Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Gene Ontology annotation based on curation of immunofluorescence data
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease.
RIF-1, a novel nuclear receptor corepressor that associates with the nuclear matrix.
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Human LRIF1, originally called RIF-1, directly interacts with RARalpha in vivo and in vitro.
"Here we report the cloning and
characterization of a novel protein RIF1 (receptor interacting factor) that
interacts with RARalpha in vivo and in vitro."
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LRIF1 also binds multiple other nuclear receptors, with its RARalpha-interaction region mapped to residues 512-674.
"GST-pull down assays show that RIF1 also interacts with a number of other
NRs. The interaction domain of RIF1 for RARalpha is located at the C-terminal
region of RIF1, between amino acids 512 and 674."
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LRIF1 is a nuclear-matrix protein whose nuclear localization depends on a nuclear-localization signal.
"RIF1 is localized exclusively
in the cell nucleus and specifically to the nuclear matrix. Mutation of the
nuclear localization signal abolishes this nuclear localization and causes RIF1
to appear in the cytoplasm."
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A distal LRIF1 repression domain inhibits ligand-dependent RARalpha transcription, partly through histone-deacetylase recruitment.
"RIF1 contains a strong transcriptional
repression domain that robustly inhibits ligand-dependent transcriptional
activation by RARalpha. This domain is located to the distal C-terminal 100
amino acids, distinct from the RARalpha-interaction and nuclear matrix-targeting
domains. The transcriptional repression activity of RIF1 is mediated at least in
part through direct recruitment of histone deacetylases."
Human POGZ modulates dissociation of HP1alpha from mitotic chromosome arms through Aurora B activation.
Analysis of the human HP1 interactome reveals novel binding partners.
A directed protein interaction network for investigating intracellular signal transduction.
Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway.
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Human LRIF1/HBiX1 and SMCHD1 are enriched across the inactive X and are required for its compaction.
"Here we show that Xi
compaction requires HBiX1, a heterochromatin protein 1 (HP1)-binding protein,
and structural maintenance of chromosomes hinge domain-containing protein 1
(SMCHD1), both of which are enriched throughout the Xi chromosome."
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HP1 and SMCHD1 recruit LRIF1/HBiX1 to distinct H3K9me3 and XIST-H3K27me3 inactive-X domains.
"HBiX1
localization to H3K9me3 and XIST-associated H3K27me3 (XIST-H3K27me3) domains was
mediated through interactions with HP1 and SMCHD1, respectively."
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LRIF1/HBiX1 is required to recruit SMCHD1 to H3K9me3 domains, and depletion of either protein decompacts the inactive X without requiring PRC2.
"Furthermore,
HBiX1 was required for SMCHD1 localization to H3K9me3 domains. Depletion of
HBiX1 or SMCHD1, but not Polycomb repressive complex 2 (PRC2), resulted in Xi
decompaction, similarly to XIST depletion."
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LRIF1/HBiX1 and SMCHD1 bridge two repressive chromatin-domain classes to organize inactive-X architecture.
"Thus, the molecular network involving
HBiX1 and SMCHD1 links the H3K9me3 and XIST-H3K27me3 domains to organize the
compact Xi structure."
A quantitative telomeric chromatin isolation protocol identifies different telomeric states.
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Quantitative telomeric chromatin isolation identifies and validates LRIF1 as a human telomere-associated protein.
"telomere-associated polypeptides including all THO subunits, SMCHD1 and LRIF1."
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LRIF1 and SMCHD1 show higher density at long than short human telomeres.
"with long telomeres."
Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation.
A human interactome in three quantitative dimensions organized by stoichiometries and abundances.
A High-Density Map for Navigating the Human Polycomb Complexome.
A reference map of the human binary protein interactome.
Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
LRIF1 interacts with HP1α to coordinate accurate chromosome segregation during mitosis.
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LRIF1 recruits HP1alpha to mitotic centromeres and the interaction is required for accurate chromosome segregation.
