LncRNAs comprise a heterogeneous class of thousands of RNA-encoding genes whose functions are largely unknown. This thesis describes systematic computational approaches to discover liver-expressed lncRNAs globally and then deduce their regulatory roles in response to foreign chemical and hormonal exposures. In a first study, bulk liver RNA-seq data was used to discover liver-expressed lncRNAs responsive to multiple xenobiotics in a rat model. Ortholog analysis combined with co-expression data and causal inference methods was used to infer lncRNA function and deduce gene regulatory networks, including causal effects of lncRNAs on biological pathways. This work provides a framework for understanding the widespread transcriptome-altering actions of foreign chemicals in a key-responsive mammalian tissue. In a second study, single-cell RNA-seq was employed to develop a reference catalog of 48,261 mouse liver-expressed lncRNAs, a majority novel, by transcriptome reconstruction from > 2,000 bulk public mouse liver RNA-seq datasets. Single cell RNA-seq was sufficiently sensitive to detect >30,000 mouse liver lncRNAs and characterize their dysregulation in mouse models of high fat diet-induced non-alcoholic steatohepatitis (NASH), carbon tetrachloride-induced liver fibrosis, and hepatotoxicity induced by the Ah receptor agonist TCDD. Trajectory inference algorithms uncovered lncRNA zonation patterns in five major hepatic cell populations and their dysregulation in diseased states. LncRNAs expressed in NASH-associated macrophages, closely linked to disease progression, and in collagen-producing myofibroblasts, a key source of the fibrous scar in fibrotic liver, were identified. Regulatory network analysis linked individual lncRNAs with key biological pathways and gene centrality metrics identified network-essential regulatory lncRNAs in each liver disease model. In a third study, single nucleus RNA-seq combined with single nucleus ATAC-seq mapping of open chromatin regions elucidated functional linkages between cis- and trans-regulatory elements and their downstream genes targets, notably genes showing expression sex-differences impacting metabolism and disease risk. Liver cell type-specific chromatin accessibility signatures were identified, as were sex-specific accessibility signatures for hepatocytes and their associated DNA regulatory region motifs. Integrative modalities were employed to elucidate transcription factor-based mechanisms involved in sex-specific growth hormone-regulated gene expression by identifying transcriptional and epigenetic changes during feminization of mouse liver. Together, these studies characterize lncRNA function and can motivate future experiments. / 2026-03-20T00:00:00Z
| Identifer | oai:union.ndltd.org:bu.edu/oai:open.bu.edu:2144/48455 |
| Date | 20 March 2024 |
| Creators | Karri, Kritika |
| Contributors | Waxman, David J. |
| Source Sets | Boston University |
| Language | en_US |
| Detected Language | English |
| Type | Thesis/Dissertation |
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