Project

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Bioinformatics-driven analysis of complementation and autonomy among the LTR retrotransposons of barley

Applicant Buchmann Jan
Number 143673
Funding scheme Fellowships for prospective researchers
Research institution MTT/BI Plant Genomics Lab Institute of Biotechnology University of Helsinki
Institution of higher education Institution abroad - IACH
Main discipline Molecular Biology
Start/End 01.10.2012 - 30.09.2013
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Keywords (5)

Bioinformatics; autonomous/non-autonomous elements; LTR retrotransposon; Genome Evolution; Barley

Lay Summary (English)

Lead
Cassandra elements are mobile genetic elements found in plant genomes. Until today, no autonomous Cassandra element has been identified. However, based on molecular analysis, several thousand copies of this element are expected to be found in the barley genome. The high copy number of Cassandra elements in barley hints the existence of a mechanism for cross activation of the non-autonomous Cassandra by other, autonomous mobile elements.
Lay summary

Mobile genetic elements, so called Transposable Elements (TE), can move in the genome of its host organism. i.e. they can change their position in the genomic sequence. TEs can be divided into two classes, based on the mechanism of transposition. DNA Transposons excise itself and insert in a new location while RNA Transposons produce a copy of themselves which is then inserted in a new location.

In both classes, two distinctive forms, autonomous and non-autonomous have been identified. The autonomous elements contain all informations which are needed for transposition and therefore are able to transpose by itself. In contrast, non-autonomous elements are lacking those informations and cannot move on its own.

We plan to analyze relationship between autonomous and non-autonomous retrotransposons by addressing several open questions.  First, are the non-autonomous elements are specialized to a "host" LTR retrotransposon or have they developed the ability to parasite a wide range of host  elements?  Second, do the two groups compete for the available "genome space" and proteins needed for transposition, i.e., do non-autonomous elements affect the transposition of autonomous elements as parasites?  Third, is there an evolutionary selection for a certain mode of  complementation?

We choose to analyze the Cassandra element because no autonomous form has been identified until today.  We use an in silico approach to isolate Cassandra elements in genomic sequences of grasses  as barley or sorghum. Further, Cassandra elements will be analyzed and compared to known autonomous RNA Transposons to gain insight in the relationship of autonomous and non-autonomous elements. 

Direct link to Lay Summary Last update: 30.01.2013

Responsible applicant and co-applicants

Collaboration

Group / person Country
Types of collaboration
University of Helsinki Finland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Plant Genome Evolution Conference 2013 Poster Analysis of CACTA transposons in grasses reveals intron loss as major mechanism for CACTA transposase evolution 08.09.2013 Amsterdam, Netherlands Buchmann Jan;
Finnish Plant Science Days Individual talk Analysis of DNA-Transposons in the Genome of Brachypodium distachyon Reveals Mechanisms for Intergenic Sequence Turnover 13.05.2013 Helsinki, Finland Buchmann Jan;
StatSeq workshop 5 Poster Interspecies sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity 24.04.2013 Helsinki, Finland Buchmann Jan;
Plant and Animal Genome XXI Conference Poster Interspecies sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity 12.01.2013 San Diego, United States of America Buchmann Jan;


Abstract

BackgroundLTR retrotransposons are the most abundant transposable elements in plant genomes. They are responsible for the huge variation of genome size in the flowering plants, particularly in the monocotyledons. In the Triticeae (wheat, barley, etc.) family, they can constitute up to 80% of the whole genome sequence. Their activity can influence the transcription of genes by a variety of ways, including insertional disruption of genes and epigenetic mechanisms. It has been shown that LTR retrotransposons get activated upon inducing stress conditions like drought or UV. They move by a copy and paste mechanism, leading to an additional copy after every transposition. LTR retrotransposons encode only their own set of proteins needed for transposition but are rely on the transcription machinery from their host genome. Moreover, the retrotransposons themselves interact: they are present as two groups, the autonomous and non-autonomous elements. Autonomous elements can transpose on their own, while the non-autonomous can only do so if they contain motifs to allow recognition by the machinery encoded by an autonomous element. This complementation allows the non-autonomous element to proliferate, despitetheir lack of coding capacity. This two-fold dynamic between the cell, autonomous elements, and non autonomous elements has far-reaching consequences for genome structure and evolution.AimWe plan to analyze relationship between autonomous and non-autonomousretrotransposons by addressing several open questions. First, are thenon-autonomous elements specialized to a "host" LTR retrotransposon or have they developed the ability to parasite a wide range of host elements? Second, do the two groups compete for the available "genome space" and proteins needed for transposition, i.e., do non-autonomous elements affect the transposition of autonomous elements as parasites? Third, is there an evolutionary selection for a certain mode of complementation? For this, we want to analyze if the interactionbetween autonomous and non-autonomous elements influenced the pattern of genome evolution. Experimental designIntensive generation of various types of sequence data for barley (Hordeum vulgare) is currently underway and provides an ideal resource for this project. For comparative analysis, data from wild barley (H. spontaneum) and sequences from the closely related bread wheat (Triticum aestivum) will be used. The huge amount of data needs bioinformatics approaches for screening and mining. We will focus on LTR retrotransposons of the Copia and Gypsy superfamilies. The BARE1, Bagy1, and Bagy2 families represent the main autonomous elements, and BARE2, Cassandra, and LARD will serve as non-autonomous examples. In a first approach, the host retrotransposons and the corresponding non-autonomous elements will be identified. Non-autonomous elements will be harvested by screening for the recognition signals like PBS and Psi. Comparison to autonomous elements will identify the host LTR retrotransposon. In a second approach, segments which were identified to belong to LTR retrotransposons will be clustered, aligned and categorized. The population structure and conserved features of non-autonomous elements will be analyzed. ImportanceThis work will identify new mechanism of parasitism and replication as well as influences of retrotransposons on each other and on the host genome. The effect on the host genome, which includes the movement of cellular genes linked to Cassandra and LARDs, will add information to other mechanisms as post-transcriptional gene silencing, virus resistance and genome evolution. The information gained from this project on virus-like particle (VLP) formation and subsequent nuclear targeting for DNA insertion can be used to develop retrotransposon vectors to integrate exogenous proteins into host genomes.
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