José CercaJun 2

New publication out 🆕 📤

"No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts"

https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-025-00362-z

🔍 Despite rapid speciation, niche shifts, & hybridization, we found no significant TE accumulation differences across species or hybrids.
🌵 Even in arid-adapted lineages—where genome downsizing may be expected—TEs didn’t decline.
#TransposableElements #Speciation #AdaptiveRadiation #Genomics

Amelia Cervera 🧬Feb 10
Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci.
#GenomeEditing #GeneTherapy #TransposableElements
https://www.nature.com/articles/s41587-024-02137-y
Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci - Nature Biotechnology

Transgenes are inserted into human cells by 2-RNA delivery of a retroelement protein and template.

Nature
Amelia Cervera 🧬Feb 10
Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals.
#TransposableElements #SomaticTransposition #LongReads #Arabidopsis #PlantScience #Preprint
https://www.biorxiv.org/content/10.1101/2025.02.07.637047v1
Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals

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.

bioRxiv
MOBOT MuseumFeb 10
#TransposableElements A Homage to Barbara McClintock and Hopi Zea mays, artwork series by Megan Singleton in #KernelsOfCulture #MaizeAroundTheWorld
This artwork commission is sponsored by Nancy Ridenour.
megansingleton.com
Pix: Hopi Purple and Hopi Turquoise photograph series and art book, photos by Virginia Harold
Amelia Cervera 🧬Jan 31
High short tandem repeat mutation recurrence in heat-stressed Arabidopsis thaliana lines.
#TransposableElements #Arabidopsis #HeatStress #ShortTandemRepeats #Preprint
https://www.biorxiv.org/content/10.1101/2025.01.24.634728v1
High short tandem repeat mutation recurrence in heat-stressed Arabidopsis thaliana lines

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.

bioRxiv
Lukas VFN 🇪🇺Jan 28

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"

How tiny algae shaped the evolution of giant clams

Giant clams, some of the largest mollusks on Earth, have long fascinated scientists. These impressive creatures can grow up to 4.5 feet in length and weigh over 700 pounds, making them icons of tropical coral reefs.

Phys.org
Amelia Cervera 🧬Jan 26
LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development.
#TransposableElements #Retrotransposons #LINE-1 #InducedPluripotentStemCells #BrainOrganoids #Preprint
https://www.biorxiv.org/content/10.1101/2025.01.17.633315v1
LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development

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.

bioRxiv
Amelia Cervera 🧬Nov 6, 2024

Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing

#TransposableElements #Retrotransposons #Silencing #HuSH #LINE-1

https://www.nature.com/articles/s41467-024-53761-w

Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing - Nature Communications

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.

Nature
Amelia Cervera 🧬Oct 23, 2024
Transposable elements are prevalent vectors of transgenerational epigenetic inheritance in nature.
#TransposableElements #TEs #Arabidopsis #Epigenetics #Preprint
https://www.biorxiv.org/content/10.1101/2024.09.20.614076v1.full.pdf
PLOS BiologyMay 8, 2024
Where do new genes come from? @HassanZaman91 @barricklab &co show that within the timescale of the #LTEE experiment, the co-option of #promoters, mainly from #TransposableElements, serves as the major source of raw material for #DeNovoGenes #PLOSBiology https://plos.io/4a8p6DT
Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli

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.