 RRP41A Rrp41p SKI6 Ski6p hRrp41p p12A
Species	Homo sapiens
Database cross references - EXOSC4
ExoCarta	ExoCarta_54512
Vesiclepedia	VP_54512
Entrez Gene	54512
HGNC	18189
MIM	606491
UniProt	Q9NPD3
EXOSC4 identified in sEVs derived from the following tissue/cell type
Chondrocytes	35931686
Chondrocytes	35931686
Mesenchymal stem cells	36408942
Thymus	23844026

Gene ontology annotations for EXOSC4

Molecular Function
	3'-5'-RNA exonuclease activity	GO:0000175	NAS
	RNA binding	GO:0003723	IBA
	RNA exonuclease activity	GO:0004532	IDA
	protein binding	GO:0005515	IPI
	mRNA 3'-UTR AU-rich region binding	GO:0035925	IDA
Biological Process
	maturation of 5.8S rRNA	GO:0000460	IMP
	nuclear-transcribed mRNA catabolic process	GO:0000956	IMP
	rRNA processing	GO:0006364	NAS
	RNA processing	GO:0006396	IDA
	RNA catabolic process	GO:0006401	IDA
	rRNA catabolic process	GO:0016075	IBA
	positive regulation of cell growth	GO:0030307	IMP
	U4 snRNA 3'-end processing	GO:0034475	IBA
	DNA deamination	GO:0045006	IDA
	defense response to virus	GO:0051607	IMP
	nuclear mRNA surveillance	GO:0071028	IBA
	nuclear mRNA surveillance	GO:0071028	IMP
	histone mRNA catabolic process	GO:0071044	IMP
	poly(A)-dependent snoRNA 3'-end processing	GO:0071051	IBA
Subcellular Localization
	nuclear exosome (RNase complex)	GO:0000176	IBA
	nuclear exosome (RNase complex)	GO:0000176	NAS
	cytoplasmic exosome (RNase complex)	GO:0000177	IBA
	cytoplasmic exosome (RNase complex)	GO:0000177	NAS
	exosome (RNase complex)	GO:0000178	IDA
	exosome (RNase complex)	GO:0000178	NAS
	euchromatin	GO:0000791	IMP
	nucleus	GO:0005634	IDA
	nucleoplasm	GO:0005654	IDA
	nucleoplasm	GO:0005654	TAS
	nucleolus	GO:0005730	IBA
	nucleolus	GO:0005730	IDA
	nucleolus	GO:0005730	NAS
	cytoplasm	GO:0005737	IDA
	cytoplasm	GO:0005737	NAS
	cytosol	GO:0005829	IDA
	cytosol	GO:0005829	TAS
	intracellular membrane-bounded organelle	GO:0043231	IDA
	nucleolar exosome (RNase complex)	GO:0101019	NAS

Experiment description of studies that identified EXOSC4 in sEVs

Experiment ID

497

MISEV standards
✘	Biophysical techniques
✔ CD9\|CD151\|CD63\|CD81\|CD82\|FLOT1\|FLOT2\|GAPDH\|LAMP1\|LAMP2\|RAB5A\|SDCBP\|TFRC\|TSG101\|UCHL1	Enriched markers
✘	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

35931686

Organism

Homo sapiens

Experiment description

Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression

Authors

"Varela-EirÃn M, Carpintero-FernÃ¡ndez P, GuitiÃ¡n-CaamaÃ±o A, Varela-VÃ¡zquez A, GarcÃa-Yuste A, SÃ¡nchez-Temprano A, Bravo-LÃ³pez SB, YaÃ±ez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, MayÃ¡n MD."

Journal name

Cell Death Dis

Publication year

2022

Sample

Chondrocytes

Sample name

T/C-28a2

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectometry

Experiment ID

498

MISEV standards
✔ EM	Biophysical techniques
✔ CD9\|CD151\|CD63\|CD81\|CD82\|FLOT1\|FLOT2\|GAPDH\|LAMP1\|LAMP2\|RAB5A\|SDCBP\|TFRC\|TSG101\|UCHL1	Enriched markers
✘	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

35931686

Organism

Homo sapiens

Experiment description

Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression

Authors

Journal name

Cell Death Dis

Publication year

2022

Sample

Chondrocytes

Sample name

T/C-28a2

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectometry

Experiment ID

488

MISEV standards
✔ EM	Biophysical techniques
✔ CD9\|CD81\|CD63\|GAPDH\|SDCBP\|LAMP1\|TFRC\|UCHL1\|FLOT2\|LAMP2\|FLOT1\|ICAM1\|RAB5B\|CD151\|RAB35\|TSG101\|RAB5A\|CD82	Enriched markers
✔ CANX	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Homo sapiens

Experiment description

Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells

Authors

"Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."

