Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypomethylated plants. It is, however, well-known that TEs can also be active in the soma, although the high-confidence detection of somatic events has been challenging. Here, we leveraged the high accuracy of PacBio HiFi long reads to evaluate the somatic mobility of TEs in individuals of an A. thaliana non-reference strain lacking activity of METHYLTRANSFERASE1 (MET1), a major component of the DNA methylation maintenance machinery. Most somatically mobile families coincided with those found in germline studies of hypomethylated genotypes, although the exact TE copies differed. We also discovered mobile elements that had been missed by standard TE annotation methods. Somatic TE activity was variable among individual plants, but also within TE families. Finally, our approach pointed to the possible involvement of alternative transposition as a cause for somatic hypermutability in a region that contains two closely spaced VANDAL21 elements. We conclude that long-read sequencing can reveal widespread TE transposition in the soma of A. thaliana hypomethylated mutants. Assessing somatic instead of germline mobilization is a fast and reliable method to investigate different aspects of TE mobility at the single plant level. ### Competing Interest Statement D.W. holds equity in Computomics, which advises plant breeders. D.W. also consults for KWS SE, a globally active plant breeder and seed producer. The other authors declare no competing interests.
The rise of the annual average temperature presents a strong selection pressure for many species. Sessile organisms, such as the plant Arabidopsis thaliana (A. thaliana), need to adapt to elevated temperatures. Here, we conducted a mutation accumulation experiment in A. thaliana under high temperature to monitor genetic changes over nine generations in three parallel lines compared to three lines under normal growth conditions. Whole-genome sequencing of every sample allowed us to accurately capture mutations in troublesome regions by utilizing the genotypes of both parent and offspring. Our approach revealed that high temperature treatment disproportionally increased the rate of insertions and deletions in dimeric short tandem repeats (STRs) compared to the rate of single nucleotide variants. Recurrent mutations appeared more often than expected, indicating a mutation bias along the genome sequence. Our study sheds light on the mutational landscape of a plant genome when exposed to high temperature stress and points to STRs as key genomic elements that rapidly increase the standing genetic variation available for natural selection. ### Competing Interest Statement The authors have declared no competing interest.
How tiny algae shaped the #evolution of giant clams https://phys.org/news/2025-01-tiny-algae-evolution-giant-clams.html https://www.nature.com/articles/s42003-024-07423-8
"T. maxima have evolved more genes for sensors to distinguish friendly #algae from harmful #bacteria, #viruses... it has tuned down some of its immune genes in a way that likely helps the #animals tolerate #microbes... As a result of the weakened #ImmuneSystem, its genome contains a large number of #TransposableElements left behind by viruses. These aspects highlight the tradeoffs of #symbiosis"
Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human developmental programs is lacking, in part due to the challenges associated with specific profiling and manipulation of human L1 expression. Here we show that thousands of hominoid-specific L1 integrants are expressed in human induced pluripotent stem cells and cerebral organoids. The activity of individual L1 promoters is surprisingly divergent and correlates with an active epigenetic state. Efficient on-target CRISPRi silencing of L1s revealed nearly a hundred co-opted L1-derived chimeric transcripts and L1 silencing resulted in changes in neural differentiation programs and reduced cerebral organoid size. Together, these data implicate L1s and L1-derived transcripts in hominoid-specific CNS developmental processes. ### Competing Interest Statement The authors have declared no competing interest.
Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing
#TransposableElements #Retrotransposons #Silencing #HuSH #LINE-1
The study identifies HuSH2, a paralogous complex to HuSH, centered around TASOR2, and distinct in its genomic localization and function. HuSH represses LINE-1 retrotransposons, while HuSH2 regulates interferon signaling genes.
De novo gene birth from non-genic sequence has received considerable attention due to the widespread occurrence of genes that are unique to particular species. This study shows that within the short evolutionary timescale of the iconic E. coli LTEE experiment, the co-option of promoters, principally from transposable elements, serves as the major source of raw material for new genes.
Gonadal sex determination in mice is a complex and dynamic process, crucial for the development of functional reproductive organs. The expression of genes involved in this process is regulated by a variety of genetic and epigenetic mechanisms. Recently, there has been increasing evidence that transposable elements (TEs), which are a class of mobile genetic elements, play a significant role in regulating gene expression during embryogenesis and organ development. In this study, we aimed to investigate the involvement of TEs in the regulation of gene expression during mouse embryonic gonadal development. Through bioinformatic analysis, we aimed to identify and characterize specific TEs acting as regulatory elements for sex-specific genes, as well as their potential mechanisms of regulation. We identified TE loci expressed in a time-and sex-specific manner along fetal gonad development that correlate positively and negatively with nearby gene expression, suggesting that their expression is integrated to the gonadal regulatory network. Moreover, chromatin accessibility and histone post-transcriptional modification analyses in the differentiating supporting cells revealed that TEs are acquiring sex-specific signature for promoter-, enhancer-, and silencer-like elements with some of them being proximal to critical sex determining genes. Altogether, our study introduces TEs as new potential players of the gene regulatory network controlling gonadal development in mammals.
Amelia Cervera 🧬
MOBOT Museum
Lukas VFN 🇪🇺
PLOS Biology
Isabelle Stévant