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Jurgen Schmitz - One of the best experts on this subject based on the ideXlab platform.
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De-novo emergence of SINE Retroposons during the early evolution of passerine birds
Mobile DNA, 2017Co-Authors: Alexander Suh, Jurgen Brosius, Sandra Bachg, Stephen Donnellan, Leo Joseph, Jan Ole Kriegs, Jurgen SchmitzAbstract:Background Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of Retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. Results Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant Retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri – songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. Conclusions We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.
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Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data
2016Co-Authors: Andrej Kuritzin, Jurgen Schmitz, Tabea Kischka, Gennady ChurakovAbstract:Ancient Retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p
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SOFTWARE Open Access A novel web-based TinT application and the chronology of the Primate Alu Retroposon activity
2013Co-Authors: Gennady Churakov, Norbert Grundmann, Andrej Kuritzin, Jurgen Brosius, Wojciech Makałowski, Jurgen SchmitzAbstract:Background: DNA sequences afford access to the evolutionary pathways of life. Particularly mobile elements that constantly co-evolve in genomes encrypt recent and ancient information of their host’s history. In mammals there is an extraordinarily abundant activity of mobile elements that occurs in a dynamic succession of active families, subfamilies, types, and subtypes of retroposed elements. The high frequency of Retroposons in mammals implies that, by chance, such elements also insert into each other. While inactive elements are no longer able to retropose, active elements retropose by chance into other active and inactive elements. Thousands of such directional, element-in-element insertions are found in present-day genomes. To help analyze these events, we developed a computational algorithm (Transpositions in Transpositions, or TinT) that examines the different frequencies of nested transpositions and reconstructs the chronological order of Retroposon activities. Results: By examining the different frequencies of such nested transpositions, the TinT application reconstructs the chronological order of Retroposon activities. We use such activity patterns as a comparative tool to (1) delineate the historical rise and fall of Retroposons and their relations to each other, (2) understand the Retroposon-induced complexity of recent genomes, and (3) find selective informative homoplasy-free markers of phylogeny. The efficiency of the new application is demonstrated by applying it to dimeric Alu Short INterspersed Elements (SINE
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Positions of Retroposed Elements as Landmarks of Evolution on the Bayesian-Based Placental Evolutionary Tree from Murphy et al. [ 2]
2013Co-Authors: Jan Ole Kriegs, Gennady Churakov, Jurgen Brosius, Martin Kiefmann, Ursula Jordan, Jurgen SchmitzAbstract:The resultant tree is consistent with previous studies [1, 2, 4, 5, 7, 8, 10, 38, 39] in most aspects. Note that the positions of afrotherians and xenarthras have been reversed, based on the presence of two Retroposon insertions at node 2. Gray balls represent single insertion events. Supported splitting points are labeled with Arabic numerals. Superordinal clades, in the order shown, were established by Waddell et al. [6] and supported by several major studies [1, 2, 7, 8], and are labeled with Roman numerals. The taxa shown represent only those from which we sampled LINEs and LTRs. Dotted lines indicate nodes in need of further confirmation. Asterisks represent Retroposon evidence from the literature for monophyly of Afrotheria [27], Primates [18], Rodentia [45], and Cetartiodactyla [26].
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Representative Alignments of the Presence/Absence Regions Indicating Support for the Five Investigated Evolutionary Divergences
2013Co-Authors: Jan Ole Kriegs, Gennady Churakov, Jurgen Brosius, Martin Kiefmann, Ursula Jordan, Jurgen SchmitzAbstract:Potential direct repeats are boxed. The 5′ and 3′ ends of the Retroposon insertions are partially shown in lower case letters on a gray background. Node designations corresponding to Figure 2 and the names of the supported monophyletic groups are given above the inserted elements.
Elisabetta Ullu - One of the best experts on this subject based on the ideXlab platform.
