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Genome fragments

Wandering DNA

Fragments of genetic material move from one place to another according to a non-random pattern

055_Transposons_198Laura DaviñaResearchers have increasingly identified important functions performed by fragments of DNA previously regarded as trash. Transposable elements, or transposons, are found between these segments of genetic material. These fragments can duplicate or detach themselves from where they are and install themselves in other parts of the DNA, sometimes next to essential genes or even in the middle of the structure of those genes. When investigating these unusual molecular characters, the group headed by biologist Marie-Anne Van Sluys, of the University of São Paulo (USP), deals with sugarcane genomes in a block, which is an innovative approach. The investigation has shown that the movements of these fragments are less random than previously thought and might even play an important role in the dynamics of a genome.

This broad scale analysis stemmed from the results of the Sugarcane Genome Project (Sucest), concluded in 2001. The project unveiled the sequences of the functional genome of this plant, a key element in the Brazilian economy. It revealed the existence of 276 active transposable elements – or expressed elements, in biological jargon. “In 2005, it took us two years to convince the editor of Plant Journal that the result was real and not contamination,” Marie-Anne recalls. At that time, genome-related studies conducted entirely by Brazilian researchers were uncommon and the said result was surprising. The journal published the article, after having accepted the evidence that those fragments of DNA – also referred to as transposons – had a function, even though nobody had identified this function.

Based on the results of the Sucest project and on the heightened capacity to generate and analyze enormous volumes of data, the group headed by Marie-Anne partnered with colleagues from the State of São Paulo and in 2009 started to work on the sequencing of one thousand selected fragments of the sugarcane genome. Nowadays, the research team resembles a scientific knowledge production line, which it actually is: a number of articles published this year describe major developments on how transposons function.

The most outstanding article is a study published in BMC Genomics, a collaborative effort with researchers from Paulista State University, including Fabio Nogueira, and from the State University of Campinas, including Renato Vicentini. From April to July, the article was accessed more than one thousand times on the journal’s site, earning the highly accessed label. “We were the first to show – in molecular form – how transposable elements have individualized patterns,” Marie-Anne explains. This means that when one of these DNA fragments detaches itself from its original site, its destination is not as random as scientists originally believed. Each family of transposons has a stronger tendency to install itself in specific chromosomes or chromosome regions. Marie-Anne hopes that by establishing those patterns, she will be able to describe how this interaction influences the effects of the genes.

Many of the families of transposable elements diversified a long time ago, even before plants with flowers were divided into two major groups: monocotyledons, such as corn, sugarcane and rice, whose seeds contain one cotyledon (an energy reservoir); and dicotyledons, such as shrubs and trees, whose seeds contain two cotyledons. Marie-Anne’s team mapped this diversification of the transposons related to three monocotyledon species of commercial interest (sorghum, sugarcane, and rice) in the review article, which is in the process of being published in Topics in Current Genetics.

Sugarcane is a special case, because it seems to have many more active transposable elements than other plants being studied. The biologist from USP explains that this happens because of the hybrid origin of sugarcane, the result of a combination of two wild species, the Saccharum officinarum and S. spontaneum. The end result of this hybridization is a plant that produces much more sugar and tolerates diseases better. In Marie-Anne’s opinion, the process of merging the two species caused an unbalance in the genetic functioning that might have altered how the DNA’s mobile fragments move. “The organism needs to recover its rhythm.”

The influence of those elements might be the backdrop of the plant’s identity itself. “Eighty percent of the genes in sugarcane, sorghum, and corn are common to each plant; what distinguishes one plant from the other might be gene regulation,” says Marie-Anne. In her opinion, the transposable elements could be carrying out the function of modulating the functioning of the genes.

From now onward, the studies might gain practical applications and help to improve this plant further. Sugarcane yields two thirds of the world’s sugar and is gaining growing importance as a source of renewable energy. The transposable elements may help one to identify and control the functioning of the genes, such as the genes responsible for resistance to droughts, thereby contributing to the production of varieties adapted to drier climates. However, economic aspects are not the main interest of plant geneticists, who see the genetic functioning of sugarcane as being interesting in itself, due to its hybrid origin and to the duplicates that make the species have a multiple genome, with various copies of each gene. It is fascinating to imagine that tiny fragments of DNA, that move from one side to the other inside the cell’s nucleus, like wandering gypsies, may have contributed to distinguish sugarcane from other grass species.

The Project
Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function (nº 08/52074-0); Modality Thematic Project – Bioen; Coordinator Marie-Anne Van Sluys – IB-USP; Investment R$ 2,504,444.87

Scientific articles
DOMINGUES, D. S. et al. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics. v. 13, n. 137. 16 Apr. 2012.
DE SETTA, N. et al. Noise or symphony: comparative evolutionary analysis of sugarcane transposable elements with other grasses. Topics in Current Genetics. Forthcoming.

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