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Epigenetic Reprogramming in Early Embryo Development
Published in Cristina Camprubí, Joan Blanco, Epigenetics and Assisted Reproduction, 2018
Notably, active retrotransposons are currently mobilizing in the human and mouse genome (69). Retrotransposons are also divided in two types, those containing long-terminal repeats (LTRs) on both ends, known as LTR retrotransposons or endogenous retroviruses (ERVs), and those lacking LTRs, non-LTR retrotransposons. Although in mouse both LTR and non-LTR retrotransposons continue to generate interindividual genomic variability, in humans only retrotransposons from the non-LTR retrotransposon class are currently active. Within non-LTR retrotransposons, two main types of elements can be described: The SINE family (short interspersed elements) and the LINE family (long interspersed elements). SINEs are short and non-coding sequences, while LINEs are coding sequences that generate protein products responsible for the mobilization of both LINEs and SINEs. Within LINEs, the class 1 of these elements (LINE-1s) is the evolutionary younger family of elements that continue to generate variability in our genome. From a copy number perspective, SINE elements such as Alu have accumulated more than a million copies over human evolution, while LINE-1s have generated a substantial half million copies over evolution. In sum, both LINE-1s and SINEs make up an estimated 15%–17% of the human genome due to its length (70,71).
Epigenetics from Oocytes to Embryos
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Dagnė Daškevičiūtė, Marta Sanchez-Delgado, David Monk
H3K27me3 is a polycomb-based histone modification associated with gene repression49 and can be inherited from the oocyte regulating enhancer function and lineage-specific genes.50 In the mouse zygote, H3K27me3 located in promoter regions in both the maternal and paternal genomes is lost, followed by rapid redistributions during the cleavage stages.50 The rapid erasure throughout the paternal genome is accompanied by selective depletion at maternal promoters. Recently, oocyte-derived, maternal H3K27me3-mediated imprinting has been described in mouse pre-implantation embryos for several genes, including Gab1, Phf17, Sfmbts, and Slc38a4.50 This occurs at DNA unmethylated promoter regions, but is transient, being lost by implantation, reflecting the complementary roles of H3K27me3 and 5mC in regulating imprinting. During human pre-implantation development, the H3K27me3 oocyte and embryonic profiles differ from mice. By the eight-cell cleavage stage, human embryos exhibit complete erasure on both parental genomes,43 consistent with the largely non-existent H3K27me3-mediated, germline 5mC-independent temporal imprinting.51,52 H3K27me3 also appears in intergenic regions, where it is widespread and may be involved in transcriptional repression, compensating for the lack of 5mC and H3K9me3 during reprogramming. This is especially important at repeat-rich sequences such as long terminal repeat (LTR) retrotransposons, which must be properly regulated to avoid recombination, self-duplication, and genome instability. Since 5mC is largely demethylated shortly after fertilization, silencing of LTRs requires a switch from 5mC to repressive histone modifications, including H3K27me3 and H3K9me3.53 Promoters demarked by H3K9me3 are erased at fertilization and re-established at post-implantation stages, indicating that unique sequences and LTRs have different regulatory mechanisms, likely involving ZFP-KAP1 complexes.
Gordon H. Dixon’s trace in my personal career and the quantic jump experienced in regulatory information
Published in Systems Biology in Reproductive Medicine, 2018
The tRFs are able to safeguard genome integrity against LTR-retrotransposons that escape other means of detection. Defense against transposons is complicated for the host by the challenge to discriminate self from non-self, as many genes have functional domains derived from transposons (Feschotte 2008) or harbor TE sequences in their non-coding regulatory regions (Faulkner et al. 2009). This means that transposon silencing mediated by siRNAs and piRNAs derived from the entire TE comes with potential ‘off-target’ effects on gene regulation. In contrast, the binding target site of 3ʹ CCA tRFs is downstream of the LTR promoter and upstream of their protein coding sequences, and highly conserved across LTR-retrotransposons but not in other genes. A unique target sequence recognizes and inhibits endogenous as well as infectious LTR-retrotransposons with a repertoire of 3ʹ CCA tRFs readily available in cells. Potential target sites of 3ʹ CCA tRFs are also found in human ERVs (Kawaji et al. 2008; Li et al. 2012b; Schorn et al. 2017) that also functions against exogenous HIV virus infection (Yeung et al. 2009), a fact that suggests that viral defense could have evolved from a much more widespread role for tRFs in inhibiting LTR retroelements.
Stress-induced strain and brain region-specific activation of LINE-1 transposons in adult mice
Published in Stress, 2018
Ugo Cappucci, Giulia Torromino, Assunta Maria Casale, Jeremy Camon, Fabrizio Capitano, Maria Berloco, Andrea Mele, Sergio Pimpinelli, Arianna Rinaldi, Lucia Piacentini
Mounting evidences demonstrate that mammalian non-long terminal repeat (non-LTR) retrotransposons belonging to the group of long interspersed nuclear elements (LINEs), are normally active during neurogenesis in both rodent and human tissues and appear to insert in neurally expressed genes (Erwin, Marchetto, & Gage, 2014; Muotri et al., 2005). These interesting data change the dogma that neuronal genomes are static and reveal that they are susceptible to somatic alterations; this raises the intriguing hypothesis that active mobilization of some TEs could play a functional role in normal brain physiology.
Effects of ionizing radiation at Drosophila melanogaster with differently active hobo transposons
Published in International Journal of Radiation Biology, 2019
Transposable elements (TEs) are mobile DNA fragments of genome. The classification of TEs is based on differences in their structure and mechanisms of movement in the genome. Currently, there are three classes of TEs (Kim 2014). The first class includes retrotransposons — long terminal repeat (LTR)-retrotransposons (gypsy, copia et al.), non-LTR-retrotransposons and retroviruses (I, jockey, LINEs, SINEs et al.), and retroelements (PLEs). Mechanism (DNA-RNA-DNA displacement) of their movement is associated with the synthesis of DNA chain through the formation of RNA mediator with the participation of the enzyme reverse transcriptase (Finnegan 1989). The second class of TEs is represented by DNA transposons (P, hobo, mariner et al.) encoding a transposase. A transposase is able to recognize the ends of ‘its’ element, cut it out of the chromosome and/or embed it into the chromosome of the host genome (Bazin et al. 1999). Such a mechanism of transposition (DNA-DNA displacement) leads to DNA integrity disruption and the formation of double-stranded breaks (Kaufman and Rio 1992; Khromykh et al. 2004). The third class includes helitrons and polintons which move along the genome on the rolling circle replication (Jurka et al. 2007). In some papers, passive elements of the foldback (FB) type are considered as a separate class TEs. FBs found only in plants and in the genomes of the melanogaster subgroup flies (Macas et al. 2003; Badal et al. 2013). They are distinguished by the presence of large arrays of short terminally inverted repeat (TIRs), possibly representing nonhomologous recombination targets. Mechanism of their movement is still unknown. There is an opinion that when the FB moves, a so-called ‘complex with paired ends of the transposon’ is formed the transpososome (Kim 2014).