Studies on RNA Regulation: From Enhancer RNAs to RBBP6 Isoform3

This dissertation contains two separate yet interconnected pieces of work, which shed light on the complicated RNA regulatory mechanism. The first part, as the main focus of the thesis, characterizes a large pool of human polyadenylated enhancer RNA under deficient nuclear surveillance conditions, and investigates their metabolism mechanisms. The second part elucidates the dynamic localization mechanism of RBBP6 isoform3, which inhibits pre-mRNA 3’ processing by completing with RBBP6 isoform1. Despite being composed of approximately 3 billion base pairs, only 1 to 2% of the human genome codes for proteins. The non-coding DNA regions can however function as transcription units and generate non-coding RNAs such as enhancer-derived RNAs, or eRNAs, that play crucial roles in gene expression regulation, cell differentiation, development, and diseases. Previous studies have suggested that most eRNAs are transcribed by RNA polymerase II (RNAP II), but not polyadenylated. In Chapter 3, I identify a large fraction of polyadenylated enhancer RNAs under deficient nuclear surveillance conditions via genome-wide analyses, and explore their biogenesis and degradation mechanisms. I find that the Integrator complex plays an important role in polyadenylated eRNA biogenesis, and that their exosome-dependent degradation requires two cofactor complexes containing the RNA helicase Mtr4: the PAXT/PPC complex and the NEXT complex. Additionally, the canonical poly(A) polymerases PAP-α and PAP-γ play a major role in the 3’ end processing of pA+ eRNA. Finally, I show that under deficient nuclear surveillance conditions, pA+ eRNAs accumulate in the cytoplasm and associate with polysomes, suggesting that at least some might have translation potential. I also contributed to the discovery of two novel complexes both containing the RNA helicase Mtr4, which is a master player of the nuclear surveillance system. Mtr4 and ZFC3H1 form the PAXT/PPC complex, which facilitates the turnover of polyadenylated nuclear RNAs, including prematurely terminated RNAs (ptRNAs), upstream antisense RNAs (uaRNAs), and eRNAs (see the paper in Appendix II). Mtr4 also associates with NRDE2 to form a complex, functioning in the DNA damage response pathway (see the paper in Appendix III). These works provide additional insights into the complexity and significance of the RNA helicase Mtr4. In the second part of the thesis, presented in Chapter 4, I studied a polyadenylation factor known as Retinoblastoma-binding protein 6 (RBBP6). RBBP6 was initially identified as a large multidomain protein, interacting with tumor suppressors p53 and Rb. Later, its diverse roles were uncovered in cell cycle progression, apoptosis, nucleic acid metabolism, differentiation, and mRNA processing. RBBP6 protein has four isoforms, among which the shortest isoform, iso3, has only one domain: the DWNN (Domain With No Name) domain. The DWNN domain displays high similarities with ubiquitin, implying its function as a novel ubiquitin-like modifier. However, I show that the DWNN domain is actually not a ubiquitin-like modifier, but is itself ubiquitinated. Moreover, the monoubiquitylation of iso3 can facilitate its localization at chromatin. Additionally, I find that the C-terminal tail of iso3 also plays a role in iso3 chromatin localization, presumably by interacting with other factors of the polyadenylation machinery. Pulldown experiments of iso3 followed by mass spectrometry identified Importin7 as an iso3-interacting factor that assists its cytoplasmic retention. Our results identified novel mechanisms for the dynamic localization of RBBP6 iso3, which shed light on the role of iso3 in mRNA 3’ processing and disease

Multiple Solutions to Fractional Difference Boundary Value Problems

The following fractional difference boundary value problems ▵νyt=-ft+ν-1,yt+ν-1, y(ν-2)=y(ν+b+1)=0 are considered, where 1<ν≤2 is a real number and ▵νy(t) is the standard Riemann-Liouville fractional difference. Based on the Krasnosel’skiǐ theorem and the Schauder fixed point theorem, we establish some conditions on f which are able to guarantee that this FBVP has at least two positive solutions and one solution, respectively. Our results significantly improve and generalize those in the literature. A number of examples are given to illustrate our main results

Boosting oxygen evolution over inverse spinel Fe-Co-Mn oxide nanocubes through electronic structure engineering

