Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SNW1 (SNW domain containing 1)

Written2017-08Cagla Ece Olgun and Mesut Muyan
Middle East Technical University, Department of Biological Sciences, Cankaya 06800, Ankara, Turkey; colgun@metu.edu.tr; mmuyan@metu.edu.tr

Abstract SNW1 is a spliceosomal component and transcriptional co-regulator that provides a modulatory coupling of transcription initiation and splicing. SNW1 appears to be an essential cancer cell survival factor by co-transcriptionally regulating mRNA splicing of proteins involved in cell cycle checkpoints. As a co-regulator, SNW1 is shown to attune the activity of a number of transcription factors, including nuclear hormone receptors as well as CBF1, Smad2/3, and MyoD by modulating a transition step between the repressing and activating transcription complex assembly. SNW1 is also involved in the cell cycle progression through the involvement in cell cycle checkpoint-dependent changes in gene expressions during cellular proliferation and viral infections.

Keywords SNW1; cancer; transcription regulation

(Note : for Links provided by Atlas : click)

Identity

Alias_namesSKIIP
SKI interacting protein
Alias_symbol (synonym)NCoA-62
SKIP
Prp45
PRPF45
Bx42
Other aliasHomolog Of Drosophila BX42 (Bx42)
Nuclear Receptor Coactivator NCoA-62 (NCOA-62)
SKI Interacting Protein (SKIP)
HGNC (Hugo) SNW1
LocusID (NCBI) 22938
Atlas_Id 42348
Location 14q24.3. Genomic coordinates: 14: 77717599-77761220  [Link to chromosome band 14q24]
Location_base_pair Starts at 77717601 and ends at 77761154 bp from pter ( according to hg19-Feb_2009)  [Mapping SNW1.png]
 
  Human SNW1 located on chromosome 14q24.3 is on the reverse strand. (https://www.ncbi.nlm.nih.gov/gene/22938, 2017)
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

 
  Exons are shown in boxes; introns are indicated by lines. The encoding exons are in blue. The start codon ATG and stop codon TAG are shown.
Description The human SNW1 gene contains 14 exons.
Transcription As a result of alternative splicing, SNW1 has two transcript variants (https://www.ncbi.nlm.nih.gov/gene/22938, 2017). The transcript 1, the long isoform, has 2207 nt mRNA which encodes a 571 amino acid (aa)-long protein (protein ID: NP_001305773.1). The transcript 2, which has 2146 nucleotides, differs in the 3' UTR and displays multiple coding region differences compared to transcript 1. One of the coding region differences results in a frame shift, giving rise to the isoform 2, which has 536 amino-acids with a distinct carboxyl-terminus (protein ID: NP_036377.1).
Pseudogene There is one reported pseudogene located on chromosome 1 (https://www.ncbi.nlm.nih.gov/gene/22938, 2017).

