Sydney RNA Salon

The Sydney RNA salon is co-organised by the Weatheritt lab at the Garvan Institute, the Wong lab at the Centenary Institute, and the Voineagu lab at UNSW.

We meet bi-monthly and discuss all things RNA. If you would like to join, please email 
sydneyrnaclub@gmail.com. Find us on twitter @RnaSalon. 

 


Next meeting:

Date: December 10th 2019

Location: Centenary

Guest Speaker: Dr. John Marioni (European Bioinformatics Institute, EMBL)
Title: Understanding cell fate decisions with single cell genomics
BiographyFollowing undergraduate training in mathematics and statistics, John Marioni read for a PhD in computational under the supervision of Simon Tavaré at the University of Cambridge. As a postdoc, under the supervision of Matthew Stephens at the University of Chicago, he developed approaches for analysing data generated using RNA-sequencing in the context of comparative genomics. In 2010, he started his own research group at the EMBL-European Bioinformatics Institute and, in 2015, he received a joint appointment as a Senior Group Leader at the CRUK Cambridge Institute. His group are interested in developing methods to better understand cell fate decisions in the context of normal development and cancer and, in particular, have focused on data generated using single cell genomics technologies

Guest Speaker: Dr. Gyorgy Hutvagner (University of Technology, Sydney)
Title: Post-transcriptional regulation of the miRNA pathway and miRNA isoforms
BiographyDr Gyorgy Hutvagner obtained his MSc from Biotechnology and PhD from Biology in Hungary. He has completed his postdoctoral training in The Netherlands (Plant Research International, Wageningen, 1999–2001) and in the U.S. (University of Massachusetts, Medical School, 2001–2005) winning several national and international short-term and long term fellowships. He established his own research group in 2005 in Dundee with the support of the Wellcome Trust Career Development Fellowship and the European Framework 6 grant SIROCCO. He moved to the UTS in 2011 and accepted a position at the Faculty of Engineering and Information Technology. In 2011 he was awarded with the prestigious ARC Future Fellowship.

 


October 23rd 2019 @Garvan

Guest Speaker: Dr. Sandra Cooper (University of Sydney)
Title: Biophysical space constraint for spliceosome assembly - a novel mechanism causing abnormal splicing in rare disorders
SummaryA precise genetic diagnosis is the single most important step for families with genetic disorders to enable personalized and preventative medicine. In addition to genetic variants in coding regions (exons) that can change a protein sequence, abnormal pre-mRNA splicing can be devastating for the encoded protein, inducing a frame-shift or in-frame deletion/insertion of multiple residues. Non-coding variants that disrupt splicing are extremely challenging to identify. Stemming from an initial clinical discovery in two index Australian families, we define 25 families with genetic disorders caused by a class of pathogenic non-coding splice variant due to intronic deletions. These pathogenic intronic deletions spare all consensus splice motifs, though critically shorten the minimal distance between the 5′ splice-site (5′SS) and branchpoint. The mechanistic basis for abnormal splicing is due to biophysical constraint precluding U1/U2 spliceosome assembly, which stalls in A-complexes (that bridge the 5′SS and branchpoint). Substitution of deleted nucleotides with non-specific sequences restores spliceosome assembly and normal splicing; arguing against loss of an intronic element as the primary causal basis. Incremental lengthening of 5′SS-branchpoint length in our index EMD case defines 45 - 47 nt as the critical elongation enabling (inefficient) spliceosome assembly for EMD intron-5.  The 5′SS-branchpoint space constraint mechanism, not currently factored by genomic informatics pipelines, is relevant to diagnosis and precision medicine across the breadth of Mendelian disorders and cancer genomics.

