Altruistic functions for selfish DNA

Roslin Institute, University of Edinburgh, Roslin, Scotland, UK.
Cell cycle (Georgetown, Tex.) (Impact Factor: 4.57). 10/2009; 8(18):2895-900. DOI: 10.4161/cc.8.18.9536
Source: PubMed


Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this "selfish DNA" or "junk DNA" dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo.

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Available from: Piero Carninci, Dec 14, 2013
    • "At the time, because no determined function could be correlated with this huge part of the chromatin, some termed this region as the dark matter. Further analysis showed that mobile DNA elements and their residues constitute a large portion (*45%) of the chromatin dark matter (Faulkner and Carninci, 2009). It appears that mobile DNA elements, which are also known as transposable elements (TEs), resided in eukaryotic genomes some 100 million years ago. "
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    ABSTRACT: Mobile DNA elements transposable elements (TEs) are genomic sequences capable of moving themselves independently into different parts of the genome. Viral invasion of eukaryotic genomes is assumed to be the main source of TEs. Selfish transposition of these elements could be a serious threat to the host cell, as they can insert themselves into the middle of coding genes and/or induce genomic instability. In response, through million years of evolution, cells have come up with various mechanisms such as genomic imprinting, DNA methylation, heterochromatin formation, and RNA interference to deactivate them. Interestingly, these processes have also greatly contributed to important cellular functions involved in cell differentiation, development, and differential gene expression. Propagation of TE copies during the course of evolution have resulted in increasing the genome size and providing proper space and flexibility in shaping the genome by creating new genes and establishing essential cellular structures such as heterochromatin, centromere, and telomeres. Yet, these elements are mostly labeled for playing a role in pathogenesis of human diseases. In this study, we attempt to introduce TEs as factors necessary for making us human rather than just selfish sequences or obligatory guests invading our DNA.
    No preview · Article · Jul 2015 · DNA and cell biology
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    • "Two nanoCAGE libraries were synthesized from independent harvests and deeply sequenced using Illumina technology, yielding a total of 53,158,862 tags with a length of 25 bp and corresponding to the very 5 -end of MOE capped transcripts. 31,031,749 tags were confidently mapped to the mouse genome (Faulkner et al., 2008; Hashimoto et al., 2009). The mapped nanoCAGE tags were clustered and aggregated into Tag Clusters (TCs) (Carninci et al., 2006), and the data were unified in publicly accessible tracks that can be uploaded in UCSC Genome Browser (see Supplementary Data). "
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    ABSTRACT: By coupling laser capture microdissection to nanoCAGE technology and next-generation sequencing we have identified the genome-wide collection of active promoters in the mouse Main Olfactory Epithelium (MOE). Transcription start sites (TSSs) for the large majority of Olfactory Receptors (ORs) have been previously mapped increasing our understanding of their promoter architecture. Here we show that in our nanoCAGE libraries of the mouse MOE we detect a large number of tags mapped in loci hosting Type-1 and Type-2 Vomeronasal Receptors genes (V1Rs and V2Rs). These loci also show a massive expression of Long Interspersed Nuclear Elements (LINEs). We have validated the expression of selected receptors detected by nanoCAGE with in situ hybridization, RT-PCR and qRT-PCR. This work extends the repertory of receptors capable of sensing chemical signals in the MOE, suggesting intriguing interplays between MOE and VNO for pheromone processing and positioning transcribed LINEs as candidate regulatory RNAs for VRs expression.
    Full-text · Article · Feb 2014 · Frontiers in Cellular Neuroscience
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    • "Forty four percent of the human genome and more than 85% of the maize genome consists of transposons and their relics [2,3]. New views have led to the insight that transposons have shaped the genomic landscape in almost every conceivable way: shuffling, addition and deletion of not only new coding and regulatory sequences, but of large stretches of chromosomes as well [4,5]. "
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    ABSTRACT: Background DAYSLEEPER encodes a domesticated transposase from the hAT-superfamily, which is essential for development in Arabidopsis thaliana. Little is known about the presence of DAYSLEEPER orthologs in other species, or how and when it was domesticated. We studied the presence of DAYSLEEPER orthologs in plants and propose a model for the domestication of the ancestral DAYSLEEPER gene in angiosperms. Results Using specific BLAST searches in genomic and EST libraries, we found that DAYSLEEPER-like genes (hereafter called SLEEPER genes) are unique to angiosperms. Basal angiosperms as well as grasses (Poaceae) and dicotyledonous plants possess such putative orthologous genes, but SLEEPER-family genes were not found in gymnosperms, mosses and algae. Most species contain more than one SLEEPER gene. All SLEEPERs contain a C2H2 type BED-zinc finger domain and a hATC dimerization domain. We designated 3 motifs, partly overlapping the BED-zinc finger and dimerization domain, which are hallmark features in the SLEEPER family. Although SLEEPER genes are structurally conserved between species, constructs with SLEEPER genes from grapevine and rice did not complement the daysleeper phenotype in Arabidopsis, when expressed under control of the DAYSLEEPER promoter. However these constructs did cause a dominant phenotype when expressed in Arabidopsis. Rice plant lines with an insertion in the RICESLEEPER1 or 2 locus displayed phenotypic abnormalities, indicating that these genes are functional and important for normal development in rice. We suggest a model in which we hypothesize that an ancestral hAT transposase was retrocopied and stably integrated in the genome during early angiosperm evolution. Evidence is also presented for more recent retroposition events of SLEEPER genes, such as an event in the rice genome, which gave rise to the RICESLEEPER1 and 2 genes. Conclusions We propose the ancestral SLEEPER gene was formed after a process of retro-transposition during the evolution of the first angiosperms. It may have acquired an important function early on, as mutation of two SLEEPER genes in rice, like the daysleeper mutant in A. thaliana gave a developmental phenotype indicative of their importance for normal plant development.
    Full-text · Article · Oct 2012 · BMC Plant Biology
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