Final Report Summary - ADAPTED (The role of adaptive evolution in the success of transposable elements)
Transposable elements (TEs) are DNA sequences that can replicate independently of their host’s cell replication cycle. TEs are ubiquitous components of eukaryotic organisms, and as a result of their proliferative ability over evolutionary timescales, they comprise the majority of genomes. For example, more than 50% of the human genome has been estimated to be of TE origin [1], while in plant species such as maize and wheat this fraction is even higher at ~85% [2,3].
During the life cycle of TEs, new copies can insert near or even within genes, which can prove deleterious for the host as it may severely compromise gene function. It therefore comes as no surprise that hosts have evolved mechanisms to suppress TE activity and safeguard genomic integrity. These mechanisms rely heavily on small RNA molecules that guide the deposition of silencing marks (such as DNA methylation) on the TE sequence. This process aims to generate a dense chromatin environment around the TE, which physically restricts access to DNA-binding proteins that are needed to initiate transcription of the TE sequence into mRNA; hence, the TE is silenced. However, given their abundance in genomes, TEs can surely escape silencing and proliferate. How this is happening, as well as how hosts respond to TE escape, are poorly understood processes. We sought to investigate this evolutionary interplay between TEs and host defenses, by focusing on the large and fully sequenced maize genome and one of its most prolific TEs, the Sireviruses, which constitute 20% of its genomic content. We set out the following tasks:
1. Search for sequence signatures of adaptive evolution across the Sirevirus phylogeny. Subfamilies with the most successful life histories (as measured by their population sizes) should be those that were able to adapt better against host defenses.
2. Elucidate the distribution of small RNA targeting and methylation marks along the Sirevirus sequence. The focal points of interaction between TEs and silencing mechanisms are so far unknown.
3. Identify Sireviruses that have captured host gene fragments in their genomes and investigate whether this mechanism may aid these elements to escape suppression. The hypothesis is that silencing these TEs will negatively impact on the function of the original genes.
To address these questions, we retrieved the original maize Sirevirus population from MASiVEdb [4] and produced a highly annotated set of 6,456 full-length Sireviruses that are split across five families. We also identified another 439 elements with gene fragments within their genomes. Initial phylogenetic analysis of each family did not delineate branches with sufficient bootstrap support, which hampers the search for adaptive evolution signatures. As a result, and given that two of the five families have amplified in large numbers [5], we are now comparing families (instead of subfamilies) for their rates of adaptive evolution. We anticipate completing most analyses by the end of this year.
The examination of the distribution of silencing marks, and especially small RNAs, on Sireviruses provided strong evidence for the potential importance of the cis-regulatory regions of TEs as main targets of host defenses. Sireviruses contain a complex palindrome-rich domain in the part of their sequence that controls their life cycle (i.e. the cis-regulatory region). We discovered that these palindromes are targeting hotspots, because the majority of small RNAs map to four narrow loci occupied by these motifs. Surprisingly, however, the palindromes are not identical but differ among loci, among members of the same family and among families; as a result, each palindrome is also targeted by different small RNAs. This intense interaction between cis-motifs and small RNAs suggests that this region is a template of an evolutionary arms race between Sireviruses and host defences: at first, sequence evolution of the palindromes may allow elements to escape silencing (because there will be few matching small RNAs to mediate silencing), before hosts adapt (by generating more matching small RNAs) and re-silence these elements. Hosts may in fact ‘domesticate’ few defunct old Sireviruses that inserted in the genome million years ago, because it can use their palindromes during emergencies to quickly produce matching small RNAs to younger, highly dangerous, relatives.
Finally, comparison of the distribution of silencing marks on the sequences of Sireviruses that contain and do not contain gene fragments generated highly similar patterns. This result does not support the hypothesis that gene capturing may represent an escape mechanism for TEs. That said, further research across other TE classes and host species is required to further examine this intriguing possibility.
1. Lander ES, Int Human Genome Sequencing C, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, et al.: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
2. Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, et al.: Structural and functional partitioning of bread wheat chromosome 3B. Science 2014, 345.
3. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al.: The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009, 326:1112-1115.
4. Bousios A, Minga E, Kalitsou N, Pantermali M, Tsaballa A, Darzentas N: MASiVEdb: the Sirevirus Plant Retrotransposon Database. Bmc Genomics 2012, 13.
