Usf1 upstream transcription factor 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Usf1provided by MGI
Official Full Name: upstream transcription factor 1provided by MGI
Primary source: MGI:MGI:99542
See related: Ensembl:ENSMUSG00000026641 AllianceGenome:MGI:99542
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: bHLHb11
Summary: This protein encoded by this gene is a member of the basic-Helix-Hoop-Helix-Leucine zipper (bHLH-LZ) family and encodes a protein that can act as a transcription factor. Studies indicate that the basic region interacts with DNA at E-Box motifs, while the helix-loop-helix and leucine zipper domains are involved in dimerization with different partners. This protein is involved in a wide array of biological pathways, including cell cycle regulation, immune response, and responses to ultraviolet radiation. Mice lacking most of the coding exons of this gene often lacked both whiskers and nasal fur, and were prone to epileptic seizures, while mice lacking both this gene and another family member, Usf2, displayed embryonic lethality (PMID:9520440). Mutations in the human ortholog of this gene have been associated with Familial Combined Hyperlipidemia (FCHL) in humans. Pseudogenes of this gene are found on chromosome 11 and the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]
Expression: Ubiquitous expression in whole brain E14.5 (RPKM 35.2), ovary adult (RPKM 33.6) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 H3; 1 79.4 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (171238875..171246327)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (171411307..171418954)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hematopoietic upstream stimulating factor 1 deficiency is associated with increased atherosclerosis susceptibility in LDL receptor knockout mice.
Title: Hematopoietic upstream stimulating factor 1 deficiency is associated with increased atherosclerosis susceptibility in LDL receptor knockout mice.
Data suggest that the that the upstream transcription factor 1 (USF1) is indispensable for the proper maintenance of mammalian spermatogenesis.
Title: Transcription Factor USF1 Is Required for Maintenance of Germline Stem Cells in Male Mice.
The authors found that USF1 induced miR-125a-3p levels which suppressed Chi3L1 expression. Their results suggest that lung metastasis is suppressed by knock-down of Chi3L1 through miR-125a-3p-mediated up-regulation of USF1.
Title: Suppression of metastasis through inhibition of chitinase 3-like 1 expression by miR-125a-3p-mediated up-regulation of USF1.
ILEI contributes to melanoma cell invasiveness in vivo without affecting primary tumor growth and is transcriptionally up-regulated by USF-1.
Title: Interleukin-like EMT inducer (ILEI) promotes melanoma invasiveness and is transcriptionally up-regulated by upstream stimulatory factor-1 (USF-1).
Our findings identify USF1 as a novel factor regulating HDL functionality, showing that USF1 inactivation boosts cholesterol efflux, reduces macrophage inflammation and attenuates macrophage cholesterol accumulation, linking improved macrophage cholesterol metabolism and inflammatory pathways to the antiatherogenic function of USF1 deficiency.
Title: USF1 deficiency alleviates inflammation, enhances cholesterol efflux and prevents cholesterol accumulation in macrophages.
Mice lacking Usf1 displayed increased BAT-facilitated, diet-induced thermogenesis with up-regulation of mitochondrial respiratory chain complexes, as well as increased BAT activity even at thermoneutrality and after BAT sympathectomy
Title: USF1 deficiency activates brown adipose tissue and improves cardiometabolic health.
USF1 exclusively bound to the CACGTG E-box motifs in the brain cortex neuron proximal promoter regions. Importantly, functional annotation of the USF1-binding targets revealed an enrichment of genes related to lysosomal functions.
Title: Genome-wide analyses in neuronal cells reveal that upstream transcription factors regulate lysosomal gene expression.
Propose that USF1 is an important modulator of molecular and behavioral circadian rhythms in mammals via DNA-binding of the CLOCK:BMAL1 complex.
Title: Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice.
USF1 but not USF2 supports OPN expression in LRP6-VKO vascular smooth muscle lineage, and immunoprecipitation confirmed increased USF1 association with OPN chromatin.
Title: Vascular smooth muscle LRP6 limits arteriosclerotic calcification in diabetic LDLR-/- mice by restraining noncanonical Wnt signals.
They underscore the new role of USF1 and give new clues of how p53 loss of function can occur in any cell type.
Title: p53 requires the stress sensor USF1 to direct appropriate cell fate decision.

