Host Protein General Information (ID: PT0535)
  Protein Name
Heterogeneous nuclear ribonucleoprotein U (HNRNPU)
  Gene Name
HNRNPU
  Host Species
Homo sapiens
  Uniprot Entry Name
HNRPU_HUMAN
  Subcellular Location
nucleus; cytoskeleton; cytoplasm and cytosol
  External Link
NCBI Gene ID
3192
Uniprot ID
Q00839
Ensembl ID
ENSG00000153187
HGNC ID
HGNC:5048
  Function in Host
DNA- and RNA-binding protein involved in several cellularprocesses such as nuclear chromatin organization, telomere-lengthregulation, transcription, mRNA alternative splicing and stability, Xist-mediated transcriptional silencing and mitotic cell progression. Plays a role in the regulation ofinterphase large-scale gene-rich chromatin organization throughchromatin-associated RNAs (caRNAs) in a transcription-dependent manner, and thereby maintains genomic stability. Required for the localization of thelong non-coding Xist RNA on the inactive chromosome X (Xi) and thesubsequent initiation and maintenance of X-linked transcriptional genesilencing during X-inactivation. Plays a role as a RNApolymerase II (Pol II) holoenzyme transcription regulator. Promotes transcription initiation bydirect association with the core-TFIIH basal transcription factorcomplex for the assembly of a functional pre-initiation complex withPol II in a actin-dependent manner. Blocks Pol II transcription elongation activity by inhibiting the C-terminal domain (CTD) phosphorylation of Pol II and dissociates fromPol II pre-initiation complex prior to productive transcriptionelongation. Positively regulates CBX5-inducedtranscriptional gene silencing and retention of CBX5 in the nucleus. Negatively regulates glucocorticoid-mediatedtranscriptional activation. Key regulator oftranscription initiation and elongation in embryonic stem cells uponleukemia inhibitory factor (LIF) signaling. Involved inthe long non-coding RNA H19-mediated Pol II transcriptional repression. Participates in the circadian regulation of the coreclock component ARNTL/BMAL1 transcription. Plays a rolein the regulation of telomere length. Plays a role asa global pre-mRNA alternative splicing modulator by regulating U2 smallnuclear ribonucleoprotein (snRNP) biogenesis. Plays arole in mRNA stability. Component of the CRD-mediated complex that promotesMYC mRNA stabilization. Enhances the expression ofspecific genes, such as tumor necrosis factor TNFA, by regulating mRNAstability, possibly through binding to the 3'-untranslated region (UTR). Plays a role in mitotic cell cycle regulation. Involved in the formation of stablemitotic spindle microtubules (MTs) attachment to kinetochore, spindleorganization and chromosome congression. Phosphorylation at Ser-59 by PLK1 is required for chromosome alignementand segregation and progression through mitosis. Contributes also to the targeting of AURKA to mitotic spindle MTs. Binds to double- and single-stranded DNA and RNA, poly (A), poly (C) and poly (G) oligoribonucleotides. Bindsto chromatin-associated RNAs (caRNAs). Associateswith chromatin to scaffold/matrix attachment region (S/MAR) elements ina chromatin-associated RNAs (caRNAs) -dependent manner . Binds to the XistRNA. Binds the long non-coding H19 RNA. Binds to SMN1/2 pre-mRNAs at G/U-rich regions. Binds to small nuclear RNAs (snRNAs). Binds to the 3'-UTR of TNFA mRNA. Binds (via RNA-binding RGG-box region) to the long non-coding Xist RNA;this binding is direct and bridges the Xist RNA and the inactivechromosome X (Xi). Also negatively regulates embryonicstem cell differentiation upon LIF signaling. Requiredfor embryonic development. Binds to brown fat long non-coding RNA 1 (Blnc1); facilitates the recruitment of Blnc1 by ZBTB7Brequired to drive brown and beige fat development and thermogenesis. [1-8]
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  Related KEGG Pathway
Spliceosome hsa03040            Pathway Map 
  3D Structure

Function of This Protein During Virus Infection
Virus NameSARS-COV-2 Protein Function Pro-viral [9]
Infected TissueLung Infection Time24 h
Infected CellA549 Cells (Adenocarcinomic Human alveolar basal epithelial cells) Cellosaurus IDCVCL_H249 
Method DescriptionTo detect the role of host protein HNRNPU in viral infection, HNRNPU protein Knockout A549 Cells were infected with SARS-COV-2 for 24 h , and the effects on infection was detected through qRT-PCR.
