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Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages.

ABSTRACT: Post-transcriptional regulation, often mediated by miRNAs and RNA-binding proteins at the 3' untranslated regions (UTRs) of mRNAs, is implicated in important roles in the output of transcriptome. To decipher this layer of gene regulation, it is essential to measure global mRNA expression quantitatively in a 3'-UTR-specific manner. Here we establish an experimental and bioinformatics pipeline that simultaneously determines 3'-end formation by leveraging local nucleotide composition and quantitatively measures mRNA expression by sequencing polyadenylated transcripts. When applied to purified mouse embryonic skin stem cells and their daughter lineages, we identify 18,060 3' UTRs representing 12,739 distinct mRNAs that are abundantly expressed in the skin. We determine that ?78% of UTRs are formed by using canonical A[A/U]UAAA polyadenylation signals, whereas ?22% of UTRs use alternative signals. By comparing to relative and absolute mRNA abundance determined by qPCR, our RNA-seq approach can precisely measure mRNA fold-change and accurately determine the expression of mRNAs over four orders of magnitude. Surprisingly, only 829 out of 12,739 genes show differential 3'-end usage between embryonic skin stem cells and their immediate daughter cells, whereas the numbers increase to 933 genes when comparing embryonic skin stem cells with the more remotely related hair follicle cells. This suggests an evolving diversity instead of switch-like dynamics in 3'-end formation during development. Finally, core components of the miRNA pathway including Dicer, Dgcr8, Xpo5, and Argonautes show dynamic 3'-UTR formation patterns, indicating a self-regulatory mechanism. Together, our quantitative analysis reveals a dynamic picture of mRNA 3'-end formation in tissue stem cell lineages in vivo.

SUBMITTER: Wang L

PROVIDER: S-EPMC3677251 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages.

Wang Li L Dowell Robin D RD Yi Rui R

RNA (New York, N.Y.) 20130116 3

Post-transcriptional regulation, often mediated by miRNAs and RNA-binding proteins at the 3' untranslated regions (UTRs) of mRNAs, is implicated in important roles in the output of transcriptome. To decipher this layer of gene regulation, it is essential to measure global mRNA expression quantitatively in a 3'-UTR-specific manner. Here we establish an experimental and bioinformatics pipeline that simultaneously determines 3'-end formation by leveraging local nucleotide composition and quantitati ...[more]

PMID: 23325109

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Project description:In multicellular organisms, transcription regulation is one of the central mechanisms modelling lineage differentiation and cell-fate determination. Transcription requires dynamic chromatin configurations between promoters and their corresponding distal regulatory elements. It is believed that their communication occurs within large discrete foci of aggregated RNA polymerases termed transcription factories in three-dimensional nuclear space. However, the dynamic nature of chromatin connectivity has not been characterized at the genome-wide level. Here, through a chromatin interaction analysis with paired-end tagging approach using an antibody that primarily recognizes the pre-initiation complexes of RNA polymerase II, we explore the transcriptional interactomes of three mouse cells of progressive lineage commitment, including pluripotent embryonic stem cells, neural stem cells and neurosphere stem/progenitor cells. Our global chromatin connectivity maps reveal approximately 40,000 long-range interactions, suggest precise enhancer-promoter associations and delineate cell-type-specific chromatin structures. Analysis of the complex regulatory repertoire shows that there are extensive colocalizations among promoters and distal-acting enhancers. Most of the enhancers associate with promoters located beyond their nearest active genes, indicating that the linear juxtaposition is not the only guiding principle driving enhancer target selection. Although promoter-enhancer interactions exhibit high cell-type specificity, promoters involved in interactions are found to be generally common and mostly active among different cells. Chromatin connectivity networks reveal that the pivotal genes of reprogramming functions are transcribed within physical proximity to each other in embryonic stem cells, linking chromatin architecture to coordinated gene expression. Our study sets the stage for the full-scale dissection of spatial and temporal genome structures and their roles in orchestrating development.

Dataset Information

Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages.

Publications

Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages.

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