A high-resolution map of transcription in the yeast genome

Department of Biochemistry, Stanford University, Palo Alto, California, United States
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 05/2006; 103(14):5320-5. DOI: 10.1073/pnas.0601091103
Source: PubMed

ABSTRACT There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.

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    DESCRIPTION: PhD Thesis 2006 - Duke University Abstract: Genomes of living organisms contain genes that code for proteins. Non‐coding DNA can be found both surrounding and within genes. Higher organisms harbor large amounts of this non‐coding DNA, and the reasons for this are not clear. Here, in three projects performed with the root of the plant Arabidopsis thaliana, I studied the relationship between non‐coding DNA sequences and gene transcription using, in each project respectively 1) DNA constructs with the Green Fluorescent Protein reporter gene inserted into plants, 2) gene expression data from cell‐sorting microarray experiments and the annotation of the A. thaliana genome and 3) homologous sequences obtained from related species. I found that: 1) in a sample of 61 transcription factors expressed in a tissue‐specific manner in the root, the upstream intergenic sequence of the gene limited to three kilobases is generally sufficient to drive its correct mRNA expression pattern; 2) a genome‐wide study of the relationship between the mRNA expression of a gene across tissues of the root and the length of its associated sequences shows that intergenic and gene non‐coding sequences have opposite relationships with gene expression; 3) for seven genes expressed at varying degrees of specificity in the root, a negative correlation between the rate of evolution of their upstream intergenic sequence and the intensity and specificity of their expression pattern is observed. In the Discussion, I will argue that these results are consistent with the view that the bulk of non‐coding DNA has a regulatory action on gene transcription via organizing the structure of the genome within the nucleus. I will discuss the reason for the importance of nuclear structure and its implication for our understanding of evolution in the context of living organisms as complex systems.

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