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作者： Calvert-Joshua, Tracey University of the Western Cape

学位级别：master

Kidney cancers, of which clear cell renal cell carcinoma comprises an estimated 70%, have been placed amongst the top ten most common cancers in both males and females. With a mortality rate that exceeds 40%, kidney cancer is considered the most lethal cancer of the genitourinary system. Despite advances in its treatment, the mortality- and incidence rates across all stages of the disease have continued to climb. Since the release of the Human Genome Project in the early 2000’s, most genetics studies have focused on the protein coding region of the human genome, which accounts for a mere 2% of the entire genome. It has been suggested that diverting our focus to the other 98% of the genome, which was previously dismissed as non-functional “junk dna”, could possibly contribute significantly to our understanding of the underlying mechanisms of complex *** this study a whole genome sequencing somatic mutation data set from the International Cancer Genome Consortium was used. The non-coding somatic mutations within the promoter, intronic, 5-prime untranslated and 3-prime untranslated regions of clear cell renal cell carcinoma-implicated genes were extracted and submitted to RegulomDB for their functional *** expected, most of the variants were located within the intronic regions and only a small subset of identified variants was predicted to be deleterious. Although the variants all belonged to a selected subset of kidney cancer-associated genes, the genes frequently mutated in the non-coding regions were not the same genes that were frequently mutated in the whole exome studies (where the focus is on the coding sequences). This indicates that with whole genome sequencing studies a new set of genes/variants previously unassociated with the clear cell renal cell carcinoma could be identified. In addition, most of the non-coding somatic variants fell within multiple transcriptions factor binding sites. Since many of these variants were also deleterious (a

关键词： non-coding dna Gene dysregulation Aberrant methylation Renal cell carcinoma Clear cell renal cell carcinoma

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noncoding Genomics in Gastric Cancer and the Gastric Precancerous Cascade: Pathogenesis and Biomarkers

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DISEASE MARKERS 2015年第1期2015卷 1-14页

作者： Sandoval-Borquez, Alejandra Saavedra, Kathleen Carrasco-Avino, Gonzalo Garcia-Bloj, Benjamin Fry, Jacqueline Wichmann, Ignacio Corvalan, Alejandro H. Pontificia Univ Catolica Chile Adv Ctr Chron Dis ACCDiS Santiago 8330034 Chile Univ La Frontera Sci & Technol Bioresource Nucleus BIOREN Temuco 4811230 Chile Univ La Frontera Grad Program Appl Cell & Mol Biol Temuco 4811230 Chile Pontificia Univ Catolica Chile UC Ctr Invest Oncol CITO Santiago 8330034 Chile Univ Chile Dept Pathol Santiago 8380453 Chile Icahn Sch Med Mt Sinai Dept Pathol New York NY 10029 USA Pontificia Univ Catolica Chile Fac Med Dept Hematol Oncol Santiago 8330034 Chile

Gastric cancer is the fifth most common cancer and the third leading cause of cancer-related death, whose patterns vary among geographical regions and ethnicities. It is a multifactorial disease, and its development depends on infection by Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV), host genetic factors, and environmental factors. The heterogeneity of the disease has begun to be unraveled by a comprehensive mutational evaluation of primary tumors. The low-abundance of mutations suggests that other mechanisms participate in the evolution of the disease, such as those found through analyses of noncoding genomics. noncoding genomics includes single nucleotide polymorphisms (SNPs), regulation of gene expression through dna methylation of promoter sites, miRNAs, other noncoding RNAs in regulatory regions, and other topics. These processes and molecules ultimately control gene expression. Potential biomarkers are appearing from analyses of noncoding genomics. This review focuses on noncoding genomics and potential biomarkers in the context of gastric cancer and the gastric precancerous cascade.

