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EEF1E1-BLOC1S5

Written2020-03Luigi Cristiano
Aesthetic and medical biotechnologies research unit, Prestige, Terranuova Bracciolini, Italy; prestige.infomed@gmail.com - luigicristiano@libero.it

Abstract EEF1E1-BLOC1S5 is a long non-coding RNA that derives from the read-through transcription between the neighboring EEF1E1 and BLOC1S5 genes. This review collects the data on DNA/RNA and the diseases where it is involved.

Keywords EEF1E1-BLOC1S5; EEF1E1-MUTED; EEF1E1-BLOC1S5 readthrough; lncRNA

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)EEF1E1-BLOC1S5 readthrough
EEF1E1-MUTED
lnc-EEF1E1-2
HGNC (Hugo) EEF1E1-BLOC1S5
LocusID (NCBI) 100526837
Atlas_Id 62733
Location 6p24.3  [Link to chromosome band 6p24]
Location_base_pair Starts at 8013567 and ends at 8102595 bp from pter ( according to hg19-Feb_2009)  [Mapping EEF1E1-BLOC1S5.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
EEF1E1-BLOC1S5/ZNF384EEF1E1-BLOC1S5/NCOR1EEF1E1-BLOC1S5/NSMCE4A
CDYL/EEF1E1-BLOC1S5

DNA/RNA

 
  Figure. 1. EEF1E1-BLOC1S5 lncRNA. The figure shows the locus on chromosome 6 for EEF1E1-BLOC1S5 (reworked from https://www.ncbi.nlm.nih.gov/gene; http://grch37.ensembl.org; www.genecards.org)
Description EEF1E1-BLOC1S5 was identified for the first time by Prakash and colleagues in 2010 (Prakash et al, 2010). It starts at 8,013,567 nt and ends at 8,102,595 nt from pter with a length of 89,029 bp. It counts 7 exons and the current reference sequence is NC_000006.12. Near to the genomic sequence of EEF1E1-BLOC1S5 there is a strong promoter transcriptional element that is located at +1.0 kb. Enhancer transcriptional elements are located at +38.2 Kb and at +18.1 Kb respectively.
Transcription EEF1E1-BLOC1S5 counts 2,992 bp and it is a long non-coding RNA with reference sequence NR_037618.1. It derives from the read-through transcription between the neighboring EEF1E1 (eukaryotic translation elongation factor 1 epsilon 1) and MUTED (muted homolog) genes on chromosome 6. MUTED gene, alias BLOC1S5 (biogenesis of lysosomal organelles complex 1 subunit 5), is a component of BLOC-1 (biogenesis of lysosome-related organelles complex 1) complex that is involved in the biogenesis of organelles like melanosomes and platelet-dense granules.
It is a chimeric RNA, i.e. an RNA with a sequence derived from two genes and its transcriptional and post-transcriptional regulations could be the same as those of the other known-genes (He et al, 2018).
It was not possible to find experimentally a protein product for this chimeric RNA (Fagerberg et al, 2014), although in some databases is reported a theoretical protein product of 151 amino acids, with a predicted weight of 17,02 kDa and isoelectric point of 7.39 (https://www.uniprot.org/uniprot/C9J1V9; http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?g=ENSG00000265818;r=6:8015726-8102530;t=ENST00000397456). Therefore EEF1E1-BLOC1S5 is a candidate for nonsense-mediated mRNA decay (NMD) because it is unlikely to produce a protein product.

Protein

Expression EEF1E1-BLOC1S5 ncRNA is transcribed (but not translated) widely in human tissues and normal cells. In memory B cells, it was found that the EEF1E1-BLOC1S5 is downregulated in the early gene expression (Day3-Day 0) following seasonal trivalent influenza vaccination in older individuals (Haralambieva et al, 2016)

