Showing papers by "Wei Xie published in 2009"
TL;DR: Genome-wide data and high-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprograming and that reprogramming does not lead to genomic instability, and suggest that iPSCs should be considered a unique subtype of pluripotent cell.
1,036 citations
TL;DR: The results suggest that K56Ac is involved in the human core transcriptional network of pluripotency, and more accurately reflects the epigenetic differences between hESCs and somatic cells than other active histone marks such as H3 K4 trimethylation and K9 acetylation.
200 citations
TL;DR: This study proposes a statistical method to identify the patterns of NFRs from a genome-wide measurement of nucleosome occupancy based on an appropriately designed segmental semi-Markov model, which can capture each NFR pattern and output its quantitative characterizations.
Abstract: Background
Nucleosome free regions (NFRs) play important roles in diverse biological processes including gene regulation A genome-wide quantitative portrait of each individual NFR, with their starting and ending positions, lengths, and degrees of nucleosome depletion is critical for revealing the heterogeneity of gene regulation and chromatin organization By averaging nucleosome occupancy levels, previous studies have identified the presence of NFRs in the promoter regions across many genes However, evaluation of the quantitative characteristics of individual NFRs requires an NFR calling method
Methodology
In this study, we propose a statistical method to identify the patterns of NFRs from a genome-wide measurement of nucleosome occupancy This method is based on an appropriately designed segmental semi-Markov model, which can capture each NFR pattern and output its quantitative characterizations Our results show that the majority of the NFRs are located in intergenic regions or promoters with a length of about 400–600bp and varying degrees of nucleosome depletion Our quantitative NFR mapping allows for an investigation of the relative impacts of transcription machinery and DNA sequence in evicting histones from NFRs We show that while both factors have significant overall effects, their specific contributions vary across different subtypes of NFRs
Conclusion
The emphasis of our approach on the variation rather than the consensus of nucleosome free regions sets the tone for enabling the exploration of many subtler dynamic aspects of chromatin biology
17 citations