Transposable elements donate lineage-specific regulatory sequences to host genomes

Mariño-Ramírez, Leonardo; Lewis, Kenneth C.; Landsman, David; Jordan, I. King

doi:10.1159/000084965

Cited by 89 publications

(81 citation statements)

References 105 publications

(47 reference statements)

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“…A number of researchers have argued that transposable elements offer an obvious and ideal substrate for the evolution of lineage-specific functions [89][90][91][92][93] . Transposable elements contain a variety of functional subunits that can be exapted and modified by the host genome 89,91 , and they can mediate duplication of existing CNEs to distant genomic locations through transduction or chimaerism 92 .…”

Section: Conserved Sequence Elementsmentioning

confidence: 99%

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen¹,

Wakefield²,

Aken³

et al. 2007

Nature

661

592

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We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

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Section: Conserved Sequence Elementsmentioning

confidence: 99%

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen¹,

Wakefield²,

Aken³

et al. 2007

Nature

661

592

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“…It is important to bear in mind that mobile elements are taxonomically specific and so will contribute lineagespecific regulatory sequences to host genomes [228,229]. Table 11a gives a list of mobile element exaptations as regulatory sites documented in the genome sequence record.…”

Section: Evolution Of Regulatory Circuits By Mobile Elementsmentioning

confidence: 99%

How life changes itself: The Read–Write (RW) genome

Shapiro

2013

Physics of Life Reviews

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The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

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“…Furthermore, despite the strong conservation of gene expression patterns across different maize lines, Mutator transposition programmed by transcriptionally active MuDR can induce a 25% change in the anther transcriptome, reflecting widespread insertion of the Mutator transposon into genes encoding transcription factors (Skibbe et al, 2009). Our data show that 14 of 24 Mutator insertion sites in P. pubescens FL-cDNAs are located in genes encoding transcription factors, which indicates that Mutator transposons may influence host growth and development by influencing the regulatory factor of gene expression (Marino-Ramirez et al, 2005).…”

Section: Discussionmentioning

confidence: 78%

“…There are relatively few TEs within the FL-cDNA sequences compared to the genome average (TEs represent 0.32% of FL-cDNAs but >20% of GSSs), which indicates that most TEs are not expressed in P. pubescens transcriptome due to the tight regulation of TEs (Jiao and Deng, 2007). However, the presence of TEs in and around genes appears to be essential for the growth and development of the host organism (Lockton and Gaut, 2009;Pritham, 2009), because they are involved in the regulation of gene expression (Marino-Ramirez et al, 2005;Feschotte, 2008). In a seminal study, Jordan et al (2003) reported that nearly 25% of experimentally characterized human promoters contain TE sequences, including empirically defined cis-regulatory elements.…”

Section: Discussionmentioning

confidence: 99%

Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats

Zhou

Liu²,

Tang³

2011

Genet. Mol. Res.

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ABSTRACT. Phyllostachys pubescens is a woody bamboo with the highest ecological, economic, and cultural values of all bamboos in Asia. There is more genomic data available for P. pubescens than for any other bamboo species, including 2.12-Mb genome survey sequences (GSS) and 11.4-Mb full-length cDNA sequences (FLcDNAs) currently deposited in GenBank. Analysis of these sequences revealed that transposable elements (TEs) are abundant, diverse and polyphyletic in the P. pubescens genome, of which Ty3-gypsy and Ty1-copia are the two most abundant families. Phylogenic analysis showed that both elements probably arose before the Bambusoideae separated from the other Poaceae subfamilies. We found evidence that the distribution of some intragenic TEs correlated with transcript profiles, of which Mutator elements preferred to insert in the transcripts of transcription factors. Additionally, we found that the abundance of SSRs in TEs (4.56%) was significantly higher than in GSS (0.098%) and in FL-cDNAs (2.60%) in P. pubescens genome, and TA/AT and 3027 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 10 (4): 3026-3037 (2011) Structure and evolution of Phyllostachys pubescens genome CT/AG repeats were found to be intimately associated with En/Spm and Mutator elements, respectively. Our data provide a glimpse of the structure and evolution of P. pubescens genome, although large-scale sequencing of the genome would be required to fully understand the architecture of the P. pubescens genome.

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Transposable elements donate lineage-specific regulatory sequences to host genomes

Cited by 89 publications

References 105 publications

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

How life changes itself: The Read–Write (RW) genome

Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats

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