Implicated in

Note LncRNAs are nowadays considered as emerging key regulators of cellular processes and they are often aberrantly expressed in various diseases (Kumar et al, 2019). EEF1E1-BLOC1S5 is not been still well-characterized, i.e. it is still unclear its physiologic role in the cell and its involvement in diseases when its expression is altered, however it is involved in some genomic translocations with the creation of several fusion genes (Table.1).
Name5' end3' endLoc1Loc2DescriptionTypeDiseaseOrganCodeRef.
CDYL/EEF1E1-BLOC1S5CDYLEEF1E1-BLOC1S56p25.16p24.3t(6;6)(p24;p25)TranslocationCancer(?)-1
EEF1E1-BLOC1S5EEF1E1BLOC1S56p24.36p24.3Readthrough transcriptionFusion gene(?)(?)--
EEF1E1-BLOC1S5/NSMCE4AEEF1E1-BLOC1S5NSMCE4A6p24.310q26.13t(6;10)(p24;q26)Translocation(?)Normal cells--
EEF1E1-BLOC1S5/NCOR1EEF1E1-BLOC1S5NCOR16p24.317p12t(6;17)(p24;p12)TranslocationCancerProstate-2
EEF1E1-BLOC1S5/ZNF384EEF1E1-BLOC1S5ZNF3846p24.312p13.31t(6;12)(p24;p13)TranslocationCancerProstate-2

Table.1 EEF1E1-BLOC1S5 rearrangements: translocations and fusion genes (reworked from: http://www.tumorfusions.org; https://mitelmandatabase.isb-cgc.org/; http://quiver.archerdx.com; http://atlasgeneticsoncology.org//Bands/6p24.html#REFERENCES; https://fusionhub.persistent.co.in/home.html). [ (?) ] unknown; [ 1 ] Campbell et al, 2020; [ 2 ] Robinson et al, 2015; [ - ] no reference
  
Entity Prostate cancer
Note Two genomic translocations were found in prostate cancer samples derived from patients, i.e. the t(6;17)(p24;p12) EEF1E1-BLOC1S5/NCOR1 and the t(6;12)(p24;p13) EEF1E1-BLOC1S5/ZNF384 (Robinson et al., 2015).
The t(6;17)(p24;p12) EEF1E1-BLOC1S5/NCOR1 is originated by the fusion of EEF1E1-BLOC1S5 gene at 5'-end with "nuclear receptor corepressor 1" (NCOR1) gene at 3' end while the t(6;12)(p24;p13) EEF1E1-BLOC1S5/ZNF384 NCOR1 is originated by the fusion of EEF1E1-BLOC1S5 gene at 5'-end with "zinc finger protein 384" ( ZNF384) gene at 3'. There are no data about the respective chimeric transcripts or proteins and the role of these genomic alterations is still unknown.
  
  
Entity Cystic fibrosis
Note EEF1E1-BLOC1S5 is found to be over-expressed in cystic fibrosis (CF) airway tissues respect control tissues and it may play an important role in the pathophysiology of CF lung disease. However, further studies are needed to understanding its exact role in this disease (Kumar et al, 2019).
  

Bibliography

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics
Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto CA, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M
Mol Cell Proteomics 2014 Feb;13(2):397-406
PMID 24309898
 
Transcriptional signatures of influenza A/H1N1-specific IgG memory-like B cell response in older individuals
Haralambieva IH, Ovsyannikova IG, Kennedy RB, Zimmermann MT, Grill DE, Oberg AL, Poland GA
Vaccine 2016 Jul 25;34(34):3993-4002
PMID 27317456
 
Transcriptional-Readthrough RNAs Reflect the Phenomenon of "A Gene Contains Gene(s)" or "Gene(s) within a Gene" in the Human Genome, and Thus Are Not Chimeric RNAs
He Y, Yuan C, Chen L, Lei M, Zellmer L, Huang H, Liao DJ
Genes (Basel) 2018 Jan 16;9(1)
PMID 29337901
 
Pan-cancer analysis of whole genomes
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Nature 2020 Feb;578(7793):82-93
PMID 32025007
 
Comparative analyses of long non-coding RNA profiles in vivo in cystic fibrosis lung airway and parenchyma tissues
Kumar P, Sen C, Peters K, Frizzell RA, Biswas R
Respir Res 2019 Dec 16;20(1):284
PMID 31842871
 
