Project description:HNRNPK is part of the minimally deleted region (MDR) in AML del(9q). To understand the function of hnRNP K in pathogenesis of this AML subtype, we analyzed the function of hnRNP K as an RNA binding protein in myeloid cells. Co-immunoprecipitated RNAs from hnRNP K and non-related control immunoprecipitation as well as input RNA were subjected to next generation sequencing. This analysis revealed an interaction of hnRNP K with 1076 RNAs, among them many mRNAs encoding transcription factors involved in myeloid differentiation and AML pathogenesis.
Project description:To inform the mechanism of hnRNP H dysfunction in methamphetamine-induced dopamine release and behavior, we surveyed mRNA targets of hnRNP H via cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in striatal tissue at baseline and at 30 min post-MA (2 mg/kg, i.p.). To integrate identification of hnRNP H targets with the impact of Hnrnph1 mutation and methampetamine on downstream gene expression and splicing, we analyzed the transcriptome of the parallel samples used in CLIP-seq.
Project description:The regulation of post-transcriptional modifications of pre-mRNA by alternative splicing is important for cellular function, development and immunity The receptor tyrosine phosphatase CD45, which is expressed on all hematopoietic cells, is known for its role in the development and activation of T cells. To investigate the role of hnRNP L further, we have generated conditional hnRNP L knockout mice carrying floxed alleles and the T-cell specific Lck-Cre recombinase transgene. The Lck-Cre transgene is active in DN3, DN4 as well as in DP and SP cells. We found that deletion of hnRNP L results in a decreased thymic cellularity caused by a partial block at the transition stage between DN4 and DP cells. In addition, hnRNP L-/- thymocytes express aberrant levels of the CD45RA splice isoform and show high levels of phosphorylated Lck at the activator tyrosine Y394 but lacking phosphorylation of the inhibitory tyrosine Y505. This is indicative of an increased basal Lck activation and correlated with a higher proliferation rate of DN4 cells in hnRNP L-/- mice. Deletion of hnRNP L also blocked egress of SP cells to peripheral lymphoid organs and the migration of SP thymocytes in response to the chemokines CCL21 and SDF-1a. Since we found that actin polymerization was also compromised in hnRNP L-/- SP cells, we propose that a defect in the signal transduction cascade downstream of the chemokine receptors CCR7 and CXCR4 caused by the absence of hnRNP L is responsible for this phenotype. Our results indicate that hnRNPL regulates pre-T cell development and migration by regulating CD45 pre-mRNA splicing and chemokine receptor signaling. RNA-seq from Thymocytes from WT mice compared to KO (hnRNP L) mice
Project description:The regulation of post-transcriptional modifications of pre-mRNA by alternative splicing is important for cellular function, development and immunity The receptor tyrosine phosphatase CD45, which is expressed on all hematopoietic cells, is known for its role in the development and activation of T cells. To investigate the role of hnRNP L further, we have generated conditional hnRNP L knockout mice carrying floxed alleles and the T-cell specific Lck-Cre recombinase transgene. The Lck-Cre transgene is active in DN3, DN4 as well as in DP and SP cells. We found that deletion of hnRNP L results in a decreased thymic cellularity caused by a partial block at the transition stage between DN4 and DP cells. In addition, hnRNP L-/- thymocytes express aberrant levels of the CD45RA splice isoform and show high levels of phosphorylated Lck at the activator tyrosine Y394 but lacking phosphorylation of the inhibitory tyrosine Y505. This is indicative of an increased basal Lck activation and correlated with a higher proliferation rate of DN4 cells in hnRNP L-/- mice. Deletion of hnRNP L also blocked egress of SP cells to peripheral lymphoid organs and the migration of SP thymocytes in response to the chemokines CCL21 and SDF-1a. Since we found that actin polymerization was also compromised in hnRNP L-/- SP cells, we propose that a defect in the signal transduction cascade downstream of the chemokine receptors CCR7 and CXCR4 caused by the absence of hnRNP L is responsible for this phenotype. Our results indicate that hnRNPL regulates pre-T cell development and migration by regulating CD45 pre-mRNA splicing and chemokine receptor signaling.
Project description:This experiment identifies hnRNP A1 binding sites transcriptome-wide in Hela cells. HeLa cells with inducible expression of T7-tagged hnRNP A1 were grown to approximately 90% confluence and then subject to iCLIP analysis (following the protocol from Huppertz et al. 2014 (iCLIP: protein-RNA interactions at nucleotide resolution)). The iCLIP library was sequenced using Illumina's HighSeq 1500
Project description:Limited knowledge of the downstream targets of hnRNP A2/B1 has, however, precluded a clear understanding of their roles in cancer cell growth. To define the pathways in which this protein acts we have now carried out microarray experiments with total RNA from Colo16 epithelial cells transfected with an shRNA that markedly suppresses hnRNP A2/B1 expression. The microarray data identified 123 genes, among 22283 human gene probe sets, with altered expression levels in hnRNP A2/B1-depleted cells. Ontological analysis showed that many of these downstream targets are involved in regulation of the cell cycle and cell proliferation and that this group of proteins is significantly over-represented amongst the affected proteins. The changes detected in the microarray experiments were confirmed by real-time PCR for a subset of proliferation-related genes. Immunoprecipitation-RT-PCR demonstrated that hnRNP A2/B1 formed complexes with the transcripts of many of the verified downstream genes, suggesting that hnRNP A2/B1 contributes to the regulation of these genes.