ExoCarta: Gene summary

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Gene description for EXOSC2
Gene name	exosome component 2
Gene symbol	EXOSC2
Other names/aliases	RRP4 Rrp4p hRrp4p p7
Species	Homo sapiens
Database cross references - EXOSC2
ExoCarta	ExoCarta_23404
Vesiclepedia	VP_23404
Entrez Gene	23404
HGNC	17097
MIM	602238
UniProt	Q13868
EXOSC2 identified in exosomes derived from the following tissue/cell type
Bone marrow mesenchymal stem cells	36408942
Bone marrow mesenchymal stem cells	36408942
Bone marrow mesenchymal stem cells	36408942
Bone marrow mesenchymal stem cells	36408942
Mesenchymal stem cells	36408942

Gene ontology annotations for EXOSC2

Molecular Function
	3'-5'-RNA exonuclease activity	GO:0000175	TAS
	RNA binding	GO:0003723	IBA
	RNA exonuclease activity	GO:0004532	IDA
	protein binding	GO:0005515	IPI
	7S RNA binding	GO:0008312	TAS
Biological Process
	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	GO:0000467	IBA
	nuclear-transcribed mRNA catabolic process	GO:0000956	IBA
	rRNA processing	GO:0006364	TAS
	RNA processing	GO:0006396	IDA
	RNA catabolic process	GO:0006401	IDA
	positive regulation of cell growth	GO:0030307	IMP
	U4 snRNA 3'-end processing	GO:0034475	IBA
	CUT catabolic process	GO:0071034	IBA
	nuclear polyadenylation-dependent rRNA catabolic process	GO:0071035	IBA
	TRAMP-dependent tRNA surveillance pathway	GO:0071038	IBA
	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	IDA
	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
	nucleus	GO:0005634	IDA
	nucleoplasm	GO:0005654	IDA
	nucleoplasm	GO:0005654	TAS
	nucleolus	GO:0005730	IDA
	cytoplasm	GO:0005737	IDA
	cytosol	GO:0005829	IDA
	cytosol	GO:0005829	TAS
	nucleolar exosome (RNase complex)	GO:0101019	NAS

Experiment description of studies that identified EXOSC2 in exosomes

Experiment ID

489

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

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

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 6

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

490

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

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

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 7

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

491

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

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

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 8

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

492

MISEV standards
✔ EM	Biophysical techniques
✔ Cd9\|Cd81\|Cd63\|Gapdh\|Sdcbp\|Lamp1\|Aqp1\|Rab5a\|Icam1\|Cd82\|Itga2b\|Tsg101\|Lamp2\|Rab35\|Flot1\|Flot2\|Cd151\|Rab5b\|Tfrc\|Uchl1	Enriched markers
✔ Canx	Negative markers
✔ NTA	Particle analysis

Identified molecule

Protein

Identification method

Mass spectrometry

PubMed ID

36408942

Organism

Rattus norvegicus

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

Bone marrow mesenchymal stem cells

Sample name

BMSC - Passage 9

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

Protein-protein interactions for EXOSC2

Protein Interactor

ExoCarta ID

Identification method

PubMed

Species

RIT1

6016

Negative Genetic

Homo sapiens

SLIT2

9353

Affinity Capture-MS

Homo sapiens

EXOSC7

23016

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

MRPL48

Two-hybrid

Homo sapiens

DIS3

22894

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

FBXL4

26235

Affinity Capture-MS

Homo sapiens

PPIE

10450

Affinity Capture-MS

Homo sapiens

KPNB1

3837

Co-fractionation

Homo sapiens

UBC

7316

Affinity Capture-MS

Homo sapiens

CAND1

55832

Affinity Capture-MS

Homo sapiens

EIF4E2

Affinity Capture-MS

Homo sapiens

PEX1

5189

Affinity Capture-MS

Homo sapiens

USP36

Affinity Capture-MS

Homo sapiens

GALNT13

114805

Two-hybrid

Homo sapiens

C1D

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

RNF8

Two-hybrid

Homo sapiens

METTL22

Affinity Capture-MS

Homo sapiens

PRC1

9055

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

NPM1

4869

Affinity Capture-MS

Homo sapiens

MDC1

Affinity Capture-MS

Homo sapiens

ZNF408

Two-hybrid		Homo sapiens
Two-hybrid		Homo sapiens

MALSU1

Affinity Capture-MS

Homo sapiens

RSRC1

Affinity Capture-MS

Homo sapiens

EXOSC4

54512

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
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

EXOSC6

118460

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

MECP2

4204

Affinity Capture-MS

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

COMMD4

54939

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

EXOSC9

5393

Co-fractionation		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

AURKA

6790

Affinity Capture-MS

Homo sapiens

DIS3L

Affinity Capture-MS		Homo sapiens
Affinity Capture-Western		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

