scholarly journals Genetic Innovation in Vertebrates: Gypsy Integrase Genes and Other Genes Derived from Transposable Elements

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Domitille Chalopin ◽  
Delphine Galiana ◽  
Jean-Nicolas Volff
Keyword(s):  
Transposable Elements ◽  
Regulatory Sequences ◽  
Biological Functions ◽  
Dna Rearrangements ◽  
Dna Transposons ◽  
New Genes ◽  
Molecular Domestication ◽  
Genome Analyses ◽  
Ability To Drive

Due to their ability to drive DNA rearrangements and to serve as a source of new coding and regulatory sequences, transposable elements (TEs) are considered as powerful evolutionary agents within genomes. In this paper, we review the mechanism of molecular domestication, which corresponds to the formation of new genes derived from TE sequences. Many genes derived from retroelements and DNA transposons have been identified in mammals and other vertebrates, some of them fulfilling essential functions for the development and survival of their host organisms. We will particularly focus on the evolution and expression of Gypsy integrase (GIN) genes, which have been formed from ancient event(s) of molecular domestication and have evolved differentially in some vertebrate sublineages. What we describe here is probably only the tip of the evolutionary iceberg, and future genome analyses will certainly uncover new TE-derived genes and biological functions driving genetic innovation in vertebrates and other organisms.

scholarly journals Why did the Tc1-like elements of mollusks acquired the spliceosomal introns?

2019 ◽  
Author(s):  
M.V. Puzakov ◽  
L.V. Puzakova ◽  
S.V. Cheresiz
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Inverted Repeats ◽  
Considerable Influence ◽  
Dna Transposons ◽  
Spliceosomal Introns ◽  
New Genes ◽  
Eukaryotic Genes ◽  
Low Copy Number ◽  
Diverse Groups

AbstractTransposable elements are the DNA sequences capable of transpositions within the genome and, thus, exerting a considerable influence on the genome functioning and structure and providing the source of new genes. Transposable elements are classified into retrotransposons and the DNA transposons. IS630/Tc1/mariner superfamily of DNA transposons is one of the most diverse groups broadly represented among the eukaryotes. We identified a new group of Tc1-like elements in the mollusks, which we named TLEWI. These DNA transposons are characterized by the low copy number, the lack of terminal inverted repeats and the presence of DD36E signature and the spliceosomal introns in transposase sequence. Their prevalence among the mollusks is limited to subclass Pteriomorpha (Bivalvia). Since TLEWI possess the features of domesticated TE and the structure similar to the eukaryotic genes, which is not typical for the DNA transposons, we consider the hypothesis of co-optation of TLEWI gene by the bivalves.

scholarly journals Role of Transposable Elements in Gene Regulation in the Human Genome

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 118
Author(s):  
Arsala Ali ◽  
Kyudong Han ◽  
Ping Liang
Keyword(s):  
Gene Regulation ◽  
Transposable Elements ◽  
Regulatory Sequences ◽  
Rna Sequences ◽  
Expression Of Genes ◽  
Wide Range ◽  
Lineage Specificity ◽  
Regulatory Rnas ◽  
Potential Factors ◽  
Interspersed Repeats

Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans.

scholarly journals How Barbara McClintock discovered transposable elements in maize

2012 ◽  
Vol 10 (4) ◽  
pp. 3-13
Author(s):  
Keyword(s):  
Transposable Elements ◽  
Chromosomal Location ◽  
Chromosome Breakage ◽  
Dna Transposons ◽  
Barbara Mcclintock ◽  
Controlling Elements ◽  
Earthquake Event ◽  
Maize Kernels ◽  
The Relationship

The paper describes the early part of Barbara McClintock`s work on DNA transposons in maize, in which she discovered the Ac-Ds family of mobile "controlling elements". An account is first given of the cytology of the system that was used to generate intact chromosomes having "sticky" (broken) ends. Cytogenetical aspects of the chromatid and chromosome breakage-fusion-bridge cycles, deriving from breakage, are then described, which leads on to the way in which variegation in phenotypes of the maize kernels could be "read" in terms of chromosome breakage. The "genetic earthquake" event of 1944, triggered by introducing broken chromosomes into a zygote from both parents, lead to the discovery of Ds and Ac. Finding mobility of Ds from one chromosomal location to another was pure serendipity: the transposition showed itself while experiments were being undertaken to accurately map Ds. A similar chance observation revealed transposition of Ac as well, and then the relationship between the two elements was elucidated in terms of their autonomous and non-autonomous nature.