Journal name

Proteomics

Publication year

2023

Sample

Mesenchymal stem cells

Sample name

UCMSC

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Western blotting
Mass spectometry

Experiment ID

217

MISEV standards
✔ EM	Biophysical techniques
✔ TSG101\|CD81\|CD9\|CD63	Enriched markers
✘	Negative markers
✔ NTA	Particle analysis

Identified molecule

protein

Identification method

Mass spectrometry

PubMed ID

23844026

Organism

Homo sapiens

Experiment description

Characterization of human thymic exosomes.

Authors

"Skogberg G, Gudmundsdottir J, van der Post S, Sandstrom K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O."

Journal name

PLoS One

Publication year

2013

Sample

Thymus

Sample name

Normal-Thymus

Isolation/purification methods

Differential centrifugation
Filtration
Ultracentrifugation

Flotation density

Molecules identified in the study

Protein

Methods used in the study

Mass spectrometry

Protein-protein interactions for EXOSC4

Protein Interactor

ExoCarta ID

Identification method

PubMed

Species

UBE2H

7328

Affinity Capture-MS

Homo sapiens

PSMA6

5687

Co-fractionation

Homo sapiens

SPATS2

Affinity Capture-MS

Homo sapiens

RIT1

6016

Negative Genetic

Homo sapiens

UTP18

Affinity Capture-MS

Homo sapiens

SLIT2

9353

Affinity Capture-MS

Homo sapiens

EXOSC7

23016

Two-hybrid		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

MRPL48

Affinity Capture-MS

Homo sapiens

MED17

Affinity Capture-MS

Homo sapiens

WDR3

Affinity Capture-MS

Homo sapiens

SKIV2L

6499

Two-hybrid		Homo sapiens
Two-hybrid		Homo sapiens

RPS4X

6191

Affinity Capture-MS

Homo sapiens

PSMA4

5685

Co-fractionation

Homo sapiens

GTF2IRD1

Two-hybrid

Homo sapiens

RPL37A

6168

Affinity Capture-MS

Homo sapiens

DHPS

1725

Affinity Capture-MS

Homo sapiens

NOP56

10528

Co-fractionation

Homo sapiens

DDX47

51202

Co-fractionation

Homo sapiens

UTP3

57050

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

WDR36

134430

Affinity Capture-MS

Homo sapiens

RPS3

6188

Affinity Capture-MS

Homo sapiens

USP36

Affinity Capture-Western		Homo sapiens
Affinity Capture-MS		Homo sapiens

PSIP1

11168

Co-fractionation

Homo sapiens

CAPZB

832

Affinity Capture-MS

Homo sapiens

EXOSC2

23404

Two-hybrid		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Cross-Linking-MS (XL-MS)		Homo sapiens
Two-hybrid		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

C1D

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

H1FX

8971

Co-fractionation

Homo sapiens

SMPD4

55627

Two-hybrid

Homo sapiens

FBXW7

Synthetic Lethality		Homo sapiens
Affinity Capture-MS		Homo sapiens

RPS10

6204

Affinity Capture-MS

Homo sapiens

ETFA

2108

Affinity Capture-MS

Homo sapiens

OBSL1

23363

Affinity Capture-MS

Homo sapiens

TSEN15

116461

Two-hybrid

Homo sapiens

TOM1

10043

Co-fractionation

Homo sapiens

ABCE1

6059

Affinity Capture-MS

Homo sapiens

RSRC1

Affinity Capture-MS

Homo sapiens

EXOSC4

54512

Two-hybrid		Homo sapiens
Two-hybrid		Homo sapiens

EED

Affinity Capture-MS

Homo sapiens

ATG16L1

55054

Affinity Capture-MS

Homo sapiens

MTDH

92140

Affinity Capture-MS

Homo sapiens

EXOSC6

118460

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

SPATA5L1

79029

Affinity Capture-MS

Homo sapiens

MECP2

4204

Affinity Capture-MS

Homo sapiens

CTPS1

1503

Co-fractionation

Homo sapiens

MPHOSPH6

10200

Co-fractionation		Homo sapiens
Reconstituted Complex		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

