Clark laboratory: Transcriptomics and Neurogenetics

• 
  Head of Laboratory
  Dr Mike Clark

  michael.clark@unimelb.edu.au

  View researcher's webpage

  +61 3 9035 3669

Research Overview

We work at the intersection of genomics and neuroscience, utilising transcriptomic (RNA-Seq, Nanopore long-read sequencing, targeted RNA sequencing and single cell sequencing) and functional genomic approaches to investigate gene expression and function in the human brain and in neuropsychiatric disorders. Our laboratory has three main areas of investigation.

1. Risk genes for neuropsychiatric disorders

• Many genes in our DNA confer risk to disease, including neuropsychiatric disorders such as schizophrenia and bipolar disorder, but how they confer risk is generally unknown. We are interested in studying these genes, both protein coding and noncoding (i.e.: long noncoding RNAs) and how their expression can change to cause disease risk. We utilise both post-mortem human brain and neurons derived from induced pluripotent stem cells (iPSCs) to help answer these questions.

2. The role of gene isoforms in brain development

• Almost all human genes express multiple RNA products, (known as isoforms) through processes such as alternative splicing. Switches between isoforms play crucial roles in brain development, but we have previously lacked the technologies to systematically identify and functionally characterise the isoforms involved. Using long-read single-cell RNA sequencing approaches we helped develop, we are examining gene isoforms in stem-cell and organoid models of brain development and in-vivo.

3. Novel applications and tools for Nanopore sequencing

• We work to develop and utilise novel sequencing methods and informatic tools. Previously we co-developed targeted RNA sequencing to enable highly sensitive detection and quantification of genes of interest. More recently we have focused on utilising Nanopore sequencing, a technology that can sequence both DNA and native RNA. We are applying Nanopore sequencing to many research questions as well as developing novel applications and tools for this technology such as NanoCount, NanoSplicer and BLAZE.

In addition, we have interests in multiple aspects of RNA biology including noncoding RNAs and RNA post-transcriptional regulation.

Staff

Dr Ric De Paoli-Iseppi, Research Fellow

Shweta Joshi, PhD Student

Sefi Prawer, PhD Student

Josie Gleeson, PhD Student

Anran Li, MSc Student

Anthea Hull, MSc Student

Ching Yin (Andrew) Wan, MSc (Bioinformatics) Student

Ria Agarwal, Hons student

Manveer Chauhan, Hons student

Collaborators

Matt Richie, Walter and Eliza Hall Institute, Aus

Heejung Shim, University of Melbourne, Aus

Clare Parish, The Florey Institute of Neuroscience and Mental Health, Aus

Paul Harrison, University of Oxford, UK

Wilfried Haerty, Earlham Institute, UK

Zameel Cader, University of Oxford, UK

Daniel Weinberger, Lieber Institute for Brain Development, USA

Lachlan Coin, Doherty Institute, Aus

Christine Wells, University of Melbourne, Aus

Tony Hannan, The Florey Institute of Neuroscience and Mental Health, Aus

Funding

MRFF Early to Mid-Career Researchers (2023-2028): The missing heritability of human disease: discovery to implementation
NHMRC Investigator Grant (2021-2025): Elucidating the pathological role and predictive value of mental health disorder risk genes.
ARC Discovery Project (2020 - 2023): The role of gene isoforms in human brain development.
Brain and Behavior Foundation (2019-2020): Elucidating the Expression and Splicing of Neuropsychiatric Disease Genes in Human Brain
NHMRC CJ Martin Biomedical Fellowship (2014-2020)
MRC Research Grant (2017-2019): Brain-enriched voltage-gated calcium channel isoforms: novel, genetically informed, therapeutic targets for psychiatric disorders
Wellcome Trust Seed Award (2016-2017): Capture NanoporeSeq: A novel technique for targeted full-length transcript sequencing and gene expression analysis
EMBO Long Term Fellowship (2014-2016)

Research Publications

1. You Y, Prawer YDJ, De Paoli-Iseppi R, Hunt CPJ, Parish CL, Shim H* and Clark MB*. (2023) Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE. Genome Biol. 24: 66 (*Corresponding authors).
2. You, Y, Clark MB*, Shim H*.(2022). NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing. Bioinformatics. btac359 (*Corresponding authors).
3. Gleeson J, Leger A, Prawer YDJ, Lane TA, Harrison PJ, Haerty W, Clark MB. (2022). Accurate expression quantification from nanopore direct RNA sequencing with NanoCount. Nucleic Acids Res. 50: e19
4. Pokhilko A, Handel AE, Curion F, Volpato V, Whiteley ES, Bøstrand S, Newey SE, Akerman CJ, Webber C, Clark MB*, Bowden B*, Cader MZ*. (2021). Targeted single cell RNA-sequencing of transcription factors facilitates biological insights from human cell experimental models. Genome Res. 31: 1069-1081 (* Corresponding authors).
5. Clark MB*, Wrzesinski T*, García-Bea A, Hall NAL, Kleinman JE, Hyde T, Weinberger DR, Harrison PJ, Haerty W, Tunbridge EM. (2020) Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain. Mol Psychiatry 25: 37–47. (* Joint first authors).
6. Clark MB*, Mercer TR*, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Lê Cao K, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME (2015). Quantitative gene profiling of long-noncoding RNAs with targeted RNA sequencing. Nature Methods. 12:339- 342 (* Joint first authors).
7. Mercer TR*, Clark MB*, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS (2015). Genome-wide discovery of human splicing branchpoints. Genome Res. 25: 290-303 (* Joint first authors).
8. Mercer TR*, Clark MB*, Crawford J*, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. (2014). Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc. 9:989-1009. (* Joint first authors).
9. Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME, Mattick JS. (2012). Genome-wide analysis of long noncoding RNA stability. Genome Res. 22: 885-898.
10. Amaral PP*, Clark MB*, Gascoigne DK*, Dinger ME, Mattick JS. (2011). lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-151. (* Joint first authors).