Submit: New GeneRIF Correction See all GeneRIFs (36)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (4)
Targeted (4) 1 citation
Not Applicable (1) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_4129-4130:996679399:1 (e-PCR)
- UniSTS:269327

Usf1 (e-PCR), detects polymorphism
- UniSTS:144737

Usf1 (e-PCR), detects polymorphism
- UniSTS:527601

Homology

Homologs of the Usf1 gene: The Usf1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, and zebrafish.
Orthologs from Annotation Pipeline: 388 organisms have orthologs with human gene Usf1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
contributes_to DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables bHLH transcription factor binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to insulin stimulus	ISO Inferred from Sequence Orthology more info
involved_in glucose metabolic process	ISO Inferred from Sequence Orthology more info
involved_in late viral transcription	ISO Inferred from Sequence Orthology more info
involved_in lipid homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription from RNA polymerase II promoter by glucose	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription from RNA polymerase II promoter by glucose	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to UV	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to hypoxia	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IC Inferred by Curator more info	PubMed
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: upstream stimulatory factor 1

Names: Upstream stimulatory factor 1 (Major late transcription factor 1); major late transcription factor 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001305676.1 → NP_001292605.1 upstream stimulatory factor 1 isoform 1

See identical proteins and their annotated locations for NP_001292605.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in its 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).

Source sequence(s)

AK142437, AW555090, BE995823, CJ050979

Consensus CDS

CCDS15495.1

UniProtKB/Swiss-Prot

Q61069

UniProtKB/TrEMBL

A0A8C6HZ27, Q3UQH7

Related

ENSMUSP00000125729.2, ENSMUST00000161241.8

Conserved Domains (2) summary

pfam15744
Location:145 → 284

UPF0492; Uncharacterized protein family UPF0492

cd18924
Location:196 → 260

bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
NM_001305677.1 → NP_001292606.1 upstream stimulatory factor 1 isoform 1

See identical proteins and their annotated locations for NP_001292606.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2, and 3 encode the same isoform (1).

Source sequence(s)

AK142437, AW555090, BE995823, CJ050979

Consensus CDS

CCDS15495.1

UniProtKB/Swiss-Prot

Q61069

UniProtKB/TrEMBL

A0A8C6HZ27, Q3UQH7

Conserved Domains (2) summary

pfam15744
Location:145 → 284

UPF0492; Uncharacterized protein family UPF0492

cd18924
Location:196 → 260

bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
NM_001305678.1 → NP_001292607.1 upstream stimulatory factor 1 isoform 2

See identical proteins and their annotated locations for NP_001292607.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site at an internal exon compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG to encode an isoform (2) that has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK142437, AW555090, BE995823, CJ050979, DV653810

UniProtKB/TrEMBL

A0A6P5PBF1, Q3UQH7, Q8R4E5

Conserved Domains (2) summary

pfam15744
Location:86 → 225

UPF0492; Uncharacterized protein family UPF0492

cd18924
Location:137 → 201

bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
NM_009480.3 → NP_033506.1 upstream stimulatory factor 1 isoform 1

See identical proteins and their annotated locations for NP_033506.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. The 5' terminal exon of this transcript was described in PMID:8938446, and is supported by RNASeq data. Variants 1, 2, and 3 encode the same isoform (1).

Source sequence(s)

AC087229, AK142437, AW555090, BE995823

Consensus CDS

CCDS15495.1

UniProtKB/Swiss-Prot

Q61069

UniProtKB/TrEMBL

A0A8C6HZ27, Q3UQH7

Related

ENSMUSP00000128913.2, ENSMUST00000167546.2

Conserved Domains (2) summary

pfam15744
Location:145 → 284

UPF0492; Uncharacterized protein family UPF0492

cd18924
Location:196 → 260

bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

171238875..171246327

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030253053.2 → XP_030108913.1 upstream stimulatory factor 1 isoform X2

UniProtKB/TrEMBL

A0A6P5PBF1, Q8R4E5

Conserved Domains (2) summary

pfam15744
Location:86 → 225

UPF0492; Uncharacterized protein family UPF0492

cd18924
Location:137 → 201

bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
XM_030253052.2 → XP_030108912.1 upstream stimulatory factor 1 isoform X1

UniProtKB/Swiss-Prot

Q61069

UniProtKB/TrEMBL

A0A8C6HZ27, Q3UQH7

Conserved Domains (2) summary

pfam15744
Location:145 → 284

UPF0492; Uncharacterized protein family UPF0492

cd18924
Location:196 → 260

bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
XM_030253055.1 → XP_030108915.1 upstream stimulatory factor 1 isoform X2

UniProtKB/TrEMBL

A0A6P5PBF1, Q8R4E5

Conserved Domains (2) summary

pfam15744
Location:86 → 225

UPF0492; Uncharacterized protein family UPF0492

cd18924
Location:137 → 201

bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins