Indiana University-Purdue University Indianapolis (IUPUI) / The human genome generates a vast number of functionally and structurally diverse noncoding transcripts, incorporated into complex networks which modulate the activity of classic pathways. Long noncoding RNAs (lncRNA) have been shown to exhibit diverse regulatory roles in various physiological and pathological processes. Hypoxia, a key feature of the tumor microenvironment, triggers adaptive responses in cancer cells that involve hundreds of genes. While the coding component of hypoxia signaling has been extensively studied, much less information is available regarding its noncoding arm. My doctoral work identified and functionally characterized a novel hypoxia-inducible lncRNAs encoded from the miR193b-host gene (MIR193BHG) locus, on chromosome 16. In the pursuit of understanding how MIR193BHG responds to hypoxia, we discovered a more complex transcriptional control of MIR193BHG by hypoxia. Ectopic expression of MIR193BHG in breast cancer cell lines in vitro and in xenografts significantly represses cell invasion, as well as the metastasis to lung and liver. Conversely, inhibition of MIR193BHG promotes cancer cell invasiveness and metastasis. RNAseq followed by pathway analysis revealed that MIR193BHG is a negative modulator of cholesterol biosynthesis pathway. MIR193BHG exerts a highly coordinated effect on the expression of cholesterol biosynthetic genes which leads to a measurable impact on the total cellular cholesterol content. The role of MIR193BHG in cholesterol metabolism also provided a mechanistic explanation for the sex maturation associated SNPs located in vicinity of this gene locus. Our work also provided preliminary insights into the functional mechanism of MIR193BHG by showing that its modulation of genes in cholesterol synthesis is predominantly at transcriptional level. Overall, my dissertation project identified a non-canonical hypoxia-inducible lncRNA, MIR193BHG, which modulates breast cancer invasion and metastasis via finetuning of cholesterol synthesis.

Pervasive transcription is widespread amongst eukaryotic genomes, and produces long noncoding RNAs (lncRNAs) in addition to classically annotated transcripts such as messenger RNAs (mRNAs). LncRNAs are heterogeneous in length and map to intergenic regions or overlap with annotated genes. Analogous to mRNAs, lncRNAs are transcribed by RNA polymerase II, regulated by common transcription factors, and possess 5’ caps and perhaps 3’ poly(A) tails. However, lncRNAs perform distinct functions, acting as scaffolds for ribonucleoprotein complexes or directing proteins to nucleic acid targets. The act of transcribing a lncRNA can also affect the local chromatin environment. Furthermore, whereas mRNAs are predominantly turned over in the cytoplasm, both nuclear and cytoplasmic pathways reportedly participate in lncRNA degradation. In this study, I address the question of when and how lncRNAs and mRNAs are distinguished in the cell. Messenger RNAs interact with a defined series of protein factors governing their production, processing and decay, and I hypothesised that lncRNAs might be similarly regulated. I therefore sought to determine which mRNA-binding proteins, if any, also bind lncRNAs. I reasoned that this would reveal the point at which lncRNAs and mRNAs diverge, and how differences in their biogenesis and turnover equip them for different roles. I selected factors from key stages of mRNA metabolism in Saccharomyces cerevisiae, and identified their transcriptome-wide targets using CRAC (crosslinking and analysis of cDNAs). CRAC can detect interactions with low abundance transcripts under physiological conditions, and reveal where within each transcript a protein is bound. Analyses of binding sites in mature mRNAs and intron-containing pre-mRNAs revealed the order in which the tested factors interact with mRNAs, and which region they bind. The poly(A)-binding protein Nab2 bound throughout mRNAs, consistent with an architectural role, whereas the cytoplasmic decay factors Xrn1 and Ski2 bound to poly(A) tails, which might act as hubs to coordinate turnover. The RNA packaging factors Tho2 and Gbp2, and nuclear surveillance factors Mtr4 and Trf4 bound abundantly to intron-containing premRNAs, indicating that they act during or shortly after transcription. The tested factors bound lncRNAs to various extents. LncRNA binding was most abundant for Mtr4 and Trf4, moderate for Tho2, Gbp2, the cap binding complex component Sto1, and the 3’ end processing factors Nab2, Hrp1 and Pab1, and lowest for Xrn1, Ski2 and the export receptor Mex67. This suggests that early events in lncRNA and mRNA biogenesis are similar, but unlike mRNAs, most lncRNAs are retained and degraded in the nucleus. Analyses of two documented classes of lncRNA, cryptic unstable transcripts (CUTs) and stable unannotated transcripts (SUTs), revealed some differences. SUTs were most similar to mRNAs, with canonical cleavage and polyadenylation signals flanking their 3’ ends, and poly(A) tails bound by the poly(A)-binding protein Pab1. CUTs lacked these characteristics, and in comparison to SUTs bound more abundantly to Mtr4 and Trf4 and less so to Ski2, Xrn1 and Mex67. Furthermore, CUTs accumulated upon Hrp1 depletion, suggesting that Hrp1 functions non-canonically to promote CUT turnover. Mtr4, Trf4 and Nab2 also bound abundantly to promoter-proximal RNA fragments generated from ~1000 protein coding genes. These fragments possessed short oligo(A) tails (hallmarks of nuclear surveillance substrates), were not bound to cytoplasmic factors, and apparently correspond to a population of ~150-200 nt promoter-proximal lncRNAs. Notably, CRAC analyses of Mtr4 and Sto1 targets in yeast subjected to a media shift revealed widespread changes in the abundance and surveillance of mRNAs, promoter-proximal transcripts and CUTs, which at many loci were arranged in a complex transcriptional architecture. Overall, the transcriptome-wide binding analyses presented here reveal that lncRNAs diverge from mRNAs prior to export, and are predominantly retained in the nucleus. Transcript fate is apparently determined during 3’ end processing, with CUTs diverging from mRNAs early in transcription via a distinct termination pathway coupled to rapid turnover, and SUTs diverging during or shortly after cleavage and polyadenylation, making them more stable and perhaps prone to escape to the cytoplasm. Promoter-proximal transcripts might arise from termination associated with an early checkpoint in Pol II transcription. The diverse behaviours of lncRNAs arise from their association with distinct subsets of RNA binding proteins, some of which perform different roles when bound to different types of transcript. In conclusion, my results provide the foundation for a mechanistic understanding of how distinct classes of non-coding Pol II transcripts are produced, and how they can perform diverse functions throughout the nucleus.

Evidências sugerem que somente cerca de 2% do genoma codifica proteínas, mas que a maior parte dos 80% restante possui atividade transcricional. Por não ser codificadora de proteínas, essa fração do genoma foi considerada como \'DNA lixo\'. Entretanto, estudos mais recentes e análises pós-ENCODE vem demonstrando que parte significativa destes RNAs não-codificantes desempenham papéis importantes em processos biológicos essenciais e também em doenças. Os RNAs longos não codificadores (lncRNAs) embora tradicionalmente conhecidos pelo imprintinggenômico, vem demonstrando diversos mecanismos de regulação da expressão gênica, principalmente emnível pós transcricional. Um destes lncRNAs que está envolvido principalmente com a metastase em câncer é o HOTAIR. O melanoma tem sido utilizado como modelo de progressao do câncer por suas etapas bem definidas e por isso já tem apresentado alguns lncRNAs envolvidos na melanomagenese e progressão do melanoma, tal como o HOTAIR. Assim, neste trabalho foi analisado a expressão de lncRNAs de amostras de melanócito e melanoma, sendo que as amostras malignas representam as principais fases de progressão deste tipo de câncer. Foram analisados os níveis de expressão relativa. Além disso, foi realizado a expressão diferencial dos grupos representativos do melanoma. Foram encontrados lncRNAs com valores de expressão e significância (p-ajustado <0,01 e fold change >1) que podem ser indicativos de expressão associada a progressão do melanoma. Os lncRNAs mais diferencialmente expressos foram avaliados quanto a sua capacidade de interação proteína-RNA e literatura científica disponível e então foram selecionados para posteriores ensaios funcionais. / Evidence suggests that only about 2% of the genome encodes protein, but most remaining 80% has transcriptional activity. Since they do not coding for proteins, this fraction of the genome was considered \'junk DNA\', However, recent studies and post-ENCODE analisys has shown that significant part of these non-coding RNAs play important roles in essential biological processes and in disease. Long noncoding RNAs (lncRNAs) although traditionally known for genomic imprinting, has demonstrated several mechanisms of regulation of gene expression, especially at the post transcriptional level. One of these lncRNAs that is involved primarily with metastasis in câncer is HOTAIR. Melanoma has been used as a model of câncer progression by its well-defined steps, and so it has been presented some lncRNAs involved in melanoma progression and melanomagenese, as HOTAIR was demonstrated. In this work it was analyzed the expression of lncRNAs of melanocyte and melanoma samples, and malignant samples represent the main stages of progression of this type of câncer. Relative expression levels were analyzed. Furthermore, it was performed differential expression of representative melanoma groups. lncRNAs found with expression values and significance (p-adjusted <0.01 and fold change> 1) may be indicative of expression associated with melanoma progression. The lncRNAs more differentially expressed were evaluated for their ability to interact protein-RNA and available scientific literature and then were selected for further functional assays.