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Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei
BMC Genomics, 2012Co-Authors: Christian Tschudi, Huafang Shi, Joseph B Franklin, Elisabetta UlluAbstract:Background At the core of the RNA interference (RNAi) pathway in Trypanosoma brucei is a single Argonaute protein, Tb AGO1, with an established role in controlling Retroposon and repeat transcripts. Recent evidence from higher eukaryotes suggests that a variety of genomic sequences with the potential to produce double-stranded RNA are sources for small interfering RNAs (siRNAs). Results To test whether such endogenous siRNAs are present in T. brucei and to probe the individual role of the two Dicer-like enzymes, we affinity purified Tb AGO1 from wild-type procyclic trypanosomes, as well as from cells deficient in the cytoplasmic ( Tb DCL1) or nuclear ( Tb DCL2) Dicer, and subjected the bound RNAs to Illumina high-throughput sequencing. In wild-type cells the majority of reads originated from two classes of Retroposons. We also considerably expanded the repertoire of trypanosome siRNAs to encompass a family of 147-bp satellite-like repeats, many of the regions where RNA polymerase II transcription converges, large inverted repeats and two pseudogenes. Production of these newly described siRNAs is strictly dependent on the nuclear DCL2. Notably, our data indicate that putative centromeric regions, excluding the CIR147 repeats, are not a significant source for endogenous siRNAs. Conclusions Our data suggest that endogenous RNAi targets may be as evolutionarily old as the mechanism itself.
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distinct and overlapping roles for two dicer like proteins in the rna interference pathways of the ancient eukaryote trypanosoma brucei
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Kristin L Patrick, Christian Tschudi, Klaus Ersfeld, Nikolay G Kolev, Elisabetta UlluAbstract:Trypanosoma brucei is one of the most ancient eukaryotes where RNA interference (RNAi) is operational and is the only single-cell pathogen where RNAi has been extensively studied and used as a tool for functional analyses. Here, we report that the T. brucei RNAi pathway, although relying on a single Argonaute protein (AGO1), is initiated by the activities of two distinct Dicer-like enzymes. Both TbDCL1, a mostly cytoplasmic protein, and the previously undescribed nuclear enzyme TbDCL2 contribute to the biogenesis of siRNAs from Retroposons. However, TbDCL2 has a predominant role in generating siRNAs from chromosomal internal repeat transcripts that accumulate at the nucleolus in RNAi-deficient cells and in initiating the endogenous RNAi response against Retroposons and repeats alike. Moreover, siRNAs generated by both TbDCL1 and TbDCL2 carry a 5′-monophosphate and a blocked 3′ terminus, suggesting that 3′ end modification is an ancient trait of siRNAs. We thus propose a model whereby TbDCL2 fuels the T. brucei nuclear RNAi pathway and TbDCL1 patrols the cytoplasm, posttranscriptionally silencing potentially harmful nucleic acid parasites that may access the cytoplasm. Nevertheless, we also provide evidence for cross-talk between the two Dicer-like enzymes, because TbDCL2 is implicated in the generation of 35- to 65-nucleotide intermediate transcripts that appear to be substrates for TbDCL1. Our finding that dcl2KO cells are more sensitive to RNAi triggers than wild-type cells has significant implications for reverse genetic analyses in this important human pathogen.
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small sense and antisense rnas derived from a telomeric Retroposon family in giardia intestinalis
Eukaryotic Cell, 2005Co-Authors: Elisabetta Ullu, Hugo D Lujan, Christian TschudiAbstract:Sequencing of a library of small RNAs from Giardia intestinalis identified a novel class of small sense and antisense RNAs homologous to the Retroposon family GilT/Genie1 that is located at certain telomeres. These small RNAs may contribute to silencing GilT expression via the RNA interference pathway.
