Transposon Silencing of Small RNAs

Transposons and fragments of transposable elements make up approximately half of the human genome; mobilization of these elements can destabilize the genome and lead to disease-associated mutations. In 2003, miRNAs and siRNAs were known to silence target mRNAs, but small RNAs had not been directly linked to transposon control. In August of that year, Aravin et al. reported the developmental profile of Drosophila small RNAs by using conventional sequencing technology. These pioneering studies identified a novel class of “repeat associated” siRNAs and hypothesized that they control transposon activity and chromatin structure. It is now clear that these “rasiRNAs” bind to Piwi clade Argonaute proteins and that Piwi-interacting RNAs (piRNAs) have a conserved function in genome maintenance and germline development.This PaperPick refers to “The Small RNA Profile during Drosophila melanogaster Development” by A.A. Aravin, M. Lagos-Quintana, A. Yalcin, M. Zavolan, D. Marks, B. Snyder, T. Gaasterland, J. Meyer, and T. Tuschl, published in August 2003.Video AbstractDr. Thomas Tuschl discusses the context for the work on small RNA profiling during Drosophila development and elaborates on our current understanding of some of the classes of small RNAs originally described by Aravin et al

Rapid evolution and conserved function of the piRNA pathway

Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host-pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence

Biogenesis and germline functions of piRNAs

Small interfering RNAs and microRNAs are generated from double-stranded RNA precursors by the Dicer endonucleases, and function with Argonaute-family proteins to target transcript destruction or to silence translation. A distinct class of 24- to 30-nucleotide-long RNAs, produced by a Dicer-independent mechanism, associates with Piwi-class Argonaute proteins. Studies in flies, fish and mice implicate these Piwi-associated RNAs (piRNAs) in germline development, silencing of selfish DNA elements, and in maintaining germline DNA integrity. However, whether piRNAs primarily control chromatin organization, gene transcription, RNA stability or RNA translation is not well understood, neither is piRNA biogenesis. Here, we review recent studies of piRNA production and function, and discuss unanswered questions about this intriguing new class of small RNAs

Pareto Optimal Strategies for Event Triggered Estimation

Although resource-limited networked autonomous systems must be able to efficiently and effectively accomplish tasks, better conservation of resources often results in worse task performance. We specifically address the problem of finding strategies for managing measurement communication costs between agents. A well understood technique for trading off communication costs with estimation accuracy is event triggering (ET), where measurements are only communicated when useful, e.g., when Kalman filter innovations exceed some threshold. In the absence of measurements, agents can use implicit information to achieve results almost as well as when explicit data is always communicated. However, there are no methods for setting this threshold with formal guarantees on task performance. We fill this gap by developing a novel belief space discretization technique to abstract a continuous space dynamics model for ET estimation to a discrete Markov decision process, which scalably accommodates threshold-sensitive ET estimator error covariances. We then apply an existing probabilistic trade-off analysis tool to find the set of all optimal trade-offs between resource consumption and task performance. From this set, an ET threshold selection strategy is extracted. Simulated results show our approach identifies non-trivial trade-offs between performance and energy savings, with only modest computational effort.Comment: 8 pages, accepted to IEEE Conference on Decision and Control 202

Chance-Constrained Multi-Robot Motion Planning under Gaussian Uncertainties

We consider a chance-constrained multi-robot motion planning problem in the presence of Gaussian motion and sensor noise. Our proposed algorithm, CC-K-CBS, leverages the scalability of kinodynamic conflict-based search (K-CBS) in conjunction with the efficiency of the Gaussian belief trees used in the Belief-A framework, and inherits the completeness guarantees of Belief-A's low-level sampling-based planner. We also develop three different methods for robot-robot probabilistic collision checking, which trade off computation with accuracy. Our algorithm generates motion plans driving each robot from its initial state to its goal while accounting for the evolution of its uncertainty with chance-constrained safety guarantees. Benchmarks compare computation time to conservatism of the collision checkers, in addition to characterizing the performance of the planner as a whole. Results show that CC-K-CBS can scale up to 30 robots.Comment: Submitted to 2023 IEEE International Conference on Intelligent Robots and Systems (IROS

