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PTBP1 (polypyrimidine tract binding protein 1)

Written2012-02Laura Fontana
Department of Medicine, Surgery, Dentistry, Medical Genetics, Universita degli Studi di Milano, Italy

(Note : for Links provided by Atlas : click)

Identity

Other namesHNRNP-I
HNRNPI
HNRPI
PTB
PTB-1
PTB-T
PTB2
PTB3
PTB4
pPTB
HGNC (Hugo) PTBP1
LocusID (NCBI) 5725
Atlas_Id 46504
Location 19p13.3  [Link to chromosome band 19p13]
Location_base_pair Starts at 797392 and ends at 812327 bp from pter ( according to hg19-Feb_2009)  [Mapping PTBP1.png]
Fusion genes
(updated 2016)
PLEKHH3 (17q21.2) / PTBP1 (19p13.3)PTBP1 (19p13.3) / MALAT1 (11q13.1)PTBP1 (19p13.3) / PTBP1 (19p13.3)
PTBP1 (19p13.3) / UBE3C (7q36.3)

DNA/RNA

 
  Shematic representation of PTB mRNA alternative splicing. Alternative splicing of PTB mRNA, as described below, originates four isoforms. Green boxes represent exons and thin black lines represent introns (not to scale).
Description The PTBP1 locus spans 14936 bases on the short arm of chromosome 19 and is composed of 14 exons.
Transcription PTBP1 results from skipping of exon 9 (3203 bp mRNA and 531 amino acid protein). Three additional isoforms are generated by alternative splicing: PTBP2 (3260 bp mRNA and 550 amino acid protein) and PTBP4 (3281 mRNA protein and 557 amino acid protein) derive from exon 9 inclusion using two alternative 3' splice sites, while PTB-T has been reported to result from alternative splicing of exons 2-10 (Sawicka et al., 2004).
Pseudogene PTBP1P (polypyrimidine tract binding protein 1 pseudogene), chromosome location 14q23.3, starts at 65745938 and ends at 65748375 bp from pter (according to hg19-Feb_2009).