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argonaute protein in the early divergent eukaryote trypanosoma brucei control of small interfering rna accumulation and Retroposon transcript abundance
Molecular and Cellular Biology, 2004Co-Authors: Huafang Shi, Christian Tschudi, Appolinaire Djikeng, Elisabetta UlluAbstract:Members of the Argonaute protein family have been linked through a combination of genetic and biochemical studies to RNA interference (RNAi) and related phenomena. Here, we describe the characterization of the first Argonaute protein (AGO1) in Trypanosoma brucei, the earliest divergent eukaryote where RNAi has been described so far. AGO1 is predominantly cytoplasmic and is found in a ribonucleoprotein particle with small interfering RNAs (siRNAs), and this particle is present in a soluble form, as well as associated with polyribosomes. A genetic knockout of AGO1 leads to a loss of RNAi, and concomitantly, endogenous Retroposon-derived siRNAs as well as siRNAs derived from transgenic double-stranded RNA are reduced to almost undetectable levels. Furthermore, AGO1 deficiency leads to an increase in Retroposon transcript abundance via mechanisms operating at the transcriptional level and at the RNA stability level. Our results suggest that AGO1 function is required for production and/or stabilization of siRNAs and provide the first evidence for an Argonaute protein being involved in the regulation of Retroposon transcript levels.
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rna interference in trypanosoma brucei cloning of small interfering rnas provides evidence for Retroposon derived 24 26 nucleotide rnas
RNA, 2001Co-Authors: Appolinaire Djikeng, Christian Tschudi, Elisabetta UlluAbstract:In animals and protozoa, gene-specific double-stranded RNA (dsRNA) triggers degradation of homologous cellular RNAs, a phenomenon known as RNA interference (RNAi). In vitro and in vivo dsRNA is processed by a nuclease to produce 21‐25-nt small interfering RNAs (siRNAs) that guide target RNA degradation. Here we show that activation of RNAi in Trypanosoma brucei by expression or electroporation of actin dsRNA results in production of actin siRNAs and that 10% of these RNAs sediment as high-molecular-weight complexes at 100,000 3 g. To characterize actin siRNAs, we established a cloning and enrichment strategy starting from 20‐30 nt RNAs isolated from high-speed pellet and supernatant fractions. Sequence analysis revealed that actin siRNAs are 24‐26 nt long and their distribution relative to actin dsRNA was similar in the two fractions. By sequencing over 1,300 fragments derived from the high-speed pellet fraction RNA, we found abundant 24‐26-nt-long fragments homologous to the ubiquitous Retroposon INGI and the site-specific Retroposon SLACS. Northern hybridization with strand-specific probes confirmed that Retroposon-derived 24‐26-nt RNAs are present in both supernatant and high-speed pellet fractions and that they are constitutively expressed. We speculate that RNAi in trypanosomes serves a housekeeping function and is likely to be involved in silencing Retroposon transcripts.
Christian Tschudi - One of the best experts on this subject based on the ideXlab platform.
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Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei
BMC Genomics, 2012Co-Authors: Christian Tschudi, Huafang Shi, Joseph B Franklin, Elisabetta UlluAbstract:Background At the core of the RNA interference (RNAi) pathway in Trypanosoma brucei is a single Argonaute protein, Tb AGO1, with an established role in controlling Retroposon and repeat transcripts. Recent evidence from higher eukaryotes suggests that a variety of genomic sequences with the potential to produce double-stranded RNA are sources for small interfering RNAs (siRNAs). Results To test whether such endogenous siRNAs are present in T. brucei and to probe the individual role of the two Dicer-like enzymes, we affinity purified Tb AGO1 from wild-type procyclic trypanosomes, as well as from cells deficient in the cytoplasmic ( Tb DCL1) or nuclear ( Tb DCL2) Dicer, and subjected the bound RNAs to Illumina high-throughput sequencing. In wild-type cells the majority of reads originated from two classes of Retroposons. We also considerably expanded the repertoire of trypanosome siRNAs to encompass a family of 147-bp satellite-like repeats, many of the regions where RNA polymerase II transcription converges, large inverted repeats and two pseudogenes. Production of these newly described siRNAs is strictly dependent on the nuclear DCL2. Notably, our data indicate that putative centromeric regions, excluding the CIR147 repeats, are not a significant source for endogenous siRNAs. Conclusions Our data suggest that endogenous RNAi targets may be as evolutionarily old as the mechanism itself.
