A5003086706- CRISPR and Genetic Engineering
- Genetics, Aging, and Longevity in Model Organisms
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- MicroRNA in disease regulation
- RNA Interference and Gene Delivery
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Plant Virus Research Studies
- Advanced biosensing and bioanalysis techniques
- Plant Reproductive Biology
- Genomics and Phylogenetic Studies
- Photosynthetic Processes and Mechanisms
- Plant nutrient uptake and metabolism
- Plant and Fungal Interactions Research
- Insurance, Mortality, Demography, Risk Management
- Plant Stress Responses and Tolerance
- Plant Disease Resistance and Genetics
- Selenium in Biological Systems
- Cancer-related molecular mechanisms research
- Animal Genetics and Reproduction
- RNA regulation and disease
- Energy and Environment Impacts
- Epigenetics and DNA Methylation
Colorado State University
2015-2025
Harvard University
2011-2013
Massachusetts General Hospital
2011-2013
Oregon State University
2006-2012
Stanford University
2012
Stanford Medicine
2012
The University of Tokyo
2010
Institut des Sciences des Plantes de Montpellier
2008
Biocom
2007
Summary AUXIN RESPONSE FACTORS (ARFs) are transcription factors involved in auxin signal transduction during many stages of plant growth development. ARF10 , ARF16 and ARF17 targeted by microRNA160 (miR160) Arabidopsis thaliana . Here, we show that negative regulation miR160 plays important roles seed germination post‐germination. Transgenic plants expressing an miR160‐resistant form which has silent mutations the miRNA target site (termed mARF10 ), exhibited developmental defects such as...
MicroRNAs and trans -acting siRNAs (ta-siRNAs) have important regulatory roles in development. Unlike other developmentally molecules, small RNAs are not known to act as mobile signals during Here, we show that low-abundant, conserved ta-siRNAs, termed tasiR-ARFs, move intercellularly from their defined source of biogenesis on the upper (adaxial) side leaves lower (abaxial) create a gradient patterns abaxial determinant AUXIN RESPONSE FACTOR3. Our observations ramifications for function...
Abstract In RNA-directed silencing pathways, ternary complexes result from small RNA-guided ARGONAUTE (AGO) associating with target transcripts. Target transcripts are often silenced through direct cleavage (slicing), destabilization slicer-independent turnover mechanisms, and translational repression. Here, wild-type active-site defective forms of several Arabidopsis thaliana AGO proteins involved in posttranscriptional were used to examine functions, including RNA binding, interaction RNA,...
RNA silencing can be initiated by endogenous or exogenously delivered siRNAs. In Caenorhabditis elegans, guided primary siRNAs is inefficient and therefore requires an siRNA amplification step involving RNA-dependent polymerases (RdRPs). Many factors involved in localize to protein- RNA-rich nuclear pore-associated P granules the germline, where they are thought surveil mRNAs as exit nucleus. Mutator class genes required for siRNA-mediated both germline somatic cells, but their specific...
MicroRNA (miRNA)-guided cleavage initiates entry of primary transcripts into the transacting siRNA (tasiRNA) biogenesis pathway involving RNA-DEPENDENT RNA POLYMERASE6, DICER-LIKE4, and SUPPRESSOR OF GENE SILENCING3. Arabidopsis thaliana TAS1 TAS2 families yield tasiRNA that form through miR173-guided initiation–cleavage target several encoding pentatricopeptide repeat proteins unknown function. Here, TAS1c locus was modified to produce synthetic (syn) an endogenous transcript PHYTOENE...
Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements animals. In Caenorhabditis elegans , mutator ( mut ) class genes mediate siRNA-guided repression of transposons as well exogenous RNAi, but their endogenous RNA pathways are not well-understood. To characterize the small RNAs dependent on genes, populations from a null allele mut-16 regulatory mg461 that disables only somatic RNAi were subjected to deep sequencing. Additionally,...
Transacting siRNA (tasiRNA) biogenesis in Arabidopsis is initiated by microRNA (miRNA) –guided cleavage of primary transcripts. In the case TAS3 tasiRNA formation, ARGONAUTE7 (AGO7)–miR390 complexes interact with transcripts at two sites, resulting recruitment RNA-DEPENDENT RNA POLYMERASE6 for dsRNA biosynthesis. An extensive screen mutants specific defects or function was done. This yielded numerous ago7 mutants, one dcl4 mutant, and that accumulated low levels miR390. A direct genome...
