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published_or_final_version / Computer Science / Master / Master of Philosophy

RNA-seq sequencing has revolutionized the landscape of whole transcriptome sequencing and analysis. With its capacity of sequencing in a high-throughput and low-cost way, it produced ever increasingly amount of RNA-seq reads that are mines of treasure in biological and therapeutic studies. However, due to the complex nature and relatively un-developed knowledge base of transcription process, many challenges exist in the modeling and investigation of RNA-seq read data. It is of high importance to develop efficient computational tools to satisfy these needs. The first part of this thesis concentrates on algorithms for both upstream and downstream analysis of RNA-seq data. For the upstream, we aim to tackle down the problems of RNA-seq reads alignment where the segmental alignment causes the major difficulty. By employing a strategy of rigid extensive tries on read segmentations indices, we implemented an accurate algorithm for returning two-segmental alignments based on bi-directional BWT. For the downstream analysis, we study two types of gene fusion events which play a critical role in the formation of cancers. Unlike previous down-scoping-search methods, we applied a search-validate approach to design the framework. By introducing key techniques such as masking, two-segmental alignment and retention of multiple maps, we developed an efficient and robust tool for detecting gene fusions with high accuracy that proved by extensive simulation and real data tests. Optical mapping is a cutting edge technique for the study of genomic structural variations which address the defect and limitation of paired-end sequencing. It was designed with great improvement in accuracy, resolution and throughput than current techniques. Also, it produces much longer molecules which enables us to explore genomic regions rich in repetitive sequences. Optical mapping has the potential to enable us to draw a complete picture of the genome structure polymorphism and it is important for us to design tools for analysis of the data. The second part of the thesis is dedicated to the algorithms for both upstream and downstream analysis of optical map data. For the upstream, we formulated a robust scoring function, which combines the effectiveness of heuristic functions and the accuracy of statistical functions. Based on it, we implemented the high performance OMDP algorithm. For the downstream, we developed BP-OMDP which makes use of both split-mapping and disparity of coverage depth to call inversions in NA12878 human genome sample. / published_or_final_version / Computer science / Doctoral / Doctor of Philosophy

Mixed lineage leukemia (MLL) gene undergoes chromosomal translocation with over 60 different fusion partner genes in human leukemias. The resultant MLL-fusion oncoproteins are profoundly implicated in leukemias with poor prognosis. Epigenetic dysregulations have been frequently reported in MLL-rearranged leukemogenesis. Our study aims to investigate the correlations between epigenetic alterations, including both histone modification and DNA methylation, and gene dysregulation in MLL-rearranged leukemia. My study focused on MLL-EEN fusion protein, which causes an onset of acute myeloid leukemia (AML). A novel Mll-Een expressing cell line, VLA33, was derived from the bone marrow of Mll-Een knockin mouse with AML phenotype. The cells were mainly myeloblast cells, possessing clonogenic ability and showed upregulation of Hoxa cluster genes. Previous study demonstrated that the protein arginine methyltransferase 1 (PRMT1) plays a significant role in MLL-EEN leukemogenesis through conferring H4R3 asymmetric dimethylation (H4R3me2a) mark on HoxA9 locus. Consistently, our ChIP analysis demonstrated enrichment of H4R3me2a at the Hoxa promoters while knockdown of Prmt1 attenuated the expression of Hoxa genes and reduced in vitro clonogenic potential of VLA33 cells. CD41, Runx1 and Tgm2 genes, which showed elevated expression in VLA33 cells, were identified as potential target genes of Mll-Een/Prmt1 complex. However, enrichment of active H4R3me2a was only observed at Runx1 promoters, but not at the regulatory regions of CD41 and Tgm2. Inhibition of Prmt1 by inhibitor AMI-1 reduced Runx1 and CD41 expression. Although Prmt1 knockdown reduced the enrichment of H4R3me2a at Runx1 promoter, it did not suppress the expression of Runx1. These data suggest the involvement of other regulatory mechanism and Prmt1 is not the sole factor causing gene dysregulation. CD41 is a marker of murine definitive hematopoietic progenitors. Interestingly, the CD41+ VLA33 cells demonstrated a trend of enhanced self-renewal ability in colony-forming assay as compared with CD41-/low cells. The CD41 expression was positively correlated with Mll-Een and Prmt1 expression. In addition, CD41+ cells expressed higher level of Hoxa9, Bmi-1, Runx1, Tal-1 and Lmo2 genes that are associated with HSC activities, suggesting reactivation of stem-cell regulatory program in CD41+ leukemia cells, which confer as leukemia stem cell population. The association between DNA methylation and MLL-EEN leukemogenesis was also investigated. The results demonstrated the establishment of stem cell Hox code, which was correlated with DNA hypomethylation status at Hox gene promoters in Mll-Een leukemia cells. Besides, Hox activation through DNA hypomethylation was independent of Prmt1-mediated histone modification, but was found associated with reduction of Bmi-1 binding at Hox loci. In conclusion, my study identified novel dysregulated genes in Mll-Een leukemogenesis. My findings provide insight into the reactivation of stem-cell program in leukemia cells through epigenetic dysregulation, which furthers our understanding of MLL-rearranged leukemogenesis. / published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / toc / Computer Science and Information Systems / Master / Master of Philosophy

Thesis (M. Phil.)--University of Hong Kong, 2008. / Also available in print.

Thesis (M. Phil.)--University of Hong Kong, 2008. / Also available online.

published_or_final_version / abstract / Pathology / Master / Master of Philosophy

Errata and corrections pasted on front end paper. / Copies of three of author's previously published articles contained in back pocket. / Bibliography: leaves 178-219. / ix, 219, [130] leaves, [31] leaves of plates : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis aims to generate a library of chromosomally derived transcriptional promoter ::lacZ fusion mutants in an environmental isolate of L. monocytogenes (DRDC8). A lacZ transcriptional fusion mutant that displayed increased B-galactosidase activity in response to the calcium chelater EGTA is investigated in detail. / Thesis (Ph.D.)--University of Adelaide, Dept. of Microbiology and Immunology, 1997

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [80]-88).