Guest Speaker: Dr. Chen Davidovich (Monash University)
Title: RNA facilitates context-dependent regulation of the histone methyltransferase PRC2
Summary:  Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that maintains cell identity during development in all multicellular organisms. At the molecular level, PRC2 mark repressed genes and chromatin domains with the H3K27me3 repressive epigenetic mark. In addition to its four core subunits, PRC2 comprises multiple accessory subunits that vary in their composition during cellular differentiation and define different types of holo-PRC2 complexes. PRC2 binds to RNA with low sequence specificity [1,2] and preference to G-tracts and G-quadruplex-forming sequences [3]. The interactions between PRC2 to some of its accessory subunits increase its enzymatic activity, while RNA inhibits it. We recently mapped the RNA-binding surfaces of PRC2 and identified an RNA-binding patch within its allosteric regulatory site, adjacent to the methyltransferase centre [4]. Accordingly, RNA-mediated inhibition of PRC2 is relieved by allosteric activation using H3K27me3 histone-tail peptides. Most common types of holo-PRC2 complexes bind RNA, providing a unified model to explain how RNA and allosteric stimuli antagonistically regulate the enzymatic activity of PRC2. I will present new data from our ongoing work, revealing how RNA regulates PRC2 within the context of transcriptional regulation.


August 21st 2019 @UNSW

Guest Speaker: Dr.Ellis Patrick (University of Sydney)
Title: Deconstructing a molecular network of the aging frontal cortex
SummaryThe Accelerated Medicine Program in Alzheimer’s Disease (AMP-AD) is performing multi-level ‘omics analysis on post-mortem tissues taken from large numbers of AD patients from several large cohorts. RNA-Seq analysis of the AD brain transcriptome has the promise of providing important mechanistic clues to the molecular aetiology of AD, however, analysis of transcriptional profiling data from post mortem brain tissue is complicated because of the significant inter-individual variability in cellular composition. We examined transcriptomic profiles of bulk tissue-level profiles from the cortex of 542 subjects from the Rush Memory Aging Project (MAP) and Religious Orders Study (ROS) and evaluated several methods for predicting cell type proportions from this bulk tissue expression data. We compared these methods and used immunohistochemistry-based image analysis to demonstrated that “molecular pathology” can be used to effectively describe the proportions of neurons, astrocytes, microglia, oligodendrocytes and endothelial cells in brain tissue. Further to this, we demonstrated that these approaches can also be used to isolate cell sub-types that are associated with disease progression. Specifically, we identified a module of genes that capture the behaviour of microglia associated with both the accumulation of tau pathology and cognitive decline. These results demonstrate that by accepting that tissue-level gene expression data captures a complex cocktail of cell-type and disease relevant signal, bioinformatics approaches can be used to deconstruct and model this complexity.

Guest Speaker: Dr.Tara Roberts (Western Sydney University)
Title: Identification of co-ordinated intron retention as a novel regulatory mechanism during the LPS response in macrophages
Summary:  The response to LPS is highly dynamic yet tightly regulated. While our understanding of gene expression has expanded we have a lesser understanding of post-transcriptional regulation. We treated bone marrow derived macrophages (BMM) with LPS and performed RNA sequencing. Analysis showed significant regulation of intron retention. Intron retention is a form of alternative splicing where introns are retained in the mature poly-adenylated transcript. In mammals, intron retention predominantly acts to decrease protein expression from the intron containing transcript often via increased degradation of the transcript by the nonsense mediated decay pathway. In contrast, retention of introns can cause transcript storage in the nucleus and subsequent further splicing allows later protein expression. In BMMs intron retention was dramatically increased at 2 hours post-LPS but decreased by 6 hours. Transcripts containing retained introns were enriched for interferon-inducible genes, pathogen recognition pathways (including Caspase 1 &4, gasdermin) and negative regulation of immune responses (including PD-L1, ubiquitin ligases). These findings were validated by qPCR. We analysed intron retention in BMM defective in nonsense mediated decay but this did not alter the expression of most intron retained transcripts. This rapid burst of intron retention coupled with the lack of effect of NMD deficiency suggests that here intron retention is a mechanism to control the timing of translation of a subset of LPS induced transcripts. This work is the first to describe the regulation of intron retention as part of the innate immune response and as such reveals an additional layer of complexity to immune regulation.


