Impact of a Rounding Checklist Implementation in the Trauma Intensive Care Unit on Clinical Outcomes.

We aimed to evaluate the effectiveness of an intensive care unit (ICU) round checklist, FAST HUGS BID (Feeding, Analgesia, Sedation, Thromboembolic prophylaxis, Head-of-bed elevation, Ulcer prophylaxis, Glycemic control, Spontaneous breathing trial, Bowel regimen, Indwelling catheter removal, and De-escalation of antibiotics-abbreviated as FD hereafter), in improving clinical outcomes in patients with severe trauma. We included patients admitted to our trauma ICU from 2016 to 2020 and divided them into two groups: before (before-FD, 2016-2017) and after (after-FD, 2019-2020) implementation of the checklist. We compared patient characteristics and clinical outcomes, including ICU and hospital length of stay (LOS) and in-hospital mortality. Survival analysis was performed using Kaplan-Meier curves and multivariable logistic regression models; furthermore, multiple linear regression analysis was used to identify independent factors associated with ICU and hospital LOS. Compared with the before-FD group, the after-FD group had significantly lower in-hospital mortality and complication rates, shorter ICU and hospital LOS, and reduced duration of mechanical ventilation. Moreover, implementation of the checklist was a significant independent factor in reducing ICU and hospital LOS and in-hospital mortality. Implementation of the FD checklist is associated with decreased ICU and hospital LOS and in-hospital mortality.

B-Cell-Mediated Immunity Predicts Survival of Patients With Estrogen Receptor-Positive Breast Cancer.

PURPOSE: The estrogen receptor-positive (ER+) breast cancer (BC), which constitutes the majority of BC cases, exhibits highly heterogeneous clinical behavior. To aid precision treatments, we aimed to find molecular subtypes of ER+ BC representing the tumor microenvironment and prognosis. METHODS: We analyzed RNA-seq data of 113 patients with BC and classified them according to the PAM50 intrinsic subtypes using gene expression profiles. Among them, we further focused on 44 patients with luminal-type (ER+) BC for subclassification. The Cancer Genome Atlas (TCGA) data of patients with BC were used as a validation data set to verify the new classification. We estimated the immune cell composition using CIBERSORT and further analyzed its association with clinical or molecular parameters. RESULTS: Principal component analysis clearly divided the patients into two subgroups separately from the luminal A and B classification. The top differentially expressed genes between the subgroups were distinctly characterized by immunoglobulin and B-cell-related genes. We could also cluster a separate cohort of patients with luminal-type BC from TCGA into two subgroups on the basis of the expression of a B-cell-specific gene set, and patients who were predicted to have high B-cell immune activity had better prognoses than other patients. CONCLUSION: Our transcriptomic approach emphasize a molecular phenotype of B-cell immunity in ER+ BC that may help to predict disease prognosis. Although further researches are required, B-cell immunity for patients with ER+ BC may be helpful for identifying patients who are good responders to chemotherapy or immunotherapy.

Clinicogenetic characteristics and the effect of radiation on the neural stem cell niche in subventricular zone-contacting glioblastoma.

