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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Combinatorial role of two paralogous splicing factors, hnRNP L and L-like, in multiple-exon regulation of CD45 alternative splicing

ABSTRACT: The goal of this study was to investigate the role of hnRNP L-like in alternative pre-mRNA splicing in human B-cells through an RNA-Seq approach. RNA-Seq was performed in DG75 cell line with over expression of hnRNP L-like or GFP as control.

ORGANISM(S): Homo sapiens

SUBMITTER: Lee-Hsueh Hung

PROVIDER: E-GEOD-33013 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.

Preussner Marco M Schreiner Silke S Hung Lee-Hsueh LH Porstner Martina M Jäck Hans-Martin HM Benes Vladimir V Rätsch Gunnar G Bindereif Albrecht A

Nucleic acids research 20120308 12

CD45 encodes a trans-membrane protein-tyrosine phosphatase expressed in diverse cells of the immune system. By combinatorial use of three variable exons 4-6, isoforms are generated that differ in their extracellular domain, thereby modulating phosphatase activity and immune response. Alternative splicing of these CD45 exons involves two heterogeneous ribonucleoproteins, hnRNP L and its cell-type specific paralog hnRNP L-like (LL). To address the complex combinatorial splicing of exons 4-6, we in ...[more]

PMID: 22402488

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Combinatorial role of two paralogous splicing factors, hnRNP L and L-like, in multiple-exon regulation of CD45 alternative splicing

Project description:The goal of this study was to investigate the role of hnRNP L-like in alternative pre-mRNA splicing in human B-cells through an RNA-Seq approach.

2012-03-29 | GSE33013 | GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)

Project description:Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and auto-regulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells. CLIPseq for hnRNP A1, hnRNP A2/B1, hnRNP F, hnRNP M, and hnRNP U in human 293T cells

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Effect of cellular and viral miRNAs on target RNA half-life in three human B-cell lines

Project description:Total, nascent and unlabeled RNA were prepared following 1h of labeling with 100 µM 4-thiouridine and 3 replicates analyzed by Affymetrix Gene ST 1.0 arrays Transcript half-lives were determined in DG75-eGFP, DG75-10/12 and BCBL-1 based on nascent/total RNA ratios; unlabeled RNA was analyzed in addition

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Identification of KSHV, EBV and cellular miRNA targets in human B-cells using RIP-Chip

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