Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Targeted RNA-seq of BCP-ALL pediatric patients

ABSTRACT: Targeted RNA-seq of pediatric infant (<1year of age at diagnosis) patients affected by B-cell precursor Acute Lymphoblastic leukemia (BCP-ALL). The aim of the study is to identify fusion gene rearrangements involved in childhood leukemia, using a custom targeted panel for RNA analysis by NGS.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-9971 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP126086

REPOSITORIES: biostudies-arrayexpress

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Publications

Recurrent genetic fusions redefine MLL germ line acute lymphoblastic leukemia in infants.

Fazio Grazia G Bardini Michela M De Lorenzo Paola P Grioni Andrea A Quadri Manuel M Pedace Lucia L Corral Abascal Lilia L Palamini Sonia S Palmi Chiara C Buldini Barbara B Vinti Luciana L Parasole Rosanna R Barisone Elena E Zecca Marco M Favre Claudio C Locatelli Franco F Conter Valentino V Rizzari Carmelo C Valsecchi Maria Grazia MG Biondi Andrea A Cazzaniga Giovanni G

Blood 20210401 14

PMID: 33512459

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Project description:Non-coding sense and antisense germline transcription within the immunoglobulin heavy chain locus precedes V(D)J recombination and has been proposed to be associated with Igh locus accessibility, although its precise role remains elusive. However, no global analysis of germline transcription throughout the Igh locus has been done. Therefore, we performed directional RNAseq, demonstrating the locations and extent of both sense and antisense transcription throughout the Igh locus. Surprisingly, the majority of antisense transcripts are localized around two PAIR elements in the distal IghV region. Importantly, long-distance loops measured by 3C are observed between these two active PAIR promoters and Eμ, the start site of Iμ germline transcription, in a lineage- and stage-specific manner, even though this antisense transcription is Eμ-independent. YY1-/- pro-B cells are greatly impaired in distal VH gene rearrangement and Igh locus compaction, and we demonstrate that YY1 deficiency greatly reduces antisense transcription and PAIR-Eμ interactions. ChIP-seq shows high level YY1 binding only at Eμ, but low levels near some antisense promoters. PAIR-Eμ interactions are not disrupted by DRB, which blocks transcription elongation without disrupting transcription factories once they are established, but the looping is reduced after heat shock treatment, which disrupts transcription factories. We propose that transcription-mediated interactions, most likely at transcription factories, initially compact the Igh locus, bringing distal VH genes close to the DJH rearrangement, which is adjacent to Eμ. Therefore, we hypothesize that one key role of non-coding germline transcription is to facilitate locus compaction, allowing distal VH genes to undergo efficient rearrangement. In order to determine the amount and location of sense and antisense non-coding RNA in the Igh locus, we prepared total RNA from CD19+ RAG1-/- pro-B cells. Samples were either pre-enriched in custom Agilent arrays, or directly sequenced. Data from one sample for each condition is included as reflected in the publication.

Dataset Information

Targeted RNA-seq of BCP-ALL pediatric patients

Publications

Recurrent genetic fusions redefine MLL germ line acute lymphoblastic leukemia in infants.

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