Protein

Note SNW domain containing protein 1 is also known as nuclear protein SkiP, nuclear receptor coactivator NcoA-62 or Ski interacting protein (SKIP).
Description The genes encoding SNW proteins are present throughout eukaryotic phylla, including lower eukaryotes, plants, fungi and animals. There is only one gene per genome, which encodes for a 60-80 kDa protein that predominantly localizes to the nucleus (Folk at al., 2004). SNW1 is suggested to contain protein interaction domains as well as a carboxyl-terminally located dimerization domain (Folk at al., 2004).
Expression SNW1 is expressed in the brain, endocrine tissues, bone marrow and immune system, muscle, lung, liver, gall bladder, pancreas, gastrointestinal tract, kidney, urinary bladder, male and female specific tissues, adipose and soft tissues and skin, in which the expression levels are high except kidney (http://www.proteinatlas.org/ENSG00000100603-SNW1/tissue, 2017).
Localisation SNW1 localizes in the nucleus (Dahl et al., 1998).
Function SNW1 acts as a co-regulator for transcriptions regulated by vitamin D and RARA / RARB / RARG (retinoic acid receptors) as well as steroid hormone receptors including NR3C1 (glucocorticoid receptor), ESR1 / ESR2 (estrogen receptors), and AR (androgen receptor) (Folk at al., 2004). SNW1 also plays critical roles in the function of v-Ski avian retroviral oncogene, bone morphogenetic protein (BMP) during vertebrate embryogenesis (Wu et al, 2011), telomere function (Lackner et al, 2011) and Notch signaling-mediated transcription (Vasquez-Del Carpio, 2013). SNW1 is reported to counteract transcriptional repression induced by RB1 (retinoblastoma protein) as well (Prathapam et al. 2002). In addition to being a transcriptional co-regulator, SNW1 is an integral component of spliceosome by interacting with the U5 small nuclear ribonucleoprotein (snRNP) subcomplex of the activated spliceosome as a part of the PRPF19/nineteen complex (NTC) (Neubauer et al, 1998; Makarova et al, 2004). SNW1 inactivation is reported to cause a rapid loss of sister chromatid cohesion (Van Der Lelij et al, 2014) mitotic spindle and cytokinesis defects (Kittler et al, 2004; Kittler et al, 2005). It is also suggested that the involvement of SNW1 in the p21-gene specific splicing is critical for cancer cell survival under stress (Chen et al, 2011).
Homology Homologs of SNW1 are found in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog (https://www.ncbi.nlm.nih.gov/gene/22938, 2017).

Mutations

Note There are no gene mutations described for SNW1.

Implicated in

  
Entity Bladder cancer
Note SNW1 displays a higher expression in bladder tumor tissue than surrounding normal adjacent tissues. Higher expression of SNW1 appears to be correlated with poor prognosis of bladder cancer. It is also reported that high-grade urothelial carcinoma samples express higher levels of SNW1 compared with low-grade urothelial carcinoma samples (Wang et al., 2014).
  
  
Entity Breast cancer
Note Immunohistochemical and western blot analyses of breast carcinoma samples showed that the SNW1 expression is augmented in breast cancer tissues compared with adjacent noncancerous tissues. SNW1 overexpression appears to have a positive correlation with the histological grade of cancerous tissues. Moreover, it is suggested that there is an inverse relationship between the SNW1 expression and pathologic prognostic parameters including estrogen (ER) and progesterone receptors status. In ER positive cell models derived from breast carcinoma, there is a lower expression of SNW1 when it is compared with the expression levels of SNW1 in ER negative cell models (Liu et al., 2014).
  
  
Entity Hepatocellular carcinoma
Note Expression analyses of SNW1 with samples of hepatocellular carcinoma patients and normal liver samples revealed that SNW1 is overexpressed in cancerous cells when compared with noncancerous liver samples. There is a positive correlation between high SNW1 expression and aggressiveness of hepatocellular carcinoma (Liu et al., 2013).
  
  
Entity Malignant pleural mesothelioma
Note As in other cancer types, SNW1 is overexpressed in malignant pleural mesotheliomas (MPM) patients, which is correlated with poor prognosis. Overexpression of SNW1 also correlates with a reduced survival rate in MPM patient cohort (Turkcu et al., 2016).
  

Bibliography

SKIP counteracts p53-mediated apoptosis via selective regulation of p21 Cip1 mRNA splicing
Chen, Y., Zhang, L., & Jones, K. A
Genes and Development 2011; 25(7): 701-16.
PMID 21460037
 
The Ski oncoprotein interacts with Skip, the human homolog of Drosophila Bx42
Dahl, R., Wani, B., & Hayman, M. J.
Oncogene 1998; 16(12): 1579-86.
PMID 9569025
 
Trancriptional coregulator SNW/SKIP: the concealed tie of dissimilar pathways
Folk P., Puta F., Skruzny M.
Cellular and Molecular Life Sciences 2004; 61(6): 629-40
PMID 15052407
 
RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells.
Kittler R., Pelletier L., Ma C., Poser I., Fischer S., Hyman A.A., Buchholz, F.
PNAS 2005; 102(7): 2396-401.
PMID 15695330
 
A siRNA-based screen for genes involved in chromosome end protection.
Lackner D.H., Durocher D., Karlseder J.
PLoS One 2011; 6(6): e21407.
PMID 21760879
 
