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Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development

ABSTRACT: Mammalian development is an intricate process regulated by multiple gene isoforms and their epigenetic states, which are yet undefined. Using integrative massive parallel sequencing and bioinformatics approach, we built genome-wide inventory of transcript variants, their promoters and histone modification states during normal development, using mouse cerebellum as model system. The data we integrated consists of 29,589 (4,792 novel) promoters that transcribe 61,525 (12,796 novel) distinct mRNAs, corresponding to 14,508 protein-coding and 9,862 non-coding genes. While 68% of the multi-transcript genes exhibit alternative splicing, 78% use alternative transcriptional events that are regulated during cerebellar development through H3K4me3 and H3K27me3. The data presented highlight the magnitude of alternative promoters and transcriptional termination as major source of transcriptome diversity along with alternative splicing. We also show that alternative promoters differentially activated during normal cerebellar development are aberrantly used in medulloblastoma, emphasizing the importance of studying gene regulation and function at the isoform-level. Study of transcriptome diversity in cerebellar development. We performed mRNA-seq and ChIP-seq experiments. mRNA-seq were performed on total RNA isolated from two P0, P5, P15 and adult cerebellum using 10 microgram of total RNA as the starting material for sequencing library prep. For each stage, mRNA-seq data was obtained from two lanes of a flowcell. For ChIP-seq experiments, solubilized chromatin was prepared by pooling multiple cerebellum tissues (3-18) and then ChIP-enriched DNA (using anti-RNAP II, anti-H3K4me3, anti-H3K27me3, or negative control IgG antibodies) were isolated. 10 microgram of ChIP-enriched DNA was used to prepare the ChIP-seq library for sequencing in a single lane.

ORGANISM(S): Mus musculus  

SUBMITTER: Louise C Showe   Valérie Baubet  Ravi Gupta  Hyunsoo Kim  Ramana V Davuluri  Priyankara Wickramasinghe  Naida Dahmane  Sharmistha Pal 

PROVIDER: E-GEOD-23525 | ArrayExpress | 2011-06-07



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Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development.

Pal Sharmistha S   Gupta Ravi R   Kim Hyunsoo H   Wickramasinghe Priyankara P   Baubet Valérie V   Showe Louise C LC   Dahmane Nadia N   Davuluri Ramana V RV  

Genome research 20110628 8

Despite our growing knowledge that many mammalian genes generate multiple transcript variants that may encode functionally distinct protein isoforms, the transcriptomes of various tissues and their developmental stages are poorly defined. Identifying the transcriptome and its regulation in a cell/tissue is the key to deciphering the cell/tissue-specific functions of a gene. We built a genome-wide inventory of noncoding and protein-coding transcripts (transcriptomes), their promoters (promoterome  ...[more]

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