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|Mutation Type||critical splice donor site|
|Coordinate||54,939,596 bp (GRCm38)|
|Base Change||A ⇒ G (forward strand)|
|Gene Name||TNFAIP3 interacting protein 1|
|Synonym(s)||ABIN1, VAN, A20-binding inhibitor of NF-kappa B activation, Nef|
|Chromosomal Location||54,910,785-54,962,917 bp (-)|
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an A20-binding protein which plays a role in autoimmunity and tissue homeostasis through the regulation of nuclear factor kappa-B activation. Mutations in this gene have been associated with psoriatic arthritis, rheumatoid arthritis, and systemic lupus erythematosus. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
PHENOTYPE: Mice homozygous for a null allele exhibit perinatal lethality associated with anemia and focal apoptosis in the fetal liver. Mice homozygous for a gene trap allele exhibit partial prenatal lethality and SLE-like inflammatory disease. [provided by MGI curators]
|Amino Acid Change|
|Institutional Source||Beutler Lab|
|Gene Model||predicted gene model for protein(s): [ENSMUSP00000018482] [ENSMUSP00000099791] [ENSMUSP00000099792] [ENSMUSP00000104513] [ENSMUSP00000104514] [ENSMUSP00000104517] [ENSMUSP00000122836] [ENSMUSP00000116721]|
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Predicted Effect||probably null|
|Alleles Listed at MGI|
|Mode of Inheritance||Autosomal Recessive|
|Last Updated||2018-10-02 3:51 PM by External Program|
|Record Created||2016-07-12 9:26 PM by Tao Yue|
The trinity phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R4475, some of which showed reduced frequencies of B2 cells (Figure 1) with concomitant increased frequencies of B1a cells (Figure 2), B1b cells (Figure 3), and CD11c+ dendritic cells (Figure 4). Some mice showed susceptibility to dextran sodium sulfate-induced colitis at 7 (Figure 5) and 10 days (Figure 6) post-DSS treatment. The level of OVA-specific IgE after OVA/alum administration was increased (Figure 7).
The causative mutation for the above phenotypes was validated to be in Pi4ka by CRISPR-mediated targeting of the Tnip1.
|Nature of Mutation|
Whole exome HiSeq sequencing of the G1 grandsire identified 39 mutations. All of the above phenotypes were linked by continuous variable mapping to a mutation in Tnip1: a T to C transition at base pair 54,939,596 (v38) on chromosome 11, or base pair 23,345 in the GenBank genomic region NC_000077 within the donor splice site of intron 3. The strongest association was found with a recessive model of inheritance to the total IgE phenotype, wherein three variant homozygotes departed phenotypically from 13 homozygous reference mice and 16 heterozygous mice with a P value of 1.169 x 10-29 (Figure 8).
The effect of the mutation at the cDNA and protein levels have not examined, but the mutation is predicted to result in skipping of the 138-base pair exon 3. Skipping of exon 3 would result in an in-frame deletion of 46 amino acids beginning after amino acid 46 of the protein, which is normally 647 amino acids long.
Genomic numbering corresponds to NC_000077. The donor splice site of intron 3, which is destroyed by the trinity mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red.
Tnip1 encodes ABIN1 (A20-binding inhibitors of NF-κB activation-1; alternatively, TNIP1 or NAF1 [NEF-associated factor-1]). ABIN1 is a member of the ABIN family, which also includes ABIN2 and ABIN3.
ABIN1 has four ABIN homology domains (AHDs), three coiled-coil regions (amino acids 39-72, 209-270, and 311-551), a nuclear localization signal (amino acids 537-543), a proline-rich C-terminus (amino acids 552-647), and nuclear receptor (NR) interaction motifs (Figure 9) (1). ABIN1 has several nuclear receptor (NR) interaction motifs, including two putative NR boxes (LXXLL [L = leucine, X = any amino acid]; amino acids 45-49 and amino acids 260-264) and two corepressor (CoRNR) boxes (LXXXI/LXXXI/L [I = isoleucine]; amino acids 235-243 and 432-440). Amino acids 95 to 425 are required for ABIN1 interaction with Nef, while amino acids 444 to 601 are required for NEMO binding and ABIN1’s inhibitory activity towards TNF-induced NF-κB activation.
The AHDs are regions of high homology between the members of the ABIN family. AHD1 mediates A20 binding and AHD2 is responsible for NF-κB activation. AHD2 corresponds to a ubiquitin-binding domain (UBD; alternatively, UBAN [UBD in ABIN proteins and NEMO] domain) that shares sequence homology with UBDs in NEMO and the NEMO-like protein, optineurin (2). The functions of the AHD3 and AHD4 domains are unknown.