HIST1H4A

8359

Affinity Capture-MS

Homo sapiens

MEPCE

56257

Affinity Capture-MS

Homo sapiens

UTP15

84135

Affinity Capture-MS

Homo sapiens

DRG1

4733

Affinity Capture-MS

Homo sapiens

RBM7

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

RPL5

6125

Affinity Capture-MS

Homo sapiens

DEK

7913

Co-fractionation

Homo sapiens

CHMP4B

128866

Affinity Capture-MS

Homo sapiens

BARD1

580

Affinity Capture-MS

Homo sapiens

EXOSC5

56915

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

SBK3

Two-hybrid

Homo sapiens

BICD2

23299

Proximity Label-MS

Homo sapiens

WDR43

23160

Affinity Capture-MS

Homo sapiens

SPDYE4

Affinity Capture-MS

Homo sapiens

HECTD1

25831

Affinity Capture-MS

Homo sapiens

ST6GALNAC1

Two-hybrid

Homo sapiens

PLXNA3

55558

Affinity Capture-MS

Homo sapiens

ZFC3H1

196441

Affinity Capture-MS

Homo sapiens

Exosc1

Affinity Capture-MS

Mus musculus

PTGR2

145482

Affinity Capture-MS

Homo sapiens

RAN

5901

Co-fractionation		Homo sapiens
Co-fractionation		Homo sapiens

WDR46

Affinity Capture-MS

Homo sapiens

ANLN

54443

Affinity Capture-MS

Homo sapiens

SFPQ

6421

Affinity Capture-MS

Homo sapiens

ASXL2

Affinity Capture-MS

Homo sapiens

KHSRP

8570

Affinity Capture-Western

Homo sapiens

FANCD2

Affinity Capture-MS

Homo sapiens

HBS1L

10767

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

RC3H2

Affinity Capture-MS

Homo sapiens

GPX1

2876

Co-fractionation

Homo sapiens

DCAF13

25879

Affinity Capture-MS

Homo sapiens

PSMA2

5683

Co-fractionation

Homo sapiens

LRRC47

57470

Affinity Capture-MS

Homo sapiens

UPF3A

Affinity Capture-Western

Homo sapiens

NXF1

10482

Affinity Capture-RNA

Homo sapiens

COG2

22796

Cross-Linking-MS (XL-MS)

Homo sapiens

PSPC1

55269

Affinity Capture-MS

Homo sapiens

LUM

4060

Affinity Capture-MS

Homo sapiens

ZCCHC8

55596

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

EXOSC3

51010

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

DHPS

1725

Affinity Capture-MS

Homo sapiens

WDR75

Affinity Capture-MS

Homo sapiens

SKIV2L2

23517

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

DDRGK1

65992

Affinity Capture-MS

Homo sapiens

UPF2

26019

Affinity Capture-Western

Homo sapiens

GNB2L1

10399

Affinity Capture-MS

Homo sapiens

RPS16

6217

Affinity Capture-MS

Homo sapiens

EXOSC10

5394

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

PLEKHA4

57664

Affinity Capture-MS

Homo sapiens

GIGYF2

26058

Affinity Capture-MS

Homo sapiens

PRRC2A

7916

Affinity Capture-MS

Homo sapiens

HDGF

3068

Affinity Capture-MS

Homo sapiens

NT5DC3

51559

Affinity Capture-MS

Homo sapiens

MNDA

4332

Affinity Capture-MS

Homo sapiens

OSTM1

28962

Affinity Capture-Western

Homo sapiens

THOP1

7064

Affinity Capture-MS

Homo sapiens

G3BP2

9908

Affinity Capture-MS

Homo sapiens

DYNC1H1

1778

Cross-Linking-MS (XL-MS)

Homo sapiens

UFL1

23376

Affinity Capture-MS

Homo sapiens

NCL

4691

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

STAG2

10735

Co-fractionation

Homo sapiens

UPF1

5976

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

ORC1

Affinity Capture-MS

Homo sapiens

ZFP36L1

Affinity Capture-Western

Homo sapiens

KRAS

3845

Negative Genetic

Homo sapiens

C9orf72

Affinity Capture-MS

Homo sapiens

PHF10

Affinity Capture-MS

Homo sapiens

100

RC3H1

149041

Affinity Capture-MS

Homo sapiens

101

PRMT1

3276

Affinity Capture-MS

Homo sapiens

102

EXOSC1

51013

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

103

NVL

Affinity Capture-MS

Homo sapiens

104

EXOSC8

Affinity Capture-MS		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

105

PARN

Co-fractionation

Homo sapiens

View the network

Pathways in which EXOSC2 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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