Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-Seq of control and ELL2-depleted MPC11 plasmacytoma cell lines

ABSTRACT: We report RNA-Seq data from MPC11 plasmacytoma cell lines transduced with either control hairpins (shGFP) or hairpins targeting the transcriptional elongation factor ELL2. ELL2 has been identified as regulating the alternative splicing and polyadenylation of immunoglobulin pre-mRNA, and is highly expressed by plasma cells but not other B cells. Notably, ELL2 drives the accumulation of transcripts encoding secreted immunoglobulin at the expense of membrane-associated transcripts. This study sought to examine the impact of ELL2 on mRNA processing at the transcriptome level, and found that ELL2 controls the alternative processing of 12% of annotated transcripts in MPC11 cells. Examination of pre-mRNA splicing patterns in either control or ELL2-depleted cells

ORGANISM(S): Mus musculus

SUBMITTER: Tarmo Äijö

PROVIDER: E-GEOD-40285 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells.

Benson Micah J MJ Aijö Tarmo T Chang Xing X Gagnon John J Pape Utz J UJ Anantharaman Vivek V Aravind L L Pursiheimo Juha-Pekka JP Oberdoerffer Shalini S Liu X Shirley XS Lahesmaa Riitta R Lähdesmäki Harri H Rao Anjana A

Proceedings of the National Academy of Sciences of the United States of America 20120918 40

B cells and plasma cells possess distinct RNA processing environments that respectively promote the expression of membrane-associated Ig by B cells versus the secretion of Ig by plasma cells. Through a combination of transcriptional profiling and screening using a lentiviral short-hairpin RNA interference library, we show that both the splicing factor hnRNPLL and the transcription elongation factor ELL2 modulate the ratio of secreted versus membrane-encoding Ighg2b transcripts in MPC11 plasmacyt ...[more]

PMID: 22991471

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Project description:Purpose: This study aimed to identify differentially expressed genes including alternative splice variants in embryonic ventricles following in utero caffeine treatment. Methods: Pregnant CD-1 mice were injected with 20 mg/kg of caffeine or vehicle control daily from embryonic day (E) 6.5-9.5. On E10.5, total RNA was isolated from embryonic ventricles and used for transcriptomic RNA sequencing with Illumina HiSeq 2000 (1X75bp). RNA-seq reads were aligned to the mouse genome (build mm10) with the Tophat for Illumina tool in the PSU galaxy platform. Counting and annotation of RNA-seq reads as well as alternative splicing analysis were performed with Partek Genomics Suite version 6.11. Differential expression of gene and transcript reads between treatments was analyzed with R package EdgeR. Genes/transcripts with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Differentially expressed genes were defined as genes with altered expression at either gene or transcript level. Unique differentially expressed genes were identified by combining the results from annotations with the RefSeq Transcripts (2013-05-10) or Ensembl Transcripts release 71 databases. Results: Differential expression analysis revealed that 59 genes and 451 transcripts were significantly up-regulated, and 65 genes and 398 transcripts were down-regulated by prenatal caffeine treatment (fold change >1.5 or <-1.5; p-value with FDR<0.05). In total, 900 unique genes were identified to have altered expression either at the gene or transcription level. Further analysis with Partek GS revealed that 183 genes had abnormal alternative splicing at the exon level after in utero caffeine treatment. Conclusions: In utero caffeine exposure caused gene expression changes in embryonic ventricles and these changes may lead to long-term effects on cardiac morphology and function. mRNA profiles in E10.5 heart ventricles treated with caffeine were generated by deep sequencing (n=2 for vehicle, n=3 for caffeine), using Illumina HiSeq 2000.

Dataset Information

RNA-Seq of control and ELL2-depleted MPC11 plasmacytoma cell lines

Publications

Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells.

Similar Datasets

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