The ubiquitin binding domain of ABIN1 is required for interaction of ABIN1 with TBK1(see the record for pioneer)/IKKi as well as the ABIN1-mediated inhibition of IFN-β production upon poly(I:C) transfection or virus infection (3). Ubiquitination of ABIN1 prevents autoimmunity by regulating the strength of TLR-MyD88-associated signaling (4). Mice expressing a mutant ABIN1Asp485Asn that did not bind either K63-linked or linear polyubiquitin chains exhibited enlarged spleens, lymph nodes, and Peyer’s Patches as well as spontaneous formation of germinal centers, isotype switching, and production of autoreactive antibodies.
The human and mouse TNIP1 genes undergo alternative splicing to generate several variants (1). See Table 1 for a list of the human ABIN1 variants. Mouse Tnip1 produces two splice variants that generate proteins that have different N-termini due to translation initiation from two different methionines (5-7).
Table 1. Human ABIN1 isoforms
The trinity mutation is predicted to result in skipping of the 138-base pair exon 3. Skipping of exon 3 would result in an in-frame deletion of 46 amino acids beginning after amino acid 46 of the protein; exon 3 encodes the N-terminal AHD domain.
TNIP1 is ubiquitously expressed, with high expression in peripheral blood lymphocytes, spleen, and skeletal muscle (2). ABIN-1 is predominantly cytoplasmic, but can putatively shuttle between the cytosol and the nucleus (8;9). The human TNIP1 splice variants show variation in expression (Table 1).
The rapid and transient activation of NF-κB complexes in response to a wide range of stimuli such as proinflammatory cytokines, DNA damaging agents, TLR agonists, and viruses is typically regulated by the canonical NF-κB pathway (Figure 10). These signals are mediated by various cell surface or intracellular receptors including the TNF receptor (TNFR) superfamily, the TIR domain family, BCR, TCR, nucleotide binding oligomerization domain (NOD)-like receptors and retinoic acid-inducible gene 1 (RIG-1) like helicases (RLHs). Receptor activation promotes the recruitment of adaptor proteins resulting in specific signaling complexes that converge on and activate the IKK complex composed of IKK-1, IKK-2 and NEMO [for review see (10;11)]. In the resting cell, NF-κB dimers are kept inactive in the cytoplasm through their association with the IκB inhibitory molecules IκBα, IκBβ, and IκBε (12). In response to stimulation, the IκB proteins are phosphorylated by the IKK complex at conserved serine residues resulting in K48-linked polyubiquitination of IκB molecules and subsequent proteolysis. Degradation of IκBs allows the NF-κB dimers to translocate into the nucleus, where they are able to activate the transcription of target genes (10;11). Genetic studies have demonstrated that the IKK-2 and NEMO subunits of the IKK complex are required for canonical NF-κB activation (13), while IKK-1 and the NF-κB inducing kinase (NIK; see the record for lucky) are required for the non-canonical or alternative NF-κB pathway (14). The non-canonical NF-κB pathway drives the post-translational processing of p100 to mature p52, and results in the activation of p52/RelB heterodimers (10;15-17).
ABIN1 is an A20 (see the record for lasvegas)-binding protein that regulates NF-κB activation through its association with A20. A20 plays a key role in the negative regulation of inflammation and immunity by regulating the nuclear factor (NF)-κB pathway as well as programmed cell death [reviewed in (18-20)]. A20 interacts with several proteins known to participate in NF-κB signaling pathways, including RIP1 and TRAF2 downstream of TNFR1; TRAF6 downstream of the TLRs and IL-1R; RIP2 downstream of NOD2; and NEMO (18-20). ABIN1 also inhibits p105 processing, which potentiates the NF-κB activity of ABIN1 (21). A20 is thought to inhibit NF-κB activity through both its deubiquitinating and ubiquitinating activities (22). In the case of RIP1, A20 first removes the activating K63-linked polyubiquitin chain, and then adds K48-polyubiquitin chains to target RIP1 for proteasomal degradation (22). A20 is also known to deubiquitinate TRAF6 (23), RIP2 (24) and NEMO, although the role of NEMO ubiquitination in NF-κB activation remains unclear (25;26). However, none of these proteins are targets of A20 K48-linked ubiquitination (19;20). A20 also inhibits NF-κB activation by targeting the RIP1 associated molecule TRAF2 to the lysosomes for degradation, an activity that does not require its ubiquitin modifying property (27). Other mechanisms A20 employs to interfere with the NF-κB pathway include TRAF6 binding, which prevents TRAF6 from interacting with the E2 conjugating enzymes UBCH13 and UBCH5 and inhibits its E3 ligase function. A20 also disrupts the interaction between UBCH13 and the E3 ubiquitin ligases cIAP1 (cellular inhibitor of apoptosis protein 1) and TRAF2 upon TNF stimulation. A20 is also required for K48-linked ubiquitination and subsequent degradation of UBCH13 and UBCH5 (28). In B and T cells that express A20 constitutively, activation of the NF-κB pathway in response to BCR and TCR stimulation requires A20 inactivation. This occurs via proteolytic processing by MALT1, as well as proteasomal degradation (29;30).