"Here, we identified a PXVXL-containing
protein, ligand-dependent nuclear receptor-interacting factor 1 (LRIF1), which
recruits HP1α to the centromere of mitotic chromosomes and its interaction with
HP1α is essential for accurate chromosome segregation during mitosis."
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LRIF1 directly binds the HP1alpha chromoshadow domain through a conserved C-terminal PXVXL motif.
"LRIF1
interacts directly with HP1α chromoshadow domain via an evolutionarily conserved
PXVXL motif within its C-terminus."
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The LRIF1-HP1alpha interaction supports inner-centromere Aurora B activity; motif mutation disrupts HP1 targeting and chromosome segregation.
"Importantly, the LRIF1-HP1α interaction is
critical for Aurora B activity in the inner centromere. Mutation of PXVXL motif
of LRIF1 leads to defects in HP1α centromere targeting and aberrant chromosome
segregation."
Independent Mechanisms Target SMCHD1 to Trimethylated Histone H3 Lysine 9-Modified Chromatin and the Inactive X Chromosome.
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Mouse LRIF1 and HP1gamma form the principal loading route for SMCHD1 at H3K9me3-marked chromosome-arm sites.
"We further show that the principal mechanism for
chromatin loading of SMCHD1 involves an LRIF1-mediated interaction with HP1γ at
trimethylated histone H3 lysine 9 (H3K9me3)-modified chromatin sites on the
chromosome arms."
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In mouse cells, inactive-X loading of SMCHD1 can occur through a pathway parallel to the H3K9me3-LRIF1-HP1 route.
"A parallel pathway accounts for chromatin loading at a minority
of sites, notably the inactive X chromosome."
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The study explicitly identifies its LRIF1 reagent as the mouse homolog of human HBiX1, constraining direct species transfer.
"Proteomic screening revealed that SMCHD1 interacts with LRIF1, the mouse homolog of HBiX1, and with HP1 protein paralogs."
Homozygous nonsense variant in LRIF1 associated with facioscapulohumeral muscular dystrophy.
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A homozygous LRIF1 variant selectively eliminated the long protein isoform and caused D4Z4 relaxation with inappropriate DUX4 expression.
"This mutation resulted in the absence of the
long isoform of LRIF1 protein, D4Z4 chromatin relaxation, and DUX4 and DUX4
target gene expression in myonuclei, all molecular and epigenetic hallmarks of
FSHD."
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LRIF1 binds D4Z4, and long-isoform knockdown in muscle cells derepresses DUX4 and its targets.
"In concordance, LRIF1 was shown to bind to the D4Z4 repeat, and knockdown
of the LRIF1 long isoform in muscle cells results in DUX4 and DUX4 target gene
expression."
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The study identifies LRIF1 loss as an FSHD2 mechanism through D4Z4 chromatin relaxation in skeletal muscle.
"This study further
reinforces the unifying genetic mechanism, which postulates that FSHD is caused
by D4Z4 chromatin relaxation, resulting in inappropriate DUX4 expression in
skeletal muscle."
SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action.
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SMCHD1 and LRIF1 provide an auxiliary layer of D4Z4 repression, while somatic loss of either alone does not recreate the underlying D4Z4 chromatin changes.
"We show
that somatic loss-of-function of either SMCHD1 or LRIF1 does not result in D4Z4
chromatin changes and that SMCHD1 and LRIF1 form an auxiliary layer of D4Z4
repressive mechanisms."
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SMCHD1 and the long LRIF1 isoform bind the LRIF1 promoter and repress LRIF1 transcription.
"We uncover that SMCHD1, together with the long isoform of
LRIF1, binds to the LRIF1 promoter and silences LRIF1 expression."
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SMCHD1-LRIF1 binding dependencies and transcriptional consequences differ between D4Z4 and the LRIF1 promoter.
"The
interdependency of SMCHD1 and LRIF1 binding differs between D4Z4 and the LRIF1
promoter, and both loci show different transcriptional responses to either early
developmentally or somatically perturbed chromatin function of SMCHD1 and LRIF1."
UniProtKB/Swiss-Prot record for human LRIF1 (Q5T3J3)