Chromatin Dynamics Regulate Transcriptional Homeostasis

Eukaryotic promoters are inherently bidirectional and allow RNA Polymerase II to transcribe both coding and noncoding RNAs. Dynamic disassembly and reassembly is a prominent feature of nucleosomes around eukaryotic promoters. While H3K56 acetylation (H3K56Ac) enhances turnover events of these promoter-proximal nucleosomes, the chromatin remodeler INO80C ensures their proper positioning. In my dissertation, I explore how chromatin dynamics regulate transcriptional homeostasis. In the first part, I investigate the role of H3K56Ac on the nascent transcriptome throughout the eukaryotic cell cycle. I find that H3K56Ac is a global, positive regulator for coding and noncoding transcription by promoting both initiation and elongation/termination. On the contrary, I find that H3K56Ac represses promiscuous transcription following replication fork passage by ensuring efficient nucleosome assembly during S-phase. In addition, I show that there is a stepwise increase in transcription in the S-G2 transition, and this response to gene dosage imbalance does not require H3K56Ac. This study clearly shows that a single histone modification, H3K56Ac can exert both positive and negative effects on transcription at different cell cycle stages. In the second part, I investigate the role of the chromatin remodeler INO80C on the nascent transcription around replication origins. I show that INO80C, together with the transcription factor Mot1, prevents cryptic transcription around yeast replication origins, and the loss of these proteins lead to an increase in DNA double strand breaks. I hypothesize that recruitment of INO80C ensures proper positioning of nucleosomes around origins and the exclusion of RNA Pol II to prevent cryptic initiation. Together these findings indicate that H3K56Ac regulates transcription globally by enhancing nucleosome turnover, and it prevents cryptic transcription and reinforces transcriptional fidelity by promoting efficient nucleosome assembly in the S-phase. In addition, INO80C maintains genome stability by preventing cryptic transcription around the origins

Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast

Dynamic disruption and reassembly of promoter-proximal nucleosomes is a conserved hallmark of transcriptionally active chromatin. Histone H3-K56 acetylation (H3K56Ac) enhances these turnover events and promotes nucleosome assembly during S phase. Here we sequence nascent transcripts to investigate the impact of H3K56Ac on transcription throughout the yeast cell cycle. We find that H3K56Ac is a genome-wide activator of transcription. While H3K56Ac has a major impact on transcription initiation, it also appears to promote elongation and/or termination. In contrast, H3K56Ac represses promiscuous transcription that occurs immediately following replication fork passage, in this case by promoting efficient nucleosome assembly. We also detect a stepwise increase in transcription as cells transit S phase and enter G2, but this response to increased gene dosage does not require H3K56Ac. Thus, a single histone mark can exert both positive and negative impacts on transcription that are coupled to different cell cycle events

Monocyte to high-density lipoprotein cholesterol ratio is predictive of in-hospital and five-year mortality in ST-segment elevation myocardial infarction

Background: We assessed the value of monocyte to high-density lipoprotein cholesterol ratio (MHR) in predicting in-hospital and 5-year mortality and major adverse cardiovascular events (MACE) in ST-segment elevation myocardial infarction (STEMI) patients. Methods: A group of 1,598 patients were enrolled and divided into tertiles according to MHR values. The effects of different variables on clinical outcomes were assessed by Cox regression analysis. Results: MHR was found as an independent predictor of in-hospital mortality (HR = 3.745, 95% CI 1.308–5.950), in-hospital MACE (HR 1.501, 95% CI 1.015–1.993, p = 0.022) and 5-year mortality (HR = 2.048, 95% CI 1.225–4.091, p = 0.014) and 5-year MACE (HR 1.285, 95% CI 1.064–1.552, p = 0.009). Conclusions: MHR is an independent predictor of in-hospital and long term mortality and MACE in STEMI

INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins

The proper coordination of transcription with DNA replication and repair is central for genomic stability. We investigate how the INO80C chromatin remodeling enzyme might coordinate these genomic processes. We find that INO80C co-localizes with the origin recognition complex (ORC) at yeast replication origins and is bound to replication initiation sites in mouse embryonic stem cells (mESCs). In yeast, INO80C recruitment requires origin sequences but does not require ORC, suggesting that recruitment is independent of pre-replication complex assembly. In both yeast and ESCs, INO80C co-localizes at origins with Mot1 and NC2 transcription factors, and genetic studies suggest that they function together to promote genome stability. Interestingly, nascent transcript sequencing demonstrates that INO80C and Mot1 prevent pervasive transcription through origin sequences, and absence of these factors leads to formation of new DNA double-strand breaks. We propose that INO80C and Mot1/NC2 function through distinct pathways to limit origin transcription, maintaining genomic stability

