A5055424418- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Engineering and Material Science Research
- CRISPR and Genetic Engineering
- Cancer-related gene regulation
- Smart Materials for Construction
- Epigenetics and DNA Methylation
- Advanced biosensing and bioanalysis techniques
- Fungal and yeast genetics research
- Gene Regulatory Network Analysis
- Ubiquitin and proteasome pathways
- Head and Neck Cancer Studies
- Cancer Diagnosis and Treatment
- Ferroptosis and cancer prognosis
- Lung Cancer Treatments and Mutations
- Enzyme Structure and Function
- Redox biology and oxidative stress
- Plant Gene Expression Analysis
- Nuclear Structure and Function
- Histone Deacetylase Inhibitors Research
- Cancer-related Molecular Pathways
- Protein Structure and Dynamics
- Glycosylation and Glycoproteins Research
University of Oxford
2014-2020
Ludwig Cancer Research
2020
Daresbury Laboratory
2010
University of Cambridge
2010
Science and Technology Facilities Council
2010
RNA polymerase II (Pol2) movement through chromatin and the co-transcriptional processing fate of nascent transcripts is coordinated by transcription elongation factors (TEFs) such as polymerase-associated factor 1 (Paf1), but it not known whether TEFs have gene-specific functions. Using strand-specific nucleotide resolution techniques, we show that levels Paf1 on Pol2 vary between genes, are controlled dynamically environmental via promoters, reflect export encoded transcript. High promote...
Genes from yeast to mammals are frequently subject non-coding transcription of their antisense strand; however the genome-wide role for remains elusive. As influences chromatin structure, we took a approach assess which features associated with nascent transcription, and contrast these sense transcription. We describe distinct architecture at promoter gene body specifically marked by reduced H2B ubiquitination, H3K36 H3K79 trimethylation increased levels H3 acetylation, remodelling enzymes,...
Antisense transcription is widespread in genomes. Despite large differences gene size and architecture, we find that yeast human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature related to biological function for transcription. Using quantitative RNA-FISH, observed changes sense transcript distributions nuclei cytoplasm as levels were altered. To determine the mechanistic underlying these distributions, developed mathematical...
Gene transcription responds to stress and metabolic signals optimize growth survival. Histone H3 (H3) lysine 4 trimethylation (K4me3) facilitates state changes, but how levels are coordinated with the environment is unclear. Here, we show that isomerization of at alanine 15-proline 16 (A15-P16) peptide bond influenced by 14 (K14) controls gene-specific K4me3 balancing actions Jhd2, demethylase, Spp1, a subunit Set1 K4 methyltransferase complex. Acetylation K14 favors A15-P16trans...
In yeast, many tandemly arranged genes show peak expression in different phases of the metabolic cycle (YMC) or carbon sources, indicative regulation by a bi-modal switch, but it is not clear how these switches are controlled. Using native elongating transcript analysis (NET-seq), we that transcription itself component switches, facilitating reciprocal gene clusters. HMS2, encoding growth-regulated factor, between sense- antisense-dominant states also coordinate up- and down-regulation at...
CRISPRi, an adapted CRISPR-Cas9 system, is proposed to act as a strand-specific roadblock repress transcription in eukaryotic cells using guide RNAs (sgRNAs) target catalytically inactive Cas9 (dCas9) and offers alternative genetic interventions for studying pervasive antisense transcription. Here, we successfully use click chemistry construct DNA templates sgRNA expression show, rather than acting simply roadblock, sgRNA/dCas9 binding creates environment that permissive...
Abstract H3K4me3 is a near-universal histone modification found predominantly at the 5’ region of genes, with well-documented association gene activity. has been ascribed roles as both an instructor expression and also downstream consequence expression, yet neither convincingly proven on genome-wide scale. Here we test these relationships using combination bioinformatics, modelling experimental data from budding yeast in which levels have massively ablated. We find that loss no effect...
ABSTRACT CRISPRi, an adapted CRISPR-Cas9 system, is proposed to act as a strand-specific roadblock repress transcription in eukaryotic cells using guide RNAs (sgRNAs) target catalytically inactive Cas9 (dCas9) and offers alternative genetic interventions for studying pervasive antisense transcription. Here we successfully use click chemistry construct DNA templates sgRNA expression show, rather than acting simply roadblock, binding of sgRNA/dCas9 creates environment that permissive...
Abstract Antisense transcription is widespread in genomes. Despite large differences gene size and architecture, we find that yeast human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature related to biological function for transcription. Using quantitative RNA-FISH, observed changes sense transcript distributions nuclei cytoplasm as levels were altered. To determine the mechanistic underlying these distributions, developed...