关键词： non-coding dna STOMACH cancer CARCINOGENESIS BIOCHEMICAL markers dna methylation

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A Statistical Framework to Predict Functional non-coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

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SCIENTIFIC REPORTS 2015年第1期5卷 10576-10576页

作者： Lu, Qiongshi Hu, Yiming Sun, Jiehuan Cheng, Yuwei Cheung, Kei-Hoi Zhao, Hongyu Yale Univ Sch Publ Hlth Dept Biostat New Haven CT 06520 USA Yale Univ Program Computat Biol & Bioinformat New Haven CT USA Yale Univ Sch Med Yale Ctr Med Informat New Haven CT USA Yale Univ Sch Med Dept Emergency Med New Haven CT USA VA Connecticut Healthcare Syst West Haven CT USA

Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://***

关键词： HUMAN genome non-coding dna non-coding RNA GENE expression EXPECTATION-maximization algorithms

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TRRUST: a reference database of human transcriptional regulatory interactions

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SCIENTIFIC REPORTS 2015年第1期5卷 11432-11432页

作者： Han, Heonjong Shim, Hongseok Shin, Donghyun Shim, Jung Eun Ko, Yunhee Shin, Junha Kim, Hanhae Cho, Ara Lee, Eiru Kim Tak Kim, Hyojin Kim, Kyungsoo Yang, Sunmo Bae, Dasom Yun, Ayoung Kim, Sunphil Kim, Chan Yeong Cho, Hyeon Jin Kang, Byunghee Shin, Susie Lee, Insuk Yonsei Univ Dept Biotechnol Coll Life Sci & Biotechnol Seoul 120749 South Korea

The reconstruction of transcriptional regulatory networks (TRNs) is a long-standing challenge in human genetics. Numerous computational methods have been developed to infer regulatory interactions between human transcriptional factors (TFs) and target genes from high-throughput data, and their performance evaluation requires gold-standard interactions. Here we present a database of literature-curated human TF-target interactions, TRRUST (transcriptional regulatory relationships unravelled by sentence-based text-mining, http://***/trrust), which currently contains 8,015 interactions between 748 TF genes and 1,975 non-TF genes. A sentence-based text-mining approach was employed for efficient manual curation of regulatory interactions from approximately 20 million Medline abstracts. To the best of our knowledge, TRRUST is the largest publicly available database of literature-curated human TF-target interactions to date. TRRUST also has several useful features: i) information about the mode-of-regulation;ii) tests for target modularity of a query TF;iii) tests for TF cooperativity of a query target;iv) inferences about cooperating TFs of a query TF;and v) prioritizing associated pathways and diseases with a query TF. We observed high enrichment of TF-target pairs in TRRUST for top-scored interactions inferred from high-throughput data, which suggests that TRRUST provides a reliable benchmark for the computational reconstruction of human TRNs.

关键词： GENE regulatory networks TRANSCRIPTION factors GENE targeting HUMAN genome non-coding dna GENETIC regulation

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Sequential splicing of a group II twintron in the marine cyanobacterium Trichodesmiume

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SCIENTIFIC REPORTS 2015年第1期5卷 16829-16829页

作者： Pfreundt, Ulrike Hess, Wolfgang R. Univ Freiburg Fac Biol D-79104 Freiburg Germany

The marine cyanobacterium Trichodesmium is unusual in its genomic architecture as 40% of the genome is occupied by non-coding dna. Although the majority of it is transcribed into RNA, it is not well understood why such a large non-coding genome fraction is maintained. Mobile genetic elements can contribute to genome expansion. Many bacteria harbor introns whereas twintrons, introns-in-introns, are rare and not known to interrupt protein-coding genes in bacteria. Here we show the sequential in vivo splicing of a 5400 nt long group II twintron interrupting a highly conserved gene that is associated with RNase HI in some cyanobacteria, but free-standing in others, including Trichodesmium erythraeum. We show that twintron splicing results in a putatively functional mRNA. The full genetic arrangement was found conserved in two geospatially distinct metagenomic datasets supporting its functional relevance. We further show that splicing of the inner intron yields the free intron as a true circle. This reaction requires the spliced exon reopening (SER) reaction to provide a free 5' exon. The fact that Trichodesmium harbors a functional twintron fits in well with the high intron load of these genomes, and suggests peculiarities in its genetic machinery permitting such arrangements.

