A5001630082- RNA Research and Splicing
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Breast Cancer Treatment Studies
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- Breast Lesions and Carcinomas
- MRI in cancer diagnosis
- Nuclear Structure and Function
- Cancer Diagnosis and Treatment
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Breast Implant and Reconstruction
- Single-cell and spatial transcriptomics
- Ultrasound and Hyperthermia Applications
- CRISPR and Genetic Engineering
- Cancer Research and Treatments
- DNA and Nucleic Acid Chemistry
- Bacterial Genetics and Biotechnology
- Gene expression and cancer classification
- RNA regulation and disease
- Extracellular vesicles in disease
- Bone health and treatments
- Multiple and Secondary Primary Cancers
- Obstructive Sleep Apnea Research
Friedrich Miescher Institute
2015-2023
Sophia Genetics (Switzerland)
2020-2021
Cardiff and Vale University Health Board
2021
University of Edinburgh
2012-2018
Queen's University
2018
Wellcome Trust
2015-2018
Kingston General Hospital
2017-2018
European Bioinformatics Institute
2015-2018
London Health Sciences Centre
2014-2018
NOSM University
2017-2018
Highlights•mESCs grown in three different conditions show distinct transcriptomes•Global intercellular variation is at similar levels all conditions•2i and a2i maintain pluripotency with metabolic variation•Correlation analysis identifies additional network genesSummaryEmbryonic stem cell (ESC) culture are important for maintaining long-term self-renewal, they influence cellular state. Here, we report single RNA-sequencing of mESCs cultured conditions: serum, 2i, the alternative ground state...
Eukaryotic genomes generate a heterogeneous ensemble of mRNAs and long noncoding RNAs (lncRNAs). LncRNAs are both transcribed by Pol II acquire 5' caps poly(A) tails, but only translated into proteins. To address how these classes distinguished, we identified the transcriptome-wide targets 13 RNA processing, export, turnover factors in budding yeast. Comparing maturation pathways lncRNAs revealed that transcript fate is largely determined during 3' end formation. Most targeted for nuclear...
SummaryThe exosome plays major roles in RNA processing and surveillance but the vivo target range substrate acquisition mechanisms remain unclear. Here we apply crosslinking (CRAC) to nucleases (Rrp44, Rrp6), two structural subunits (Rrp41, Csl4) a cofactor (Trf4) of yeast exosome. Analysis wild-type Rrp44 catalytic mutants showed that both CUT SUT classes non-coding RNA, snoRNAs and, most prominently, pre-tRNAs other Pol III transcripts are targeted for oligoadenylation degradation....
RNA decay is crucial for mRNA turnover and surveillance misregulated in many diseases. This complex system challenging to study, particularly mammals, where it remains unclear whether pathways perform specialized versus redundant roles. Cytoplasmic links translation are enigmatic. By directly profiling factor targets normal aberrant mouse embryonic stem cells (mESCs), we uncovered extensive pathway specialization crosstalk with translation. XRN1 (5′-3′) mediates cytoplasmic bulk whereas...
Article10 June 2016Open Access Transparent process Strand-specific, high-resolution mapping of modified RNA polymerase II Laura Milligan Wellcome Trust Centre for Cell Biology, University Edinburgh, UK Search more papers by this author Vân A Huynh-Thu School Informatics, Department Electrical Engineering and Computer Science, Liège, Belgium Clémentine Delan-Forino Alex Tuck Friedrich Miescher Institute Biomedical Research, Basel, Switzerland European Molecular Biology Laboratory,...
TRIM71/LIN-41, a phylogenetically conserved regulator of development, controls stem cell fates. Mammalian TRIM71 exhibits both RNA-binding and protein ubiquitylation activities, but the functional contribution either activity relevant primary targets remain poorly understood. Here, we demonstrate that shapes transcriptome mouse embryonic cells (mESCs) predominantly through its activity. We reveal binds 3′ untranslated region (UTR) hairpin motifs it acts by target degradation. mutations...