Small RNAs—including piRNAs, miRNAs, and endogenous siRNAs—bind Argonaute proteins to form RNA silencing complexes that target coding genes, transposons, aberrant RNAs. To assess the requirements for siRNA formation activity in Caenorhabditis elegans, we developed a GFP-based sensor 22G siR-1, one of set abundant siRNAs processed from precursor mapping X chromosome, X-cluster. Silencing is also dependent on partially complementary, unlinked 26G siR-O7 siRNA. We show acts trans initiate The...
The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA populations. However, these have been limited by several factors, including representational artifacts and lack established statistical analysis. Furthermore, massive HTS data sets present new problems related processing mapping a reference genome. Here, we show that cluster-based sequencing-by-synthesis technology is highly reproducible as quantitative profiling tool for...
Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory found in fungi, plants, and animals. Some endogenous siRNAs required to silence transposons or function chromosome segregation; however, the specific roles most unclear. The helicase gene eri-6/7 was identified nematode Caenorhabditis elegans by enhanced response exogenous double-stranded (dsRNAs) null mutant. encodes homologous RNA factors Armitage Drosophila, SDE3 Arabidopsis, Mov10 humans. Here we show...
Abstract Piwi-interacting RNAs (piRNAs) and small interfering (siRNAs) are distinct classes of required for proper germline development. To identify the roles piRNAs siRNAs in regulating gene expression Caenorhabditis elegans, we subjected mRNAs from gonads piRNA siRNA defective mutants to high-throughput sequencing. We show that an abundant class known as WAGO-class 22G-RNAs spermatogenic oogenic genes. also broadly transposon silencing, whereas largely dispensable. piRNAs, however, have a...
piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, piRNA target genes is mediated by mutator complex, which synthesizes high levels siRNAs through activity an RNA-dependent RNA polymerase. However, steps between mRNA recognition pathway siRNA amplification complex are unknown. Here, we identify Tudor domain protein, SIMR-1, as acting downstream production upstream complex-dependent biogenesis. Interestingly, SIMR-1 also localizes...
Caenorhabditis elegans contains 25 Argonautes, of which, ALG-1 and ALG-2 are known to primarily interact with miRNAs. ALG-5 belongs the AGO subfamily Argonautes that includes ALG-2, but its role in small RNA pathways is unknown. We analyzed by high-throughput sequencing RNAs associated ALG-5, as well changes mRNA expression alg-5, alg-1 alg-2 mutants. show defines a distinct branch miRNA pathway affecting genes involved immunity, defense, development. In contrast which associate most miRNAs...
Abstract A major challenge to our understanding of translational control has been deconvolving the individual impact specific regulatory factors have on complex dynamics mRNA translation. MicroRNAs (miRNAs), for example, guide Argonaute and associated proteins target mRNAs, where they direct gene silencing in multiple ways that are not well understood. To better deconvolve these dynamics, we developed technology directly visualize quantify human Argonaute2 (Ago2) translation subcellular...
The nematode Caenorhabditis elegans contains each of the broad classes eukaryotic small RNAs, including microRNAs (miRNAs), endogenous small-interfering RNAs (endo-siRNAs), and piwi-interacting (piRNAs). To better understand evolution these regulatory we deep-sequenced from C. three closely related nematodes: briggsae , remanei brenneri . results reveal a fluid landscape RNA pathways with essentially no conservation individual sequences aside subset miRNAs. We identified 54 miRNA families...
RNA interference (RNAi) mediates antiviral defense in many eukaryotes. Caenorhabditis elegans mutants that disable RNAi are more sensitive to viral infection. Many enhance have also been identified; these mutations may reveal genes normally down-regulated defense. About one-third of the score synMuv B genes, identified 30 years ago unrelated screens for increased growth factor signaling. encode dREAM complex chromatin-regulatory proteins found nearly all animals and plants. We show mRNAs...
Piwi-interacting RNAs (piRNAs) regulate many biological processes through mechanisms that are not fully understood. In Caenorhabditis elegans, piRNAs intersect the endogenous RNA interference (RNAi) pathway, involving a distinct class of small called 22G-RNAs, to gene expression in germline. absence piRNAs, 22G-RNA production from genes is reduced, pointing role for facilitating RNAi. Here, however, we show gain, rather than lose, 22G-RNAs which some instances coincident with silencing....