Comparative Analysis of Bivalent Domains in Mammalian Embryonic Stem Cells

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• 作者：Anna Mantsoki (20)
  Anagha Joshi (20)
  
  20. Division of Developmental Biology ; The Roslin Institute and Royal (Dick) School of Veterinary Studies ; University of Edinburgh ; Edinburgh ; UK
  
• 关键词：ChIP sequencing ; embryonic stem cells ; chromatin ; H3K4me3 ; H3K27me3 ; bivalent promoters ; developmental genes ; comparative genomics
• 刊名：Lecture Notes in Computer Science
• 出版年：2015
• 出版时间：2015
• 年：2015
• 卷：9043
• 期：1
• 页码：391-402
• 全文大小：400 KB
• 参考文献：1. Azuara, V. (2006) Chromatin signatures of pluripotent cell lines. Nature Cell Biology 8: pp. 532-538 CrossRef
  2. Bannister, A., Kouzarides, T. (2011) Regulation of chromatin by histone modifications. Cell Research 21: pp. 381-395 CrossRef
  3. Barrett, T., Wilhite, S.E., Ledoux, P.: NCBI GEO: archive for functional genomics data sets鈥攗pdate (2013)
  4. Benaglia, T. (2009) mixtools: An R Package for Analyzing Finite Mixture Models. Journal of Statistical Software 32: pp. 1-29
  5. Bernstein, B. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: pp. 315-326 CrossRef
  6. Bernstein, B.E. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotech. 28: pp. 1045-1048 CrossRef
  7. Dennis, G., et al.: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biology, 4(5), P3 (2003)
  8. Haider, S., et al.: BioMart Central Portal鈥攗nified access to biological data (2009)
  9. Harrow, J., et al.: GENCODE: The reference human genome annotation for The ENCODE Project (2012)
  10. Langmead, B., et al.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (2009)
  11. Li, H., et al.: The sequence alignment/map format and SAMtools (2009)
  12. Marks, H. (2012) The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149: pp. 590-604 CrossRef
  13. Mikkelsen, T. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: pp. 553-560 CrossRef
  14. Mohn, F. (2008) Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Molecular Cell 30: pp. 755-766 CrossRef
  15. Oksanen, J., et al.: vegan: Community Ecology Package (2013)
  16. Pan, G. (2007) Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1: pp. 299-312 CrossRef
  17. Pearson, J., Lemons, D., McGinnis, W. (2005) Modulating Hox gene functions during animal body patterning. Nature reviews. Genetics, 6: pp. 893-904
  18. Quinlan, A.R., Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: pp. 841-842 CrossRef
  19. Ringrose, L., Paro, R. (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annual Review of Genetics 38: pp. 413-443 CrossRef
  20. Andrews, S.: FastQC A Quality Control tool for High Throughput Sequence Data (2010)
  21. Sharov, A.A., Ko, M.S. (2007) Human {ES} cell profiling broadens the reach of bivalent domains. Cell Stem Cell 1: pp. 237-238 CrossRef
  22. Thomson, J. (1998) Embryonic stem cell lines derived from human blastocysts. Science 282: pp. 1145-1147 CrossRef
  23. Voigt, P., Tee, W.-W., Reinberg, D. (2013) A double take on bivalent promoters. Genes & Development 27: pp. 1318-1338 CrossRef
  24. Wilson, N. (2010) Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 7: pp. 532-544 CrossRef
  25. Xiao, S. (2012) Comparative epigenomic annotation of regulatory DNA. Cell 149: pp. 1381-1392 CrossRef
  26. Zang, C. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: pp. 1952-1958 CrossRef
  27. Zhao, X.D. (2007) Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1: pp. 286-298 CrossRef
  
• 作者单位：Bioinformatics and Biomedical Engineering
• 丛书名：978-3-319-16482-3
• 刊物类别：Computer Science
• 刊物主题：Artificial Intelligence and Robotics
  Computer Communication Networks
  Software Engineering
  Data Encryption
  Database Management
  Computation by Abstract Devices
  Algorithm Analysis and Problem Complexity
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1611-3349

文摘

Bivalent promoters are defined by the presence of both activating (H3K4me3) and repressive (H3K27me3) chromatin marks. In this paper, we first identified high confidence bivalent promoters in murine ES cells integrating data across eight studies using two methods; peak-based and cutoff-based. We showed that peak-based method is more reliable as promoters are more enriched for developmental regulators than the cutoff-based method. We further identified bivalent promoters in human and pig using the peak-based method to show that the bivalent promoters conserved across species were highly enriched for embryonic developmental processes.