Compositional Gradients in<i>Gramineae</i>Genes

Wong, Gane Ka‐Shu; Wang, Jun; Lin, Tao; Tan, Jun; Zhang, Shiping; Passey, Douglas A.; Yu, Jun

doi:10.1101/gr.189102

Cited by 165 publications

(188 citation statements)

References 26 publications

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“…Consistent with the previous report (12), most Arabidopsis genes are moderate genes, yet nearly half of the maize and rice genes exhibit a negative GC gradient (Fig. 2).…”

Section: Gc-rich Internalsupporting

confidence: 78%

“…As mentioned above, many grass genes are associated with a negative gradient in GC content in the direction of transcription, and therefore the 5′ ends of genes are more GC rich than their 3′ ends (12). Thus, we hypothesize that the high GC content of Pack-MULEs in maize and rice is due to the presence of large numbers of genes with negative GC gradients, coupled with an acquisition preference for the 5′ regions.…”

Section: Gc-rich Internalmentioning

confidence: 99%

“…In general, the Gramineae (grass) genomes contain many more GC-rich genes than the genomes of dicot plants such as Arabidopsis (11). Most of the variation in GC content occurring among genes in grasses is present in the form of a negative gradient in the direction of transcription (12). This negative gradient is defined by higher GC content at the 5′ end of genes than that at the 3′ end, and genes with a negative gradient are more abundant in rice than in Arabidopsis (12).…”

mentioning

confidence: 99%

“…This negative gradient is defined by higher GC content at the 5′ end of genes than that at the 3′ end, and genes with a negative gradient are more abundant in rice than in Arabidopsis (12). Several hypotheses, including transcription-coupled DNA repair (12), GC-biased gene conversion (13,14), and translational advantage (15), have been proposed to explain the emergence of GC richness and the formation of a negative GC gradient among grass genes. However, none of these hypotheses fully explains the dramatic difference in GC gradient among individual genes (also see Results).…”

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confidence: 99%

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Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

Jiang

Ferguson

Slotkin

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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In monocots, many genes demonstrate a significant negative GC gradient, meaning that the GC content declines along the orientation of transcription. Such a gradient is not observed in the genes of the dicot plant Arabidopsis. In addition, a lack of homology is often observed when comparing the 5′ end of the coding region of orthologous genes in rice and Arabidopsis. The reasons for these differences have been enigmatic. The presence of GC-rich sequences at the 5′ end of genes may influence the conformation of chromatin, the expression level of genes, as well as the recombination rate. Here we show that Pack-Mutator-like transposable elements (PackMULEs) that carry gene fragments specifically acquire GC-rich fragments and preferentially insert into the 5′ end of genes. The resulting Pack-MULEs form independent, GC-rich transcripts with a negative GC gradient. Alternatively, the Pack-MULEs evolve into additional exons at the 5′ end of existing genes, thus altering the GC content in those regions. We demonstrate that Pack-MULEs modify the 5′ end of genes and are at least partially responsible for the negative GC gradient of genes in grasses. Such a unique and global impact on gene composition and gene structure has not been observed for any other transposable elements.gene duplication | gene modification

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“…Consistent with the previous report (12), most Arabidopsis genes are moderate genes, yet nearly half of the maize and rice genes exhibit a negative GC gradient (Fig. 2).…”

Section: Gc-rich Internalsupporting

confidence: 78%

Section: Gc-rich Internalmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

Jiang

Ferguson

Slotkin

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…Our results also corroborate data from Xia et al (26), who detected decreasing GC content along the coding regions in genes of various animals, from humans to Xenopus laevis. Compositional gradients were also found in genes of monocot, but not dicot, plants (27).…”

Section: Discussionmentioning

confidence: 77%

GC/AT-content spikes as genomic punctuation marks

Zhang

Kasif

Cantor

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

111

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Large-scale analysis of the GC-content distribution at the gene level reveals both common features and basic differences in genomes of different groups of species. Sharp changes in GC content are detected at the transcription boundaries for all species analyzed, including human, mouse, rat, chicken, fruit fly, and worm. However, two substantially distinct groups of GC-content profiles can be recognized: warm-blooded vertebrates including human, mouse, rat, and chicken, and invertebrates including fruit fly and worm. In vertebrates, sharp positive and negative spikes of GC content are observed at the transcription start and stop sites, respectively, and there is also a progressive decrease in GC content from the 5 untranslated region to the 3 untranslated region along the gene. In invertebrates, the positive and negative GC-content spikes at the transcription start and stop sites are preceded by spikes of opposite value, and the highest GC content is found in the coding regions of the genes. Cross-correlation analysis indicates high frequencies of GC-content spikes at transcription start and stop sites. The strong conservation of this genomic feature seen in comparisons of the human͞mouse and human͞rat orthologs, and the clustering of genes with GC-content spikes on chromosomes imply a biological function. The GC-content spikes at transcription boundaries may reflect a general principle of genomic punctuation. Our analysis also provides means for identifying these GC-content spikes in individual genomic sequences.gene clustering ͉ gene ontology ͉ transcription start site ͉ transcription stop site

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Methods and Utility of EST and Whole Genome Sequencing

Rabinowicz

Martienssen

2004

Handbook of Plant Biotechnology

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Since the Human Genome Project started in 1990 numerous large‐scale genomic sequencing projects have been conducted by different consortia of laboratories. As a result, the complete genetic information of an ever growing number of higher eukaryotes is now available in the public databases, which constitute an invaluable resource for biological research. Although eukaryote genomes are very large, most of their DNA is repetitive and do not code for genes. This is particularly true for plants, where repetitive DNA can account for more than 90 % of the genome, posing a major challenge to pursue full genomic sequencing. Large‐scale sequencing of cDNA (EST sequencing) is an efficient way to specifically sequence expressed genes, although no more than half of the genes can be recovered with this strategy. Gene targeted genomic sequencing approaches, like methylation filtration, overcome some of the limitations of EST sequencing and constitute an affordable alternative for plant genomic sequencing.

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Compositional Gradients inGramineaeGenes

Cited by 165 publications

References 26 publications

Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

GC/AT-content spikes as genomic punctuation marks

Methods and Utility of EST and Whole Genome Sequencing

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