TEMP: a computational method for analyzing transposable element polymorphism in populations

Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate the frequencies of transposition events in the population and pinpoint junctions of high frequency transposition events at nucleotide resolution. Simulation data indicate that TEMP outperforms other algorithms such as PoPoolationTE, RetroSeq, VariationHunter and GASVPro. TEMP also performs well on whole-genome human data derived from the 1000 Genomes Project. We applied TEMP to characterize the TE frequencies in a wild Drosophila melanogaster population and study the inheritance patterns of TEs during hybrid dysgenesis. We also identified sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production. TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git. Acids Research

Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection

BACKGROUND: High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume \u3e70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Another challenge of preparing RNA-Seq libraries is to preserve the strand information of the RNAs. DESIGN: Here, we describe a procedure for preparing RNA-Seq libraries from 1 to 4 mug total RNA without poly(A) selection. Our method combines the deoxyuridine triphosphate (dUTP)/uracil-DNA glycosylase (UDG) strategy to achieve strand specificity with AMPure XP magnetic beads to perform size selection. Together, these steps eliminate gel purification, allowing a library to be made in less than two days. We barcode each library during the final PCR amplification step, allowing several samples to be sequenced in a single lane without sacrificing read length. Libraries prepared using this protocol are compatible with Illumina GAII, GAIIx and HiSeq 2000 platforms. DISCUSSION: The RNA-Seq protocol described here yields strand-specific transcriptome libraries without poly(A) selection, which provide approximately 90% mappable sequences. Typically, more than 85% of mapped reads correspond to protein-coding genes and only 6% derive from non-coding RNAs. The protocol has been used to measure RNA transcript identity and abundance in tissues from flies, mice, rats, chickens, and frogs, demonstrating its general applicability

Distinct Functions for the Drosophila piRNA Pathway in Genome Maintenance and Telomere Protection

Transposons and other selfish DNA elements can be found in all phyla, and mobilization of these elements can compromise genome integrity. The piRNA (PIWI-interacting RNA) pathway silences transposons in the germline, but it is unclear if this pathway has additional functions during development. Here we show that mutations in the Drosophila piRNA pathway genes, armi, aub, ago3, and rhi, lead to extensive fragmentation of the zygotic genome during the cleavage stage of embryonic divisions. Additionally, aub and armi show defects in telomere resolution during meiosis and the cleavage divisions; and mutations in lig-IV, which disrupt non-homologous end joining, suppress these fusions. By contrast, lig-IV mutations enhance chromosome fragmentation. Chromatin immunoprecipitation studies show that aub and armi mutations disrupt telomere binding of HOAP, which is a component of the telomere protection complex, and reduce expression of a subpopulation of 19- to 22-nt telomere-specific piRNAs. Mutations in rhi and ago3, by contrast, do not block HOAP binding or production of these piRNAs. These findings uncover genetically separable functions for the Drosophila piRNA pathway. The aub, armi, rhi, and ago3 genes silence transposons and maintain chromosome integrity during cleavage-stage embryonic divisions. However, the aub and armi genes have an additional function in assembly of the telomere protection complex

Adaptive evolution targets a piRNA precursor transcription network [preprint]

In Drosophila, transposon-silencing piRNAs are derived from heterochromatic clusters and a subset of euchromatic transposon insertions, which are transcribed from internal non-canonical initiation sites and flanking canonical promoters. Rhino binds to Deadlock, which recruits TRF2 to promote non-canonical transcription of these loci. Cuff co-localizes with Rhino and Del. The role of Cuff is less well understood, but the cuff gene shows hallmarks of adaptive evolution, which frequently targets functional interactions within host defense systems. We show that Drosophila simulans cuff is a dominant negative allele when expressed in Drosophila melanogaster, where it traps Deadlock, TRF2 and the transcriptional co-repressor CtBP in stable nuclear complexes. Cuff promotes Rhino and Deadlock localization, driving non-canonical transcription. CtBP, by contrast, suppresses canonical cluster and transposon transcription, which interferes with downstream non-canonical transcription and piRNA production. Cuff, TRF2 and CtBP thus form a network that balances canonical and non-canonical piRNA precursor transcription