In addition to inhibiting NF-κB activity, A20 further affects inflammation by inhibiting interferon (IFN) regulator factor 3 (IRF3) activation downstream of RIG-I and TLR3, which normally results in the production of IFN-β (31;32). A20 appears to affect IRF3 activation at the level of TBK1 and IKK-ε, which are required for IRF3 activation (31). A20 also may negatively regulate mitogen activated protein kinase (MAPK) signaling downstream of TNF, IL-1, and LPS stimulation (33-35), although this activity appears to be cell specific. Finally, A20 is also important in apopotosis and cell survival by protecting certain cell types from TNF-induced apoptosis (33;36), Fas-induced apoptosis (37) and p53-induced apoptosis following viral infection (38). In addition, A20 downregulation may be important in activation-induced cell death (AICD) in T cells (39). The ubiquitin-editing activity of A20 is likely important in its anti-apoptotic role as A20 can deubiquitinate K63-linked caspase-8, which is a common component of both TNF- and Fas-induced apoptosis. Caspase-8 ubiquitination is required for caspase-8 aggregation, leading to its full activation and processing (40). A20 can also inhibit necrosis. In some cell types, A20 overexpression has been reported to be pro-apoptotic. These paradoxical effects may be due to a balance that exists between the direct anti-apoptotic effect of A20 and an indirect pro-apoptotic effect caused by its NF-κB inhibitory function (19).
In TNF (see the record for Panr1)-associated signaling, ligand binding promotes TNFR-1 binding to TNFR-associated death domain (TRADD) protein. TNF receptor-associated factor 2 (TRAF2) and/or TRAF5 as well as the Ser/Thr kinase receptor-interacting protein (RIP) are subsequently recruited to the receptor complex. Activation of the TAB2/TAK1 complex activates the IKK complex to phosphorylate IκB, resulting in release of NF-κB for translocation to the nucleus and activation of gene expression. TNFR1 activates JNK through sequential recruitment of TRAF2, MEKK1 and MKK7. MAPK activation involves signaling through TRADD, RIP and MKK3. TRADD recruitment to TNFR1 also leads to the induction of apoptosis through FAS-associated death domain (FADD) protein, caspase-8 and caspase-3. ABIN1 inhibits caspase 8 recruitment to FADD subsequently preventing caspase 8 cleavage and programmed cell death.
ABIN1 is also a negative regulator of antiviral signaling (4). Reduced expression of ABIN1 caused increased IFN-β production upon virus infection. ABIN1 associates with TAX1BP1 and A20 to recruit these proteins to the noncanonical IκB kinases TBK1 and IKKi in response to poly(I:C) transfection. The ABIN1 and TAX1BP1 complex disrupted interactions between the E3 ubiquitin ligase TRAF3 (see the record for Hulk) and TBK1/IKKi to attenuate lysine 63-linked polyubiquitination of TBK1/IKKi.
ABIN1 is also an atypical nuclear receptor coregulator (41;42). ABIN1 targets agonist-bound PPARα, subsequently reducing PPARα transcriptional activity. ABIN1 is also a corepressor of ligand-bound retinoic acid receptors, RARα and RARγ (42).
ABIN1 can inhibit EGFR (see the record for Velvet)-associated signaling by interacting with ERK2 and subsequently blocking ERK1 (see the record for wabasha)/ERK2 nuclear translocation. In EGFR signaling, ligand binding induces the formation of EGFR homo- or heterodimers and the activation of intrinsic receptor tyrosine kinase activity, resulting in trans-phosphorylation of cytoplasmic tyrosine residues (Figure 11). Trans-phosphorylation of receptor tyrosines creates binding sites for SH2 domain- and PTB domain-containing proteins, which recruit complexes that propagate downstream signaling. These proteins include the adapters Grb2, Nck, Crk, and Shc, phosphatases PTP-1B and SHP-1 (see the record for spin), tyrosine kinases Src and Abl, PLC-γ, and p120RasGAP [reviewed in (43)]. Their binding leads to substrate phosphorylation and the activation of multiple pathways, including the Ras-MAPK, Src and Abl family kinase, JNK, STAT and PLC-γ pathways. These in turn regulate transcriptional programs controlling cell proliferation, death and differentiation, as well as signaling cascades controlling cell adhesion, motility and migration.