关键词： TRICHODESMIUM non-coding dna INTRONS RNA splicing GENOMES

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Analysis of a dna region from low-copy-number plasmid pYAN-1 of Sphingobium yanoikuyae responsible for plasmid stability

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BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY 2014年第3期78卷 510-515页

作者： Hayashi, Hiroe Kurusu, Yasuroh Tokyo Univ Agr & Technol United Grad Sch Agr Sci Fuchu Tokyo Japan Ibaraki Univ Coll Agr Dept Bioresource Sci Ami Ibaraki 30003 Japan

We identified and analyzed a dna region that is required for the stable maintenance of plasmids in the genus Sphingomonas. This dna fragment, a 244 bp, is localized in the upstream region of the repA gene of low-copy-number small plasmid pYAN-1 (4896 bp) of Sphingobium yanoikuyae. It has four inverted repeats and one direct repeat for possible secondary structures. We were able to stabilize not only another unstable plasmid, pYAN-2, in the genus Sphingomonas, but also the unstable plasmid pSC101 without par locus in Escherichia coli. The copy-number levels between the unstable plasmid and the parental plasmid were similar, and these results suggest that the stabilization of unstable plasmids by this dna region of pYAN-1 was not due to an increase in plasmid copy number. We concluded that the stabilization of the plasmid was due to a plasmid partition mechanism encoded by a dna fragment of pYAN-1.

关键词： sphingomonad plasmid partition non-coding dna

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The Most Deeply Conserved noncoding Sequences in Plants Serve Similar Functions to Those in Vertebrates Despite Large Differences in Evolutionary Rates

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PLANT CELL 2014年第3期26卷 946-961页

作者： Burgess, Diane Freeling, Michael Univ Calif Berkeley Dept Plant & Microbial Biol Berkeley CA 94720 USA

In vertebrates, conserved noncoding elements (CNEs) are functionally constrained sequences that can show striking conservation over >400 million years of evolutionary distance and frequently are located megabases away from target developmental genes. Conserved noncoding sequences (CNSs) in plants are much shorter, and it has been difficult to detect conservation among distantly related genomes. In this article, we show not only that CNS sequences can be detected throughout the eudicot clade of flowering plants, but also that a subset of 37 CNSs can be found in all flowering plants (diverging similar to 170 million years ago). These CNSs are functionally similar to vertebrate CNEs, being highly associated with transcription factor and development genes and enriched in transcription factor binding sites. Some of the most highly conserved sequences occur in genes encoding RNA binding proteins, particularly the RNA splicing-associated SR genes. Differences in sequence conservation between plants and animals are likely to reflect differences in the biology of the organisms, with plants being much more able to tolerate genomic deletions and whole-genome duplication events due, in part, to their far greater fecundity compared with vertebrates.

关键词： non-coding dna PLANT dna PLANT genomes EUDICOTYLEDONES TRANSCRIPTION factors

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Short noncoding dna fragments improve the immune potency of electroporation-mediated HBV dna vaccination

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GENE THERAPY 2014年第7期21卷 703-708页

作者： Peng, J. Shi, S. Yang, Z. Ding, Q. Hai, W. Tang, H. Yang, Y. Bernstein, J. R. Peyda, P. Xu, Y. Shanghai Jiao Tong Univ Sch Biomed Engn Med X Res Inst Shanghai 200030 Peoples R China Shanghai Jiao Tong Univ Sch Pharm Shanghai 200030 Peoples R China Univ Calif Los Angeles Dept Mol & Med Pharmacol Los Angeles CA USA

Electroporation (EP)-mediated dna immunization can elicit effective immune responses in a variety of animals, and is widely used in research studies and clinical trials. However, high-pulse voltage, high dna dose and multiple immunizations are still required to achieve considerable immune responses. To further improve the efficiency of EP-mediated dna immunization, many parameters have been tried and optimized in recent years. In our early research, we found that the short noncoding dna fragments (sf-dna) can significantly enhance EP-mediated transgene expression of reporter genes. In this study, we tested the effect of sf-dna on the immune potency of EP-mediated hepatitis B virus (HBV) dna vaccination in a mouse model. The results show that the use of sf-dna in EP-mediated HBV dna vaccination leads to an enhanced expression of the HBV surface antigen, resulting in higher cellular and humoral responses. Furthermore, the immune responses in the sf-dna-mediated 120 V cm(-1) EP immunization group were higher than that of the 200 V cm(-1) EP without sf-dna groups. These data suggest that the sf-dna can be used as an effective helper molecule to improve the immune response of EP-mediated HBV dna vaccination, which may make the EP-mediated dna vaccination more effective and suitable for animal and clinical application.