Eukaryotic genomes produce RNAs lacking protein-coding potential, with enigmatic roles. We integrated three approaches to study large intervening noncoding RNA (lincRNA) gene functions. First, we profiled mouse embryonic stem cells and neural precursor at single-cell resolution, revealing lincRNAs expressed in specific cell types, subpopulations, or cycle stages. Second, assembled a transcriptome-wide atlas of nuclear lincRNA degradation by identifying targets the exosome cofactor Mtr4....
Yeast Npl3 is a highly abundant, nuclear-cytoplasmic shuttling, RNA-binding protein, related to metazoan SR proteins. Reported functions of include transcription elongation, splicing and RNA 3’ end processing. We used UV crosslinking analysis cDNA (CRAC) map precise binding sites, strand-specific tiling arrays look at the effects loss on all transcripts across genome. found that binds diverse species, both coding non-coding, sites indicative roles in early pre-mRNA processing formation....
Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding their functional features or mechanisms action is currently lacking. Here we study Meteor, lncRNA transcribed near the gene encoding EOMES, pleiotropic transcription factor various processes throughout development and adult tissues. Using wide array perturbation techniques, show that elongation through Meteor locus required for Eomes activation mouse embryonic stem cells, with...
Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these very difficult to follow in vivo. In consequence, pre-ribosome structure composition have largely been inferred from purified analyzed vitro. Here we describe techniques for kinetic analyses of the living cells Saccharomyces cerevisiae. To allow this, vivo probing by DMS modification was combined with affinity purification newly synthesized 20S pre-rRNA over...
Numerous links exist between co-transcriptional RNA processing and the transcribing RNAPII. In particular, pre-mRNA splicing was reported to be associated with slowed RNAPII elongation. Here, we identify a site of ubiquitination (K1246) in catalytic subunit close DNA entry path. Ubiquitination increased absence Bre5-Ubp3 ubiquitin protease complex. Bre5 binds vivo, preference for exon 2 regions intron-containing pre-mRNAs poly(A) proximal sites. Ubiquitinated showed similar enrichment. The...
While the activity of multiprotein complexes is crucial for cellular metabolism, little known about mechanisms that collectively control expression their components. Here, we investigate regulations targeting biogenesis nuclear pore complex (NPC), macromolecular assembly mediating nucleocytoplasmic exchanges. Systematic analysis RNA-binding proteins interactomes, together with in vivo and vitro assays, reveal a subset NPC mRNAs are specifically bound by Hek2, yeast hnRNP K-like protein....
We have examined the kinetics of triple helix formation oligonucleotides that contain nucleotide analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine (bis-amino-U, BAU), which forms very stable base triplets with AT. Triplex stability is determined by both number and location modifications. BAU-containing generate triplexes extremely slow kinetics, as evidenced 14 degrees C hysteresis between annealing melting profiles even when heated at a rate 0.2 min(-1). The association were...
The RNA component of signal recognition particle (SRP) is transcribed by polymerase III, and most steps in SRP biogenesis occur the nucleolus. Here, we examine processing quality control yeast (scR1). In common with other pol III transcripts, scR1 terminates a U-tract, mature retains U4–5 sequence at its 3′ end. cells lacking exonuclease Rex1, longer U5–6 tail that presumably represents primary transcript. U-tract protected from aberrant La homologue, Lhp1 overexpressed apparently competes...
PURPOSE The ability of next-generation sequencing (NGS) assays to interrogate thousands genomic loci has revolutionized genetic testing. However, translation the clinic is impeded by false-negative results that pose a risk patients. In response, regulatory bodies are calling for reliability measures be reported alongside NGS results. Existing methods estimate do not account sample- and position-specific variability, which can significant. Here, we report an approach computes metrics every...
Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing U1 snRNA with a 5′ splice site (5′SS). In mammals, many contain weak 5′SSs that are not efficiently recognized the canonical snRNP, suggesting alternative mechanisms exist. Here, we develop cross-linking immunoprecipitation coupled high-throughput sequencing method, BCLIP-seq, identify NRDE2 (nuclear RNAi-defective 2), and CCDC174 (coiled-coil domain-containing 174) as novel...