ABIN1 regulates HIV-1 infection by preventing CD40-mediated downregulation of HIV-Nef (2). Nef enhances HIV replication and infectivity in T cells by down-regulating cell surface expression of CD4 and major histocompatibility complex class I molecules. ABIN1 also interacts with the HIV-1 protein Matrix (8). Matrix is a component of the HIV pre-integration complex (PIC). ABIN1 putatively regulates the nuclear import of the PIC as well as nuclear export of the gag precursor polyprotein and viral genomic RNA during virion production.
ABIN1 interacts with and negatively regulates μ-opioid receptor (MOR) (44). The MOR is a Gi/o protein-coupled receptor that mediates analgesic, euphoric, and reward effects. The receptor-mediated phosphorylation, ubiquitination, and internalization of MOR was reduced in cells that coexpressed MOR and ABIN-1.
Mutations in and/or aberrant expression of human TNIP1 are associated with psoriasis (45), psoriatic arthritis (46), rheumatoid arthritis (47), asthma, systemic lupus erythematosus (48), systemic sclerosis (49), and leukemia-lymphoma.
Tnip1-deficient and Tnip1-mutant mice exhibited prenatal lethality (incomplete penetrance) due to fetal liver apoptosis, hypoplasia, and anemia (50;51). Surviving mice exhibited increased numbers of neutrophil in the peripheral blood and spleen, B cell numbers in the spleen and lymph node and monocytes in the blood as well as increased immunoglobulin (IgA, IgG, IgM, and IgE) levels, increased susceptibility to systemic lupus erythematosus, increased anti-double stranded DNA antibody levels, glomerulonephritis, anemia, and reduced body weights compared to wild-type controls (50-52). Cells from the Tnip1-deficient mice showed hypersensitivity to TNF-induced cell death. Tnip1 mutant mice exhibited increased numbers of B cell numbers in the spleen and lymph node and monocytes in the blood.
The trinity phenotype indicates loss of ABIN1trinity function.
trinity(F):5'- TGAGTCACTGCAGTCTTCTG -3'
trinity(R):5'- ATGAAGTCAGTCCGTAGCCAGG -3'
trinity_seq(F):5'- TCTGCAGTCCCCAGAAGATCTG -3'
trinity_seq(R):5'- AAGTCAGTCCGTAGCCAGGTTTAG -3'
Genotyping is performed by amplifying the region containing the mutation using PCR, followed by sequencing of the amplified region to detect the mutation.
trinity_PCR_F: 5’- TGAGTCACTGCAGTCTTCTG-3’
trinity_PCR_R: 5’- ATGAAGTCAGTCCGTAGCCAGG-3’
trinity_SEQ_F: 5’- TCTGCAGTCCCCAGAAGATCTG-3’
trinity_SEQ_R: 5’- AAGTCAGTCCGTAGCCAGGTTTAG-3’
1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40X
6) 72°C 10:00
7) 4°C hold
The following sequence of 401 nucleotides is amplified:
tgagtcactg cagtcttctg cagtccccag aagatctgac tttctatgga tgctgtaacc
aaaagatgta cacagggaaa aggtctgcat gggaatgggt aggccctgtg gtgttcaggg
cctgggcagg ctgtattcag agaaggcagg gcttctggac tcttctggta cctgtgagct
cagccaggtc atcaaaggag accaaggagg gggcagatgt cggtggtgac agctcgctgt
ccttgaccag ctcctctgcc ttctgccgga gtctggacgc ttccatctga gactcctcca
gaagctcccc tagagacaag gcggagaagc acaggattta tccagcccaa agcacggctc
tccccatccc tgccctaaac ctggctacgg actgacttca t
Primer binding sites are underlined and the sequencing primer is highlighted; the mutated nucleotide is shown in red text (Chr. (+) = A>G).
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|Science Writers||Anne Murray|
|Illustrators||Diantha La Vine|
|Authors||Tao Yue, Xue Zhong, Jin Huk Choi, Takuma Misawa, Emre Turer, and Bruce Beutler|
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