SDCBP

6386

Two-hybrid

Homo sapiens

COMMD4

54939

Affinity Capture-MS

Homo sapiens

EEF1A1

1915

Two-hybrid

Homo sapiens

GAR1

54433

Affinity Capture-MS

Homo sapiens

EXOSC9

5393

Two-hybrid		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Two-hybrid		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

E2F4

Affinity Capture-MS

Homo sapiens

TTC37

9652

Co-fractionation

Homo sapiens

DIS3L

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

SRP9

6726

Affinity Capture-MS

Homo sapiens

DIS3

22894

Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens

HIST1H4A

8359

Affinity Capture-MS

Homo sapiens

NOL6

65083

Affinity Capture-MS

Homo sapiens

DRG1

4733

Affinity Capture-MS

Homo sapiens

Nudt21

68219

Two-hybrid

Mus musculus

RBM7

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

RPL18A

6142

Affinity Capture-MS

Homo sapiens

PWP2

5822

Affinity Capture-MS

Homo sapiens

CIRH1A

84916

Affinity Capture-MS

Homo sapiens

NTRK1

4914

Affinity Capture-MS

Homo sapiens

IFI16

3428

Affinity Capture-MS

Homo sapiens

HIST1H1E

3008

Co-fractionation

Homo sapiens

DXO

Two-hybrid

Homo sapiens

EXOSC5

56915

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

AKR1A1

10327

Two-hybrid

Homo sapiens

HECTD1

25831

Affinity Capture-MS

Homo sapiens

ZFC3H1

196441

Affinity Capture-MS

Homo sapiens

RRP1B

23076

Affinity Capture-MS

Homo sapiens

Exosc1

Affinity Capture-MS

Mus musculus

ZCCHC8

55596

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

HNRNPD

3184

Two-hybrid

Homo sapiens

PSMA3

5684

Co-fractionation

Homo sapiens

HBS1L

10767

Reconstituted Complex		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

LRRC59

55379

Affinity Capture-MS

Homo sapiens

RC3H2

Affinity Capture-MS

Homo sapiens

DCAF13

25879

Affinity Capture-MS

Homo sapiens

PHF1

Affinity Capture-MS

Homo sapiens

SHQ1

Affinity Capture-MS

Homo sapiens

FAHD1

81889

Two-hybrid

Homo sapiens

LRRC47

57470

Affinity Capture-MS

Homo sapiens

GADD45GIP1

Two-hybrid

Homo sapiens

HNRNPA1

3178

Affinity Capture-MS

Homo sapiens

UPF3A

Affinity Capture-Western

Homo sapiens

EIF2S2

8894

Affinity Capture-MS

Homo sapiens

PDCD11

22984

Affinity Capture-MS

Homo sapiens

SLTM

79811

Affinity Capture-MS

Homo sapiens

PAPD5

64282

Affinity Capture-MS

Homo sapiens

GIGYF2

26058

Affinity Capture-MS

Homo sapiens

PSPC1

55269

Affinity Capture-MS

Homo sapiens

HMGB3

3149

Co-fractionation

Homo sapiens

LUM

4060

Affinity Capture-MS

Homo sapiens

ZC3H18

Affinity Capture-MS

Homo sapiens

RBM14-RBM4

100526737

Affinity Capture-MS

Homo sapiens

EXOSC3

51010

Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-MS		Homo sapiens
Two-hybrid		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