Fossil fuels are urgent to be replaced with renewable energies to achieve carbon neutrality. Intermittent renewable energies such as solar and wind could be stored in chemical bonds, such as hydrogen and carbon-containing chemicals through water and CO2 electrolyzers respectively. Those two energy systems share a common anodic reaction, the sluggish oxygen evolution reaction (OER), which currently relies on precious noble metals to achieve a reasonable energy conversion efficiency. Herein, tuning the d-band center of Fe-based inverse spinel oxides has been achieved through compositions and morphologies engineering. Ternary Mn0.5Co0.5Fe2O4 nanocubes exhibit oxygen evolution activity superior to the benchmark RuO2. Mössbauer and in-situ infrared spectra combined with density functional theory calculations prove that the optimized d-band center offers a balanced adsorption strength of intermediate *OOH on Mn0.5Co0.5Fe2O4 nanocubes. This work provides a promising approach to the design and synthesis of highly efficient electrocatalysts beyond oxygen evolution.</p

High-purity recycling of hematite and Zn/Cu mixture from waste smelting slag

In this study, Zn/Cu-bearing smelting slag was recycled via an integrated acid dissolution and hematite precipitation method. The slag was dissolved in nitric acid to generate an acid solution containing 23.5 g/L Fe, 4.45 g/L Zn and 2.81 g/L Cu, which was subjected to hydrothermal treatment with the addition of levulinic acid (LA). More than 99.95% of the initial Fe content was removed as hematite particles with diameters of approximately 200 nm, and the residual Fe concentration in the acid was 0.43 mg/L. The generated hematite contained 97.3% Fe2O3, 0.64% ZnO and 0.58% CuO. Greater than 99% of the initial Zn and Cu was retained in the acid and further precipitated as Zn/Cu-bearing solids by adjusting the solution pH to 9. The precipitated Zn/Cu-bearing solids contained 33.6% Zn and 21.7% Cu, whereas the Fe content was less than 0.2%. This paper is the first report of an environmentally friendly approach for recycling smelting slag without generating any hazardous waste

Estimation of biogenic VOC emissions and their corresponding impact on ozone and secondary organic aerosol formation in China

Biogenic volatile organic compounds (BVOC) play an important role in global environmental chemistry and climate. In the present work, biogenic emissions from China in 2017 were estimated based on the Model of Emissions of Gases and Aerosols from Nature (MEGAN). The effects of BVOC emissions on ozone and secondary organic aerosol (SOA) formation were investigated using the WRF-CMAQ modeling system. Three parallel scenarios were developed to assess the impact of BVOC emissions on China's ozone and SOA formation in July 2017. Biogenic emissions were estimated at 23.54 Tg/yr, with a peak in the summer and decreasing from southern to northern China. The high BVOC emissions across eastern and southwestern China increased the surface ozone levels, particularly in the BTH (Beijing-Tianjin-Hebei), SCB (Sichuan Basin), YRD (Yangtze River Delta) and central PRD (Pearl River Delta) regions, with increases of up to 47 μg m−3 due to the sensitivity of VOC-limited urban areas. In summer, most SOA concentrations formed over China are from biogenic sources (national average of 70%). And SOA concentrations in YRD and SCB regions are generally higher than other regions. Excluding anthropogenic emissions while keeping biogenic emissions unchanged results that SOA concentrations reduce by 60% over China, which indicates that anthropogenic emissions can interact with biogenic emissions then facilitate biogenic SOA formation. It is suggested that controlling anthropogenic emissions would result in reduction of both anthropogenic and biogenic SOA.Peer reviewe

Sarcopenia-related Traits, Body Mass Index and Ovarian Cancer Risk: Investigation of Causal Relationships Through Multivariable Mendelian Randomization Analyses