关键词： non-coding dna ELECTROPORATION HEPATITIS B vaccination dna vaccines CLINICAL trials TRANSGENES VACCINE effectiveness

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Repetitive elements dynamics in cell identity programming, maintenance and disease

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CURRENT OPINION IN CELL BIOLOGY 2014年 31卷 67-73页

作者： Bodega, Beatrice Orlando, Valerio Ist Nazl Genet Mol INGM Romeo & Enrica Invernizzi Genome Biol Unit I-20126 Milan Italy 4700 King Abdullah Univ Sci & Technol KAUST Environm Epigenet Res Program Biol Environm Sci & Engn Div Thuwal 239556900 Saudi Arabia

The days of 'junk dna' seem to be over. The rapid progress of genomics technologies has been unveiling unexpected mechanisms by which repetitive dna and in particular transposable elements (TEs) have evolved, becoming key issues in understanding genome structure and function. Indeed, rather than 'parasites', recent findings strongly suggest that TEs may have a positive function by contributing to tissue specific transcriptional programs, in particular as enhancer-like elements and/or modules for regulation of higher order chromatin structure. Further, it appears that during development and aging genomes experience several waves of TEs activation, and this contributes to individual genome shaping during lifetime. Interestingly, TEs activity is major target of epigenomic regulation. These findings are shedding new light on the genome-phenotype relationship and set the premises to help to explain complex disease manifestation, as consequence of TEs activity deregulation.

关键词： non-coding dna GENOMICS TRANSPOSONS PHENOTYPE GENETIC transcription CELLULAR aging

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Two Histone/Protein Acetyltransferases, CBP and p300, Are Indispensable for Foxp3⁺ T-Regulatory Cell Development and Function

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MOLECULAR AND CELLULAR BIOLOGY 2014年第21期34卷 3993-4007页

作者： Liu, Yujie Wang, Liqing Han, Rongxiang Beier, Ulf H. Akimova, Tatiana Bhatti, Tricia Xiao, Haiyan Cole, Philip A. Brindle, Paul K. Hancock, Wayne W. Univ Penn Childrens Hosp Philadelphia Dept Pathol & Lab Med Div Transplant Immunol Philadelphia PA 19104 USA Univ Penn Childrens Hosp Philadelphia Biesecker Ctr Study Pediat Liver Dis Philadelphia PA 19104 USA Univ Penn Perelman Sch Med Philadelphia PA 19104 USA Univ Penn Childrens Hosp Philadelphia Dept Pediat Div Nephrol Philadelphia PA 19104 USA Univ Penn Childrens Hosp Philadelphia Philadelphia PA 19104 USA Perelman Sch Med Philadelphia PA USA Johns Hopkins Univ Sch Med Dept Pharmacol & Mol Sci Baltimore MD 21205 USA St Jude Childrens Res Hosp Dept Biochem Memphis TN 38105 USA

T-regulatory (Treg) cells are important to immune homeostasis, and Treg cell deficiency or dysfunction leads to autoimmune disease. A histone/protein acetyltransferase (HAT), p300, was recently found to be important for Treg function and stability, but further insights into the mechanisms by which p300 or other HATs affect Treg biology are needed. Here we show that CBP, a p300 paralog, is also important in controlling Treg function and stability. Thus, while mice with Treg-specific deletion of CBP or p300 developed minimal autoimmune disease, the combined deletion of CBP and p300 led to fatal autoimmunity by 3 to 4 weeks of age. The effects of CBP and p300 deletion on Treg development are dose dependent and involve multiple mechanisms. CBP and p300 cooperate with several key Treg transcription factors that act on the Foxp3 promoter to promote Foxp3 production. CBP and p300 also act on the Foxp3 conserved noncoding sequence 2 (CNS2) region to maintain Treg stability in inflammatory environments by regulating pCREB function and GATA3 expression, respectively. Lastly, CBP and p300 regulate the epigenetic status and function of Foxp3. Our findings provide insights into how HATs orchestrate multiple aspects of Treg development and function and identify overlapping but also discrete activities for p300 and CBP in control of Treg cells.

关键词： T cells AUTOIMMUNE diseases RESEARCH HISTONE acetyltransferase MICE as laboratory animals non-coding dna THERAPEUTIC use

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