Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development

The role of retroelements in Parkinson's disease development

Parkinson's disease is the second most common neurodegenerative disease characterized by accumulation of alpha-synuclein and Lewy bodies in the brain's substantia nigra. Genetic studies indicate an association of various SNPs, many of which are located in intergenic and intronic regions, where retrotransposons and non-coding RNA genes derived from them reside, with this disease. Therefore, we hypothesize the influence of SNPs in retroelement genes on Parkinson's disease development. A susceptibility factor is retrotransposons activation with age, since the disease is associated with aging. We hypothesized that alpha-synuclein accumulates in the brain due to its interaction with transcripts of activated retroelements. As a result of a defective antiviral response and a large number of RNA targets for this protein, its aggregates form Lewy bodies in neurons with inflammation and neurodegeneration development in the substantia nigra. As evidence, data are presented on the role of alpha-synuclein in the antiviral response with binding to RNA viruses, which are characterized by the ability to activate retroelements that have evolved from exogenous viruses integrated into the human genome. Activation of LINE1s in the brain, endogenous retroviruses, and LINE1s in the blood serum of Parkinson's disease patients was detected. An additional mechanism contributing to the progression of the disease is mitochondrial dysfunction due to insertions of Alu elements into their genomes using LINE1 enzymes. Mechanisms of activated retrotransposons' influence on microRNAs that evolved from them are described. Analysis of the scientific literature allowed us to identify 35 such microRNAs (miR-1246, -1249, -1271, -1273, -1303, -151, -211, -28, -31, -320b, -320d, -330, -335, - 342, -374a, -374b, -421, -4293, -4317, -450b, -466, -487b, -493, -495, -5095, -520d, -576, -585, -6088, -619, -625, -626, -769, -885, -95) associated with Parkinson's disease, which may become promising targets for its treatment and diagnosis.

Investigation of chimeric transcripts derived from LINE-1 and Alu retrotransposons in cerebellar tissues of individuals with autism spectrum disorder (ASD)

LINE-1 and Alu retrotransposons are components of the human genome and have been implicated in many human diseases. These elements can influence human transcriptome plasticity in various mechanisms. Chimeric transcripts derived from LINE-1 and Alu can also impact the human transcriptome, such as exonization and post-transcriptional modification. However, its specific role in ASD neuropathology remains unclear, particularly in the cerebellum tissues. We performed RNA-sequencing of post-mortem cerebellum tissues from ASD and unaffected individuals for transposable elements profiling and chimeric transcript identification. The majority of free transcripts of transposable elements were not changed in the cerebellum tissues of ASD compared with unaffected individuals. Nevertheless, we observed that chimeric transcripts derived from LINE-1 and Alu were embedded in the transcripts of differentially expressed genes in the cerebellum of ASD, and these genes were related to developments and abnormalities of the cerebellum. In addition, the expression levels of these genes were correlated with the significantly decreased thickness of the molecular layer in the cerebellum of ASD. We also found that global methylation and expression of LINE-1 and Alu elements were not changed in ASD, but observed in the ASD sub-phenotypes. Our findings showed associations between transposable elements and cerebellar abnormalities in ASD, particularly in distinct phenotypic subgroups. Further investigations using appropriate models are warranted to elucidate the structural and functional implications of LINE-1 and Alu elements in ASD neuropathology.

Post-transcriptional and translational regulation of plant gene expression by transposons

Transposons are mobile DNA sequences that can move within the genome and integrate in new genomic locations. They are widespread in eukaryotes and prokaryotes and can influence gene expression when landing within or nearby a gene. Although transposon-induced regulation of gene expression at the transcriptional level has been extensively studied, there has been less focus on regulation at the post-transcriptional and translational levels. Recent studies in maize (Zea mays) and other plant species suggest that transposon insertions can affect RNA processing, RNA stability, protein translation and protein stability. We will describe the diverse mechanisms by which transposons can influence gene expression at the post-transcriptional and translational levels, and discuss the interactions between these mechanisms.

Genetic features and genomic targets of human KRAB-zinc finger proteins

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on close to a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.

An update on post-transcriptional regulation of retrotransposons

Retrotransposons, including LINE-1, Alu, SVA, and endogenous retroviruses, are one of the major constituents of human genomic repetitive sequences. Through the process of retrotransposition, some of them occasionally insert into new genomic locations by a copy-paste mechanism involving RNA intermediates. Irrespective of de novo genomic insertions, retrotransposon expression can lead to DNA double-strand breaks and stimulate cellular innate immunity through endogenous patterns. As a result, retrotransposons are tightly regulated by multi-layered regulatory processes to prevent the dangerous effects of their expression. In recent years, significant progress was made in revealing how retrotransposon biology intertwines with general post-transcriptional RNA metabolism. Here, I summarize current knowledge on the involvement of post-transcriptional factors in the biology of retrotransposons, focusing on LINE-1. I emphasize general RNA metabolisms such as methylation of adenine (m⁶ A), RNA 3'-end polyadenylation and uridylation, RNA decay and translation regulation. I discuss the effects of retrotransposon RNP sequestration in cytoplasmic bodies and autophagy. Finally, I summarize how innate immunity restricts retrotransposons and how retrotransposons make use of cellular enzymes, including the DNA repair machinery, to complete their replication cycles.