Protein

 
  Schematic representation of PTBP1 protein structure. Each RNA recognition motif (RRM) has different binding affinity for pyrimidine-rich sequences on mRNA. The N-terminal domain encloses partially overlapping nuclear localisation (NLS) and export signals (NES). Blue boxes representing RRMs are not drawn to scale.
Description 57 kDa protein belonging to the heterogeneous nuclear ribonucleoprotein family (hnRNP). PTBP1 has four RNA recognition motifs (RRMs) and a conserved N-terminal domain that harbors both nuclear localisation and export signals (NLS and NES). Through the RRMs, PTBP1 binds to the transcript at multiple sites within large pyrimidine tracts leading to conformational changes suitable for functional mRNA processing (Sawicka et al., 2004).
Expression PTBP1 is ubiquitously expressed in human tissues emerging as a pleiotropic splicing regulator. PTBP1 expression levels have been associated with myoblast and neural precursor differentiation through specific modulation of the splicing pattern (Clower et al., 2010). In the brain, in particular, the switch from PTBP1 to nPTB expression drives the differentiation towards the neuronal lineage: PTBP1 is expressed in neural precursors and glial cells, while post-mitotic neurons express only nPTB (Boutz et al., 2007). Recently a strong PTBP1 expression has been found in embryonic stem cells, particularly those in the brain cortex and subventricular zone, where PTBP1 appears essential for cell division after implantation (Shibayama et al., 2009; Suckale et al., 2011).
Localisation PTBP1 shuttles between the nucleus and the cytoplasm. Cytoplasmic localisation is mainly achieved by PKA-mediated phosphorylation of a specific serine residue (Ser-16) within the nuclear localisation signal. Cytoplasmic accumulation of PTB occurs during cell stress (Sawicka et al., 2008). PTBP1 has also been identified as a key component in maintaining the integrity of the perinucleolar compartment, a sub-nuclear structure predominantly found in transformed cells (Wang et al., 2003).
Function PTB was originally identified as a regulator of alternative splicing (Garcia-Blanco et al., 1989) but other roles in mRNA processing have been described (Sawicka et al., 2008).
Alternative splicing regulation: PTBP1 commonly acts as repressor of alternative splicing favouring skipping of alternative exons. Different models of PTBP1 activity have been proposed (Spellman and Smith, 2006): 1) binding competition with the splicing factor U2AF65 at the 3' splice site of alternative exons; 2) polymerization of PTBP1 molecules on the alternative exon masking splicing enhancer sequences; and 3) looping out of alternative exon by PTBP1 binding of flanking intronic sequences. Targets of PTBP1-mediated repression of exon inclusion comprise α-tropomiosin, α-actinin, GABAAγ2 (gamma-aminobutyric acid Aγ2), c-src and FGFR2 (fibroblast growth factor receptor 2) (Li et al., 2007; Spellman et al., 2005). Recent evidences indicate that PTBP1 may also favour exon inclusion depending on the position of its binding sites relative to the target exon. Upon binding to the upstream intron and/or within the exon, PTBP1 represses exon inclusion, while by binding to the downstream intron, it activates exon inclusion. The PTBP1 position-dependent activity relies on the splice site features: in particular included exons show weaker 5' splice sites, whereas skipped exons have longer polypyrimidine tracts (Llorian et al., 2010).
PTBP1 pre-mRNA undergoes PTBP1-mediated alternative splicing too, as part of an autoregulatory feedback loop: high levels of PTBP1 induce skipping of exon 11 and hence mRNA degradation via the nonsense-mediated mRNA decay (Spellman et al., 2005).
3'-end processing: PTBP1 both promotes and inhibits the mRNA 3'-end cleavage required for polyadenylation. PTBP1 may prevent mRNA polyadenylation through competition with the cleavage stimulating factor (CstF), or stimulate polyadenylation by binding to pyrimidine-rich upstream elements (USEs).
mRNA transport: evidences for a role of PTBP1 in mRNA transport come from experiments in Xenopus, where the PTBP1 homologue (VgRBP60) is involved in the localisation of the Vg1 mRNA. In vertebrates PKA-activated PTBP1 is involved in α-actin mRNA localisation at neurite terminals.
mRNA stability: PTBP1 increases the stability of specific transcript by binding to the untraslated regions of mRNA and consequently competing with factors involved in mRNA degradation. Transcripts with PTB-mediated increased stability include those of insulin, VEGF (vascular endothelial growth factor), CD154 (cluster of differentiation 154) and iNOS (inducible nitric oxide synthase).
Viral translation and replication: PTBP1 acts as an ITAF (IRES -internal ribosomal entry site- trans-acting factor) for mRNA translation of virus belonging to the Picornaviridae family and lacking cap structure. PTBP1 seems to have a role as a viral RNA chaperone that stabilizes or alters IRES structure to direct ribosomes to the correct start codon.
IRES-mediated translation: PTBP1 favours cap-independent translation of few cellular RNAs under cell stress, apoptosis or infection through ribosome recruitment to IRES. In this case, PTBP1 cytoplasmic relocalisation is required.
Homology PTBP1 shares 70-80% homology with other two proteins: nPTB (neural PTB), expressed in adult brain, muscle and testis, and ROD1 (regulator of differentiation 1) only expressed in hematopoietic cells. PTB also regulates alternative splicing of its homologues, in particular the nonsense-mediated decay of nPTB transcripts and the non-productive splicing of ROD1 (Sawicka et al., 2008).

Mutations

Somatic Three synonymous mutations have been reported in cancer samples: c.510C>T (p.A170A) in kidney carcinoma (Dalgliesh et al., 2010), c.1416C>T (p.F472F) in melanoma (Wei et al., 2011) and c.501G>A (p.S167S) in squamous cell carcinoma of the mouth (Stransky et al., 2011). Moreover five missense mutations have been identified in other cancer samples: c.932C>T (p.A311V) in ovarian carcinoma (Cancer Genome Atlas Research Network, 2011), c.413C>T (p.T138I) in skin squamous cell carcinoma (Durinck et al., 2011), c.212C>T (p.T71M), c.666C>G (p.F222L) and c.928G>A (p.G310R) in squamous cell carcinomas of the mouth and larynx (Durinck et al., 2011; Stransky et al., 2011).

