Isochore chromosome maps of eukaryotic genomes

Oliver, José Luis Tejera; Bernaola‐Galván, Pedro; Carpena, Pedro; Román-Roldán, Ramón

doi:10.1016/s0378-1119(01)00641-2

Cited by 90 publications

(64 citation statements)

References 44 publications

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“…For MHC class II sequence, as the subwindow size is reduced to around 2.5 kb, the ANOVA test result is typically significant (Fig.1). This is consistent to the definition of isochores as "fairly homogeneous" (as versus "strictly homogeneous") segments above a size of 3 kb [21,22], and justifies the "coarse graining" procedure to locate isochore boundaries in [9].…”

Section: Discussionsupporting

confidence: 81%

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Bernaola‐Galván

Carpena

et al. 2002

Genome Biol

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Section: Discussionsupporting

confidence: 81%

“…The exact borders of the two isochore sequences are determined by a segmentation procedure [9,10] and an online resource on isochore mapping [11]). We first repeat the test in [4] that these two sequences, when viewed as a collection of many 20 kb windows, are sampled from a binomial distribution.…”

Section: Resultsmentioning

confidence: 99%

Untitled

Bernaola‐Galván

Carpena

et al. 2002

Genome Biol

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“…The first is that ORFs with similar G+C content at the 3rd codon position are significantly clustered (Bradnam et al, 1999;Oliver et al, 2001). The second is that adjacent pairs of genes, as well as nearby non-adjacent pairs, show correlated expression independent of their orientation, and that genes with similar functions tend to occur in adjacent positions along the chromosomes (Cohen et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

Relationship between G+C content, ORF‐length and mRNA concentration in Saccharomyces cerevisiae

Marı́n

Gallardo

Kato

et al. 2003

Yeast

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RNA biogenesis is a tightly-regulated process. The levels and timing of expression of a gene depends on its particular function. However, gene expression levels may also depend on structural features. Here we describe the analysis of gene expression of 4977 ORFs using DNA microarrays covering the whole genome of three different S. cerevisiae strains, wild-type and tho2 and thp1 mutants with a general effect on mRNA biogenesis. We show that transcripts from G+C-rich ORFs accumulate at higher concentrations than those from G+C-poor ones, in different ORF-length categories in all strains tested. In addition, we found a negative correlation between ORF length and G+C content. Our results indicate that length and G+C content of a gene have a clear effect on its levels of expression. We discuss the biological relevance of these results, as well as different ways that these structural features could modulate mRNA biogenesis.

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“…Some of these properties have been shown primarily for mammals and birds, whereas other properties are apparently found in a wide range of eukaryotes. Thus, gene density has been found to correlate with GC also in Drosophila (Jabbari and Bernardi, 2000;Myers et al, 2000), Arabidopsis , and in the heterogeneous chromosome 3 of yeast (Oliver et al, 2001).…”

Section: Resultsmentioning

confidence: 93%