ResultsIt is reported that Knockdown of HNRNPU leads to the reduced viral particles production 50% compared with control group.

Host Protein - Virus RNA Network

 Full List of Virus RNA Interacting with This Protien
            RNA Region: 3'-UTR (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [10]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
3'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: 3'-UTR (hCoV-19/IPBCAMS-YL01/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [11]
              Strains Name
hCoV-19/IPBCAMS-YL01/2020
              Strains Family
Beta (B.1.351)
              RNA Binding Region
3'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7.5.1 cells (Hepatocyte derived cellular carcinoma cell) Huh7.5.1 cells (Hepatocyte derived cellular carcinoma cell)  (CVCL_E049 )
              Cell Originated Tissue Liver
              Infection Time 30 h
              Interaction Score Affinity = 0.957
              Method Description PrismNet; pull-down western (STAR methods); Mass spectrometry
           RNA Region: 5'-UTR (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [10]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
5'-UTR
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line) Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: ORF10 (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [10]
              Strains Name
hCoV-19/Not Specified Virus Strain
              Strains Family
Beta (B.1.351)
              RNA Binding Region
ORF10
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line) Huh7 cells (human liver cell line); Calu-3 cells (human lung cancer cell line)  (CVCL_0336;CVCL_0609 )
              Cell Originated Tissue Liver; Lung
              Interaction Score P-value < 0.05
              Method Description RNA pull-down assays; liquid chromatography with tandem mass spectrometry (LC-MS/MS); Wilcoxon test; MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS)
           RNA Region: N region (hCoV-19/Wuhan-Hu-1/2019 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCoV-19/Wuhan-Hu-1/2019
              Strains Family
Beta (B.1.351)
              RNA Binding Region
N region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Interaction Type Potential binding protein
              Infection Cells HepG2 cells (hepatocellular carcinoma cell line) HepG2 cells (hepatocellular carcinoma cell line)  (CVCL_0027 )
              Cell Originated Tissue Liver
              Method Description ENCODE project database; Pysster model; DeepRiPe (Section 3.6; 3.7; 3.8; 3.9); ClustalO (72) algorithm
           RNA Region: 3'-UTR site; a peak within the S protein-coding region adjacent to the start codon  (hCoV-19/IPBCAMS-YL01/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [13], [14], [15]
              Strains Name
hCoV-19/IPBCAMS-YL01/2020
              Strains Family
Beta (B.1.351)
              RNA Binding Region
3'-UTR site; a peak within the S protein-coding region adjacent to the start codon
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Interaction Type known to be direct binder
              Interaction Binding Type Single stranded RNA binding
              Infection Cells Huh7.5.1 cells (Hepatocyte derived cellular carcinoma cell) Huh7.5.1 cells (Hepatocyte derived cellular carcinoma cell)  (CVCL_E049 )
              Cell Originated Tissue Liver
              Infection Time 30 h
              Interaction Score MIST = 0.992357128
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)
           RNA Region: Not Specified Virus Region (hCoV-SARS/Manitoba/2003 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCoV-SARS/Manitoba/2003
              Strains Family
Beta
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome-related coronavirus (HCoV-SARS)
              Interaction Type Potential binding protein
              Infection Cells HepG2 cells (hepatocellular carcinoma cell line) HepG2 cells (hepatocellular carcinoma cell line)  (CVCL_0027 )
              Cell Originated Tissue Liver
              Method Description ENCODE project database; Pysster model; DeepRiPe (Section 3.6; 3.7; 3.8; 3.9); ClustalO (72) algorithm
           RNA Region: Not Specified Virus Region (hCov-OC43/VR-759 Quebec/2019 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCov-OC43/VR-759 Quebec/2019