BACKGROUND AND PURPOSE: Neural stem cells (NSCs) in the subventricular zone (SVZ) are recognized as the cellular origin of glioblastoma (GBM) and a potential therapeutic target. However, the characteristics of SVZ contacting GBM (SVZ + GBM) and radiotherapeutic strategies for NSCs are still controversial. Here, we investigated the clinicogenetic features of SVZ + GBM and evaluated the dose effect of NSC irradiation depending on SVZ involvement. MATERIALS AND METHODS: We identified 125 patients with GBM treated with surgery followed by chemoradiotherapy. The genomic profiles were obtained by next-generation sequencing targeting 82 genes. NSCs in the SVZ and hippocampus were contoured using standardized methods, and dosimetric factors were analyzed. SVZ + GBM was defined as GBM with SVZ involvement in a T1 contrast-enhanced image. Progression-free survival (PFS) and overall survival (OS) were used as endpoints. RESULTS: The number of patients with SVZ + GBM was 95 (76%). SVZ + GBM showed lower PFS than GBM without SVZ involvement (SVZ-GBM) (median 8.6 vs. 11.5 months, p = 0.034). SVZ contact was not associated with any specific genetic profile but was an independent prognostic factor in multivariate analysis. In SVZ + GBM, patients receiving high doses to the ipsilateral NSC region showed significantly better OS (HR = 1.89, p = 0.011) and PFS (HR = 1.77, p = 0.013). However, in SVZ-GBM, high doses to the ipsilateral NSC region were associated with worse OS (HR = 0.27, p = 0.013) and PFS (HR = 0.37, p = 0.035) in both univariate and multivariate analyses. CONCLUSION: SVZ involvement in GBM was not associated with distinct genetic features. However, irradiation of NSCs was associated with better prognosis in patients with tumors contacting the SVZ.

Impact of spinal injury on mortality in patients with major trauma: A propensity-matched cohort study.

Major trauma is defined as a significant injury or injury that has the potential to be life-threatening and is quantitatively identified as an injury severity score (ISS) >15. Spinal injuries are common in patients with major trauma; however, because spinal injury is not independently included in the ISS calculation, the impact of spinal injury on mortality in patients with major trauma has not been fully elucidated. The purpose of this study is to identify the association between spinal injury and mortality in patients with major trauma. From January 1, 2016, to December 31, 2020, retrospective analysis was conducted on 2893 major trauma adult patients admitted to a level 1 trauma center. There were 781 patients in the spinal injury group and 2112 patients in the group without spinal injury. After matching the 2 groups 1:1, we compared injury mechanism, mortality, cause of death, intensive care unit length of stay (ICU LOS), and duration of ventilator use between spinal injury group and matched cohorts. Falls and traffic accidents were the most common injury mechanisms in the spinal injury group and the matched cohort, respectively. The mortality was significantly lower in the spinal injury group compared with the matched cohort (4.0% vs 7.9%, P = .001), and the ICU LOS was longer than the matched cohort (8.8 ± 17.4 days vs 7.2 ± 11.7 days, P = .028). In the spinal injury group, multiple organ failure (MOF) was the most common cause of death (41.9%), while that in the matched cohort was central nervous system (CNS) damage (61.3%). In patients with major trauma, spinal injury may act as a shock absorber for internal organs, which is thought to lower the mortality rate.

Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions.

Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.

Predictors of Post-chemoradiotherapy Pulmonary Complication in Locally Advanced Non-Small Cell Lung Cancer.

PURPOSE: We investigated the clinical effects and predictive factors of severe post-chemoradiotherapy pulmonary complications (PCPC) in locally advanced non-small cell lung cancer (LA-NSCLC). Materials and Methods: Medical records of 317 patients who underwent definitive concurrent chemoradiation (CCRT) for LA-NSCLC were reviewed retrospectively. PCPC was defined as an event of admission or emergency department visit for acute or subacute pulmonary inflammatory complications, including pneumonitis and pneumonia, within 6 months after CCRT initiation. Patient characteristics, baseline lung function tests, radiation dosimetric parameters, and laboratory tests were analyzed to investigate their association with PCPC. Prognostic endpoints were disease progression rate (DPR) and overall survival (OS). RESULTS: PCPC was reported in 53 patients (16.7%). The OS of patients with PCPC was significantly worse (35.0% in 2 years) than that of patients without PCPC (67.0% in 2 years, p < 0.001). However, 2-year DPRs were 77.0% and 70.7% in patients with and without PCPC, respectively, which were not significantly different (p=0.087). In multivariate logistic regression, PCPC was independently associated with grade ≥ 1 hypoalbuminemia during CCRT (odds ratio [OR], 5.670; 95% confidence interval [CI], 2.487 to 13.40; p < 0.001), lower diffusing capacity of carbon monoxide (DLCO) (per mL/min/mmHg; OR, 0.855; 95% CI, 0.743 to 0.974; p=0.022), and higher lung V5 (per 10%; OR, 1.872; 95% CI, 1.336 to 2.699; p < 0.001). CONCLUSION: PCPC might be a clinical endpoint to evaluate complications and predict the survival of patients subjected to CCRT for LA-NSCLC. Hypoalbuminaemia, DLCO, and lung V5 might predict PCPC in LA-NSCLC.

