A5004223504- Plant Molecular Biology Research
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Genetics and Neurodevelopmental Disorders
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Photosynthetic Processes and Mechanisms
- RNA Research and Splicing
- RNA regulation and disease
- Light effects on plants
- Plant Reproductive Biology
- Plant Disease Resistance and Genetics
- Genetic Mapping and Diversity in Plants and Animals
- Plant Genetic and Mutation Studies
- Wheat and Barley Genetics and Pathology
- Plant Gene Expression Analysis
University of Massachusetts Chan Medical School
2016-2022
ETH Zurich
2009-2016
University of Zurich
2009
Max Planck Institute for Developmental Biology
2009
Polycomb group (PcG) proteins are essential to maintain gene expression patterns during development. Transcriptional repression by PcG involves trimethylation of H3K27 (H3K27me3) Repressive Complex 2 (PRC2) in animals and plants. PRC1 binds H3K27me3 is required for transcriptional animals, but plants PRC1-like activities have remained elusive. One candidate protein that could be involved functions LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), because LHP1 associates with genes marked vivo has a...
In eukaryotic cells, histones are subject to a large number of posttranslational modifications whose sequential or combinatorial action affects chromatin structure and genome function. We identified acetylation at Lys-36 in histone H3 (H3K36ac) as new modification plants. The H3K36ac is evolutionary conserved seed plants, including the gymnosperm Norway spruce (Picea abies) angiosperms rice (Oryza sativa), tobacco (Nicotiana tabacum), Arabidopsis (Arabidopsis thaliana). Arabidopsis, highly...
Significance Fragile X syndrome (FXS), the most prevalent monogenic form of autism, is caused by loss FMRP, an RNA binding protein. In absence translation dysregulated, but restoration translational homeostasis rescues and thus could suggest new treatments for disorder. Using ribosome profiling metabolic profiling, we show that, in FMRP-deficient mouse brain, there are few specific disturbances. Instead, widespread imbalance levels. This destabilization FMRP targets other mRNAs based on...
Abstract Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present reference strain. An alternative are tiling arrays, previous designs have not allowed simultaneous analysis both strands on single array. We introduce AGRONOMICS1, new microarray that contains complete paths genome strands, with average one 25mer probe per 35-bp...
Abstract Background Histone variants establish structural and functional diversity of chromatin by affecting nucleosome stability histone-protein interactions. H3.3 is an H3 histone variant that incorporated into outside S-phase in various eukaryotes. In animals, associated with active transcription possibly maintenance transcriptional memory. Plant variants, which evolved independently their animal counterparts, are much less well understood. Results We profile the distribution Arabidopsis...
Despite advances in understanding the pathophysiology of Fragile X syndrome (FXS), its molecular basis is still poorly understood. Whole brain tissue expression profiles have proved surprisingly uninformative, therefore we applied single cell RNA sequencing to profile an FMRP deficient mouse model with higher resolution. We found that absence results highly type specific gene changes are strongest among neuronal types, where FMRP-bound mRNAs were prominently downregulated. Metabolic pathways...
Abstract Post‐translational chromatin modifications are an important regulatory mechanism in light signalling and circadian clock function. The regulation of diurnal transcript level changes requires fine‐tuning the expression generally active genes depending on prevailing environmental conditions. We investigated association histone H3K4me3, H3K9ac, H3K9me2, H3S10p, H3K27ac, H3K27me3 H3S28p with using immunoprecipitations followed by sequencing (ChIP‐Seq) fully expanded leaves 6 Arabidopsis...
DNA accessibility is an important layer of regulation DNA-dependent processes. Methods that measure at local and genome-wide scales have facilitated a rapid increase in the knowledge chromatin architecture animal yeast systems. In contrast, much less known about organization plants. We developed robust DNase I-polymerase chain reaction (PCR) protocol for model plant Arabidopsis (Arabidopsis thaliana). probed by digesting nuclei with gradient I followed locus-specific PCR. The reduction PCR...
Dysregulated protein synthesis is a major underlying cause of many neurodevelopmental diseases including fragile X syndrome. In order to capture subtle but biologically significant differences in translation these disorders, robust technique required. One powerful tool study translational control ribosome profiling, which based on deep sequencing mRNA fragments protected from ribonuclease (RNase) digestion by ribosomes. However, this approach has been mainly applied rapidly dividing cells...
Abstract Despite advances in understanding the pathophysiology of Fragile X syndrome (FXS), its molecular bases are still poorly understood. Whole brain tissue expression profiles have proved surprisingly uninformative. We applied single cell RNA sequencing to profile a FXS mouse model. found that results highly type specific effect and it is strongest among different neuronal types. detected downregulation mRNAs bound by FMRP this prominent neurons. Metabolic pathways including translation...
Abstract Fragile X syndrome (FXS) is caused by inactivation of the FMR1 gene and loss encoded FMRP, an RNA binding protein that represses translation some its target transcripts. Here we use ribosome profiling RNA-seq to investigate dysregulation in mouse brain cortex. We find most changes occupancy on hundreds mRNAs are largely driven transcript abundance. Many downregulated mRNAs, which mostly responsible for neuronal synaptic functions, highly enriched FMRP targets. metabolic labeling...