Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through the reverse transcription process using an RNA transposition intermediate. (wikipedia.org)
Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. (biomedcentral.com)
Transposable elements were initially viewed as "selfish" DNA or "parasitic" elements because of their deleterious effects on host genomes [ 7 ]. (biomedcentral.com)
Transposable elements can be considered as a source of raw material for primitive genomes, tools of genetic innovation, and ancestors of modern genes (e.g., ncRNA) [ 15 ]. (biomedcentral.com)
Transposable elements are able to affect conserved and divergent chromatin looping and contribute to cell- and species-specific gene regulation [ 11 ]. (biomedcentral.com)
Transposable elements (TEs) can be classified into two groups according to their mechanism of movement. (encyclopedia.pub)
DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. (lookformedical.com)
00:00:04.20 And my lab studies transposable elements. (ibiology.org)
00:00:11.12 In the first talk I introduced transposable elements by describing their discovery by Barbara McClintock, 00:00:21.02 how they move, and how that discovery over the years was recognized as a major revolution in biology 00:00:28.25 as it became appreciated that transposable elements 00:00:31.27 are the major component of most of the genomes of higher eukaryotes. (ibiology.org)
00:00:37.16 In this talk I am going to go into detail about how my lab 00:00:41.20 studies the evolutionary impact of transposable elements on genomes. (ibiology.org)
00:00:47.02 And how we develop strategies to identify elements 00:00:51.14 that have an impact on transposable elements. (ibiology.org)
00:01:32.22 So to review the first part, we talked about the genetic analysis of transposable elements, 00:01:41.21 how genetic analysis led to the discovery of transposable elements, 00:01:47.06 and I used this spotted corn kernel as an example to tell you really how powerful the genetic analysis was. (ibiology.org)
00:01:53.12 So when you see a spotted corn kernel like this, 00:01:57.05 we know, the geneticist knows, that the reason that kernel is spotted 00:02:02.07 is because there are active transposable elements. (ibiology.org)
that is the spots reflect the movement of transposable elements. (ibiology.org)
00:02:55.24 McClintock and others were able to deduce this just by looking at the behavior 00:03:02.15 of transposable elements in crosses. (ibiology.org)
00:03:14.26 And that is that by its very nature genetics depends on the analysis of mutant alleles, 00:03:20.23 and so the transposable elements that were being studied were the ones causing mutations. (ibiology.org)
00:03:36.28 So, I mentioned in the first talk that genomes are up to 50-80% 00:03:42.28 of the genome sequence is derived from transposable elements. (ibiology.org)
these are a special class of transposable elements that cause mutations. (ibiology.org)
00:04:12.13 So McClintock as I also described in the first talk, 00:04:18.07 not only discovered transposable elements, 00:04:21.11 but she hypothesized that they were also tools that diversify organisms. (ibiology.org)
00:04:29.14 And to review, she hypothesized that transposable elements that are in the genome 00:04:35.15 do not move around frequently, 00:04:38.02 that there are conditions, such as changes in climate for example, 00:04:42.09 that could activate transposable elements. (ibiology.org)
SINEs2
and non-LTR retrotransposons, including long interspersed nuclear elements (LINEs, such as the L1 element [ 7 ] ) and short interspersed nuclear elements (SINEs, such as the Alu element [ 8 ] ). (encyclopedia.pub)
The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. (lookformedical.com)
Maize1
In maize, a miniature inverted-repeat transposable element (MITE) inserted into the promoter of the NAC gene ( ZmNAC111 ) has been found to enhance drought tolerance at the seedling stage [ 20 ]. (biomedcentral.com)
Retrotransposons2
These retrotransposons are regulated by a family of short non-coding RNAs termed as PIWI [P-element induced wimpy testis]-interacting RNAs (piRNAs). (wikipedia.org)
Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. (lookformedical.com)
Transposons3
In addition to having a role in the suppression of genomic transposons, various roles of piRNAs have been recently reported like regulation of 3' UTR of protein-coding genes via RNAi, transgenerational epigenetic inheritance to convey a memory of past transposon activity, and RNA-induced epigenetic silencing. (wikipedia.org)
DNA transposons encode a transposase which, when translated, catalyses the excision of the transposase gene and its flanking region and its insertion into a different genomic location: a 'jumping' DNA element. (wikipedia.org)
In contrast, Subclass II transposons, such as members of the Helitron superfamily [ 9 ] , follow a copy-and-paste mechanism, during which the element generates copies of itself which integrate into the genome. (encyclopedia.pub)
Genomic2
However, it has been proven that more than 62% of genomic DNA serves as a template for transcription, which indicates that there are abundant non-coding RNAs (ncRNAs) in human transcriptome [ 2 , 3 ]. (ijbs.com)
00:00:57.26 In the first part I talk about the transition from genetic approaches to genomic approaches 00:01:04.14 in order to identify elements that in fact impact genome evolution. (ibiology.org)
Genome7
Initially, piRNAs were described as repeat-associated siRNAs (rasiRNAs) because of their origin from the repetitive elements such as transposable sequences of the genome. (wikipedia.org)
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. (lookformedical.com)
00:02:10.05 The other thing the genetics tells us is exactly where in the genome that active transposable element is. (ibiology.org)
00:02:48.25 Those are the elements that don't make transposase 00:02:51.27 but are able to move if there is an autonomous element in the genome. (ibiology.org)