scholarly journals “What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Biology ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 25 ◽  
Author(s):  
Roberta Moschetti ◽  
Antonio Palazzo ◽  
Patrizio Lorusso ◽  
Luigi Viggiano ◽  
René Massimiliano Marsano
Keyword(s):  
Transposable Elements ◽  
Transcriptional Control ◽  
Environmental Changes ◽  
Model Organism ◽  
Model Organisms ◽  
Regulatory Sequences ◽  
Transcriptional Pattern ◽  
Constitutive Components ◽  
Host Genes

Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome’s structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE–host interactions in any complex eukaryotic genome.

scholarly journals Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1089 ◽  
Author(s):  
Rocio Enriquez-Gasca ◽  
Poppy A. Gould ◽  
Helen M. Rowe
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transposable Elements ◽  
Essential Gene ◽  
Expression Patterns ◽  
Genetic Material ◽  
Endogenous Retroviruses ◽  
Host Gene ◽  
New Genes ◽  
Host Genes

The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.

scholarly journals Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes

2020 ◽  
Vol 375 (1795) ◽  
pp. 20190347 ◽  
Author(s):  
Vasavi Sundaram ◽  
Joanna Wysocka
Keyword(s):  
Gene Regulation ◽  
Transposable Elements ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Regulatory Function ◽  
Specific Gene ◽  
Regulatory Sequences ◽  
Dependent Manner ◽  
Unique Contribution ◽  
Regulatory Potential

Eukaryotic gene regulation is mediated by cis -regulatory elements, which are embedded within the vast non-coding genomic space and recognized by the transcription factors in a sequence- and context-dependent manner. A large proportion of eukaryotic genomes, including at least half of the human genome, are composed of transposable elements (TEs), which in their ancestral form carried their own cis -regulatory sequences able to exploit the host trans environment to promote TE transcription and facilitate transposition. Although not all present-day TE copies have retained this regulatory function, the preexisting regulatory potential of TEs can provide a rich source of cis -regulatory innovation for the host. Here, we review recent evidence documenting diverse contributions of TE sequences to gene regulation by functioning as enhancers, promoters, silencers and boundary elements. We discuss how TE-derived enhancer sequences can rapidly facilitate changes in existing gene regulatory networks and mediate species- and cell-type-specific regulatory innovations, and we postulate a unique contribution of TEs to species-specific gene expression divergence in pluripotency and early embryogenesis. With advances in genome-wide technologies and analyses, systematic investigation of TEs' cis -regulatory potential is now possible and our understanding of the biological impact of genomic TEs is increasing. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

scholarly journals Conservation patterns’ analysis of 18,364 candidate human-specific regulatory sequences revealed two distinct pathways of the human regulatory DNA divergence

2015 ◽  
Author(s):  
Gennadi Glinsky
Keyword(s):  
Transposable Elements ◽  
Regulatory Networks ◽  
Homo Sapiens ◽  
Functional Divergence ◽  
Regulatory Sequences ◽  
Conservation Patterns ◽  
Genomic Regulatory Networks ◽  
Species Specific ◽  
Regulatory Dna ◽  
Human Specific

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the idea that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Here, conservation patterns analysis of 18,364 regulatory DNA segments comprising candidate HSRS was carried out using the most recent releases of the reference genomes’ databases of humans and nonhuman primates (NHP) and defining the sequence conservation threshold as the minimum ratio of bases that must remap of 1.00. Present analyses identified 5,535 candidate HSRS defined by either the acceleration of mutation rates on the human lineage or the functional divergence from chimpanzee that are highly conserved in NHP and appear to evolve by the exaptation of ancestral DNA pathway. This pathway seems mechanistically distinct from the evolution of regulatory DNA driven by the species-specific expansion of transposable elements. It is proposed that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: i) exaptation of the highly conserved ancestral regulatory DNA segments; ii) human-specific insertions of transposable elements.

Sign in / Sign up

Export Citation Format

Share Document