Radiosensitivity is associated with antitumor immunity in estrogen receptor-negative breast cancer.

PURPOSE: This study evaluated radiosensitivity and the tumor microenvironment (TME) to identify characteristics of breast cancer patients who would benefit most from radiation therapy. METHODS: We analyzed 1903 records from the Molecular Taxonomy of Breast Cancer International Consortium cohort using the radiosensitivity index and gene expression deconvolution algorithms, CIBERSORT and xCell, that estimates the TME composition of tumor samples. In this study, patients were stratified according to TME and radiosensitivity. We performed integrative analyses of clinical and immuno-genomic data to characterize molecular features associated with radiosensitivity. RESULTS: Radiosensitivity was significantly associated with activation of antitumor immunity. In contrast, radioresistance was associated with a reactive stromal microenvironment. The immuno-genomic analysis revealed that estrogen receptor (ER) pathway activity was correlated with suppression of antitumor immunity. In ER-negative disease, the best prognosis was shown in the immune-high and radiosensitive group patients, and the lowest was in the immune-low and radioresistant group patients. In ER-positive disease, immune signature and radiosensitivity had no prognostic significance. CONCLUSION: Taken together, these results suggest that tumor radiosensitivity is associated with activation of antitumor immunity and a better prognosis, particularly in patients with ER-negative breast cancer.

Prediction and clinical impact of delayed lymphopenia after chemoradiotherapy in locally advanced non-small cell lung cancer.

Introduction: The dosimetric factors of radiotherapy have an acute impact on the host immune system during chemoradiotherapy (CRT) in locally advanced non-small cell lung cancer (NSCLC). However, even after CRT, a substantial number of patients remain immunosuppressed with delayed lymphopenia. Therefore, we aimed to evaluate clinical and dose-volumetric predictors of delayed lymphopenia after CRT in locally advanced NSCLC. Materials and methods: We retrospectively reviewed 272 patients with locally advanced NSCLC who received definitive CRT from January 2012 to August 2020. Differential blood count data, including serum albumin values, were obtained at baseline, during and at first follow up after CRT. Acute and delayed lymphopenia events were defined as grade III/IV lymphopenia developed during or 4-12 weeks after CRT completion, which accounted for 84% and 10% of cases, respectively. Dose-volume histogram parameters for planned target volume, whole body, heart, lung, great vessels, spleen, esophagus and thoracic vertebral bodies were evaluated. Results: Multivariate analysis revealed that patients with delayed lymphopenia were associated with inferior overall survival (HR 2.53, P = 0.001) and progression-free survival (HR 1.98, P = 0.006). However, there was no significant survival difference between groups stratified by acute lymphopenia. On multivariable logistic regression models, lung V5, baseline ALC, during-CRT ALC, and albumin nadir were significant predictors for delayed lymphopenia. Furthermore, the nomogram for delayed lymphopenia based on these variables had good discrimination (area under the curve, 0.905). Conclusions: In this study, we investigated the prognostic significance of delayed lymphopenia and identified clinico-dosimetric parameters to predict delayed lymphopenia.

Synthetic PPAR Agonist DTMB Alleviates Alzheimer's Disease Pathology by Inhibition of Chronic Microglial Inflammation in 5xFAD Mice.