              Strains Family
Beta
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Human coronavirus OC43 (HCov-OC43)
              Interaction Type Potential binding protein
              Infection Cells HepG2 cells (hepatocellular carcinoma cell line) HepG2 cells (hepatocellular carcinoma cell line)  (CVCL_0027 )
              Cell Originated Tissue Liver
              Method Description ENCODE project database; Pysster model; DeepRiPe (Section 3.6; 3.7; 3.8; 3.9); ClustalO (72) algorithm
           RNA Region: Not Specified Virus Region (hCov-NL63/Amsterdam/2004 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCov-NL63/Amsterdam/2004
              Strains Family
Alpha
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Human Coronavirus NL63 (HCov-NL63)
              Interaction Type Potential binding protein
              Infection Cells HepG2 cells (hepatocellular carcinoma cell line) HepG2 cells (hepatocellular carcinoma cell line)  (CVCL_0027 )
              Cell Originated Tissue Liver
              Method Description ENCODE project database; Pysster model; DeepRiPe (Section 3.6; 3.7; 3.8; 3.9); ClustalO (72) algorithm
           RNA Region: Not Specified Virus Region (hCov-MERS/Jeddah/2012 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCov-MERS/Jeddah/2012
              Strains Family
Beta
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Middle East respiratory syndrome-related coronavirus (HCov-MERS)
              Interaction Type Potential binding protein
              Infection Cells HepG2 cells (hepatocellular carcinoma cell line) HepG2 cells (hepatocellular carcinoma cell line)  (CVCL_0027 )
              Cell Originated Tissue Liver
              Method Description ENCODE project database; Pysster model; DeepRiPe (Section 3.6; 3.7; 3.8; 3.9); ClustalO (72) algorithm
           RNA Region: Not Specified Virus Region (hCoV-HKU1/Hong Kong/2004 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCoV-HKU1/Hong Kong/2004
              Strains Family
Beta
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Human coronavirus HKU1 (HCoV-HKU1)
              Interaction Type Potential binding protein
              Infection Cells HepG2 cells (hepatocellular carcinoma cell line) HepG2 cells (hepatocellular carcinoma cell line)  (CVCL_0027 )
              Cell Originated Tissue Liver
              Method Description ENCODE project database; Pysster model; DeepRiPe (Section 3.6; 3.7; 3.8; 3.9); ClustalO (72) algorithm
           RNA Region: Not Specified Virus Region (hCov-229E/Würzburg/2000 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCov-229E/Würzburg/2000
              Strains Family
Alpha
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Human coronavirus 229E (HCov-229E)
              Interaction Type Potential binding protein
              Infection Cells HepG2 cells (hepatocellular carcinoma cell line) HepG2 cells (hepatocellular carcinoma cell line)  (CVCL_0027 )
              Cell Originated Tissue Liver
              Method Description ENCODE project database; Pysster model; DeepRiPe (Section 3.6; 3.7; 3.8; 3.9); ClustalO (72) algorithm
           RNA Region: Not Specified Virus Region (hCoV-19/USA/WA1/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [16]
              Strains Name
hCoV-19/USA/WA1/2020
              Strains Family
Alpha (B.1.1.7)
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7.5 cells (Hepatocyte derived cellular carcinoma cell) Huh7.5 cells (Hepatocyte derived cellular carcinoma cell)  (CVCL_7927 )
              Cell Originated Tissue Liver
              Infection Time 48 h
              Interaction Score FDR ≤ 0.05
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)
           RNA Region: Not Specified Virus Region (hCoV-19/France/IDF-220-95/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [9]
              Strains Name
hCoV-19/France/IDF-220-95/2020
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Interaction Type Direct interaction
              Infection Cells HEK293 Cells (Human embryonic kidney cell) HEK293 Cells (Human embryonic kidney cell)  (CVCL_0045 )
              Cell Originated Tissue Kidney
              Infection Time 48 h
              Interaction Score SAINT score ≥ 0.79
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)