June 19th  2019 @Centenary

Guest Speaker: Dr. Martin Smith (Garvan Institute of Medical Research)
Title: “Dissecting RNA Biology, One Molecule at a Time”
Summary: “High-throughput transcriptomic and epigenomic studies have substantiated the prevalence and dynamics of regulatory regions in the human genome, including the surprising diversity and contentious function of long non-coding RNAs. What additional layers of complexity can single-cell and single-molecule sequencing technologies unravel? How will the observation of native molecules in real-time improve our understanding of health and disease? I will describe genomic and computational strategies for functional transcriptome annotation, with emphasis on single molecule sequencing, epitranscriptomics, and characterisation of structural motifs in incRNAs.”
 
Guest Speaker: Dr. Rippei Hayashi (Australian National University)
Title: “Mechanism of piRNA substrate selection”
Summary: “Transposons in animals are silenced by small RNAs called piRNAs. piRNAs are produced from single-stranded precursor RNAs using dedicated biogenesis machinery. The pool of piRNAs determines the specificity of silencing, however, how the piRNA biogenesis machinery selects its substrate RNA is not well understood. We found that, in Drosophila ovarian somatic cells, the simple Uridine content of RNA determines the rate of piRNA production genome-wide. gypsy retrotransposons are the major active transposons in this tissue. Like many other retroelements, gypsy genomes are highly biased towards Adenosine, making a piRNA precursor transcript containing antisense sequences of gypsy ideal for piRNA production.”

 

April 17th 2019 @ Garvan

Guest Speaker: Dr. David Humphreys (Victor Chang Cardiac Research Institute)
Title: “Enhancing circular RNA analysis by cross examination of back and canonical forward splicing using Ularcirc”
Summary: “Circular RNAs (circRNA) are a unique class of transcripts that can only be identified from sequence alignments spanning discordant junctions, commonly referred to as backsplice junctions (BSJ). The challenges of detecting a BSJ from short read high throughput sequencing (HTS) data has steered software development to focus primarily on algorithmic methods to accurately capture BSJs. Canonical splicing is also linked with circRNA biogenesis either from the parental transcript or internal to the circRNA, and is often not considered in circRNA studies.  Here I will present Ularcirc, the first software tool that integrates the visualization of both BSJ and forward splicing junctions (FSJ) and provides downstream analysis (sequence retrieval, ORF, miRNA binding) of selected circRNA candidates. Ularcirc utilises the output of CIRI, circExplorer, or the raw chimeric output of the STAR aligner and assembles BSJ count table to allow multi-sample analysis. We have used Ularcirc to identify and characterise circRNA from public and in-house generated data sets and demonstrate how it can be used to (i) discover novel splicing patterns of parental transcripts, (ii) detect internal splicing patterns of circRNA, and (iii) reveal the complexity of BSJ formation. Furthermore, we identify circRNA that have potential open reading frames longer than their linear sequence. Finally, we have detected and validated the presence of a novel class of circRNA generated from ApoA4 transcripts whose BSJ derive from multiple non-canonical splicing sites within coding exons. Ularcirc can be accessed via https://github.com/VCCRI/Ularcirc.”

Guest speaker: Professor Jennifer Gamble (The University of Sydney - School of Medicine)
Title: “Blockmirs: A new class of oligonucleotide drugs.”
Summary: “Therapeutic targeting of miRNAs has been proposed and indeed there are some success stories. However, miRNAs can have a large number of targets with diverse activity. Classic antagomirs may therefore show non-specific activity. We have used a novel Blockmir technology, to develop a drug that inhibits a miRNA-specific target interaction. The drug, CD5-2 has profound effects in chronic inflammatory diseases.”