High SKIP expression is correlated with poor prognosis and cell proliferation of hepatocellular carcinoma
Liu, G., Huang, X., Cui,X., Zang, J., Wei, L., Ni, R., Lu, C.
Med. Oncol. 2013; 30(3): 537
PMID 23696020
 
Expression and prognostic role of SKIP in human breast carcinoma
Liu, X., Ni, Q., Xu, J., Sheng, C., Wang, Q., Chen, J., Yang S., Wang, H.
Journal of Molecular Histology 2014; 45(2): 169-80.
PMID 24150787
 
A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing
Makarova O.V., Makarov E.M., Urlaub H., Will C.L., Gentzel M., Wilm M., Lührmann R.
EMBO Journal 2004; 23(12): 2381-91
PMID 15175653
 
Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex.
Neubauer G., King A, Rappsilber J., Calvio C., Watson M., Ajuh P., Sleeman J., Lamond A., Mann M.
Nature Genetics 1998; 20(1): 46-50.
PMID 9731529
 
Skip interacts with the retinoblastoma tumor suppressor and inhibits its transcriptional repression activity
Prathapam, T., Kühne, C., & Banks, L.
Nucleic Acids Research 2002; 30(23): 5261-68
PMID 12466551
 
Comparison of SKIP expression in malignant pleural mesotheliomas with Ki-67 proliferation index and prognostic parameters
Turkcu G., Alabalik U., Keles A.N., Ibiloglu I., Kucukoner M., Selimoglu Sen H., & Buyukbayram H.
Pol. J. Pathol 2016; 67(2): 108-13.
PMID 27543864
 
Assembly of a Notch Transcriptional Activation Complex Requires Multimerization
Vasquez-Del Carpio, R., Kaplan, F. M., Weaver, K. L., VanWye, J. D., Alves-Guerra, M.C., Robbins, D. J., & Capobianco, A. J.
Molecular and Cellular Biology 2011; 31(7): 1396-408.
PMID 21245387
 
SKIP expression is correlated with clinical prognosis in patients with bladder cancer
Wang L., Zhang M., Wu Y., Huang Y., Shi Z., & Huang H.
Int. J. Clin. Exp. Pathol. 2014; 7(4): 1695-701.
PMID 24817966
 
SNW1 Is a Critical Regulator of Spatial BMP Activity, Neural Plate Border Formation, and Neural Crest Specification in Vertebrate Embryos
Wu M.Y., Ramel M.C., Howell M., Hill C.S.
Plos Biology 2011; 9(2): e1000593
PMID 21358802
 
SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs.
van der Lelij P., Stocsits R.R., Ladurner R., Petzold G., Kreidl E., Koch B., Schmitz J., Neumann B., Ellenberg J., Peters J.M.
EMBO J. 2014; 33(22): 2643-58.
PMID 25257309
 

Citation

This paper should be referenced as such :
Olgun, CE; Muyan, M
SNW1 (SNW domain containing 1);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/SNW1ID42348ch14q24.html


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 4 ]
  t(3;14)(q27;q24) EIF4G1/SNW1
t(8;14)(q24;q24) NDRG1/SNW1
t(8;14)(q24;q24) RPL8/SNW1
t(11;14)(p15;q24) IGF2/SNW1