MPZL1

9019

Two-hybrid

Homo sapiens

100

SKIV2L2

23517

Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

101

DDRGK1

65992

Affinity Capture-MS

Homo sapiens

102

RPS29

6235

Affinity Capture-MS

Homo sapiens

103

ADAR

103

Affinity Capture-MS

Homo sapiens

104

UPF2

26019

Affinity Capture-Western

Homo sapiens

105

EIF4E2

Affinity Capture-MS

Homo sapiens

106

RPS16

6217

Affinity Capture-MS

Homo sapiens

107

RPL13

6137

Affinity Capture-MS

Homo sapiens

108

EXOSC10

5394

Two-hybrid		Homo sapiens
Affinity Capture-Western		Homo sapiens
Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Two-hybrid		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

109

PLEKHA4

57664

Affinity Capture-MS

Homo sapiens

110

ESR2

Affinity Capture-MS

Homo sapiens

111

TXNDC16

57544

Affinity Capture-MS

Homo sapiens

112

LIG3

3980

Affinity Capture-MS

Homo sapiens

113

PPARA

Two-hybrid

Homo sapiens

114

FBXL6

Affinity Capture-MS

Homo sapiens

115

TP53

7157

Synthetic Growth Defect

Homo sapiens

116

NMI

Co-fractionation

Homo sapiens

117

IVNS1ABP

Affinity Capture-MS

Homo sapiens

118

OSTM1

28962

Affinity Capture-Western

Homo sapiens

119

CHAMP1

Affinity Capture-MS

Homo sapiens

120

THOP1

7064

Affinity Capture-MS

Homo sapiens

121

KPNA6

23633

Co-fractionation

Homo sapiens

122

KNOP1

400506

Affinity Capture-MS

Homo sapiens

123

SMURF1

57154

Affinity Capture-MS

Homo sapiens

124

PTPN2

5771

Affinity Capture-MS

Homo sapiens

125

WTAP

9589

Two-hybrid

Homo sapiens

126

TBL3

10607

Affinity Capture-MS

Homo sapiens

127

PRRC2B

Two-hybrid

Homo sapiens

128

NEK1

Two-hybrid

Homo sapiens

129

WDR18

57418

Affinity Capture-MS

Homo sapiens

130

PSMA1

5682

Co-fractionation

Homo sapiens

131

UFL1

23376

Affinity Capture-MS

Homo sapiens

132

LRRC8D

55144

Two-hybrid

Homo sapiens

133

NCL

4691

Affinity Capture-MS

Homo sapiens

134

PSMA5

5686

Co-fractionation

Homo sapiens

135

EIF2B4

8890

Affinity Capture-MS

Homo sapiens

136

UPF1

5976

Affinity Capture-Western

Homo sapiens

137

CBX8

57332

Affinity Capture-MS

Homo sapiens

138

CIT

11113

Affinity Capture-MS

Homo sapiens

139

KRAS

3845

Negative Genetic

Homo sapiens

140

HNRNPU

3192

Affinity Capture-MS

Homo sapiens

141

C9orf72

Affinity Capture-MS

Homo sapiens

142

PHF10

Affinity Capture-MS

Homo sapiens

143

PSMC4

5704

Co-fractionation

Homo sapiens

144

PRMT1

3276

Affinity Capture-MS

Homo sapiens

145

EXOSC1

51013

Two-hybrid		Homo sapiens
Two-hybrid		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

146

EXOSC8

Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Co-fractionation		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens
Affinity Capture-MS		Homo sapiens

147

PARN

Co-fractionation

Homo sapiens

View the network

Pathways in which EXOSC4 is involved

Pathway	Evidence	Source
ATF4 activates genes in response to endoplasmic reticulum stress	TAS	Reactome
Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA	TAS	Reactome
Cellular responses to stimuli	TAS	Reactome
Cellular responses to stress	TAS	Reactome
Deadenylation-dependent mRNA decay	TAS	Reactome
KSRP (KHSRP) binds and destabilizes mRNA	TAS	Reactome
Major pathway of rRNA processing in the nucleolus and cytosol	TAS	Reactome
Metabolism of RNA	TAS	Reactome
mRNA decay by 3' to 5' exoribonuclease	TAS	Reactome
PERK regulates gene expression	TAS	Reactome
Regulation of mRNA stability by proteins that bind AU-rich elements	TAS	Reactome
rRNA processing	TAS	Reactome
rRNA processing in the nucleus and cytosol	TAS	Reactome
Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA	TAS	Reactome
Unfolded Protein Response (UPR)	TAS	Reactome

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