5. Bousios A, Kourmpetis YAI, Pavlidis P, Minga E, Tsaftaris A, Darzentas N: The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant Journal 2012, 69:475-488.
During the life cycle of TEs, new copies can insert near or even within genes, which can prove deleterious for the host as it may severely compromise gene function. It therefore comes as no surprise that hosts have evolved mechanisms to suppress TE activity and safeguard genomic integrity. These mechanisms rely heavily on small RNA molecules that guide the deposition of silencing marks (such as DNA methylation) on the TE sequence. This process aims to generate a dense chromatin environment around the TE, which physically restricts access to DNA-binding proteins that are needed to initiate transcription of the TE sequence into mRNA; hence, the TE is silenced. However, given their abundance in genomes, TEs can surely escape silencing and proliferate. How this is happening, as well as how hosts respond to TE escape, are poorly understood processes. We sought to investigate this evolutionary interplay between TEs and host defenses, by focusing on the large and fully sequenced maize genome and one of its most prolific TEs, the Sireviruses, which constitute 20% of its genomic content. We set out the following tasks:
1. Search for sequence signatures of adaptive evolution across the Sirevirus phylogeny. Subfamilies with the most successful life histories (as measured by their population sizes) should be those that were able to adapt better against host defenses.
2. Elucidate the distribution of small RNA targeting and methylation marks along the Sirevirus sequence. The focal points of interaction between TEs and silencing mechanisms are so far unknown.
3. Identify Sireviruses that have captured host gene fragments in their genomes and investigate whether this mechanism may aid these elements to escape suppression. The hypothesis is that silencing these TEs will negatively impact on the function of the original genes.
To address these questions, we retrieved the original maize Sirevirus population from MASiVEdb [4] and produced a highly annotated set of 6,456 full-length Sireviruses that are split across five families. We also identified another 439 elements with gene fragments within their genomes. Initial phylogenetic analysis of each family did not delineate branches with sufficient bootstrap support, which hampers the search for adaptive evolution signatures. As a result, and given that two of the five families have amplified in large numbers [5], we are now comparing families (instead of subfamilies) for their rates of adaptive evolution. We anticipate completing most analyses by the end of this year.
The examination of the distribution of silencing marks, and especially small RNAs, on Sireviruses provided strong evidence for the potential importance of the cis-regulatory regions of TEs as main targets of host defenses. Sireviruses contain a complex palindrome-rich domain in the part of their sequence that controls their life cycle (i.e. the cis-regulatory region). We discovered that these palindromes are targeting hotspots, because the majority of small RNAs map to four narrow loci occupied by these motifs. Surprisingly, however, the palindromes are not identical but differ among loci, among members of the same family and among families; as a result, each palindrome is also targeted by different small RNAs. This intense interaction between cis-motifs and small RNAs suggests that this region is a template of an evolutionary arms race between Sireviruses and host defences: at first, sequence evolution of the palindromes may allow elements to escape silencing (because there will be few matching small RNAs to mediate silencing), before hosts adapt (by generating more matching small RNAs) and re-silence these elements. Hosts may in fact ‘domesticate’ few defunct old Sireviruses that inserted in the genome million years ago, because it can use their palindromes during emergencies to quickly produce matching small RNAs to younger, highly dangerous, relatives.
Finally, comparison of the distribution of silencing marks on the sequences of Sireviruses that contain and do not contain gene fragments generated highly similar patterns. This result does not support the hypothesis that gene capturing may represent an escape mechanism for TEs. That said, further research across other TE classes and host species is required to further examine this intriguing possibility.
1. Lander ES, Int Human Genome Sequencing C, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, et al.: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
2. Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, et al.: Structural and functional partitioning of bread wheat chromosome 3B. Science 2014, 345.
3. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, et al.: The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009, 326:1112-1115.
4. Bousios A, Minga E, Kalitsou N, Pantermali M, Tsaballa A, Darzentas N: MASiVEdb: the Sirevirus Plant Retrotransposon Database. Bmc Genomics 2012, 13.
5. Bousios A, Kourmpetis YAI, Pavlidis P, Minga E, Tsaftaris A, Darzentas N: The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant Journal 2012, 69:475-488.