External links

Nomenclature
HGNC (Hugo)SNW1   16696
Cards
AtlasSNW1ID42348ch14q24
Entrez_Gene (NCBI)SNW1  22938  SNW domain containing 1
AliasesBx42; FUN20; NCOA-62; PRPF45; 
Prp45; SKIIP; SKIP; SKIP1
GeneCards (Weizmann)SNW1
Ensembl hg19 (Hinxton)ENSG00000100603 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000100603 [Gene_View]  ENSG00000100603 [Sequence]  chr14:77717601-77761154 [Contig_View]  SNW1 [Vega]
ICGC DataPortalENSG00000100603
TCGA cBioPortalSNW1
AceView (NCBI)SNW1
Genatlas (Paris)SNW1
WikiGenes22938
SOURCE (Princeton)SNW1
Genetics Home Reference (NIH)SNW1
Genomic and cartography
GoldenPath hg38 (UCSC)SNW1  -     chr14:77717601-77761154 -  14q24.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SNW1  -     14q24.3   [Description]    (hg19-Feb_2009)
EnsemblSNW1 - 14q24.3 [CytoView hg19]  SNW1 - 14q24.3 [CytoView hg38]
Mapping of homologs : NCBISNW1 [Mapview hg19]  SNW1 [Mapview hg38]
OMIM603055   
Gene and transcription
Genbank (Entrez)AF045184 AK292274 AK293619 AK302246 AK316087
RefSeq transcript (Entrez)NM_001318844 NM_012245
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SNW1
Cluster EST : UnigeneHs.445498 [ NCBI ]
CGAP (NCI)Hs.445498
Alternative Splicing GalleryENSG00000100603
Gene ExpressionSNW1 [ NCBI-GEO ]   SNW1 [ EBI - ARRAY_EXPRESS ]   SNW1 [ SEEK ]   SNW1 [ MEM ]
Gene Expression Viewer (FireBrowse)SNW1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)22938
GTEX Portal (Tissue expression)SNW1
Human Protein AtlasENSG00000100603-SNW1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13573   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13573  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13573
Splice isoforms : SwissVarQ13573
PhosPhoSitePlusQ13573
Domains : Interpro (EBI)SKI-int_prot_SKIP    SKI-int_prot_SKIP_SNW-dom   
Domain families : Pfam (Sanger)SKIP_SNW (PF02731)   
Domain families : Pfam (NCBI)pfam02731   
Conserved Domain (NCBI)SNW1
DMDM Disease mutations22938
Blocks (Seattle)SNW1
SuperfamilyQ13573
Human Protein Atlas [tissue]ENSG00000100603-SNW1 [tissue]
Peptide AtlasQ13573
HPRD04340
IPIIPI00013830   IPI00943237   IPI00910816   IPI01025618   IPI01025271   IPI01025390   
Protein Interaction databases
DIP (DOE-UCLA)Q13573
IntAct (EBI)Q13573
FunCoupENSG00000100603
BioGRIDSNW1
STRING (EMBL)SNW1
ZODIACSNW1
Ontologies - Pathways
QuickGOQ13573
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  generation of catalytic spliceosome for second transesterification step  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  transcription coactivator activity  transcription corepressor activity  RNA binding  Notch binding  protein binding  nucleus  nucleoplasm  nucleoplasm  spliceosomal complex  regulation of transcription by RNA polymerase II  transcription initiation from RNA polymerase II promoter  Notch signaling pathway  positive regulation of transcription of Notch receptor target  cyclin/CDK positive transcription elongation factor complex  viral process  nuclear matrix  nuclear body  nuclear speck  enzyme binding  positive regulation of transforming growth factor beta receptor signaling pathway  nuclear hormone receptor binding  intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  vitamin D receptor binding  retinoic acid receptor binding  positive regulation by host of viral transcription  positive regulation by host of viral transcription  positive regulation of Notch signaling pathway  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  SMAD binding  positive regulation of mRNA splicing, via spliceosome  retinoic acid receptor signaling pathway  regulation of retinoic acid receptor signaling pathway  androgen receptor binding  positive regulation of neurogenesis  positive regulation of histone H3-K4 methylation  regulation of vitamin D receptor signaling pathway  positive regulation of vitamin D receptor signaling pathway  U2-type catalytic step 2 spliceosome  catalytic step 2 spliceosome  post-mRNA release spliceosomal complex  cellular response to retinoic acid  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  generation of catalytic spliceosome for second transesterification