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Sense-Antisense lncRNA Pair Encoded by Locus 6p22.3 Determines Neuroblastoma Susceptibility via the USP36-CHD7-SOX9 Regulatory Axis.

Cancer cell | 2018

Trait-associated loci often map to genomic regions encoding long noncoding RNAs (lncRNAs), but the role of these lncRNAs in disease etiology is largely unexplored. We show that a pair of sense/antisense lncRNA (6p22lncRNAs) encoded by CASC15 and NBAT1 located at the neuroblastoma (NB) risk-associated 6p22.3 locus are tumor suppressors and show reduced expression in high-risk NBs. Loss of functional synergy between 6p22lncRNAs results in an undifferentiated state that is maintained by a gene-regulatory network, including SOX9 located on 17q, a region frequently gained in NB. 6p22lncRNAs regulate SOX9 expression by controlling CHD7 stability via modulating the cellular localization of USP36, encoded by another 17q gene. This regulatory nexus between 6p22.3 and 17q regions may lead to potential NB treatment strategies.

Pubmed ID: 29533783 RIS Download

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This is a list of tools and resources that we have found mentioned in this publication.


Fiji (tool)

RRID:SCR_002285

Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.

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Subread (tool)

RRID:SCR_009803

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

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TopHat (tool)

RRID:SCR_013035

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

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HA-Tag Antibody (F-7) (antibody)

RRID:AB_627809

This monoclonal targets HA-Tag

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Mono- and polyubiquitinylated conjugates, mAb (FK2) (antibody)

RRID:AB_10541840

This monoclonal targets Mono- and polyubiquitinylated conjugates mAb (FK2)

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Monoclonal Anti-Neurofilament 200 (Phos. and Non-Phos.) antibody produced in mouse (antibody)

RRID:AB_477257

This monoclonal targets Neurofilament 200 (Phos. and Non-Phos.) antibody produced in mouse

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Anti-Sox9 (antibody)

RRID:AB_2239761

This polyclonal targets Sox9

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Anti-USP36 antibody produced in rabbit (antibody)

RRID:AB_1858682

This polyclonal targets USP36 antibody produced in rabbit

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Anti-alpha-Tubulin, clone DM1A (antibody)

RRID:AB_310035

This monoclonal targets alpha-Tubulin clone DM1A

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Rabbit Normal igg Control antibody, Unconjugated (antibody)

RRID:AB_145841

This unknown targets Rabbit Normal igg Control antibody

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Anti-HaloTag pAb (antibody)

RRID:AB_713650

This polyclonal targets HaloTag pAb

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USP36 antibody (antibody)

RRID:AB_1271430

This polyclonal targets Human USP36

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