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distinct and overlapping roles for two dicer like proteins in the rna interference pathways of the ancient eukaryote trypanosoma brucei
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Kristin L Patrick, Christian Tschudi, Klaus Ersfeld, Nikolay G Kolev, Elisabetta UlluAbstract:Trypanosoma brucei is one of the most ancient eukaryotes where RNA interference (RNAi) is operational and is the only single-cell pathogen where RNAi has been extensively studied and used as a tool for functional analyses. Here, we report that the T. brucei RNAi pathway, although relying on a single Argonaute protein (AGO1), is initiated by the activities of two distinct Dicer-like enzymes. Both TbDCL1, a mostly cytoplasmic protein, and the previously undescribed nuclear enzyme TbDCL2 contribute to the biogenesis of siRNAs from Retroposons. However, TbDCL2 has a predominant role in generating siRNAs from chromosomal internal repeat transcripts that accumulate at the nucleolus in RNAi-deficient cells and in initiating the endogenous RNAi response against Retroposons and repeats alike. Moreover, siRNAs generated by both TbDCL1 and TbDCL2 carry a 5′-monophosphate and a blocked 3′ terminus, suggesting that 3′ end modification is an ancient trait of siRNAs. We thus propose a model whereby TbDCL2 fuels the T. brucei nuclear RNAi pathway and TbDCL1 patrols the cytoplasm, posttranscriptionally silencing potentially harmful nucleic acid parasites that may access the cytoplasm. Nevertheless, we also provide evidence for cross-talk between the two Dicer-like enzymes, because TbDCL2 is implicated in the generation of 35- to 65-nucleotide intermediate transcripts that appear to be substrates for TbDCL1. Our finding that dcl2KO cells are more sensitive to RNAi triggers than wild-type cells has significant implications for reverse genetic analyses in this important human pathogen.
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small sense and antisense rnas derived from a telomeric Retroposon family in giardia intestinalis
Eukaryotic Cell, 2005Co-Authors: Elisabetta Ullu, Hugo D Lujan, Christian TschudiAbstract:Sequencing of a library of small RNAs from Giardia intestinalis identified a novel class of small sense and antisense RNAs homologous to the Retroposon family GilT/Genie1 that is located at certain telomeres. These small RNAs may contribute to silencing GilT expression via the RNA interference pathway.
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argonaute protein in the early divergent eukaryote trypanosoma brucei control of small interfering rna accumulation and Retroposon transcript abundance
Molecular and Cellular Biology, 2004Co-Authors: Huafang Shi, Christian Tschudi, Appolinaire Djikeng, Elisabetta UlluAbstract:Members of the Argonaute protein family have been linked through a combination of genetic and biochemical studies to RNA interference (RNAi) and related phenomena. Here, we describe the characterization of the first Argonaute protein (AGO1) in Trypanosoma brucei, the earliest divergent eukaryote where RNAi has been described so far. AGO1 is predominantly cytoplasmic and is found in a ribonucleoprotein particle with small interfering RNAs (siRNAs), and this particle is present in a soluble form, as well as associated with polyribosomes. A genetic knockout of AGO1 leads to a loss of RNAi, and concomitantly, endogenous Retroposon-derived siRNAs as well as siRNAs derived from transgenic double-stranded RNA are reduced to almost undetectable levels. Furthermore, AGO1 deficiency leads to an increase in Retroposon transcript abundance via mechanisms operating at the transcriptional level and at the RNA stability level. Our results suggest that AGO1 function is required for production and/or stabilization of siRNAs and provide the first evidence for an Argonaute protein being involved in the regulation of Retroposon transcript levels.