step  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  transcription coactivator activity  transcription corepressor activity  RNA binding  Notch binding  protein binding  nucleus  nucleoplasm  nucleoplasm  spliceosomal complex  regulation of transcription by RNA polymerase II  transcription initiation from RNA polymerase II promoter  Notch signaling pathway  positive regulation of transcription of Notch receptor target  cyclin/CDK positive transcription elongation factor complex  viral process  nuclear matrix  nuclear body  nuclear speck  enzyme binding  positive regulation of transforming growth factor beta receptor signaling pathway  nuclear hormone receptor binding  intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  vitamin D receptor binding  retinoic acid receptor binding  positive regulation by host of viral transcription  positive regulation by host of viral transcription  positive regulation of Notch signaling pathway  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  SMAD binding  positive regulation of mRNA splicing, via spliceosome  retinoic acid receptor signaling pathway  regulation of retinoic acid receptor signaling pathway  androgen receptor binding  positive regulation of neurogenesis  positive regulation of histone H3-K4 methylation  regulation of vitamin D receptor signaling pathway  positive regulation of vitamin D receptor signaling pathway  U2-type catalytic step 2 spliceosome  catalytic step 2 spliceosome  post-mRNA release spliceosomal complex  cellular response to retinoic acid  
Pathways : KEGGNotch signaling pathway   
REACTOMEQ13573 [protein]
REACTOME PathwaysR-HSA-72163 [pathway]   
NDEx NetworkSNW1
Atlas of Cancer Signalling NetworkSNW1
Wikipedia pathwaysSNW1
Orthology - Evolution
OrthoDB22938
GeneTree (enSembl)ENSG00000100603
Phylogenetic Trees/Animal Genes : TreeFamSNW1
HOVERGENQ13573
HOGENOMQ13573
Homologs : HomoloGeneSNW1
Homology/Alignments : Family Browser (UCSC)SNW1
Gene fusions - Rearrangements
Fusion : MitelmanEIF4G1/SNW1 [3q27.1/14q24.3]  [t(3;14)(q27;q24)]  
Fusion : MitelmanIGF2/SNW1 [11p15.5/14q24.3]  [t(11;14)(p15;q24)]  
Fusion : MitelmanLARGE/SNW1 [22q12.3/14q24.3]  [t(14;22)(q24;q12)]  
Fusion : MitelmanNDRG1/SNW1 [8q24.22/14q24.3]  [t(8;14)(q24;q24)]  
Fusion : MitelmanRPL8/SNW1 [8q24.3/14q24.3]  [t(8;14)(q24;q24)]  
Fusion PortalEIF4G1 3q27.1 SNW1 14q24.3 LUAD
Fusion PortalIGF2 11p15.5 SNW1 14q24.3 THCA
Fusion PortalLARGE 22q12.3 SNW1 14q24.3 BRCA
Fusion PortalNDRG1 8q24.22 SNW1 14q24.3 BLCA
Fusion PortalRPL8 8q24.3 SNW1 14q24.3 BRCA
Fusion : QuiverSNW1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSNW1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SNW1
dbVarSNW1
ClinVarSNW1
1000_GenomesSNW1 
Exome Variant ServerSNW1
ExAC (Exome Aggregation Consortium)ENSG00000100603
GNOMAD BrowserENSG00000100603
Genetic variants : HAPMAP22938
Genomic Variants (DGV)SNW1 [DGVbeta]
DECIPHERSNW1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSNW1 
Mutations
ICGC Data PortalSNW1 
TCGA Data PortalSNW1 
Broad Tumor PortalSNW1
OASIS PortalSNW1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSNW1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSNW1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SNW1
DgiDB (Drug Gene Interaction Database)SNW1
DoCM (Curated mutations)SNW1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SNW1 (select a term)
intoGenSNW1
NCG5 (London)SNW1
Cancer3DSNW1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603055   
Orphanet
DisGeNETSNW1
MedgenSNW1
Genetic Testing Registry SNW1
NextProtQ13573 [Medical]
TSGene22938
GENETestsSNW1
Target ValidationSNW1
Huge Navigator SNW1 [HugePedia]
snp3D : Map Gene to Disease22938
BioCentury BCIQSNW1
ClinGenSNW1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD22938
Chemical/Pharm GKB GenePA134883977
Clinical trialSNW1
Miscellaneous
canSAR (ICR)SNW1 (select the gene name)
Probes
Litterature
PubMed100 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSNW1
EVEXSNW1
GoPubMedSNW1
iHOPSNW1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Jul 16 10:01:07 CEST 2018

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.