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SREBF1 (sterol regulatory element binding transcription factor 1)

Written2019-02Seher Gök
Scientific and Technological Research Council of Turkey; Ankara-TURKEY/ seher.gok@tubitak.gov.tr

Abstract Review on SREBF1, with data on DNA, on the protein encoded and where the gene is implicated.

Keywords SREBF1; Streol regulatory element binding transcription factor 1

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)SREBP1
bHLHd1
SREBP-1c
SREBP1a
HGNC (Hugo) SREBF1
HGNC Alias symbSREBP1
bHLHd1
SREBP-1c
SREBP1a
LocusID (NCBI) 6720
Atlas_Id 42386
Location Located on 17p11.2  [Link to chromosome band 17p11]
Location_base_pair Starts at 17811349 and ends at 17837011 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping SREBF1.png]
Local_order SREBF1 spans 26,619 bp, starts at 17811349 and ends at 17837011 bp from pter (according to hg38-Dec_2013).
 
  Figure 1. Gene neighbours of LIPE on chromosome 17p11.2 (Chromosome 17 - NC_000017.11 Reference: GRCh38.p12 current assembly, NCBI Annotation Release 109).
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

DNA/RNA

 
  Figure 2. Genomic organization of the SREBF1 gene. Exons are numbered indicating the alternatively spliced a' and c' variants (adapted from Kedenko et al., 2012).
Description Orientation: Minus strand; 25669 bp; Exon count: 22; intron count: 20
Transcription SREBF1 gene has 23 transcripts (Table 1)
Table 1. Transcripts of human SREBF1 gene (Ensembl annotation Release 85).
Name  Transcript ID  bp  Protein   Biotype  
SREBF1-201  ENST00000261646.9  4178  1147  Protein coding  
SREBF1-202  ENST00000355815.8  4253  1177  Protein coding  
SREBF1-203  ENST00000395751.8  4653  216  Nonsense mediated decay  
SREBF1-204  ENST00000395756.5  3026  113  Nonsense mediated decay  
SREBF1-205  ENST00000395757.5  3696  893  Protein coding  
SREBF1-206  ENST00000423161.3  1058  325  Protein coding  
SREBF1-207  ENST00000447641.5  644  No protein  Retained intron   
SREBF1-208  ENST00000469356.3  1323  No protein  Retained intron   
SREBF1-209  ENST00000470247.1  374  No Protein  Retained intron   
SREBF1-210  ENST00000471445.5  936  No protein  Retained intron   
SREBF1-211  ENST00000476994.1  591  No protein  Retained intron   
SREBF1-212  ENST00000478616.1  882  163  Protein coding  
SREBF1-213  ENST00000485080.6  1230  110  Nonsense mediated decay  
SREBF1-214  ENST00000486311.5  473  157  Protein coding  
SREBF1-215  ENST00000487401.1  477  No protein  Retained intron   
SREBF1-216  ENST00000490796.1  698  No protein  Retained intron   
SREBF1-217  ENST00000577897.1  536  66  Protein coding  
SREBF1-218  ENST00000578469.1  588  31  Protein coding  
SREBF1-219  ENST00000580540.1  540  No protein  Retained intron   
SREBF1-220  ENST00000581707.1  695  No protein  Retained intron   
SREBF1-221  ENST00000583080.1  482  No protein  Retained intron   
SREBF1-222  ENST00000583732.1  580  No protein  Processed transcript  
SREBF1-223  ENST00000584760.1  564  No protein  Retained intron   

Protein

Note SREBF1 gene encodes 1147 amino acid sized protein which has 121675 Da molecular mass. SREBF1 is helix-loop-helix transcriptional activator required for lipid homeostasis (Figure 3). Regulates transcription of the LDL receptor gene as well as the fatty acid and cholesterol synthesis pathways. Binds to the sterol regulatory element 1 (SRE-1) (5'-ATCACCCCAC-3'). Has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').
 