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rna interference in trypanosoma brucei cloning of small interfering rnas provides evidence for Retroposon derived 24 26 nucleotide rnas
RNA, 2001Co-Authors: Appolinaire Djikeng, Christian Tschudi, Elisabetta UlluAbstract:In animals and protozoa, gene-specific double-stranded RNA (dsRNA) triggers degradation of homologous cellular RNAs, a phenomenon known as RNA interference (RNAi). In vitro and in vivo dsRNA is processed by a nuclease to produce 21‐25-nt small interfering RNAs (siRNAs) that guide target RNA degradation. Here we show that activation of RNAi in Trypanosoma brucei by expression or electroporation of actin dsRNA results in production of actin siRNAs and that 10% of these RNAs sediment as high-molecular-weight complexes at 100,000 3 g. To characterize actin siRNAs, we established a cloning and enrichment strategy starting from 20‐30 nt RNAs isolated from high-speed pellet and supernatant fractions. Sequence analysis revealed that actin siRNAs are 24‐26 nt long and their distribution relative to actin dsRNA was similar in the two fractions. By sequencing over 1,300 fragments derived from the high-speed pellet fraction RNA, we found abundant 24‐26-nt-long fragments homologous to the ubiquitous Retroposon INGI and the site-specific Retroposon SLACS. Northern hybridization with strand-specific probes confirmed that Retroposon-derived 24‐26-nt RNAs are present in both supernatant and high-speed pellet fractions and that they are constitutively expressed. We speculate that RNAi in trypanosomes serves a housekeeping function and is likely to be involved in silencing Retroposon transcripts.
Marcelo Rubinstein - One of the best experts on this subject based on the ideXlab platform.
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Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin
2013Co-Authors: Andrea Mariana Santangelo, Lucia F Franchini, Flavio S J De Souza, Viviana Florencia Bumaschny, Malcolm J Low, Marcelo RubinsteinAbstract:The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 59 distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) Retroposons, in particular to MAR1 Retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE Retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE Retroposon. In addition, we found that this CORE-SINE famil
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convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated Retroposons
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Lucia F Franchini, Rodrigo Lopezleal, Sofia Nasif, Paula Beati, Diego M Gelman, Flavio J S De Souza, Marcelo RubinsteinAbstract:The proopiomelanocortin gene (POMC) is expressed in a group of neurons present in the arcuate nucleus of the hypothalamus. Neuron-specific POMC expression in mammals is conveyed by two distal enhancers, named nPE1 and nPE2. Previous transgenic mouse studies showed that nPE1 and nPE2 independently drive reporter gene expression to POMC neurons. Here, we investigated the evolutionary mechanisms that shaped not one but two neuron-specific POMC enhancers and tested whether nPE1 and nPE2 drive identical or complementary spatiotemporal expression patterns. Sequence comparison among representative genomes of most vertebrate classes and mammalian orders showed that nPE1 is a placental novelty. Using in silico paleogenomics we found that nPE1 originated from the exaptation of a mammalian-apparent LTR retrotransposon sometime between the metatherian/eutherian split (147 Mya) and the placental mammal radiation (≈90 Mya). Thus, the evolutionary origin of nPE1 differs, in kind and time, from that previously demonstrated for nPE2, which was exapted from a CORE-short interspersed nucleotide element (SINE) Retroposon before the origin of prototherians, 166 Mya. Transgenic mice expressing the fluorescent markers tomato and EGFP driven by nPE1 or nPE2, respectively, demonstrated coexpression of both reporter genes along the entire arcuate nucleus. The onset of reporter gene expression guided by nPE1 and nPE2 was also identical and coincidental with the onset of Pomc expression in the presumptive mouse diencephalon. Thus, the independent exaptation of two unrelated Retroposons into functional analogs regulating neuronal POMC expression constitutes an authentic example of convergent molecular evolution of cell-specific enhancers.
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ancient exaptation of a core sine Retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene
PLOS Genetics, 2007Co-Authors: Andrea Mariana Santangelo, Lucia F Franchini, Flavio S J De Souza, Viviana Florencia Bumaschny, Malcolm J Low, Marcelo RubinsteinAbstract:The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5′ distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) Retroposons, in particular to MAR1 Retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE Retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE Retroposon. In addition, we found that this CORE-SINE family of Retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE Retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.