Objective: This study was aimed at exploring the causal relationships of four sarcopenia-related traits (appendicular lean mass, usual walking pace, right hand grip strength, and levels of moderate to vigorous physical activity) with body mass index (BMI) and ovarian cancer risk, by using univariable and multivariable Mendelian randomization (MR) methods. Materials and Methods: Univariable and multivariable MR was performed to estimate causal relationships among sarcopenia-related traits, BMI, and ovarian cancer risk, in aggregated genome-wide association study (GWAS) data from the UK Biobank. Genetic variants associated with each variable (P < 5 × 10−8) were identified as instrumental variables. Three methods—inverse variance weighted (IVW) analysis, weighted median analysis, and MR-Egger regression—were used. Results: Univariable MR analyses revealed positive causal effects of high appendicular lean mass (P = 0.02) and high BMI (P = 0.001) on ovarian cancer occurrence. In contrast, a genetically predicted faster usual walking pace was associated with lower risk of ovarian cancer (P = 0.03). No evidence was found supporting roles of right hand grip strength and levels of moderate to vigorous physical activity in ovarian cancer development (P = 0.56 and P = 0.22, respectively). In multivariable MR analyses, the association between a genetically predicted faster usual walking pace and lower ovarian cancer risk remained significant (P = 0.047). Conclusions: Our study highlights a role of slower usual walking pace in the development of ovarian cancer. Further studies are required to validate our findings and understand the underlying mechanisms

A Microarray Study of Middle Cerebral Occlusion Rat Brain with Acupuncture Intervention

Microarray analysis was used to investigate the changes of gene expression of ischemic stroke and acupuncture intervention in middle cerebral artery occlusion (MCAo) rat brain. Results showed that acupuncture intervention had a remarkable improvement in neural deficit score, cerebral blood flow, and cerebral infarction volume of MCAo rats. Microarray analysis showed that a total of 627 different expression genes were regulated in ischemic stroke. 417 genes were upregulated and 210 genes were downregulated. A total of 361 different expression genes were regulated after acupuncture intervention. Three genes were upregulated and 358 genes were downregulated. The expression of novel genes after acupuncture intervention, including Tph1 and Olr883, was further analyzed by Real-Time Quantitative Polymerase Chain Reaction (RT-PCR). Upregulation of Tph1 and downregulation of Olr883 indicated that the therapeutic effect of acupuncture for ischemic stroke may be closely related to the suppression of poststroke depression and regulation of olfactory transduction. In conclusion, the present study may enrich our understanding of the multiple pathological process of ischemic brain injury and indicate possible mechanisms of acupuncture on ischemic stroke

A Novel Classification of Glioma Subgroup, Which Is Highly Correlated With the Clinical Characteristics and Tumor Tissue Characteristics, Based on the Expression Levels of Gβ and Gγ Genes

PurposeGlioma is a classical type of primary brain tumors that is most common seen in adults, and its high heterogeneity used to be a reference standard for subgroup classification. Glioma has been diagnosed based on histopathology, grade, and molecular markers including IDH mutation, chromosome 1p/19q loss, and H3K27M mutation. This subgroup classification cannot fully meet the current needs of clinicians and researchers. We, therefore, present a new subgroup classification for glioma based on the expression levels of Gβ and Gγ genes to complement studies on glioma and Gβγ subunits, and to support clinicians to assess a patient’s tumor status.MethodsGlioma samples retrieved from the CGGA database and the TCGA database. We clustered the gliomas into different groups by using expression values of Gβ and Gγ genes extracted from RNA sequencing data. The Kaplan–Meier method with a two-sided log-rank test was adopted to compare the OS of the patients between GNB2 group and non-GNB2 group. Univariate Cox regression analysis was referred to in order to investigate the prognostic role of each Gβ and Gγ genes. KEGG and ssGSEA analysis were applied to identify highly activated pathways. The “estimate” package, “GSVA” package, and the online analytical tools CIBERSORTx were employed to evaluate immune cell infiltration in glioma samples.ResultsThree subgroups were identified. Each subgroup had its own specific pathway activation pattern and other biological characteristics. High M2 cell infiltration was observed in the GNB2 subgroup. Different subgroups displayed different sensitivities to chemotherapeutics. GNB2 subgroup predicted poor survival in patients with gliomas, especially in patients with LGG with mutation IDH and non-codeleted 1p19q.ConclusionThe subgroup classification we proposed has great application value. It can be used to select chemotherapeutic drugs and the prognosis of patients with target gliomas. The unique relationships between subgroups and tumor-related pathways are worthy of further investigation to identify therapeutic Gβγ heterodimer targets