Since its early discovery as a messenger, RNA has been shown to play a diverse set of regulatory, structural and even catalytic roles. The more recent understanding that the genome is pervasively transcribed stimulated the discovery of a new prevalent class of long non coding RNAs (lncRNAs). While these are lower abundant and relatively less conserved than other class of functional RNAs, lncRNAs are emerging as key players in different cellular processes in development and disease.

Eukaryotic genomes are pervasively transcribed and frequently generate long noncoding RNAs (lncRNAs). However, most lncRNAs remain uncharacterized. In this work, a set of positionally conserved intergenic lncRNAs in the fission yeast Schizosaccharomyces pombe genome are selected for further analysis. Deleting one of these lncRNA genes (ncRNA.1343) exhibited a clear phenotype: increased drug sensitivity. Further analyses revealed that deleting ncRNA.1343 also disrupted a previously unannotated lncRNA, termed nc-tgp1, transcribed in the opposite orientation of the predicted ncRNA.1343 gene and into the promoter of the phosphate-responsive permease gene tgp1+. Detailed analyses revealed that the act of transcribing nc-tgp1 into the tgp1+ promoter increases nucleosome density and prevents transcription factor access. Decreased nc-tgp1 transcription permits tgp1+ expression upon phosphate starvation, while nc-tgp1 loss induces tgp1+ in repressive phosphate-rich conditions. Notably, drug sensitivity results directly from tgp1+ expression in the absence of nc-tgp1 transcription. Similarly, lncRNA transcription upstream of pho1+, another phosphate-regulated gene, increases nucleosome density and prevents transcription factor binding to repress pho1+ in phosphate-replete cells. Importantly, the regulation of tgp1+ and pho1+ by upstream lncRNA transcription occurs in the absence of RNAi and heterochromatin components. Instead, the regulation of tgp1+ and pho1+ by upstream lncRNA transcription resembles examples of transcriptional interference reported in other organisms. Thus, tgp1+ and pho1+ are the first documented examples of genes regulated by transcriptional interference in S. pombe.

Evidências sugerem que somente cerca de 2% do genoma codifica proteínas, mas que a maior parte dos 80% restante possui atividade transcricional. Por não ser codificadora de proteínas, essa fração do genoma foi considerada como \'DNA lixo\'. Entretanto, estudos mais recentes e análises pós-ENCODE vem demonstrando que parte significativa destes RNAs não-codificantes desempenham papéis importantes em processos biológicos essenciais e também em doenças. Os RNAs longos não codificadores (lncRNAs) embora tradicionalmente conhecidos pelo imprintinggenômico, vem demonstrando diversos mecanismos de regulação da expressão gênica, principalmente emnível pós transcricional. Um destes lncRNAs que está envolvido principalmente com a metastase em câncer é o HOTAIR. O melanoma tem sido utilizado como modelo de progressao do câncer por suas etapas bem definidas e por isso já tem apresentado alguns lncRNAs envolvidos na melanomagenese e progressão do melanoma, tal como o HOTAIR. Assim, neste trabalho foi analisado a expressão de lncRNAs de amostras de melanócito e melanoma, sendo que as amostras malignas representam as principais fases de progressão deste tipo de câncer. Foram analisados os níveis de expressão relativa. Além disso, foi realizado a expressão diferencial dos grupos representativos do melanoma. Foram encontrados lncRNAs com valores de expressão e significância (p-ajustado <0,01 e fold change >1) que podem ser indicativos de expressão associada a progressão do melanoma. Os lncRNAs mais diferencialmente expressos foram avaliados quanto a sua capacidade de interação proteína-RNA e literatura científica disponível e então foram selecionados para posteriores ensaios funcionais. / Evidence suggests that only about 2% of the genome encodes protein, but most remaining 80% has transcriptional activity. Since they do not coding for proteins, this fraction of the genome was considered \'junk DNA\', However, recent studies and post-ENCODE analisys has shown that significant part of these non-coding RNAs play important roles in essential biological processes and in disease. Long noncoding RNAs (lncRNAs) although traditionally known for genomic imprinting, has demonstrated several mechanisms of regulation of gene expression, especially at the post transcriptional level. One of these lncRNAs that is involved primarily with metastasis in câncer is HOTAIR. Melanoma has been used as a model of câncer progression by its well-defined steps, and so it has been presented some lncRNAs involved in melanoma progression and melanomagenese, as HOTAIR was demonstrated. In this work it was analyzed the expression of lncRNAs of melanocyte and melanoma samples, and malignant samples represent the main stages of progression of this type of câncer. Relative expression levels were analyzed. Furthermore, it was performed differential expression of representative melanoma groups. lncRNAs found with expression values and significance (p-adjusted <0.01 and fold change> 1) may be indicative of expression associated with melanoma progression. The lncRNAs more differentially expressed were evaluated for their ability to interact protein-RNA and available scientific literature and then were selected for further functional assays.

