Tag Archives: chromatin

Erez Lieberman-Aiden Ph.D. Wednesday, April 4, 2012

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How the Genome Folds

Erez Aiden  Ph.D.

Fellow, Harvard Society of Fellows

Prinicpal Investigator, Laboratory-at-Large

Harvard University

Visiting Faculty, Google

4:00 Wednesday, April 4, 2012  Refreshments Abby Lounge 3:45

Caspary Auditorium 

Recommended Readings

Zhang Y; McCord RP, Ho YJ; et al.  2012.  Spatial organization of the mouse genome and its role in recurrent chromosomal translocations.  Cell. 148(5):908-921.  DOI: 10.1016/j.cell.2012.02.002

Sung MH and  GL Hager.  2011.  More to Hi-C than meets the eye.  Nature Genetics.  43(11):1047-1048.  DOI: 10.1038/ng.984

Yaffe E and A Tanay.  2011.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nature Genetics.  43(11):1059-U40.  DOI: 10.1038/ng.947

Fudenberg G; Getz G; Meyerson M; et al.  2011.  High order chromatic architecture shapes the landscape of chromosomal alterations in cancer.   Nature Biotechnology. 29(12):1109-U75.  DOI: 10.1038/nbt.2049

Lieberman-Aiden E; van Berkum NL; Williams L; et al.  2009.  Comprehenesive mapping of long-range interactions reveals folding principles of the human genome.  Science.  326(5950):289-293.  DOI: 10.1126/science.1181369

Guelen L; Pagie L; Brasset E; et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.   Nature.  453(7197):948-U83.  DOI: 10.1038/nature06947

Rada-Iglesias A; Ameur A; Kapronov P; et al.  2008.  Whole-genome maps opf USA and USF2 binding and histone H3 acetylation reveal new aspects of prmotoer structure and candidate genes for common human disorders.  Genome Research.  18(3):380-392.  DOI: 10.1101/gr.6880908

Xiao G; Wang X; and Ab Khodursky.  2011.  Modeling three-dimensional chromosome structures using gene expression data. Journal of the American Statistical Association.  106(493):61-72.  DOI: 10.1198/jasa.2010/ap09504   Please request copy from Markus Library.

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Recommended Readings: Howard Chang, M.D., Ph.D.

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Friday Lecture Series

Genome Regulation by Long Noncoding RNA

Howard Chang, M.D., Ph.D., early career scientist,

Howard Hughes Medical Institute; professor of dermatology,

Stanford University School of Medicine, member, Stanford Cancer Center and Stanford Institute for Stem Cell Biology and Regenerative Medicine

February 10, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

 

Recommended Readings:

Hung, T., Y. Wang, M. F. Lin, A. K. Koegel, Y. Kotake, G. D. Grant, H. M. Horlings, et al. 2011. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nature genetics 43, (7): 621-629

Rinn, J. L., M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu, S. A. Brugmann, L. H. Goodnough, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, (7): 1311-1323

Tsai, M. -C, O. Manor, Y. Wan, N. Mosammaparast, J. K. Wang, F. Lan, Y. Shi, E. Segal, and H. Y. Chang. 2010. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, (5992): 689-693

Wang, K., and H. Chang. 2011. Molecular mechanisms of long noncoding RNAs. Molecular cell 43, (6): 904-914

Wang, K. C., Y. W. Yang, B. Liu, A. Sanyal, R. Corces-Zimmerman, Y. Chen, B. R. Lajoie, et al. 2011. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, (7341): 120-126

 

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Recommended Readings: Gerald Crabtree, M.D.; June 5, 2009

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Friday Lecture Series

“Understanding the Words of Chromatin Remodeling”

Gerald Crabtree, M.D.

Stanford University

June 5, 2009

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Articles:

Wu, J. I., J. Lessard, and G. R. Crabtree. 2009. Understanding the words of chromatin regulation. Cell. 136(2):200-206.

 

Lessard, J., J. I. Wu, J. A. Ranish, M. Wan, M. M. Winslow, B. T. Staahl, H. Wu, R. Aebersold, I. A. Graef, and G. R. Crabtree. 2007. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron. 55(2):201-215.

 

Chi, T. H., M. Wan, P. P. Lee, K. Akashi, D. Metzger, P. Chambon, C. B. Wilson, and G. R. Crabtree. 2003. Sequential roles of brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development. Immunity. 19(2):169-182.

 

Rando, O. J., T. H. Chi, and G. R. Crabtree. 2003. Second messenger control of chromatin remodeling. Nature structural biology. 10(2):81-83.

 

Wu, J. I., J. Lessard, I. A. Olave, Z. Qiu, A. Ghosh, I. A. Graef, and G. R. Crabtree. 2007. Regulation of dendritic development by neuron-specific chromatin remodeling complexes. Neuron. 56(1):94-108.

 

Olave, I. A., Reck-Peterson, S. L., and Crabtree, G. R. 2002. Nuclear actin and actin-related proteins in chromatin remodeling. Annual Review of Biochemistry. 71:755-781.

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