  Figure 3. Co-crystal structure of sterol regulatory element binding protein 1a bound to an LDL Receptor promoter at 2.3 A resolution (adapted from Párraga et al., 1998).
Description The encoded protein is synthesized as a precursor that is initially attached to the nuclear membrane and endoplasmic reticulum. After cleavage, the mature protein translocates to the nucleus and activates transcription. This cleaveage is inhibited by sterols. Alternative promoter usage and splicing result in multiple transcript variants. 6 isoforms are described. Isoform 1A has been choosen as the canonical sequence (provided by RefSeq, Nov 2017). Quaternary structure of protein forms a tight complex with SCAP in the ER membrane. Efficient DNA binding of the soluble transcription factor fragment requires dimerization with another bHLH protein. Interacts with LMNA. Interacts with CEBPA, the interaction produces a transcriptional synergy (By similarity).
Post-translational modifications: 
At low cholesterol the SCAP/SREBP complex is recruited into COPII vesicles for export from the ER. In the Golgi complex SREBPs are cleaved sequentially by site-1 and site-2 protease. The first cleavage by site-1 protease occurs within the luminal loop, the second cleavage by site-2 protease occurs within the first transmembrane domain and releases the transcription factor from the Golgi membrane. Apoptosis triggers cleavage by the cysteine proteases CASP3 and CASP7 (caspase-3 and caspase-7).
Phosphorylated by AMPK (P
rotein kinase AMP-activated catalytic subunits), leading to suppress protein processing and nuclear translocation, and repress target gene expression. Phosphorylation at Ser-402 by SIK1 represses activity possibly by inhibiting DNA-binding.
Ubiquitinatylated at Lys347, Lys379, Lys587, Lys675, Lys934, Lys1070.
Expression Expressed in a wide variety of tissues, most abundant in fat and adrenal gland. In fetal tissues, lung and liver shows highest expression. Isoform SREBF-1C predominates in liver, adrenal gland and ovary, whereas isoform SREBF-1A predominates in hepatoma cell lines. Isoform SREBF-1A and isoform SREBF-1C are found in kidney, brain, white fat, and muscle.
Localisation Endoplasmic reticulum membrane, golgi membrane, nuclear envelope, nucleoplasm, nucleus, COPII - coated vesicle membrane.
Function SREBF1 Transcription factor binds to the sterol regulatory element-1 (SRE1) (5-ATCACCCCAC-3) which is a motif found in the promoter of the low density lipoprotein receptor genes and other genes that involved in sterol biosynthesis. Depletion of cholesterol leads to intra-membrane proteolysis, releasing the active portion of SREBF1 containing the basic DNA-binding region from the endoplasmic reticulum membrane. After translocation to the nucleus and binding to its specific DNA sequences, SREBF1 dimers induce the expression of target genes involved in adipogenesis and membrane biogenesis (Nohturfft and Zhang, 2009).
Homology SREBF1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito and frog (Table 2).
Table 2. Pairwise alignment of SREBF1 gene and protein sequences (in distance from human).
GeneIdentity %&
Species  Symbol   Protein  DNA  
H. Sapiens  SREBF1      
vs. P.troglodytes  SREBF1  98.7  99.0  
vs. M.mulatta   SREBF1  97.5  97.1  
vs. C.lupus  SREBF1  87.9  87.2  
vs. B.taurus  SREBF1  84.5  85.8  
vs. M.musculus  Srebf1  81.2  80.9  
vs. R.norvegicus  Srebf1  81.6  82.0  
vs.  G.gallus   SREBF1  65.8  69.5  
vs. X.tropicalis   srebf1  67.0  65.9  
vs D.reriro  srebf1  61.3  62.4  
vs D.melanogaster  HLH106  37.5  48.4  
vs. A.gambiae  AgaP_AGAP000076  39.2  49.7  

Mutations

Note 304 missense, 36 truncating and 3 inframe and 7 other mutations of SREBF1 was identified in 74247 samples from 240 studies (cBioPortal) (Figure 4).
 
  Figure 4. Mutation types observed in SREBF1 expression in literature and corresponding color codes are as follows: Green: Missense Mutations ; Black: Truncating Mutations: Nonsense, Nonstop, Frameshift deletion, Frameshift insertion, Splice site; Beige: In-frame Mutations: In-frame deletion, In-frame insertion ; Purple: Other Mutations: All other types of mutations.
Somatic 4 SNPs were registered for SREBF1 (according to SNPedia and Human Gene Mutation Database).

Implicated in

  
Entity Endometrial Cancer (EC)
Note Higher level of SREBF1 has been detected in EC cells compared to the normal endometrium, and which was more prominent in higher-grade EC. NP (rs2297508) of SREBF-1 may serve as a genetic predisposition factor for the development of EC Qui et al., 2014).
  