Functional Conservation of Nucleosome Formation Selectively Biases Presumably Neutral Molecular Variation in Yeast Genomes

One prominent pattern of mutational frequency, long appreciated in comparative genomics, is the bias of purine/pyrimidine conserving substitutions (transitions) over purine/pyrimidine altering substitutions (transversions). Traditionally, this transitional bias has been thought to be driven by the underlying rates of DNA mutation and/or repair. However, recent sequencing studies of mutation accumulation lines in model organisms demonstrate that substitutions generally do not accumulate at rates that would indicate a transitional bias. These observations have called into question a very basic assumption of molecular evolution; that naturally occurring patterns of molecular variation in noncoding regions accurately reflect the underlying processes of randomly accumulating neutral mutation in nuclear genomes. Here, in Saccharomyces yeasts, we report a very strong inverse association (r = −0.951, P < 0.004) between the genome-wide frequency of substitutions and their average energetic effect on nucleosome formation, as predicted by a structurally based energy model of DNA deformation around the nucleosome core. We find that transitions occurring at sites positioned nearest the nucleosome surface, which are believed to function most importantly in nucleosome formation, alter the deformation energy of DNA to the nucleosome core by only a fraction of the energy changes typical of most transversions. When we examined the same substitutions set against random background sequences as well as an existing study reporting substitutions arising in mutation accumulation lines of Saccharomyces cerevisiae, we failed to find a similar relationship. These results support the idea that natural selection acting to functionally conserve chromatin organization may contribute significantly to genome-wide transitional bias, even in noncoding regions. Because nucleosome core structure is highly conserved across eukaryotes, our observations may also help to further explain locally elevated transition bias at CpG islands, which are known to destabilize nucleosomes at vertebrate promoters

Patient use of complementary and alternative medicine for psoriasis vulgaris and factors believed to trigger the disease: A multicenter cross-sectional study with 1621 patients

Introduction: Due to the chronic recurrent nature of psoriasis vulgaris (PV) and lack of definitive treatment for the disease, patients often resort to alternative treatments. Physicians seem to have low awareness of this issue. Objectives: To elicit the perceptions of 1,621 PV patients on complementary and alternative medicine (CAM) and examine factors reported to worsen PV. Methods: The patients sociodemographic characteristics, Psoriasis Area Severity Index (PASI), Dermatology Life Quality Index (DLQI), disease duration, and severity were recorded, and the patients CAM use was questioned in detail. The patients were also asked about factors that worsened PV and their experiences with a gluten-free diet. Results: Of the patients, 56.51% had used CAM. The mean age, illness duration, PASI scores and DLQI of those using CAM were significantly higher. CAM use was significantly higher in those with facial, genital involvement, and arthralgia/arthritis. The patients mostly referred to CAM when PV became severe (46.4%). Of the CAM users, 45.52% used herbal topicals. The physicians of 67.03% did not inquire whether they used CAM. Of the participants, 37.73% considered that stress worsened their disease. Gluten-free diet did not affect PV symptoms in 52.22%. Conclusions: Patients CAM use is often overlooked by dermatologists. Our results showed that more than half the patients used CAM and did not share this information with their physicians. Therefore, the awareness of physicians should be increased and patients should be asked about the use of CAM and directed to the appropriate medical treatment options by physicians

Habits of using social media and the internet in psoriasis patients

Introduction: Psoriasis significantly affects the patients quality of life, which often leads patients to seek online information about this disease. Objectives: To explore the habits of patients with psoriasis related to their use of social media (SM) and the internet to obtain information about their disease. Methods: 1,520 patients completed the survey and the Dermatology Life Quality Index (DLQI) questionnaire. The Psoriasis Area Severity Index scores (PASI) and clinical data of the patients were recorded by their physicians. Results: Of the 1,114 patients that reported using SM and internet, 48.38% regularly and 31.14% sometimes resorted to obtain information about psoriasis. The use of SM and internet for psoriasis was statistically significantly higher among young people (P = 0.000), those with university or higher education (P = 0.009), higher DLQI (P = 0.000) and PASI (P = 0.011) scores, facial (P = 0.050), scalp (P = 0.032), hand (P = 0.048), genital (P = 0.001) and inverse (P = 0.000) involvement, and arthralgia/arthritis (P = 0.006). The participants mostly used the Google (86%) and Facebook (41%). More than half of the participants (62.8%) expected dermatologists to inform society that psoriasis is not contagious. Conclusions: Internet and SM being widely available and offering substantial information to be easily accessed make it very attractive for patients to use these platforms to investigate diseases, including psoriasis. If what is presented on SM conflicts with what the physician says, patients mostly trust the latter, but at the same time, they tend not to share the results of their online inquiries with their physicians