Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of wild type yeast and a mutant deficient for intron degradation using a high density tiling array for genome-wide mapping of introns

ABSTRACT: High density yeast tiling array reveals new introns and extensive meiotic splicing regulation. Knowing gene structure is vital to understanding gene function, and accurate genome annotation is essential for understanding cellular function. To this end, we have developed an assay for genome-wide mapping of introns in Saccharomyces cerevisiae. Using high-density tiling arrays we compared wild type yeast to a mutant deficient for intron degradation. Our method identified 76% of the known introns, verified the existence of an additional 18 predicted introns, and revealed six new introns. Furthermore, we discovered that all 13 meiosis-specific intronic yeast genes undergo regulated splicing, which provides post-transcriptional regulation of the genes involved in yeast cell differentiation. Moreover, we found that >10% of intronic genes in yeast are incompletely spliced during exponential growth in rich media, suggesting that meiosis is not the only cellular function regulated by splicing. The method provides a clear snapshot of the spliced transcriptome in yeast. Our tiling array assay can be used to explore a variety of cellular environments and should be readily adaptable to the study of other organisms including humans.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Molly Miranda

PROVIDER: E-MEXP-919 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing.

Juneau Kara K Palm Curtis C Miranda Molly M Davis Ronald W RW

Proceedings of the National Academy of Sciences of the United States of America 20070123 5

Knowing gene structure is vital to understanding gene function, and accurate genome annotation is essential for understanding cellular function. To this end, we have developed a genome-wide assay for mapping introns in Saccharomyces cerevisiae. Using high-density tiling arrays, we compared wild-type yeast to a mutant deficient for intron degradation. Our method identified 76% of the known introns, confirmed 18 previously predicted introns, and revealed 9 formerly undiscovered introns. Furthermor ...[more]

PMID: 17244705

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Project description:Transcription profiling of two cancer cell lines: K562 and U937. It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), linking chromatin structure and function to co- transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.

Project description:Chromatin immunoprecipitation microarray (ChIP-chip) study using 3 human cell lines (K562, U937, CD14+); of 19 histone modifications across 1% of the human genome used in the pilot phase of the ENCODE project.<br>paper abstract: It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons ("exon-intron marking"), linking chromatin structure and function to co- transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.

Dataset Information

Transcription profiling of wild type yeast and a mutant deficient for intron degradation using a high density tiling array for genome-wide mapping of introns

Publications

High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing.

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