Host Protein General Information (ID: PT1261)
  Protein Name
YTH domain-containing family protein 2 (YTHDF2)
  Gene Name
YTHDF2
  Host Species
Homo sapiens
  Uniprot Entry Name
YTHD2_HUMAN
  Protein Families
YTHDF family
  Subcellular Location
Cytoplasm; cytosol Cytoplasm; P-body Cytoplasm
  External Link
NCBI Gene ID
51441
Uniprot ID
Q9Y5A9
Ensembl ID
ENSG00000198492
HGNC ID
HGNC:31675
  Function in Host
Specifically recognizes and binds N6-methyladenosine (m6A) -containing RNAs, and regulates their stability. M6A is amodification present at internal sites of mRNAs and some non-codingRNAs and plays a role in mRNA stability and processing. Acts as a regulator of mRNA stability by promotingdegradation of m6A-containing mRNAs via interaction with the CCR4-NOTand ribonuclease P/MRP complexes, depending on the context. The YTHDF paralogs (YTHDF1, YTHDF2 and YTHDF3) sharem6A-containing mRNAs targets and act redundantly to mediate mRNAdegradation and cellular differentiation. M6A-containing mRNAs containing a binding site forRIDA/HRSP12 (5'-GGUUC-3') are preferentially degraded byendoribonucleolytic cleavage: cooperative binding of RIDA/HRSP12 andYTHDF2 to transcripts leads to recruitment of the ribonuclease P/MRPcomplex. Other m6A-containing mRNAs undergodeadenylation via direct interaction between YTHDF2 and CNOT1, leadingto recruitment of the CCR4-NOT and subsequent deadenylation of m6A-containing mRNAs. Required maternally to regulateoocyte maturation: probably acts by binding to m6A-containing mRNAs, thereby regulating maternal transcript dosage during oocyte maturation, which is essential for the competence of oocytes to sustain earlyzygotic development. Also required duringspermatogenesis: regulates spermagonial adhesion by promotingdegradation of m6A-containing transcripts coding for matrixmetallopeptidases. Also involved in hematopoietic stemcells specification by binding to m6A-containing mRNAs, leading topromote their degradation. Also acts as a regulatorof neural development by promoting m6A-dependent degradation of neuraldevelopment-related mRNA targets. Inhibits neuralspecification of induced pluripotent stem cells by binding tomethylated neural-specific mRNAs and promoting their degradation, thereby restraining neural differentiation. Regulatescircadian regulation of hepatic lipid metabolism: acts by promotingm6A-dependent degradation of PPARA transcripts. Regulates the innate immune response to infection by inhibiting thetype I interferon response: acts by binding to m6A-containing IFNBtranscripts and promoting their degradation. May alsoact as a promoter of cap-independent mRNA translation following heatshock stress: upon stress, relocalizes to the nucleus and specificallybinds mRNAs with some m6A methylation mark at their 5'-UTR, protectingdemethylation of mRNAs by FTO, thereby promoting cap-independent mRNAtranslation. Regulates mitotic entry by promoting thephase-specific m6A-dependent degradation of WEE1 transcripts. Promotes formation of phase-separated membranelesscompartments, such as P-bodies or stress granules, by undergoingliquid-liquid phase separation upon binding to mRNAs containingmultiple m6A-modified residues: polymethylated mRNAs act as amultivalent scaffold for the binding of YTHDF proteins, juxtaposingtheir disordered regions and thereby leading to phase separation. The resulting mRNA-YTHDF complexes then partition into differentendogenous phase-separated membraneless compartments, such as P-bodies, stress granules or neuronal RNA granules. May alsorecognize and bind RNAs modified by C5-methylcytosine (m5C) and act asa regulator of rRNA processing. [1-10]
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  3D Structure

Function of This Protein During Virus Infection
Virus NameSARS-COV-2 Protein Function Anti-viral [11]
Infected TissueLung Infection Time7-9 Days
Infected CellCalu-3 Cells (Human epithelial cell line) Cellosaurus IDCVCL_0609 
Method DescriptionTo detect the role of host protein YTHDF2 in viral infection, YTHDF2 protein Knockout Calu-3 Cells were infected with SARS-COV-2 for 7 - 9 Days , and the effects on infection was detected through CRISPR-based genome-wide gene-knockout screen.
ResultsIt is reported that knockout of YTHDF2 increases SARS-CoV-2 RNA levels compared with control group.