Abnormal productions of amyloid beta (Aß) plaque and chronic neuroinflammation are commonly observed in the brain of patients with Alzheimer's disease, and both of which induce neuronal cell death, loss of memory, and cognitive dysfunction. However, many of the drugs targeting the production of Aß peptides have been unsuccessful in treating Alzheimer's disease. In this study, we identified synthetic novel peroxisome proliferator-activating receptor (PPAR) agonist, DTMB, which can ameliorate the chronic inflammation and Aß pathological progression of Alzheimer's disease. We discovered that DTMB attenuated the proinflammatory cytokine production of microglia by reducing the protein level of NF-κB. DTMB also improved the learning and memory defects and reduced the amount of Aß plaque in the brain of 5xFAD mice. This reduction in Aß pathology was attributed to the changes in gliosis and chronic inflammation level. Additionally, bulk RNA-sequencing showed that genes related to inflammation and cognitive function were changed in the hippocampus and cortex of DTMB-treated mice. Our findings demonstrate that DTMB has the potential to be a novel therapeutic agent for Alzheimer's disease.

The Chromatin Accessibility Landscape of Nonalcoholic Fatty Liver Disease Progression.

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the generegulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

Retropharyngeal lymph node-sparing radiotherapy in patients with oropharyngeal carcinoma.

PURPOSE: In radiotherapy for head and neck cancer, it is crucial to define the appropriate treatment volume to determine treatment outcome and toxicity. We examined the feasibility of omitting elective high retropharyngeal lymph node (RPLN) irradiation in patients with oropharyngeal cancer. MATERIALS AND METHODS: We performed a retrospective review of 189 patients with oropharyngeal squamous cell carcinoma who were treated with definitive or postoperative radiation therapy between 2009 and 2016. Of them, 144 (76.2%) underwent ipsilateral RPLN irradiation up to the superior border of the C1 vertebral body, while the other 45 (23.8%) were irradiated up to the transverse process of the C1 vertebra. High RPLN-treated and spared group were propensity matched based on key clinical variables. RESULTS: During the follow-up period, only three patients (one in the high RPLN-treated group and two in the high RPLN-spared group) developed RPLN recurrence. There were no significant between-group differences in 5-year locoregional failure-free survival (82.8% vs. 90.6%; p = 0.14), distant metastasis-free survival (93.1% vs. 93.3%; p = 0.98) and RPLN failure-free survival (99.3% vs. 95.0%; p = 0.09). In the matched groups, high RPLN-spared patients received a lower mean ipsilateral parotid gland dose (mean, 20.8 Gy vs. 29.9 Gy; p < 0.001) and had a lower incidence of chronic xerostomia (grade 0, 43.5% vs. 13.0%; p = 0.023) at 1 year after radiotherapy compared with high RPLN-treated patients. CONCLUSION: Omission of ipsilateral high RPLN irradiation seems safe, and reduces the incidence of chronic xerostomia in patients with oropharyngeal squamous cell carcinoma.

hnRNP K supports the maintenance of RORγ circadian rhythm through ERK signaling.

Retinoic acid-related orphan receptor γ (RORγ) maintains the circadian rhythms of its downstream genes. However, the mechanism behind the transcriptional activation of RORγ itself remains unclear. Here, we demonstrate that transcription of RORγ is activated by heterogeneous nuclear ribonucleoprotein K (hnRNP K) via the poly(C) motif within its proximal promoter. Interestingly, we confirmed the binding of endogenous hnRNP K within RORγ1 and RORγ2 promoter along with the recruitment of RNA polymerase 2 through chromatin immunoprecipitation (ChIP). Furthermore, an assay for transposase accessible chromatin (ATAC)-qPCR showed that hnRNP K induced higher chromatin accessibility within the RORγ1 and RORγ2 promoter. Then we found that the knockdown of hnRNP K lowers RORγ mRNA oscillation amplitude in both RORγ and RORγ-dependent metabolic genes. Moreover, we demonstrated that time-dependent extracellular signal-regulated kinase (ERK) activation controls mRNA oscillation of RORγ and RORγ-dependent metabolic genes through hnRNP K. Taken together, our results provide new insight into the regulation of RORγ by hnRNP K as a transcriptional activator, along with its physiological significance in metabolism.

