Nicole Cloonan
A5084301986- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Pluripotent Stem Cells Research
- Chromosomal and Genetic Variations
- Pancreatic and Hepatic Oncology Research
- Malaria Research and Control
- Evolution and Genetic Dynamics
- DNA Repair Mechanisms
- Bioinformatics and Genomic Networks
- Nutrition, Genetics, and Disease
- Kruppel-like factors research
- Extracellular vesicles in disease
- Immune Cell Function and Interaction
- Genomics and Rare Diseases
- Genetic factors in colorectal cancer
- Molecular Biology Techniques and Applications
- Myeloproliferative Neoplasms: Diagnosis and Treatment
QIMR Berghofer Medical Research Institute
2002-2024
University of Auckland
2018-2023
The University of Queensland
2000-2016
Harvard University
2012
Griffith University
2004-2007
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete components with high success rates but assembly complete isoform structures poses a major challenge even when all constituent elements identified. Expression-level estimates also varied widely across methods, based on similar models. Consequently,...
Abstract Background Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance these variants remains controversial. Observational studies show that isomiR patterns non-random, hinting molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for molecules. Results To assess relevance we have performed ultra-deep miRNA-seq on ten adult human tissues, created...
Abstract Background MicroRNAs are modifiers of gene expression, acting to reduce translation through either translational repression or mRNA cleavage. Recently, it has been shown that some microRNAs can act promote suppress cell transformation, with miR-17-92 described as the first oncogenic microRNA. The association encoded a surprisingly broad range cancers not only underlines clinical significance this locus, but also suggests may regulate fundamental biological processes, and for these...
KLF1 regulates a diverse suite of genes to direct erythroid cell differentiation from bipotent progenitors. To determine the local cis -regulatory contexts and transcription factor networks in which operates, we performed ChIP-seq mouse. We found at least 945 sites genome E14.5 fetal liver cells are occupied by endogenous KLF1. Many these recovered reside gene promoters such as Hbb-b1 , but majority distant any known gene. Our data suggests directly most aspects terminal including production...
Metastasis is a complex, multistep process involved in the progression of cancer from localized primary tissue to distant sites, often characteristic more aggressive forms this disease. Despite being studied great detail recent years, mechanisms that govern remain poorly understood. In study, we identify novel role for miR-139-5p inhibition breast progression. We highlight its clinical relevance by reviewing expression across wide variety subtypes using in-house generated and online data...
Abstract Background MicroRNAs (miRNAs) bind to mRNAs and target them for translational inhibition or transcriptional degradation. It is thought that most miRNA-mRNA interactions involve the seed region at 5′ end of miRNA. The importance sites supported by experimental evidence, although there growing interest in mediated central miRNA, termed centered sites. To investigate prevalence these interactions, we apply a biotin pull-down method determine direct targets ten human miRNAs, including...
MicroRNAs are noncoding regulators of gene expression, which act by repressing protein translation and/or degrading mRNA. Many have been shown to drive tumorigenesis in cancer, but functional studies understand their mode action typically limited single-target genes. In this study, we use synthetic biotinylated miRNA pull down endogenous targets miR-182-5p. We identified more than 1000 genes as potential miR-182-5p, most a known function pathways underlying tumor biology. Specifically,...
Abstract Reprogramming of somatic cells to induced pluripotent stem involves a dynamic rearrangement the epigenetic landscape. To characterize this epigenomic roadmap, we have performed MethylC-seq, ChIP-seq (H3K4/K27/K36me3) and RNA-Seq on samples taken at several time points during murine secondary reprogramming as part Project Grandiose. We find that DNA methylation gain occurs gradually, while loss is achieved only ESC-like state. Binding sites activated factors exhibit focal...
Mechanotransduction is a strong driver of mesenchymal stem cell (MSC) fate. In vitro, variations in matrix mechanics invoke changes MSC proliferation, migration and differentiation. However, when incorporating MSCs within injectable, inherently soft hydrogels, this dominance over response substantially limits our ability to couple the ease application hydrogels with efficiently directed differentiation, especially case bone generation. Here, we identify differential miRNA expression varying...
mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood. Because the RNA intermediates in each these have finite lifetimes, extensive mechanistic dynamical information is encoded total cellular RNA. Here we report development SnapShot-Seq, set computational methods allow determination vivo rates pre-mRNA splicing, intron degradation, decay from single RNA-Seq snapshot SnapShot-Seq can detect changes specific it provides...