Recommended Readings: Joanna Wysocka, Ph.D., November 13th

Friday Lecture Series
Friday, November 13, 2015
3:45 p.m., Caspary Auditorium

Joanna Wysocka, Ph.D.
Department of Chemical and Systems Biology,
Department of Developmental Biology,
Stanford University

On Peculiarities of Being a Human: Gene Regulatory Mechanisms in Human Development and Evolution

Recommended Readings

Empirical Articles

Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., … & Wysocka, J. (2014). Reorganization of enhancer patterns in transition from naive to primed pluripoteny. Cell Stem Cell, 14(6), 838-853. doi:10.1016/j.stem.2014.04.003

Grow, E. J., Flynn, R. A., Chavez, S. L., Bayless, N. L., Wossidlo, M., Wesche, D. J., … & Wysocka, J. (2015). Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature. 522(7555), 221-225. doi:10.1038/nature14308

Prescott, S. L., Srinivasan, R., Marchetto, M. C., Grishina, I., Narvaiza, I., Selleri, L., … & Wysocka, J. (2015). Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell, 163(1), 68-83. doi:10.1016/j.cell.2015.08.036

Review Papers

Calo, E., & Wysocka, J. (2013). Modification of enhancer chromatin: what, how, and why?. Molecular Cell, 49(5), 825-837. doi:10.1016/j.molcel.2013.01.038

Buecker, C., & Wysocka, J. (2012). Enhancers as information integration hubs in development: lessons from genomics. Trends in Genetics, 28(6), 276-284. doi:10.1016/j.tig.2012.02.008

Recommended Readings: Mitchell Guttman, Monday, February 27, 2012

Monday lecture Series

Functional Integration of Large ncRNAs in the Molecular

Circuitry Controlling Cell State

Mitchell Guttman

Graduate Fellow

Broad Institute of MIT and Harvard

   Massachusetts Institute of Technology

Monday, February 27, 2012

4 p.m, Caspary Auditorium.   Refreshments 3:45 p.m.

Recommended Readings:

Yang, LG; Lin CR; Rosebfeld MG. 2011.  A lincRNA switch for embryonic stem cell fate.  Cell Research  21(12):1646-1648.  DOI:10.1038/cr.2011.166

Guttman M; Donachey J; Carey BW; et al. 2011.  lincRNAs act in the circuitry controlling pluripotency and differentiation.  NATURE.  477(7364):295-U60.   DOI:10.1038/nature10398

Loewer S; Cabili MN; Guttman M: et al.  2010.  Large intergenic non-coding RNA-RoR modeulates reprogramming of human induced pluripotent stem cells.  NATURE Genetics.  42(12):1113-   DOI: 10.1038/ng.710

Huarte M; Guttman M; Feldser D; et al.  2010.  A large intergenic noncoding RNA induced by p53 mediates global gene repression in thep53 response. Cell.  142(3):409-419.   DOI:10.1016/j.cell.2010.06.040

Guttman, M; Garber M; Levin JZ; et al.  2010.  Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.  NATURE Biotechnology.  28(5):503-U166.  DOI: 10.1038/nbt.1633

Khalil AM; Guttman M; Huarte M; et al.  2009.  Many human large intergenic noncoding RNAs associate with Chromatin-modifying complexes and affect gene expression.  PNAS.  106(28):11667-11672   DOI: 10.1073/pnas.0904715106

Guttman M; Amit I; Garber M; et al.  2009.  Chromatin signature reveals over a thousand highly conserved large no-coding RNAs in mammals.  NATURE.  458(7235):223-227.  DOI: 10.1038/nature07672


The Element That Controls Pluripotency in Stem Cells

ScienceDaily (May 7, 2009) — Scientists at UC Santa Barbara have made a significant discovery in understanding the way human embryonic stem cells function.   They explain nature’s way of controlling whether these cells will renew, or will transform to become part of an ear, a liver, or any other part of the human body.   The research team includes James Thomson, who provided an important proof to the research effort.  The new research shows that a microRNA –– a single-stranded RNA whose function is to decrease gene expression –– lowers the activity of three key ingredients in the recipe for embryonic stem cells.  This microRNA is known as miR-145.   The study is reported in the May 1 issue of the journal Cell.