Creation of bladder assembloids mimicking tissue regeneration and cancer.

Current organoid models are limited by their inability to mimic mature organ architecture and associated tissue microenvironments1,2. Here we create multilayer bladder 'assembloids' by reconstituting tissue stem cells with stromal components to represent an organized architecture with an epithelium surrounding stroma and an outer muscle layer. These assembloids exhibit characteristics of mature adult bladders in cell composition and gene expression at the single-cell transcriptome level, and recapitulate in vivo tissue dynamics of regenerative responses to injury. We also develop malignant counterpart tumour assembloids to recapitulate the in vivo pathophysiological features of urothelial carcinoma. Using the genetically manipulated tumour-assembloid platform, we identify tumoural FOXA1, induced by stromal bone morphogenetic protein (BMP), as a master pioneer factor that drives enhancer reprogramming for the determination of tumour phenotype, suggesting the importance of the FOXA1-BMP-hedgehog signalling feedback axis between tumour and stroma in the control of tumour plasticity.

Microsatellite Instability Correlated Inflammatory Markers and their Prognostic Value in the Rectal Cancer Following Neoadjuvant Chemoradiotherapy: A Hypothesis-generating Study.

BACKGROUND/AIM: This study aimed to analyze the correlation between microsatellite instability (MSI) and inflammatory markers during neoadjuvant CRT in rectal cancer and its influence on prognosis. PATIENTS AND METHODS: A total of 549 patients with locally advanced rectal cancer underwent neoadjuvant CRT. Complete blood counts before CRT, and 4-8 weeks after CRT were used to measure neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR). RESULTS: MSI was significantly associated with elevated NLR and PLR after CRT as well as with a change in NLR and PLR during CRT. Neither inflammatory markers nor MSI significantly related to survival. However, in patients with MSI, an increase in NLR and PLR before CRT was significantly correlated with poor overall survival and disease-free survival. CONCLUSION: There is correlation between inflammatory markers and MSI during CRT and it influences prognosis. Therefore, inflammatory markers might have a role in assessing the microenvironment related to MSI and the immunologic response in rectal cancer.

Genomic and Transcriptomic Characteristics According to Size of Papillary Thyroid Microcarcinoma.

It is controversial as to whether papillary thyroid microcarcinoma (PTMC) has some genomic and transcriptomic characteristics that differentiate between an early-stage lesion that would eventually evolve into the larger papillary thyroid cancer (PTC), and an occult indolent cancer in itself. To investigate this, we comprehensively elucidated the genomic and transcriptomic landscapes of PTMCs of different sizes, using a large-scaled database. This study included 3435 PTCs, 1985 of which were PTMCs. We performed targeted next-generation sequencing for 221 PTCs and integrated these data with the data including The Cancer Genome Atlas (TCGA) project. The frequency of v-raf murine sarcoma viral oncogene homolog B (BRAF)V600E mutation was higher in PTMCs >0.5 cm than that in very small PTMCs (≤0.5 cm) and decreased again in PTCs >2 cm. Among PTMCs, the prevalence of mutations in rat sarcoma (RAS) and telomerase reverse transcriptase (TERT) promoter was not significantly different according to their size, but lower than in large PTCs. There was no change in the tumor mutational burden, the number of driver mutations, and transcriptomic profiles with tumor size, among PTMCs and all PTCs. Although a few genes with differential expression and TERT promoter mutations were found in a few PTMCs, our findings showed that there were no useful genomic or transcriptomic characteristics for the prediction of the future progression of PTMC.

Bioinformatics services for analyzing massive genomic datasets.

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.

