Several reviews have been published regarding structures and potential functions of retrotransposons. Despite this knowledge, how retrotransposon functions remains largely unknown and controversial, while recent progress on retrotransposons opens up new insights into understanding their functional importance. Moreover, retrotransposon sequences may mediate genomic rearrangement through nonallelic homologous recombination. Sometimes cytoplasmic mRNA is incorporated during retrotransposon complex assembly then later, this gene sequence may be inserted into the genome by retrotransposition activity and create pseudogenes that might gain new functions during evolution. In addition, retrotransposon-contained regulatory elements such as enhancers allow target genes to acquire new expression and regulatory patterns. Alternatively, retrotransposons may provide new transcription start sites to change gene regulation and gene structure. Retrotransposons may interfere with gene expression by antisense transcription or premature transcription termination. Basically, a retrotransposition event leads to insertional mutagenesis and may change gene structure and expression, depending on insertion position and direction. The most intriguing question about retrotransposon is its biological function. Therefore, human ERVs are always regarded as genomic fossils of ancient retroviruses and descendants. Differently, ERVs such as intracisternal A-particle (IAP) are active in mice, but not mobilized in human except in some pathological conditions. During mobilization, LINE1 is transcribed and translated and then reverse transcribed and integrated back into the genome, with a slight preference for intergenic genomic regions. LINE1 is the most well-studied non-LTR retrotransposon because it is active in both mouse and human, while mobilization of SINEs relies on LINE1-encoded proteins. Non-LTR retrotransposons mainly include long/short interspersed nuclear elements (LINEs and SINEs). Mammalian retrotransposons include non-LTR retrotransposons and LTR retrotransposons (also known as endogenous retroviruses, ERVs). BackgroundĪpproximately 40% of the mammalian genome is comprised of retrotransposons, implying their important role in organizing genomic architecture, orchestrating biological processes, and contributing to species diversity and evolution. Additionally, endeavors made to unveil the roles of these mysterious elements may facilitate stem cell status conversion and manipulation of pluripotency. Further investigations on the regulatory network of retrotransposons in early embryogenesis and ESCs will provide valuable insights and a deeper understanding of retrotransposon biology. In this review, we summarize expression patterns and regulatory functions of different retrotransposons in early embryos and ESCs, as well as document molecular mechanisms controlling retrotransposon expression and their potential functions. In addition, retrotransposons may mediate epigenetic memory, regulate gene expression posttranscriptionally, defend virus infection, and so on. Some other retrotransposons reside in the vicinity of endogenous genes and are capable of regulating nearby genes and cell fate, possibly through providing alternative promoters, regulatory modules, or orchestrating high-order chromatin assembly. Some retrotransposon elements retained the capacity to retrotranspose, such as LINE1, producing genetic diversity or disease. Notably, abundant retrotransposon expression in mouse embryonic stem cells (ESCs) marks transient totipotency status, while retrotransposon enrichment in human ESCs indicates naive-like status. Retrotransposons are epigenetically silenced in most somatic tissues and become reactivated in early embryos. Increasing evidence shows that they are not just remnants of ancient retroviruses but play important roles in multiple biological processes. Retrotransposons comprise a significant fraction of mammalian genome with unclear functions.
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