京都大学 / 0048 / 新制・課程博士 / 博士(薬科学) / 甲第19974号 / 薬科博第65号 / 新制||薬科||7(附属図書館) / 33070 / 京都大学大学院薬学研究科医薬創成情報科学専攻 / (主査)教授 馬見塚 拓, 教授 緒方 博之, 教授 掛谷 秀昭 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

Recently, the discovery of noncoding RNAs (ncRNAs), such as long noncoding RNAs (lncRNAs) has altered the traditional view of gene regulation. Sequencing of genomes has brought to light the vast stretches of non-protein coding DNA regions that transcribe non-protein coding RNA. LncRNAs are multifunctional and extremely diverse. They can act as signals, decoys, scaffolds, guides, or enhancers. Several lncRNAs, such as Fendrr and Bvht, have been found to have important regulatory functions in cardiac disease and development. The Glt2-Dio3 locus, which is enriched in cardiac muscle, harbors two long intragenic RNAs, MEG3 and MEG8, and harbors one of the largest mammalian miRNA clusters. MEG3, which is termed Gtl2 in rat and mouse, contain 10 exons that are alternatively spliced and give rise to several variants. Gtl2 is conserved across human, rat, and mouse, which makes it an ideal candidate for research and a possible target for therapies. Based on the growing evidence for lncRNAs playing a role in cardiac muscle and our research on the Gtl2-Dio3 microRNAs (miRNAs), I focused on investigating the Gtl2 lncRNA in the heart. Antisense oligonucleotides (GapmeRs) were used to knockdown Gtl2 lncRNA expression levels in cultured, primary neonatal cardiomyocytes in basal and hypertrophic conditions. Although Gtl2 was effectively knocked down in basal conditions I was unable to achieve efficient knockdown in hypertrophic cardiomyocytes induced by phenylephrine treatment. Consequently, I did not observe any modulation of hypertrophy as determined by changes in the expression of Nppa and Nppb, established markers of cardiomyocyte hypertrophy.. Next, I utilized short hairpin RNA (shRNA) to knockdown Gtl2 lncRNA expression levels and obtained robust knockdown. Lastly, I designed a cardiac tropic adeno-associated virus 9 (AAV9) encoding MEG3 DNA for in vivo overexpression experiments as well as an adenovirus encoding MEG3 for in vitro overexpression experiments. These reagents will provide valuable resources for dissecting the functions of the Gtl2 lncRNA. Studies investigating the roles of Gtl2 in the diseased heart my lead to the development of other potential therapies to treat cardiac disease.

Sickle cell disease (SCD) is one of the most common hemoglobinopathies worldwide. It is caused by a homozygous mutation in codon 6 of the beta globin gene (HBB), which leads to polymerization of the variant hemoglobin and sickled red blood cells that obstruct blood vessels and reduce oxygen delivery to tissues. Patients with SCD have multiple clinical problems, including pain crises, anemia and organ damage. However, not all patients with SCD display all these clinical manifestations. One major factor for reduced occurrences of symptoms is fetal hemoglobin (HbF). HbF is the main hemoglobin in the fetus, and declines one year after birth to less than one percent of total hemoglobin. Nevertheless, there are individuals who continue to have high levels of HbF into adulthood, which is beneficial for an individual with SCD because HbF reduces the amount of sickle polymer in red blood cells. There are three major quantitative trait loci (QTL) associated with high HbF. However, these QTL account for 20-45% of HbF variance. Therefore, further investigation is required to fully understand how HbF is regulated. The HBS1L-MYB intergenic polymorphism (HMIP) on chromosome 6q23 is one of the major QTL associated with high HbF. This region is also known to regulate other erythroid-specific traits due to an enhancer element that promotes the expression of the downstream gene, MYB, which controls hemoglobin expression and erythroid proliferation and maturation. The presence of RNA polymerase II binding and a 50-bp transcript suggested that a long noncoding RNA (lncRNA) is transcribed from this region. LncRNAs are non-protein-coding transcripts greater than 200 nucleotides and are involved in gene regulation. Therefore, it was hypothesized that a lncRNA is transcribed from the enhancer of MYB and regulates hemoglobin expression. I characterized a novel lncRNA, 1283 bp in length that was differentially expressed among various tissue types, among erythroid progenitor cells with different hemoglobin makeup, and also during erythroid differentiation. Furthermore, knockdown of this lncRNA, named the HBS1L-MYB intergenic long noncoding RNA (HMI-LNCRNA), significantly increased HbF. Taken together, these observations suggest that HMI-LNCRNA can be a possible therapeutic target to increase HbF expression in patients with SCD and β-thalassemia. / 2018-05-01T00:00:00Z

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