Nomogram for Predicting the Pathological Tumor Response from Pre-treatment Clinical Characteristics in Rectal Cancer.

BACKGROUND/AIM: To develop a nomogram for predicting the pathological tumor response to preoperative chemoradiotherapy (CRT) for locally advanced rectal cancer based on pre-treatment magnetic resonance imaging (MRI) and blood test characteristics. PATIENTS AND METHODS: This retrospective study included 514 patients who underwent MRI and received preoperative CRT followed by surgical resection. Pathological tumor response was assessed as good [Dworak tumor regression grade (TRG) 3 or 4] or poor (TRG 0-2). A nomogram for good response was developed using stepwise logistic regression analysis. RESULTS: A nomogram based on longitudinal tumor diameter, extramural tumor invasion depth, carcinoembryonic antigen and hemoglobin levels, age, and interval between CRT and surgery gave an area under the receiver operating characteristic curve for a good response of 0.721 (95%CI=0.676-0.768). CONCLUSION: Our nomogram based on pre-treatment clinical characteristics can predict the tumor response to CRT, which may help identify patients who can benefit most from CRT.

hnRNP K Supports High-Amplitude D Site-Binding Protein mRNA (Dbp mRNA) Oscillation To Sustain Circadian Rhythms.

Circadian gene expression is defined by the gene-specific phase and amplitude of daily oscillations in mRNA and protein levels. D site-binding protein mRNA (Dbp mRNA) shows high-amplitude oscillation; however, the underlying mechanism remains elusive. Here, we demonstrate that heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a key regulator that activates Dbp transcription via the poly(C) motif within its proximal promoter. Biochemical analyses identified hnRNP K as a specific protein that directly associates with the poly(C) motif in vitro Interestingly, we further confirmed the rhythmic binding of endogenous hnRNP K within the Dbp promoter through chromatin immunoprecipitation as well as the cycling expression of hnRNP K. Finally, knockdown of hnRNP K decreased mRNA oscillation in both Dbp and Dbp-dependent clock genes. Taken together, our results show rhythmic protein expression of hnRNP K and provide new insights into its function as a transcriptional amplifier of Dbp.

Comparative analysis of commonly used peak calling programs for ChIP-Seq analysis.

Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq) is a powerful technology to profile the location of proteins of interest on a whole-genome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could accurately explain the binding features of target proteins detected by ChIP-Seq. Here, publicly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was compared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak prediction. There were no major differences among peak callers when analyzing point source histone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parameters, which indicates that their peak positions might not be located accurately. Our comparative results could provide a helpful guide to choose a suitable peak calling program for specific histone modifications.

The Poly(C) Motif in the Proximal Promoter Region of the D Site-Binding Protein Gene (Dbp) Drives Its High-Amplitude Oscillation.

The D site-binding protein (Dbp) supports the rhythmic transcription of downstream genes, in part by displaying high-amplitude cycling of its own transcripts compared to other circadian-clock genes. However, the underlying mechanism remains elusive. Here, we demonstrated that the poly(C) motif within the Dbp proximal promoter, in addition to an E-box element, provoked transcriptional activation. Furthermore, we generated a cell line with poly(C) deleted to demonstrate the endogenous effect of the poly(C) motif within the Dbp promoter. We investigated whether RNA polymerase 2 (Pol2) recruitment on the Dbp promoter was decreased in the cell line with poly(C) deleted. Next, assay for transposase-accessible chromatin (ATAC)-quantitative PCR (qPCR) showed that the poly(C) motif induced greater chromatin accessibility within the region of the Dbp promoter. Finally, we determined that the oscillation amplitude of endogenous Dbp mRNA of the cell line with poly(C) deleted was decreased, which affected the oscillation of other clock genes that are controlled by Dbp Taken together, our results provide new insights into the function of the poly(C) motif as a novel cis-acting element of Dbp, along with its significance in the regulation of circadian rhythms.