Project description:ATAC-seq on human cell line NCI-H929 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:To identify novel targets of the transcriptional repressor that functions to extinguish the B cell phenotype during terminal plasma cell differentiation, we assessed PRDM1 bound sequences through ChIP-Seq. We prepared PRDM1-enriched chromatin from two PRDM1 positive mutiple myeloma cell lines, U266 and NCI-H929. At least 5 PRDM1- or IgG enrichments were performed per cell line and pooled into the two respective conditions per cell line. The U226 and NCI-H929 revealed respectively, 574 and 2887 association peaks were indentified per cell line. Both cell lines displayed an intense peak at the ELL3 loci, suggesting PRDM1 association. This was validated by ChIP followed by qPCR, confirming PRDM1 association.
Project description:Most patients with multiple myeloma (MM) will eventually relapse and current treatments have limited effect. Herein, we demonstrate that succinate dehydrogenase subunitA (SDHA) was low expressed in MM patients, and patients with SDHA relatively high expression had long overall survival and progression-free survival. Furthermore, SDHA high expression inhibited proliferation and invasion in multiple myeloma (MM) cell lines and enhanced the anti-tumor and synergistic effect of chemotherapeutics. To investgate regulation of SDHA on epigenetic level, we conducted ChIP-seq experiments to compare the H3K27ac signal between H929 cells treated with DMSO and H929 cells treated with chidamide.
Project description:Here we report the use of high-throughput sequencing technologies (RNA-seq, ATAC-seq, ChIP-seq) to identify the molecular programme of the transcirption factor c-MAF (MAF) in parental (MM1.S, JJN3, H929), MAF-depleted (MM1S, JJN3) and MAF-overexpressing (MM1S, U266) multiple myeloma (MM) cells . We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) against MAF in naive MM cells , and against MAF, H3K27ac and H3K4me1 in MAF-overexpressing cells. Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on MAF-overexpressing U266 myeloma cells. In addition, we identifed the transcriptome of MAF-depleted myeloma cells 3 days after lentiviral transduction with MAF-targeting shRNA and scbl control. Our integrated -omics approach provides a comprehensive characterization of the role and function of MAF in myeloma cells and provides novel insights towards the discovery and design of molecular targets for precision therapy against MAF-overexpressing MM.
Project description:ChIP-seq data for the transcription factors (TFs) IRF4, PU.1 and SPIB from the cell lines OCI-LY3, OCI-LY10 and H929, and BATF from the cell lines OCI-Ly3 and OCI-Ly10. In addition ChIP-seq for the TFs IRF4, PU.1 and SPIB from the cell line OCI-LY3 following transfections of scramble/SPIB-siRNA. ChIP-seq data for the transcription factors (TFs) IRF4, PU.1 and SPIB from the cell lines OCI-LY3, OCI-LY10 and H929, and BATF from the cell lines OCI-Ly3 and OCI-Ly10. In addition ChIP-seq for the TFs IRF4, PU.1 and SPIB from the cell line OCI-LY3 following transfections of scramble/SPIB-siRNA.
Project description:MicroRNAs have been demonstrated to be deregulated in multiple myeloma (MM). We have previously reported the downregulation of miR-214 in MM compared to normal plasma cells. In the present study, we have explored the functional role of miR-214 in myeloma pathogenesis. Ectopic expression of miR-214 reduced cell growth and induced apoptosis of myeloma cells. In order to identify the potential direct target genes of miR-214 which could be involved in the biological pathways regulated by this miRNA, gene expression profiling of H929 myeloma cell line transfected with precursor miR-214 was carried out. Functional analysis revealed significant enrichment for DNA replication, cell cycle phase and DNA binding. We show that miR-214 directly down-regulates the expression of PSMD10, which encodes the oncoprotein gankyrin, and ASF1B, a histone chaperone required for DNA replication, by binding to their 3'-UTR. In addition, gankyrin inhibition induced an increase of P53 mRNA levels and subsequent up-regulation in CDKN1A (p21Waf1/Cip1) and BAX transcripts, which are direct transcriptional targets of p53. In conclusion, we demonstrate that miR-214 function as a tumor suppressor in myeloma by a positive regulation of p53 and inhibition of DNA replication. H929 cell line was transfected with Pre-miR™ miRNA precursors pre-miR-214 or pre-miR™ miRNA negative, non-targeting control#1 (Ambion) at 50 nM concentration, using the nucleofector II system with C-16 program (Amaxa). The experiments were performed in triplicates.
Project description:Circular RNAs (circRNAs) are covalently closed endogenous RNA molecules with tissue- and disease specific expression patterns, which have potential as diagnostic and prognostic biomarkers in cancer. The landscape of circRNA expression has not been characterized in B-cell malignancies. We quantified circular RNA expression by total RNA sequencing of four different Mantle Cell Lymphoma cell lines, REC-1, Granta-519, Z138 and UPN2 and the Multiple Myeloma cell line, H929.
Project description:We designed oligonucleotide tiling arrays spanning the t(4;14) breakpoint region on chromosome 4 to identify additional oncogenic RNAs in an unbiased fashion. Four (4) multiple myeloma bone marrow samples with t(4;14) and twelve (12) MM BM samples without t(4;14) were analyzed. Furthermore, seven (7) bladder (1 normal, 6 malignant), eight (8) colon (1 normal, 7 malignant) and eight (8) esophagus (2 normal, 6 maligant) tissue samples were analyzed. Finally, five (5) multiple myeloma cell line samples with t(4;14) - three (3) of LP-1 and two (2) of H929 - and three (3) MM cell line samples and three (3) non-MM cell line samples without t(4;14) - three (3) of U266 and three (3) of Hela - were analyzed.
Project description:To identify epigenetically silenced genes in multiple myeloma (MM) cell lines and to determine the effects of 5-aza-2-deoxycytidine and trichostatin A on gene expression. We treated 3 multiple myeloma cell lines (MM1, NCI-H929, U266) with 5-aza-2-deoxycytidine and/or trichostatin A.