Jan Ole Kriegs - One of the best experts on this subject based on the ideXlab platform.
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De-novo emergence of SINE Retroposons during the early evolution of passerine birds
Mobile DNA, 2017Co-Authors: Alexander Suh, Jurgen Brosius, Sandra Bachg, Stephen Donnellan, Leo Joseph, Jan Ole Kriegs, Jurgen SchmitzAbstract:Background Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of Retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. Results Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant Retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri – songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. Conclusions We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.
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Positions of Retroposed Elements as Landmarks of Evolution on the Bayesian-Based Placental Evolutionary Tree from Murphy et al. [ 2]
2013Co-Authors: Jan Ole Kriegs, Gennady Churakov, Jurgen Brosius, Martin Kiefmann, Ursula Jordan, Jurgen SchmitzAbstract:The resultant tree is consistent with previous studies [1, 2, 4, 5, 7, 8, 10, 38, 39] in most aspects. Note that the positions of afrotherians and xenarthras have been reversed, based on the presence of two Retroposon insertions at node 2. Gray balls represent single insertion events. Supported splitting points are labeled with Arabic numerals. Superordinal clades, in the order shown, were established by Waddell et al. [6] and supported by several major studies [1, 2, 7, 8], and are labeled with Roman numerals. The taxa shown represent only those from which we sampled LINEs and LTRs. Dotted lines indicate nodes in need of further confirmation. Asterisks represent Retroposon evidence from the literature for monophyly of Afrotheria [27], Primates [18], Rodentia [45], and Cetartiodactyla [26].
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Representative Alignments of the Presence/Absence Regions Indicating Support for the Five Investigated Evolutionary Divergences
2013Co-Authors: Jan Ole Kriegs, Gennady Churakov, Jurgen Brosius, Martin Kiefmann, Ursula Jordan, Jurgen SchmitzAbstract:Potential direct repeats are boxed. The 5′ and 3′ ends of the Retroposon insertions are partially shown in lower case letters on a gray background. Node designations corresponding to Figure 2 and the names of the supported monophyletic groups are given above the inserted elements.
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mesozoic Retroposons reveal parrots as the closest living relatives of passerine birds
Nature Communications, 2011Co-Authors: Martin Paus, Gennady Churakov, Jurgen Brosius, Jan Ole Kriegs, Martin Kiefmann, Franziska Anni Franke, Jurgen SchmitzAbstract:Zebra finches are passerine birds, but their phylogenetic relationship with non-passerine birds remains controversial. By examining Retroposon insertion loci in avian genomes, the authors reveal that parrots are the closest relatives of passerines, which may have implications for understanding the evolution of birdsong.
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mesozoic Retroposons reveal parrots as the closest living relatives of passerine birds
Nature Communications, 2011Co-Authors: Alexander Suh, Gennady Churakov, Jurgen Brosius, Jan Ole Kriegs, Martin Kiefmann, Martin Paus, Franziska Anni Franke, Jurgen SchmitzAbstract:The relationships of passerines (such as the well-studied zebra finch) with non-passerine birds is one of the great enigmas of avian phylogenetic research, because decades of extensive morphological and molecular studies yielded highly inconsistent results between and within data sets. Here we show the first application of the virtually homoplasy-free Retroposon insertions to this controversy. Our study examined ~200,000 Retroposon-containing loci from various avian genomes and retrieved 51 markers resolving early bird phylogeny. Among these, we obtained statistically significant evidence that parrots are the closest and falcons the second-closest relatives of passerines, together constituting the Psittacopasserae and the Eufalconimorphae, respectively. Our new and robust phylogenetic framework has substantial implications for the interpretation of various conclusions drawn from passerines as model organisms. This includes insights of relevance to human neuroscience, as vocal learning (that is, birdsong) probably evolved in the psittacopasseran ancestor, >30 million years earlier than previously assumed.