Integrative Clinical Genomics of Advanced Prostate Cancer
Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, Vinson J, Cao X, Vats P, Kunju LP, Hussain M, Feng FY, Tomlins SA, Cooney KA, Smith DC, Brennan C, Siddiqui J, Mehra R, Chen Y, Rathkopf DE, Morris MJ, Solomon SB, Durack JC, Reuter VE, Gopalan A, Gao J, Loda M, Lis RT, Bowden M, Balk SP, Gaviola G, Sougnez C, Gupta M, Yu EY, Mostaghel EA, Cheng HH, Mulcahy H, True LD, Plymate SR, Dvinge H, Ferraldeschi R, Flohr P, Miranda S, Zafeiriou Z, Tunariu N, Mateo J, Perez-Lopez R, Demichelis F, Robinson BD, Sboner A, Schiffman M, Nanus DM, Tagawa ST, Sigaras A, Eng KW, Elemento O, Sboner A, Heath EI, Scher HI, Pienta KJ, Kantoff P, de Bono JS, Rubin MA, Nelson PS, Garraway LA, Sawyers CL, Chinnaiyan AM
Cell 2015 Jul 16;162(2):454
PMID 28843286
 

Citation

This paper should be referenced as such :
Cristiano Luigi
EEF1E1-BLOC1S5
Atlas Genet Cytogenet Oncol Haematol. 2020;24(10):366-368.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/EEF1E1-BLOC1S5ID62733ch6p24.html


External links

Nomenclature
HGNC (Hugo)EEF1E1-BLOC1S5   49187
Cards
AtlasEEF1E1-BLOC1S5ID62733ch6p24
Entrez_Gene (NCBI)EEF1E1-BLOC1S5  100526837  EEF1E1-BLOC1S5 readthrough (NMD candidate)
AliasesEEF1E1-MUTED
GeneCards (Weizmann)EEF1E1-BLOC1S5
Ensembl hg19 (Hinxton) [Gene_View]
Ensembl hg38 (Hinxton) [Gene_View]   [Sequence]  chr6:8013567-8102595 [Contig_View]  EEF1E1-BLOC1S5 [Vega]
TCGA cBioPortalEEF1E1-BLOC1S5
AceView (NCBI)EEF1E1-BLOC1S5
Genatlas (Paris)EEF1E1-BLOC1S5
WikiGenes100526837
SOURCE (Princeton)EEF1E1-BLOC1S5
Genetics Home Reference (NIH)EEF1E1-BLOC1S5
Genomic and cartography
GoldenPath hg38 (UCSC)EEF1E1-BLOC1S5  -     chr6:8013567-8102595 -  6p24.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)EEF1E1-BLOC1S5  -     6p24.3   [Description]    (hg19-Feb_2009)
GoldenPathEEF1E1-BLOC1S5 - 6p24.3 [CytoView hg19]  EEF1E1-BLOC1S5 - 6p24.3 [CytoView hg38]
genome Data Viewer NCBIEEF1E1-BLOC1S5 [Mapview hg19]  
Gene and transcription
Genbank (Entrez)BI552521
RefSeq transcript (Entrez)
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)EEF1E1-BLOC1S5
Gene ExpressionEEF1E1-BLOC1S5 [ NCBI-GEO ]   EEF1E1-BLOC1S5 [ EBI - ARRAY_EXPRESS ]   EEF1E1-BLOC1S5 [ SEEK ]   EEF1E1-BLOC1S5 [ MEM ]
Gene Expression Viewer (FireBrowse)EEF1E1-BLOC1S5 [ Firebrowse - Broad ]
GenevisibleExpression of EEF1E1-BLOC1S5 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)100526837
GTEX Portal (Tissue expression)EEF1E1-BLOC1S5
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)EEF1E1-BLOC1S5
DMDM Disease mutations100526837
Blocks (Seattle)EEF1E1-BLOC1S5
Protein Interaction databases
BioGRIDEEF1E1-BLOC1S5
STRING (EMBL)EEF1E1-BLOC1S5
ZODIACEEF1E1-BLOC1S5
Ontologies - Pathways
Huge Navigator EEF1E1-BLOC1S5 [HugePedia]
snp3D : Map Gene to Disease100526837
BioCentury BCIQEEF1E1-BLOC1S5
ClinGenEEF1E1-BLOC1S5
Clinical trials, drugs, therapy
Protein Interactions : CTD100526837
Clinical trialEEF1E1-BLOC1S5
Miscellaneous
canSAR (ICR)EEF1E1-BLOC1S5 (select the gene name)
HarmonizomeEEF1E1-BLOC1S5
DataMed IndexEEF1E1-BLOC1S5
Probes
Litterature
PubMed1 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineEEF1E1-BLOC1S5
EVEXEEF1E1-BLOC1S5
GoPubMedEEF1E1-BLOC1S5
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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