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Your search keyword '"Xie, S. Q."' showing total 8 results
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8 results on '"Xie, S. Q."'

3. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs

Author

Brookes, E., de Santiago, I., Hebenstreit, D., Morris, K. J., Carroll, T., Xie, S. Q., Stock, J. K., Heidemann, M., Eick, D., Nozaki, N., Kimura, Hiroshi, Ragoussis, J., Teichmann, S. A., and Pombo, A.

Subjects
Polycomb-Group Proteins, RNA polymerase II, Ubiquitin-Protein Ligases/genetics/metabolism, Mice, 0302 clinical medicine, Repressor Proteins/genetics/*metabolism, Genetics, Polycomb Repressive Complex 1, 0303 health sciences, Gene knockdown, education.field_of_study, biology, Cell Cycle, Gene Expression Regulation, Developmental, Chromatin, Protein Transport, Gene Knockdown Techniques, Molecular Medicine, RNA Polymerase II, PRC1, Protein Binding, animal structures, Ubiquitin-Protein Ligases, Population, Repressor, Article, Protein Binding/genetics, Cell Line, Chromatin/metabolism, 03 medical and health sciences, Gene silencing, Animals, Cell Cycle/genetics, education, Gene, Embryonic Stem Cells, 030304 developmental biology, Energy Metabolism/genetics, Embryonic Stem Cells/cytology/*metabolism, Embroyonic stem-cells, Transcription factors, Epigenetic states, Bivalent genes, Self-renewal, Differentiation, Pluripotency, Marks, SEQ, Heterogeneity, Gene Expression Profiling, Cell Biology, RNA Polymerase II/genetics/*metabolism, Repressor Proteins, biology.protein, Energy Metabolism, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Summary Polycomb repressor complexes (PRCs) are important chromatin modifiers fundamentally implicated in pluripotency and cancer. Polycomb silencing in embryonic stem cells (ESCs) can be accompanied by active chromatin and primed RNA polymerase II (RNAPII), but the relationship between PRCs and RNAPII remains unclear genome-wide. We mapped PRC repression markers and four RNAPII states in ESCs using ChIP-seq, and found that PRC targets exhibit a range of RNAPII variants. First, developmental PRC targets are bound by unproductive RNAPII (S5p+S7p−S2p−) genome-wide. Sequential ChIP, Ring1B depletion, and genome-wide correlations show that PRCs and RNAPII-S5p physically bind to the same chromatin and functionally synergize. Second, we identify a cohort of genes marked by PRC and elongating RNAPII (S5p+S7p+S2p+); they produce mRNA and protein, and their expression increases upon PRC1 knockdown. We show that this group of PRC targets switches between active and PRC-repressed states within the ESC population, and that many have roles in metabolism., Graphical Abstract Highlights ► A unique RNAPII variant (S5p+S7p−S2p−) binds PRC targets genome-wide in ESCs ► RNAPII-S5p and PRC coincide in time and localization, and show proportional abundance ► Novel, active PRC-target genes identified in ESCs include metabolic genes ► Active PRC targets switch between on/off (active/PRC) states in the ESC population

Published
2016

8. Bayesian approach to model pedestrian crashes at signalized intersections with measurement errors in exposure.

Author

Xie SQ, Dong N, Wong SC, Huang H, and Xu P

Subjects
Bayes Theorem, Hong Kong, Humans, Population Density, Accidents, Traffic statistics & numerical data, Environment Design, Location Directories and Signs statistics & numerical data, Pedestrians statistics & numerical data
Abstract

This study intended to identify the potential factors contributing to the occurrence of pedestrian crashes at signalized intersections in a densely populated city, based on a comprehensive dataset of 898 pedestrian crashes at 262 signalized intersections during 2010-2012 in Hong Kong. The detailed geometric design, traffic characteristics, signal control, built environment, along with the vehicle and pedestrian volumes were elaborately collected. A Bayesian measurement errors model was introduced as an alternative method to explicitly account for the uncertainties in volume data. To highlight the role played by exposure, models with and without pedestrian volume were estimated and compared. The results indicated that the omission of pedestrian volume in pedestrian crash frequency models would lead to reduced goodness-of-fit, biased parameter estimates, and incorrect inferences. Our empirical analysis demonstrated the existence of moderate uncertainties in pedestrian and vehicle volumes. Six variables were found to have a significant association with the number of pedestrian crashes at signalized intersections. The number of crossing pedestrians, the number of passing vehicles, the presence of curb parking, and the presence of ground-floor shops were positively related with pedestrian crash frequency, whereas the presence of playgrounds near intersections had a negative effect on pedestrian crash occurrences. Specifically, the presence of exclusive pedestrian signals for all crosswalks was found to significantly reduce the risk of pedestrian crashes by 43%. The present study is expected to shed more light on a deeper understanding of the environmental determinants of pedestrian crashes., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Published
2018
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