00:03:31.04 Now because these elements cause mutations, there aren't many copies of them in the genome. (ibiology.org)
00:04:02.15 And as such these elements really have a minimal impact on genome evolution. (ibiology.org)
Genomes1
00:04:59.21 I will come back to this scenario at the end of the talk 00:05:02.16 when I show you how the elements that we have identified 00:05:08.00 in plant genomes fit this scenario very, very nicely. (ibiology.org)
RNAs2
Exoribonuclease-resistant RNAs (xrRNAs) are particularly interesting examples of structurally conserved elements because they actively dysregulate the messenger RNA (mRNA) degradation machinery of host cells, thereby mediating viral pathogenicity. (bvsalud.org)
Unlike linear RNAs, circRNAs form covalent-closed continuous loops without 5' to 3' polarities and poly (A) tails. (ijbs.com)
Promoter1
These elements may be found in both promoter and enhancer regions. (lookformedical.com)
Transcript1
Using bioinformatic analysis and biochemical assays, we demonstrate that the ZIKV 3' TR G4 is conserved across all ZIKV isolates and maintains its structure in a 3' TR full-length transcript. (bvsalud.org)
Copies2
The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). (lookformedical.com)
TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). (lookformedical.com)
Sequences2
Previous G4 studies on ZIKV using a quadruplex forming G-rich sequences Mapper located a potential G-quadruplex sequence in the 3' terminal region (TR) and was validated structurally using a 25-mer oligo. (bvsalud.org)
The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)
Genetic1
00:04:45.21 that this activation would generate genetic diversity in the population 00:04:51.05 by increasing the frequency of mutation, 00:04:57.15 and that some of these transposable element mutations may be adaptive. (ibiology.org)
Region1
These findings provide a path forward in potential therapeutic targeting of DDX3X or DDX17's binding to the 3' TR G4 region for novel treatments against ZIKV. (bvsalud.org)
Genes1
Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases. (lookformedical.com)
Our study also demonstrates that the human DEAD-box helicases, DDX3X132-607 and DDX17135-555, bind to the 3' TR and that DDX17135-555 unfolds the G4 present in the 3' TR. (bvsalud.org)
Type1
00:02:30.14 The other thing that the genetics tells us is the type of element that's there. (ibiology.org)
Regions1
Next, we demonstrate that the 5' and 3' terminal regions of JEV interact with nM affinity using microscale thermophoresis, and this affinity is significantly reduced when the conserved cyclization sequence is not present. (bvsalud.org)
Alus3
Here we show that intronic and intergenic SINE elements, specifically inverted-repeat Alus, are the major source of drug-induced immunogenic dsRNA. (bvsalud.org)
These inverted-repeat Alus are frequently located downstream of 'orphan' CpG islands9. (bvsalud.org)
The abundance of Alus in the human genome-more than one million copies-makes it very likely to encounter inverted pairs of Alus , which can form stem-loop structures that are favored substrates of ADAR. (peerj.com)
Repetitive elements2
Initially, piRNAs were described as repeat-associated siRNAs (rasiRNAs) because of their origin from the repetitive elements such as transposable sequences of the genome. (wikipedia.org)
In mammals, the ADAR1 enzyme targets and destabilizes inverted-repeat Alu dsRNA10, which prevents activation of the MDA5 receptor11. (bvsalud.org)
Mutations3
00:03:31.04 Now because these elements cause mutations, there aren't many copies of them in the genome. (ibiology.org)
00:03:45.04 However, the elements that cause mutations are not those elements. (ibiology.org)
00:04:45.21 that this activation would generate genetic diversity in the population 00:04:51.05 by increasing the frequency of mutation, 00:04:57.15 and that some of these transposable element mutations may be adaptive. (ibiology.org)
Short4
These retrotransposons are regulated by a family of short non-coding RNAs termed as PIWI [P-element induced wimpy testis]-interacting RNAs (piRNAs). (wikipedia.org)
These splice regulatory elements are short nucleotide sequences that are often bound by RNA-binding proteins (RBPs) that can either facilitate or inhibit the splice site recognition. (nature.com)
Mechanistically, demethylation of an intragenic CpG island immediately downstream to the 3' UTR of the short isoform was associated with antisense transcription and alternative polyadenylation of NFATc1 short isoforms. (bvsalud.org)
These short interspersed nuclear elements are ∼300 base pairs (bp) in length, specific to primates, and often embedded in introns and 3′ untranslated regions (UTRs). (peerj.com)
Protein3
Certain circRNAs, such as circRNA ankyrin repeat domain 36, circRNA homeodomain‑interacting protein kinase 3 (circHIPK3) and circRNA WD repeat domain 77, are associated with inflammation, endothelial cell apoptosis and smooth muscle cell proliferation, leading to vascular endothelial dysfunction and atherosclerosis. (spandidos-publications.com)
Circ_0005015, circRNA PWWP domain containing 2A, circRNA zinc finger protein 532, circRNA zinc finger protein 609, circRNA DNA methyltransferase 3β, circRNA collagen type I α2 chain and circHIPK3 widely affect multiple biological processes of diabetic retinopathy. (spandidos-publications.com)
In addition, circRNA homeodomain interacting protein kinase 3 (circHIPK3) has been demonstrated to be involved in DR and DCM both in vivo and in vitro ( 13 , 14 ). (spandidos-publications.com)
Show2
Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold near splice junctions. (nature.com)
00:04:59.21 I will come back to this scenario at the end of the talk 00:05:02.16 when I show you how the elements that we have identified 00:05:08.00 in plant genomes fit this scenario very, very nicely. (ibiology.org)