  
Entity Pancreatic Cancer
Note SREBF1 is highly expressed in pancreatic ductal cancer. The expression of SREBF1 is an independent risk factor affecting the overall survival of patients with pancreatic cancer (Sun et al., 2015.
  
  
Entity Hepatocellular Carcinoma (HCC)
Note SREBF1 expression is activated in HCC. Suppression of SREBF1 induced growth arrest and apoptosis whereas overexpression of SREBF1 enhanced cell proliferation in human HCC cell lines. There are a significant relationship between poor survival and high SREBF1 protein expression and correlation between high SREBF1 protein expression and high risk of mortality with statistical significance (Yamashita et al., 2008).
  
  
Entity Ovarian Cancer
Note SREBF1 protein expression was significantly higher in human ovarian cancer compared to benign and borderline ovarian tumors (Nie et al., 2013).
  
  
Entity Breast cancer
Note mRNA levels for SREBF-1c increase in a panel of primary human breast cancer samples (Yang et al., 2003).
  
  
Entity Colorectal Carcinoma
Note SREBF1 and FAS expression upregulated in colorectal carcinoma cells. It was hypothesized that, tumor cells recognize and respond to a deficiency in endogenous fatty acid synthesis by upregulating both SREBF1 and FAS expression and these findings support the model that SREBF1 participates in the transcriptional regulation of lipogenic genes in colorectal neoplasia (Li et al., 2000).
  
  
Entity Obesity and Obesity-related metabolic traits; Type 2 diabetes and Dyslipidemia
Note The SREBF1 molecular screening of 40 unrelated obese patients revealed 19 single nucleotide polymorphisms (SNPs). SNP17 (54G/C, exon 18c) is associated with morbid obesity. SNP3 (-150G/A, exon 1a), SNP5 (-36delG, exon 1a), and SNP17 are found in high linkage disequilibrium (D' > 0.8). The haplotype including wild-type alleles of these SNPs (C/G/G/T/C/G, HAP2) is identified as a risk factor for morbid obesity (P = 0.003). In the obese group, SNP3, SNP5, and SNP17 are associated with male-specific hypertriglyceridemia (P = 0.07, P = 0.01, and P = 0.05, respectively). SNP17 is also associated with type 2 diabetes (P = 0.03) (Eberlé et al., 2004).
In addition, it was shown that insulin induces SREBF1 gene expression in isolated human adipocytes and skeletal muscle and also promotes SREBF1 cleavage in human isolated adipocytes. Common insulin-resistant states, such as obesity and type 2 diabetes, are characterized by decreased expression of SREBP1c mRNA (Sewter et al., 2002).
  

Bibliography

SREBF-1 gene polymorphisms are associated with obesity and type 2 diabetes in French obese and diabetic cohorts
Eberlé D, Clément K, Meyre D, Sahbatou M, Vaxillaire M, Le Gall A, Ferré P, Basdevant A, Froguel P, Foufelle F
Diabetes 2004 Aug;53(8):2153-7
PMID 15277400
 
Genetic polymorphisms of the main transcription factors for adiponectin gene promoter in regulation of adiponectin levels: association analysis in three European cohorts
Kedenko L, Lamina C, Kiesslich T, Kapur K, Bergmann S, Waterworth D, Heid IM, Wichmann HE, Kedenko I, Kronenberg F, Paulweber B
PLoS One 2012;7(12):e52497
PMID 23285067
 
Sterol regulatory element-binding protein-1 participates in the regulation of fatty acid synthase expression in colorectal neoplasia
Li JN, Mahmoud MA, Han WF, Ripple M, Pizer ES
Exp Cell Res 2000 Nov 25;261(1):159-65
PMID 11082286
 
Sterol regulatory element-binding protein 1 is required for ovarian tumor growth
Nie LY, Lu QT, Li WH, Yang N, Dongol S, Zhang X, Jiang J
Oncol Rep 2013 Sep;30(3):1346-54
PMID 23818099
 
Coordination of lipid metabolism in membrane biogenesis
Nohturfft A, Zhang SC
Annu Rev Cell Dev Biol 2009;25:539-66
PMID 19575637
 
Co-crystal structure of sterol regulatory element binding protein 1a at 2
Párraga A, Bellsolell L, Ferré-D'Amaré AR, Burley SK
3 A resolution Structure
PMID 9634703
 
