UNCOVERING THE ROLE OF HIDDEN GENES IN BRAIN DISORDERS
Grant number: 1072662 | Funding period: 2018 - 2020
Numerous regions in our DNA influence how likely we are to develop various diseases, including brain disorders such as Autism and Schizophrenia. However, in many of these regions no genes have been found and they appear “empty”, making it difficult to uncover what’s triggering the disease. This project will use a powerful new technology to discover new genes hidden within these supposedly “empty” regions that are important in brain disorders and investigate how they contribute to disease.
Related publications (17)
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Alexandra Pokhilko, Adam E Handel, Fabiola Curion, Viola Volpato, Emma S Whiteley, Sunniva Bostrand, Sarah E Newey, Colin J Akerman, Caleb Webber, Michael B Clark, Rory Bowden, M Zameel Cader
Single-cell RNA sequencing (scRNA-seq) is a widely used method for identifying cell types and trajectories in biologically heterog..
The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools
Xueyi Dong, Luyi Tian, Quentin Gouil, Hasaru Kariyawasam, Shian Su, Ricardo De Paoli-Iseppi, Yair David Joseph Prawer, Michael B Clark, Kelsey Breslin, Megan Iminitoff, Marnie E Blewitt, Charity W Law, Matthew E Ritchie
Application of Oxford Nanopore Technologies' long-read sequencing platform to transcriptomic analysis is increasing in popularity...
Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection
Jessie J-Y Chang, Daniel Rawlinson, Miranda E Pitt, George Taiaroa, Josie Gleeson, Chenxi Zhou, Francesca L Mordant, Ricardo De Paoli-Iseppi, Leon Caly, Damian FJ Purcell, Timothy P Stinear, Sarah L Londrigan, Michael B Clark, Deborah A Williamson, Kanta Subbarao, Lachlan JM Coin
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication..
CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice
Francesca Vacante, Julie Rodor, Mukesh K Lalwani, Amira D Mahmoud, Matthew Bennett, Azzurra L De Pace, Eileen Miller, Kim Van Kuijk, Jenny de Bruijn, Marion Gijbels, Thomas C Williams, Michael B Clark, Jessica P Scanlon, Amanda C Doran, Rusty Montgomery, David E Newby, Mauro Giacca, Donal O'Carroll, Patrick WF Hadoke, Laura Denby
[Figure: see text].
Multiomic analysis elucidates Complex I deficiency caused by a deep intronic variant in NDUFB10
Guy Helman, Alison G Compton, Daniella H Hock, Marzena Walkiewicz, Gemma R Brett, Lynn Pais, Tiong Y Tan, Ricardo De Paoli-Iseppi, Michael B Clark, John Christodoulou, Susan M White, David R Thorburn, David A Stroud, Zornitza Stark, Cas Simons
The diagnosis of Mendelian disorders following uninformative exome and genome sequencing remains a challenging and often unmet nee..
Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples
Fabiola Curion, Adam E Handel, Moustafa Attar, Giuseppe Gallone, Rory Bowden, M Zameel Cader, Michael B Clark
RNA-seq is the standard method for profiling gene expression in many biological systems. Due to the wide dynamic range and complex..
The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read tools
Xueyi Dong, Luyi Tian, Quentin Gouil, Hasaru Kariyawasam, Shian Su, Ricardo De Paoli-Iseppi, Yair David Joseph Prawer, Michael Clark, Kelsey Breslin, Megan Iminitoff, Marnie Blewitt, Charity Law, Matthew Ritchie
Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity...
RNA sequencing identifies a cryptic exon caused by a deep intronic variant in NDUFB10 resulting in isolated Complex I deficiency.
Guy Helman, Alison Compton, Daniella Hock, Marzena Walkiewicz, Gemma Brett, Lynn Pais, Tiong Tan, Ricardo De Paoli-Iseppi, Michael Clark, John Christodoulou, Susan White, David Thorburn, David Stroud, Zornitza Stark, Cas Simons
The diagnosis of mitochondrial disorders remains a challenging and often unmet need. We sought to investigate a sibling pair with ..
Exploiting the Variability of CACNA1C Splicing to Identify Novel, Brain-Selective Targets for Schizophrenia and Bipolar Disorder
Nicola Hall, Michael B Clark, Tomasz Wrzesinski, Aintzane B Garcia, Syed M Husain, Joel E Kleinman, Thomas Hyde, Daniel R Weinberger, Paul J Harrison, Wilfried Haerty, Elizabeth M Tunbridge
Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain
Michael B Clark, Tomasz Wrzesinski, Aintzane B Garcia, Nicola AL Hall, Joel E Kleinman, Thomas Hyde, Daniel R Weinberger, Paul J Harrison, Wilfried Haerty, Elizabeth M Tunbridge
RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse i..
Universal Alternative Splicing of Noncoding Exons
Ira W Deveson, Marion E Brunck, James Blackburn, Elizabeth Tseng, Ting Hon, Tyson A Clark, Michael B Clark, Joanna Crawford, Marcel E Dinger, Lars K Nielsen, John S Mattick, Tim R Mercer
The human transcriptome is so large, diverse, and dynamic that, even after a decade of investigation by RNA sequencing (RNA-seq), ..
Intergenic disease-associated regions are abundant in novel transcripts
N Bartonicek, MB Clark, XC Quek, JR Torpy, AL Pritchard, JLV Maag, BS Gloss, J Crawford, RJ Taft, NK Hayward, GW Montgomery, JS Mattick, TR Mercer, ME Dinger
BACKGROUND: Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomi..
Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage
Joshua A Betts, Mahdi Moradi Marjaneh, Fares Al-Ejeh, Yi Chieh Lim, Wei Shi, Haran Sivakumaran, Romain Tropee, Ann-Marie Patch, Michael B Clark, Nenad Bartonicek, Adrian P Wiegmans, Kristine M Hillman, Susanne Kaufmann, Amanda L Bain, Brian S Gloss, Joanna Crawford, Stephen Kazakoff, Shivangi Wani, Shu W Wen, Bryan Day
Breast cancer risk is strongly associated with an intergenic region on 11q13. We have previously shown that the strongest risk-ass..
Improved definition of the mouse transcriptome via targeted RNA sequencing
Giovanni Bussotti, Tommaso Leonardi, Michael B Clark, Tim R Mercer, Joanna Crawford, Lorenzo Malquori, Cedric Notredame, Marcel E Dinger, John S Mattick, Anton J Enright
Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage,..
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing
Michael B Clark, Tim R Mercer, Giovanni Bussotti, Tommaso Leonardi, Katelin R Haynes, Joanna Crawford, Marion E Brunck, Kim-Anh Le Cao, Gethin P Thomas, Wendy Y Chen, Ryan J Taft, Lars K Nielsen, Anton J Enright, John S Mattick, Marcel E Dinger
We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and q..
Genome-wide discovery of human splicing branchpoints
Tim R Mercer, Michael B Clark, Stacey B Andersen, Marion E Brunck, Wilfried Haerty, Joanna Crawford, Ryan J Taft, Lars K Nielsen, Marcel E Dinger, John S Mattick
During the splicing reaction, the 5' intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate in..
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
Xiu Cheng Quek, Daniel W Thomson, Jesper LV Maag, Nenad Bartonicek, Bethany Signal, Michael B Clark, Brian S Gloss, Marcel E Dinger
Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for ..