Implicated in

Note
Entity Glioma
Note PTBP1 is aberrantly overexpressed in glioma with expression levels correlated with glial cell transformation. The increased expression of PTBP1 contributes to gliomagenesis by deregulating the alternative splicing of genes involved in cell proliferation and migration (McCutcheon et al., 2004; Cheung et al., 2006; Cheung et al., 2009).
FGFR-1 (fibroblast growth factor receptor-1): PTBP1 overexpression increases FGFR-1 α-exon skipping and hence the synthesis of a receptor with higher affinity for fibroblast growth factor, favouring transformed cell growth (Jin et al., 2000).
PKM (pyruvate kinase): PTBP1 overexpression leads to the re-expression of the embryonic pyruvate kinase isoform, PKM2, in transformed glial cells. The switch from PKM1, normally expressed in terminally differentiated cells, to PKM2 is achieved through the PTBP1-mediated inclusion in the PKM mRNA of exon 10, instead of exon 9. In transformed cells PKM2 promotes aerobic glycolysis and proliferation. Recently c-Myc overexpression has been demonstrated to upregulate PTBP1 transcription in transformed glial cells (David et al., 2010).
USP5 (ubiquitin specific peptidase 5): PTBP1 overexpression in GBM forces the expression of USP5 isoform 2, a protein involved in ubiquitination. USP5 isoform 2 has a low activity and favours cell growth and migration (Izaguirre et al., 2011).
  
Entity Ovarian tumour
Note PTBP1 is overexpressed in the majority of epithelial ovarian tumours and deregulates cell proliferation, anchorage-dependent growth and invasiveness. PTBP1 targets in ovarian transformed cells have not yet been identified (He et al., 2007).
  
Entity Alzheimer's disease (AD)
Note Recent evidences delineate PTBP1 as a regulator of the amyloid precursor protein (APP) in neurons. In particular, PTBP1 altered expression in neuronal cells, likely mediated by miR-124, enhances the expression of APP isoforms including exon 7 and/or 8. These isoforms have been found enriched in AD patients and associated with β-amyloid production (Smith et al., 2011).
  

Bibliography

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Polypyrimidine tract binding protein and Notch1 are independently re-expressed in glioma.
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PMID 16729017
 
Splicing factors PTBP1 and PTBP2 promote proliferation and migration of glioma cell lines.
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Brain. 2009 Aug;132(Pt 8):2277-88. Epub 2009 Jun 8.
PMID 19506066
 
The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism.
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Nature. 2010 Jan 21;463(7279):364-8. Epub 2009 Dec 13.
PMID 20010808
 
Temporal dissection of tumorigenesis in primary cancers.
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Identification and purification of a 62,000-dalton protein that binds specifically to the polypyrimidine tract of introns.
Garcia-Blanco MA, Jamison SF, Sharp PA.
Genes Dev. 1989 Dec;3(12A):1874-86.
PMID 2533575
 
Knockdown of polypyrimidine tract-binding protein suppresses ovarian tumor cell growth and invasiveness in vitro.
He X, Pool M, Darcy KM, Lim SB, Auersperg N, Coon JS, Beck WT.
Oncogene. 2007 Jul 26;26(34):4961-8. Epub 2007 Feb 19.
PMID 17310993
 
PTBP1-dependent regulation of USP5 alternative RNA splicing plays a role in glioblastoma tumorigenesis.
Izaguirre DI, Zhu W, Hai T, Cheung HC, Krahe R, Cote GJ.
Mol Carcinog. 2011 Oct 4. doi: 10.1002/mc.20859. [Epub ahead of print]
PMID 21976412
 
Fibroblast growth factor receptor-1 alpha-exon exclusion and polypyrimidine tract-binding protein in glioblastoma multiforme tumors.
Jin W, McCutcheon IE, Fuller GN, Huang ES, Cote GJ.
Cancer Res. 2000 Mar 1;60(5):1221-4.
PMID 10728679
 
Neuronal regulation of alternative pre-mRNA splicing.
Li Q, Lee JA, Black DL.
Nat Rev Neurosci. 2007 Nov;8(11):819-31. (REVIEW)
PMID 17895907
 
Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB.
Llorian M, Schwartz S, Clark TA, Hollander D, Tan LY, Spellman R, Gordon A, Schweitzer AC, de la Grange P, Ast G, Smith CW.
Nat Struct Mol Biol. 2010 Sep;17(9):1114-23. Epub 2010 Aug 15.
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Expression of the splicing regulator polypyrimidine tract-binding protein in normal and neoplastic brain.
McCutcheon IE, Hentschel SJ, Fuller GN, Jin W, Cote GJ.
Neuro Oncol. 2004 Jan;6(1):9-14.
PMID 14769134
 
Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein.
Sawicka K, Bushell M, Spriggs KA, Willis AE.
Biochem Soc Trans. 2008 Aug;36(Pt 4):641-7. (REVIEW)
PMID 18631133
 
Polypyrimidine tract-binding protein is essential for early mouse development and embryonic stem cell proliferation.
Shibayama M, Ohno S, Osaka T, Sakamoto R, Tokunaga A, Nakatake Y, Sato M, Yoshida N.
FEBS J. 2009 Nov;276(22):6658-68. Epub 2009 Oct 16.
PMID 19843185
 
In vivo regulation of amyloid precursor protein neuronal splicing by microRNAs.
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Novel modes of splicing repression by PTB.
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PMID 16403634
 
The mutational landscape of head and neck squamous cell carcinoma.
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PTBP1 is required for embryonic development before gastrulation.
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PMID 21423341
 
RNA polymerase III transcripts and the PTB protein are essential for the integrity of the perinucleolar compartment.
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Citation

This paper should be referenced as such :
Fontana, L
PTBP1 (polypyrimidine tract binding protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2012;16(7):492-495.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PTBP1ID46504ch19p13.html


External links

Nomenclature
HGNC (Hugo)PTBP1   9583
Cards
AtlasPTBP1ID46504ch19p13
Entrez_Gene (NCBI)PTBP1  5725  polypyrimidine tract binding protein 1
AliasesHNRNP-I; HNRNPI; HNRPI; PTB; 
PTB-1; PTB-T; PTB2; PTB3; PTB4; pPTB
GeneCards (Weizmann)PTBP1
Ensembl hg19 (Hinxton)ENSG00000011304 [Gene_View]  chr19:797392-812327 [Contig_View]  PTBP1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000011304 [Gene_View]  chr19:797392-812327 [Contig_View]  PTBP1 [Vega]
ICGC DataPortalENSG00000011304
TCGA cBioPortalPTBP1
AceView (NCBI)PTBP1
Genatlas (Paris)PTBP1
WikiGenes5725
SOURCE (Princeton)PTBP1
Genomic and cartography
GoldenPath hg19 (UCSC)PTBP1  -     chr19:797392-812327 +  19p13.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PTBP1  -     19p13.3   [Description]    (hg38-Dec_2013)
EnsemblPTBP1 - 19p13.3 [CytoView hg19]  PTBP1 - 19p13.3 [CytoView hg38]
Mapping of homologs : NCBIPTBP1 [Mapview hg19]  PTBP1 [Mapview hg38]
OMIM600693   
Gene and transcription
Genbank (Entrez)AB208910 BC002397 BC004383 BC013694 BC023219
RefSeq transcript (Entrez)NM_002819 NM_031990 NM_031991 NM_175847
RefSeq genomic (Entrez)NC_000019 NC_018930 NT_011295 NW_004929412
Consensus coding sequences : CCDS (NCBI)PTBP1
Cluster EST : UnigeneHs.172550 [ NCBI ]
CGAP (NCI)Hs.172550
Alternative Splicing GalleryENSG00000011304
Gene ExpressionPTBP1 [ NCBI-GEO ]   PTBP1 [ EBI - ARRAY_EXPRESS ]   PTBP1 [ SEEK ]   PTBP1 [ MEM ]
Gene Expression Viewer (FireBrowse)PTBP1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5725
GTEX Portal (Tissue expression)PTBP1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP26599 (Uniprot)
NextProtP26599  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP26599
Splice isoforms : SwissVarP26599 (Swissvar)
PhosPhoSitePlusP26599
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)HnRNP-L_PTB    Nucleotide-bd_a/b_plait    RRM_dom   
Domain families : Pfam (Sanger)RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
DMDM Disease mutations5725
Blocks (Seattle)PTBP1
PDB (SRS)1QM9    1SJQ    1SJR    2AD9    2ADB    2ADC    2EVZ    3ZZY    3ZZZ   
PDB (PDBSum)1QM9    1SJQ    1SJR    2AD9    2ADB    2ADC    2EVZ    3ZZY    3ZZZ   
PDB (IMB)1QM9    1SJQ    1SJR    2AD9    2ADB    2ADC    2EVZ    3ZZY    3ZZZ   
PDB (RSDB)1QM9    1SJQ    1SJR    2AD9    2ADB    2ADC    2EVZ    3ZZY    3ZZZ   
Structural Biology KnowledgeBase1QM9    1SJQ    1SJR    2AD9    2ADB    2ADC    2EVZ    3ZZY    3ZZZ   