Differential Gene Expression During SARS-COV-2 Infection
GEO Accession: GSE152641
Sample Type: Blood
Samples Details: Healthy Control: 24; COVID-19: 62
Platform: GPL24676 Illumina NovaSeq 6000
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GEO Accession: GSE162835
Sample Type: Nasopharyngeal Swabs
Samples Details: COVID-19 (Mild Symptoms): 37; COVID-19 (Moderate Symptoms): 10; COVID-19 (Severe Symptoms): 3
Platform: GPL24676 Illumina NovaSeq 6000
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GEO Accession: GSE175779
Sample Type: Human Bronchial Epithelial Cells
Samples Details: Healthy Control: 4 (0, 24, 48, 72 and 96 h); COVID-19: 4 (24, 48, 72 and 96 h)
Platform: GPL18573 Illumina NextSeq 500
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Protein Phosphorylation after Virus Infection
S192 [17]
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S26 [18]
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S271 [18]
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S271 [17]
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S4 [17]
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S59 [17]
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T191 [17]
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Protein Sequence Information
MSSSPVNVKKLKVSELKEELKKRRLSDKGLKAELMERLQAALDDEEAGGRPAMEPGNGSLDLGGDSAGRSGAGLEQEAAAGGDEEEEEEEEEEEGISALDGDQMELGEENGAAGAADSGPMEEEEAASEDENGDDQGFQEGEDELGDEEEGAGDENGHGEQQPQPPATQQQQPQQQRGAAKEAAGKSSGPTSLFAVTVAPPGARQGQQQAGGKKKAEGGGGGGRPGAPAAGDGKTEQKGGDKKRGVKRPREDHGRGYFEYIEENKYSRAKSPQPPVEEEDEHFDDTVVCLDTYNCDLHFKISRDRLSASSLTMESFAFLWAGGRASYGVSKGKVCFEMKVTEKIPVRHLYTKDIDIHEVRIGWSLTTSGMLLGEEEFSYGYSLKGIKTCNCETEDYGEKFDENDVITCFANFESDEVELSYAKNGQDLGVAFKISKEVLAGRPLFPHVLCHNCAVEFNFGQKEKPYFPIPEEYTFIQNVPLEDRVRGPKGPEEKKDCEVVMMIGLPGAGKTTWVTKHAAENPGKYNILGTNTIMDKMMVAGFKKQMADTGKLNTLLQRAPQCLGKFIEIAARKKRNFILDQTNVSAAAQRRKMCLFAGFQRKAVVVCPKDEDYKQRTQKKAEVEGKDLPEHAVLKMKGNFTLPEVAECFDEITYVELQKEEAQKLLEQYKEESKKALPPEKKQNTGSKKSNKNKSGKNQFNRGGGHRGRGGFNMRGGNFRGGAPGNRGGYNRRGNMPQRGGGGGGSGGIGYPYPRAPVFPGRGSYSNRGNYNRGGMPNRGNYNQNFRGRGNNRGYKNQSQGYNQWQQGQFWGQKPWSQHYHQGYY
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References
1 SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs. Cell. 2017 Jun 15;169(7):1214-1227.e18.
2 H19 inhibits RNA polymerase II-mediated transcription by disrupting the hnRNP U-actin complex. Biochim Biophys Acta. 2013 Oct;1830(10):4899-906.
3 Physical and functional interaction between heterochromatin protein 1alpha and the RNA-binding protein heterogeneous nuclear ribonucleoprotein U. J Biol Chem. 2009 Oct 9;284(41):27974-27979.
4 Actin and hnRNP U cooperate for productive transcription by RNA polymerase II. Nat Struct Mol Biol. 2005 Mar;12(3):238-44.
5 hnRNP U inhibits carboxy-terminal domain phosphorylation by TFIIH and represses RNA polymerase II elongation. Mol Cell Biol. 1999 Oct;19(10):6833-44.
6 The glucocorticoid receptor is associated with the RNA-binding nuclear matrix protein hnRNP U. J Biol Chem. 1997 Nov 7;272(45):28471-8.
7 Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur J Biochem. 1994 Apr 15;221(2):749-57.
8 Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. EMBO J. 1992 Sep;11(9):3431-40.
9 Characterization and functional interrogation of the SARS-CoV-2 RNA interactome. Cell Rep. 2022 Apr 26;39(4):110744.
10 Mapping the host protein interactome of non-coding regions in SARS-CoV-2 genome. bioRxiv. 2021 Jun; DOI:10.1101/2021.06.19.449092.
11 In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs. Cell. 2021 Apr 1;184(7):1865-1883.e20.
12 Computational Mapping of the Human-SARS-CoV-2 Protein-RNA Interactome. bioRxiv. 2021 Dec; DOI:.org/10.1101/2021.12.22.472458.
13 Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2. Cell Res. 2022 Jan;32(1):9-23.
14 Viral and cellular proteins involved in coronavirus replication. Curr Top Microbiol Immunol. 2005;287:95-131.
15 Host cell proteins interacting with the 3 end of TGEV coronavirus genome influence virus replication. Virology. 2009 Sep 1;391(2):304-14.
16 Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell. 2021 Apr 29;184(9):2394-2411.e16.
17 Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature. 2021 Jun;594(7862):246-252.
18 The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 Aug 6;182(3):685-712.e19.