Host Protein - Virus RNA Network

 Full List of Virus RNA Interacting with This Protien
            RNA Region: Not Specified Virus Region (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [12]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (liver carcinoma cell)  (CVCL_0336 )
              Cell Originated Tissue Liver
              Infection Time 24h
              Interaction Score log2FC = 1.15863E+14
              Method Description RNA antisense purification and quantitative mass spectrometry (RAP-MS); Tandem mass tag (TMT) labelling; liquid chromatography tandem mass spectrometry (LC-MS/MS); Westernblot
           RNA Region: Not Specified Virus Region (hCoV-19/England/02/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [13]
              Strains Name
hCoV-19/England/02/2020
              Strains Family
Beta (B.1.351)
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Calu-3 cells (Human lung cancer cell) Calu-3 cells (Human lung cancer cell)  (CVCL_0609 )
              Cell Originated Tissue Lung
              Infection Time 24 h
              Interaction Score P-adjust = 0.006
              Method Description UV protein-RNA crosslinking; RNA interactome capture (cRIC); RNA antisense purification coupled with mass spectrometry (RAP-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 Sequence Information
MSASSLLEQRPKGQGNKVQNGSVHQKDGLNDDDFEPYLSPQARPNNAYTAMSDSYLPSYYSPSIGFSYSLGEAAWSTGGDTAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGSTPFLGQHGFNFFPSGIDFSAWGNNSSQGQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNTIDQGMAALKLGSTEVASNVPKVVGSAVGSGSITSNIVASNSLPPATIAPPKPASWADIASKPAKQQPKLKTKNGIAGSSLPPPPIKHNMDIGTWDNKGPVAKAPSQALVQNIGQPTQGSPQPVGQQANNSPPVAQASVGQQTQPLPPPPPQPAQLSVQQQAAQPTRWVAPRNRGSGFGHNGVDGNGVGQSQAGSGSTPSEPHPVLEKLRSINNYNPKDFDWNLKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSHYEKRQEEEESVKKERQGRGK
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References
1 A Unified Model for the Function of YTHDF Proteins in Regulating m 6 A-Modified mRNA. Cell. 2020 Jun 25;181(7):1582-1595.e18.
2 Endoribonucleolytic Cleavage of m 6 A-Containing RNAs by RNase P/MRP Complex. Mol Cell. 2019 May 2;74(3):494-507.e8.
3 YTHDF3 facilitates translation and decay of N 6-methyladenosine-modified RNA. Cell Res. 2017 Mar;27(3):315-328.
4 YTHDF2 destabilizes m(6)A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. Nat Commun. 2016 Aug 25;7:12626.
5 Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. J Biol Chem. 2015 Oct 9;290(41):24902-13.
6 N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell. 2015 Jun 4;161(6):1388-99.
7 N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014 Jan 2;505(7481):117-20.
8 Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine. Cell Res. 2014 Dec;24(12):1493-6.
9 Structure of the YTH domain of human YTHDF2 in complex with an m(6)A mononucleotide reveals an aromatic cage for m(6)A recognition. Cell Res. 2014 Dec;24(12):1490-2.
10 Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012 Apr 29;485(7397):201-6.
11 Genome-wide CRISPR screens identify GATA6 as a proviral host factor for SARS-CoV-2 via modulation of ACE2. Nat Commun. 2022 Apr 25;13(1):2237.
12 The SARS-CoV-2 RNA-protein interactome in infected human cells. Nat Microbiol. 2021 Mar;6(3):339-353.
13 Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Mol Cell. 2021 Jul 1;81(13):2851-2867.e7.