SCOP (Structural Classification of Proteins)1QM9    1SJQ    1SJR    2AD9    2ADB    2ADC    2EVZ    3ZZY    3ZZZ   
CATH (Classification of proteins structures)1QM9    1SJQ    1SJR    2AD9    2ADB    2ADC    2EVZ    3ZZY    3ZZZ   
SuperfamilyP26599
Human Protein AtlasENSG00000011304
Peptide AtlasP26599
HPRD02823
IPIIPI00179964   IPI00334175   IPI00556157   IPI00183626   IPI00413691   IPI00921318   
Protein Interaction databases
DIP (DOE-UCLA)P26599
IntAct (EBI)P26599
FunCoupENSG00000011304
BioGRIDPTBP1
STRING (EMBL)PTBP1
ZODIACPTBP1
Ontologies - Pathways
QuickGOP26599
Ontology : AmiGOnucleotide binding  regulation of alternative mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  RNA binding  protein binding  nucleoplasm  nucleolus  mRNA processing  poly-pyrimidine tract binding  RNA splicing  fibroblast growth factor receptor signaling pathway  gene expression  membrane  negative regulation of RNA splicing  pre-mRNA binding  poly(A) RNA binding  negative regulation of mRNA splicing, via spliceosome  negative regulation of muscle cell differentiation  extracellular exosome  IRES-dependent viral translational initiation  
Ontology : EGO-EBInucleotide binding  regulation of alternative mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  RNA binding  protein binding  nucleoplasm  nucleolus  mRNA processing  poly-pyrimidine tract binding  RNA splicing  fibroblast growth factor receptor signaling pathway  gene expression  membrane  negative regulation of RNA splicing  pre-mRNA binding  poly(A) RNA binding  negative regulation of mRNA splicing, via spliceosome  negative regulation of muscle cell differentiation  extracellular exosome  IRES-dependent viral translational initiation  
REACTOMEP26599 [protein]
REACTOME PathwaysR-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA [pathway]
REACTOME PathwaysR-HSA-72163 mRNA Splicing - Major Pathway [pathway]
NDEx NetworkPTBP1
Atlas of Cancer Signalling NetworkPTBP1
Wikipedia pathwaysPTBP1
Orthology - Evolution
OrthoDB5725
GeneTree (enSembl)ENSG00000011304
Phylogenetic Trees/Animal Genes : TreeFamPTBP1
Homologs : HomoloGenePTBP1
Homology/Alignments : Family Browser (UCSC)PTBP1
Gene fusions - Rearrangements
Fusion : MitelmanPTBP1/UBE3C [19p13.3/7q36.3]  
Fusion: TCGAPTBP1 19p13.3 UBE3C 7q36.3 PRAD
Polymorphisms : SNP, variants
NCBI Variation ViewerPTBP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTBP1
dbVarPTBP1
ClinVarPTBP1
1000_GenomesPTBP1 
Exome Variant ServerPTBP1
ExAC (Exome Aggregation Consortium)PTBP1 (select the gene name)
Genetic variants : HAPMAP5725
Genomic Variants (DGV)PTBP1 [DGVbeta]
Mutations
ICGC Data PortalPTBP1 
TCGA Data PortalPTBP1 
Broad Tumor PortalPTBP1
OASIS PortalPTBP1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPTBP1 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PTBP1
DgiDB (Drug Gene Interaction Database)PTBP1
DoCM (Curated mutations)PTBP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PTBP1 (select a term)
intoGenPTBP1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)19:797392-812327  ENSG00000011304
CONAN: Copy Number AnalysisPTBP1 
Mutations and Diseases : HGMDPTBP1
OMIM600693   
MedgenPTBP1
Genetic Testing Registry PTBP1
NextProtP26599 [Medical]
TSGene5725
GENETestsPTBP1
Huge Navigator PTBP1 [HugePedia]
snp3D : Map Gene to Disease5725
BioCentury BCIQPTBP1
ClinGenPTBP1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5725
Chemical/Pharm GKB GenePA33934
Clinical trialPTBP1
Miscellaneous
canSAR (ICR)PTBP1 (select the gene name)
Probes
Litterature
PubMed164 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePTBP1
EVEXPTBP1
GoPubMedPTBP1
iHOPPTBP1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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