Biology subjects

Sil, S.

Publications and source records attributed to Sil, S..

4 recordsLinked to original sources

bioRxiv2024

LINE-1 ribonucleoprotein complexes bind DNA to enable nuclear entry during mitosis

Long Interspersed Nuclear Element-1 (LINE-1) is an autonomous retrotransposon that makes up a significant portion of the human genome, contributing to genetic diversity and genome evolution. LINE-1 encodes two proteins, ORF1p and ORF2p, both essential for successful retrotransposition. ORF2p has endonuclease and reverse transcription activity, while ORF1p binds RNA. Many copies of ORF1p assemble onto the LINE-1 RNA to form a ribonucleoprotein complex (RNP). However, the functional role of RNPs in the LINE-1 life cycle is unclear. Using reconstitution assays on DNA curtains, we show that L1 RNPs gain DNA binding activity only when RNA is super-saturated with ORF1p. In cells, L1 RNPs bind to chromosomes during mitosis. Mutational analysis reveals that DNA binding is crucial for nuclear entry and LINE-1 retrotransposition activity. Thus, a key function of ORF1p is to form an RNP that gains access to the genome through DNA binding upon nuclear envelope breakdown.

biophysics↗

bioRxiv2023

Effects of habitat and fruit scent on the interactions between short-tailed fruit bats and Piper plants

Piper is a mega-diverse genus of pioneer plants that contributes to the maintenance and regeneration of tropical forests. With deforestation and climate change threatening forest ecosystems, understanding the mutualism between Piper and its seed dispersers becomes especially important. In the Neotropics, Carollia bats use olfaction to forage for Piper fruit and are a main disperser of Piper seeds via consumption and subsequent defecation during flight. In return, Piper fruits provide essential nutrients for Carollia year-round. There is evidence that the types and diversity of Piper frugivores are influenced by the primary habitat of different Piper species (forest, gap), with forest Piper depending more on bats for seed dispersal; however, this pattern has not been tested broadly. We aimed to characterize and compare the interactions between Carollia and Piper across forested and gap habitats, and further investigate whether differences in fruit traits relevant to bat foraging (i.e., scent) could underlie differences in Carollia-Piper interactions. We collected nightly acoustic ultrasonic recordings and 24h camera trap data in La Selva, Costa Rica across 12 species of Piper (6 forest, 6 gap) and integrated this information with data on Carollia diet and Piper fruit scent. Merging biomonitoring modalities allowed us to characterize ecological interactions in a hierarchical manner: from general activity and presence of bats, to visitations and inspections of plants, to acquisition and consumption of fruits. We found significant differences in Carollia-Piper interactions between forested and gap habitats; however, the type of biomonitoring modality (camera trap, acoustics, diet) influenced our ability to detect these differences. Forest Piper were exclusively visited by bats, whereas gap Piper had a more diverse suite of frugivores; the annual diet of Carollia, however, is dominated by gap Piper since these plants produce fruit year-round. We found evidence that fruit scent composition significantly differs between forest and gap Piper, which highlights the possibility that bats could be using chemical cues to differentially forage for gap versus forest Piper. By integrating studies of Piper fruit scent, plant visitation patterns, and Carollia diet composition, we paint a clearer picture of the ecological interactions between Piper and Carollia, and plant-animal mutualisms more generally.

ecology↗

bioRxiv2022

Condensation of LINE-1 is required for retrotransposition

LINE-1 (L1) is the only autonomously active retrotransposon in the human genome, and accounts for 17% of the human genome. The L1 mRNA encodes two proteins, ORF1p and ORF2p. ORF1p is a homotrimeric RNA-binding protein that plays a critical role in assembling functional L1 ribonucleoprotein (RNP) complexes. Here we show that condensation of ORF1p is required for L1 retrotransposition. Using a combination of biochemical reconstitution and live-cell imaging, we demonstrate that RNA binding, electrostatic interactions, and trimer conformational dynamics together tune the properties of ORF1p assemblies to allow for efficient L1 condensate formation in cells. Furthermore, we directly relate the dynamics of ORF1p assembly to the ability to complete the entire retrotransposon life-cycle. Mutations that prevented ORF1 condensation led to loss of retrotransposition activity, while orthogonal restoration of coiled-coil conformational flexibility rescued both condensation and retrotransposition. Based on these observations, we propose that ORF1p oligomerization on L1 RNA drives the formation of a dynamic L1 condensate that is essential for retrotransposition.

cell biology↗

bioRxiv2019

Comprehensive scanning mutagenesis of human retrotransposon LINE-1 identifies motifs essential for function

Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only autonomous active transposable element in the human genome. The L1-encoded proteins ORF1p and ORF2p enable the element to jump from one locus to another via a \"copy and paste\" mechanism. ORF1p is an RNA-binding protein and ORF2p has endonuclease and reverse transcriptase activities. The huge number of truncated L1 remnants in the human genome suggests that the host has likely evolved mechanisms to prevent full L1 replication and thereby decrease the proliferation of active elements and reduce the mutagenic potential of L1. In turn, L1 appears to have a minimized length to increase the probability of successful full-length replication. This streamlining would be expected to lead to high information density. Here, we describe the construction and initial characterization of a library of 538 consecutive trialanine substitutions that scan along ORF1p and ORF2p to identify functionally important regions. In accordance with the streamlining hypothesis, retrotransposition was overall very sensitive to mutations in ORF1p and ORF2p, only 16% of trialanine mutants retained near-wild-type activity. All ORF1p mutants formed near-wild-type levels of mRNA transcripts and seventy-five percent formed near-wild-type levels of protein. Two ORF1p mutants present a unique nucleolar-relocalization phenotype. Regions of ORF2p that are sensitive to mutagenesis, but lack phylogenetic conservation were also identified. We provide comprehensive information on the regions most critical to retrotransposition. This resource will guide future studies of intermolecular interactions that form with RNA, proteins and target DNA throughout the L1 life cycle.

genetics↗