title: Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the In Cis downregulation of a gene cluster that targets NF-kB.
abstract: Non-coding RNAs are much more common than previously thought. However, for the vast majority of non-coding RNAs, the cellular function remains enigmatic. The two long non-coding RNA (lncRNA) genes DLEU1 and DLEU2 map to a critical region at chromosomal band 13q14.3 that is recurrently deleted in solid tumors and hematopoietic malignancies like chronic lymphocytic leukemia (CLL). While no point mutations have been found in the protein coding candidate genes at 13q14.3, they are deregulated in malignant cells, suggesting an epigenetic tumor suppressor mechanism. We therefore characterized the epigenetic makeup of 13q14.3 in CLL cells and found histone modifications by chromatin-immunoprecipitation (ChIP) that are associated with activated transcription and significant DNA-demethylation at the transcriptional start sites of DLEU1 and DLEU2 using 5 different semi-quantitative and quantitative methods (aPRIMES, BioCOBRA, MCIp, MassARRAY, and bisulfite sequencing). These epigenetic aberrations were correlated with transcriptional deregulation of the neighboring candidate tumor suppressor genes, suggesting a coregulation in cis of this gene cluster. We found that the 13q14.3 genes in addition to their previously known functions regulate NF-kB activity, which we could show after overexpression, siRNA-mediated knockdown, and dominant-negative mutant genes by using Western blots with previously undescribed antibodies, by a customized ELISA as well as by reporter assays. In addition, we performed an unbiased screen of 810 human miRNAs and identified the miR-15/16 family of genes at 13q14.3 as the strongest inducers of NF-kB activity. In summary, the tumor suppressor mechanism at 13q14.3 is a cluster of genes controlled by two lncRNA genes that are regulated by DNA-methylation and histone modifications and whose members all regulate NF-kB. Therefore, the tumor suppressor mechanism in 13q14.3 underlines the role both of epigenetic aberrations and of lncRNA genes in human tumorigenesis and is an example of colocalization of a functionally related gene cluster.
authors.affiliation: Cooperation Unit "Mechanisms of Leukemogenesis," University Ulm, German Cancer Research Center, DKFZ, Heidelberg, Germany.
authors.forename: Angela
authors.initials: A
authors.lastname: Garding
authors.forename: Nupur
authors.initials: N
authors.lastname: Bhattacharya
authors.forename: Rainer
authors.initials: R
authors.lastname: Claus
authors.forename: Melanie
authors.initials: M
authors.lastname: Ruppel
authors.forename: Cordula
authors.initials: C
authors.lastname: Tschuch
authors.forename: Katharina
authors.initials: K
authors.lastname: Filarsky
authors.forename: Irina
authors.initials: I
authors.lastname: Idler
authors.forename: Manuela
authors.initials: M
authors.lastname: Zucknick
authors.forename: Maïwen
authors.initials: M
authors.lastname: Caudron-Herger
authors.forename: Christopher
authors.initials: C
authors.lastname: Oakes
authors.forename: Verena
authors.initials: V
authors.lastname: Fleig
authors.forename: Ioanna
authors.initials: I
authors.lastname: Keklikoglou
authors.forename: Danilo
authors.initials: D
authors.lastname: Allegra
authors.forename: Leticia
authors.initials: L
authors.lastname: Serra
authors.forename: Sudhir
authors.initials: S
authors.lastname: Thakurela
authors.forename: Vijay
authors.initials: V
authors.lastname: Tiwari
authors.forename: Dieter
authors.initials: D
authors.lastname: Weichenhan
authors.forename: Axel
authors.initials: A
authors.lastname: Benner
authors.forename: Bernhard
authors.initials: B
authors.lastname: Radlwimmer
authors.forename: Hanswalter
authors.initials: H
authors.lastname: Zentgraf
authors.forename: Stefan
authors.initials: S
authors.lastname: Wiemann
authors.forename: Karsten
authors.initials: K
authors.lastname: Rippe
authors.forename: Christoph
authors.initials: C
authors.lastname: Plass
authors.forename: Hartmut
authors.initials: H
authors.lastname: Döhner
authors.forename: Peter
authors.initials: P
authors.lastname: Lichter
authors.forename: Stephan
authors.initials: S
authors.lastname: Stilgenbauer
authors.forename: Daniel
authors.initials: D
authors.lastname: Mertens
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002471:Cell Transformation, Neoplastic; D002843:Chromatin / Q000235:genetics; D002882:Chromosomes, Human, Pair 13 / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D015536:Down-Regulation; D044127:Epigenesis, Genetic / Q000235:genetics; D005260:Female; D057809:HEK293 Cells; D006801:Humans; D007938:Leukemia / Q000097:blood / Q000235:genetics / Q000503:physiopathology; D008297:Male; D008875:Middle Aged; D009154:Mutation; D016328:NF-kappa B / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D014166:Transferases; D025521:Tumor Suppressor Proteins / Q000097:blood / Q000235:genetics; D015854:Up-Regulation
chemical_list: D002843:Chromatin; C109421:DLEU1 lncRNA, human; C109420:DLEU2 lncRNA, human; D016328:NF-kappa B; D062085:RNA, Long Noncoding; D025521:Tumor Suppressor Proteins; D014166:Transferases