Single nucleotide polymorphism of SREBF-1 gene associated with an increased risk of endometrial cancer in Chinese women
Qiu CP, Lv QT, Dongol S, Wang C, Jiang J
PLoS One 2014 Mar 10;9(3):e90491
PMID 24614076
 
Human obesity and type 2 diabetes are associated with alterations in SREBP1 isoform expression that are reproduced ex vivo by tumor necrosis factor-alpha
Sewter C, Berger D, Considine RV, Medina G, Rochford J, Ciaraldi T, Henry R, Dohm L, Flier JS, O'Rahilly S, Vidal-Puig AJ
Diabetes 2002 Apr;51(4):1035-41
PMID 11916923
 
SREBP1 regulates tumorigenesis and prognosis of pancreatic cancer through targeting lipid metabolism
Sun Y, He W, Luo M, Zhou Y, Chang G, Ren W, Wu K, Li X, Shen J, Zhao X, Hu Y
Tumour Biol 2015 Jun;36(6):4133-41
PMID 25589463
 
Activation of lipogenic pathway correlates with cell proliferation and poor prognosis in hepatocellular carcinoma
Yamashita T, Honda M, Takatori H, Nishino R, Minato H, Takamura H, Ohta T, Kaneko S
J Hepatol 2009 Jan;50(1):100-10
PMID 19008011
 
Regulation of fatty acid synthase expression in breast cancer by sterol regulatory element binding protein-1c
Yang Yu, Morin PJ, Han WF, Chen T, Bornman DM, Gabrielson EW, Pizer ES
Exp Cell Res 2003 Jan 15;282(2):132-7
PMID 12531699
 

Citation

This paper should be referenced as such :
Seher Gök
SREBF1 (sterol regulatory element binding transcription factor 1)
Atlas Genet Cytogenet Oncol Haematol. 2020;24(1):13-17.
Free journal version : [ pdf ]   [ DOI ]


External links

Nomenclature
HGNC (Hugo)SREBF1   11289
Cards
AtlasSREBF1ID42386ch17p11
Atlas Explorer : (Salamanque)SREBF1
Entrez_Gene (NCBI)SREBF1    sterol regulatory element binding transcription factor 1
AliasesHMD; IFAP2; SREBP1; bHLHd1
GeneCards (Weizmann)SREBF1
Ensembl hg19 (Hinxton)ENSG00000072310 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000072310 [Gene_View]  ENSG00000072310 [Sequence]  chr17:17811349-17837011 [Contig_View]  SREBF1 [Vega]
ICGC DataPortalENSG00000072310
TCGA cBioPortalSREBF1
AceView (NCBI)SREBF1
Genatlas (Paris)SREBF1
SOURCE (Princeton)SREBF1
Genetics Home Reference (NIH)SREBF1
Genomic and cartography
GoldenPath hg38 (UCSC)SREBF1  -     chr17:17811349-17837011 -  17p11.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SREBF1  -     17p11.2   [Description]    (hg19-Feb_2009)
GoldenPathSREBF1 - 17p11.2 [CytoView hg19]  SREBF1 - 17p11.2 [CytoView hg38]
ImmunoBaseENSG00000072310
Genome Data Viewer NCBISREBF1 [Mapview hg19]  
OMIM158310   184756   619016   
Gene and transcription
Genbank (Entrez)AB209609 AB373958 AB373959 AH004383 AH004383
RefSeq transcript (Entrez)NM_001005291 NM_001321096 NM_001388385 NM_001388386 NM_001388387 NM_001388388 NM_001388389 NM_001388390 NM_001388391 NM_001388392 NM_001388393 NM_001388394 NM_004176
Consensus coding sequences : CCDS (NCBI)SREBF1
Gene ExpressionSREBF1 [ NCBI-GEO ]   SREBF1 [ EBI - ARRAY_EXPRESS ]   SREBF1 [ SEEK ]   SREBF1 [ MEM ]
Gene Expression Viewer (FireBrowse)SREBF1 [ Firebrowse - Broad ]
GenevisibleExpression of SREBF1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6720
GTEX Portal (Tissue expression)SREBF1
Human Protein AtlasENSG00000072310-SREBF1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)SREBF1
Human Protein Atlas [tissue]ENSG00000072310-SREBF1 [tissue]
HPRD01701
Protein Interaction databases
BioGRIDSREBF1
STRING (EMBL)SREBF1
ZODIACSREBF1
Ontologies - Pathways
Litterature
PubMed425 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSREBF1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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