Recommended Readings: Peter Reddien, Ph.D. Friday September 28, 2018

Friday Lectures

Friday, September 28, 2018  3:45 p.m.

Caspary Auditorium

Peter Reddien Ph.D.

Professor and Associate Department Head

Department of Biology

Massachusetts Institute of Technology

How Stem Cells and Positional Information Lead to Planarian Regeneration

Recommended Readings:

Science News

Lisa Girard. A blueprint for regeneration. March 15, 2018. MIT News

Empirical Articles

Fincher, Christopher T.; Wurtzel, Omri; de Hoog, Thom; et al. (2018). Cell type transcriptome atlas for the planarian Schmidtea mediterranea. SCIENCE.  360 (6391): 874-+

Atabay KD, LoCascio SA, de Hoog T, Reddien PW. (2018). Self-organization and progenitor targeting generate stable patterns in planarian regeneration. SCIENCE. 360 (6387):404-409

Scimone, M. Lucila; Cote, Lauren E.; Reddien, Peter W. (2017). Orthogonal muscle fibres have different instructive roles in planarian regeneration. NATURE. 551 (7682): 623-+  

Raz, Amelie A.; Srivastava, Mansi; Salvamoser, Ranja; et al. (2017). Acoel regeneration mechanisms indicate an ancient role for muscle in regenerative patterning. NATURE COMMUNCATIONS. 8

Wurtzel, Omri; Oderberg, Isaac M.; Reddien, Peter W. (2017). Planarian Epidermal Stem Cells Respond to Positional Cues to Promote Cell-Type Diversity. DEVELOPMENTAL CELL. 40 (5): 491-504  

Scimone, M. Lucila; Kravarik, Kellie M.; Lapan, Sylvain W.; et al. (2014). Neoblast Specialization in Regeneration of the Planarian Schmidtea mediterranea. STEM CELLS REPORTS. 3 (2): 339-352

van Wolfswinkel, Josien C.; Wagner, Daniel E.; Reddien, Peter W. (2014). Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment. CELL STEM CELL. 15 (3): 326-339

Wagner, Daniel E.; Wang, Irving E.; Reddien, Peter W. (2011). Clonogenic Neoblasts Are Pluripotent Adult Stem Cells That Underlie Planarian Regeneration. SCIENCE. 332 (6031): 811-816  

Review Paper

Tanaka, Elly M.; Reddien, Peter W. (2011). The Cellular Basis for Animal Regeneration. DEVELOPMENTAL CELL. 21 (1): 172-185

Reddien, Peter W. (2011). Constitutive gene expression and the specification of tissue identity in adult planarian biology.  TRENDS IN GENETICS. 27 (7): 277-285  

Book Chapter

Wang IE, Wagner DE, Reddien PW. (2018). Clonal Analysis of Planarian Stem Cells by Subtotal Irradiation and Single-Cell Transplantation. Planarian Regeneration. 1774:479-495

Recommended Readings: Gerald Crabtree, Ph.D. Friday February 16th, 2018

Friday Lectures

Friday, February 16th, 2018  3:45 p.m.

Caspary Auditorium

Gerald Crabtree, Ph.D.

David Korn Professor

Pathology and Developmental Biology

Stanford University

Chromatin regulation: Insights from new methods and the genomics of human disease

Recommended Readings:

Empirical Articles

Braun, Simon M. G.; Kirkland, Jacob G.; Chory, Emma J.; et al. (2017). Rapid and reversible epigenome editing by endogenous chromatin regulators. NATURE COMMUNICATIONS. 8

Stanton, Benjamin Z.; Hodges, Courtney; Calarco, Joseph P.; et al. (2017). Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. NATURE GENETICS. 49 (2): 282-288

Kadoch, Cigall; Williams, Robert T.; Calarco, Joseph P.; et al. (2017). Dynamics of BAF-Polycomb complex opposition on heterochromatin in normal and oncogenic states. NATURE GENETICS. 49 (2): 213-222

Miller, Erik L.; Hargreaves, Diana C.; Kadoch, Cigall; et al. (2017). TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24 (4): 344-+

Son, Esther Y.; Crabtree, Gerald R. (2014). The Role of BAF (mSWI/SNF) Complexes in Mammalian Neural Development. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS. 166 (3): 333-349

Hodges, Courtney; Crabtree, Gerald R. (2012). Dynamics of inherently bounded histone modification domains. PNAS. 109 (33): 13296-13301

Hathaway, Nathaniel A.; Bell, Oliver; Hodges, Courtney; et al. (2012). Dynamics and Memory of Heterochromatin in Living Cells. CELL. 149 (7): 1447-1460

Review Papers

Kadoch, Cigall; Crabtree, Gerald R. (2015). Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics. SCIENCE ADVANCES. 1 (5) 

Ho, Lena; Crabtree, Gerald R. (2010). Chromatin remodelling during development. NATURE. 463 (7280): 474-484

Book Chapter

Lessard, Julie A.; Crabtree, Gerald R. (2010). Chromatin Regulatory Mechanisms in Pluripotency. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. Book Series: Annual Review of Cell and Developmental Biology. 26: 503-532

Recommended Readings: Laura Landweber, Ph.D. Friday February 2nd, 2018

Friday Lectures

Friday, February 2nd, 2018  3:45 p.m.

Caspary Auditorium

Laura Landweber, Ph.D.


Biochemistry and Molecular Biophysics and Biological Sciences

Columbia University

RNA-programmed genome rearrangement and editing in the ciliate Oxytricha

Recommended Readings:

Science News

Greg Miller. This Bizarre Organism Builds Itself a New Genome Every Time It Has Sex. (2014, Sep 17). Wired

Empirical Articles

Khurana, Jaspreet S.; Clay, Derek M.; Moreira, Sandrine; et al.(2018). Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha. RNA. 24 (1): 18-29

Lindblad, Kelsi A.; Bracht, John R.; Williams, April E.; et al. (2017). Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development. RNA. 23 (8): 1200-1208

Chen, Xiao; Bracht, John R.; Goldman, Aaron David; et al. (2014). The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development. CELL. 158 (5): 1187-1198

Swart, Estienne C.; Bracht, John R.; Magrini, Vincent; et al. (2013). The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. PLOS BIOLOGY. 11 (1).

Goldman, Aaron David; Landweber, Laura F. (2012). Oxytricha as a modern analog of ancient genome evolution. TRENDS IN GENETICS. 28 (8): 382-388

Fang, Wenwen; Wang, Xing; Bracht, John R.; et al. (2012). Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement. CELL. 151 (6): 1243-1255

Nowacki, Mariusz; Haye, Joanna E.; Fang, Wenwen; et al. (2010). RNA-mediated epigenetic regulation of DNA copy number. PNAS. 107 (51): 22140-22144

Nowacki, Mariusz; Vijayan, Vikram; Zhou, Yi; et al. (2008). RNA-mediated epigenetic programming of a genome-rearrangement pathway. NATURE. 451 (7175): 153-U4

Review Papers

Bracht, John R.; Fang, Wenwen; Goldman, Aaron David; et al. (2013). Genomes on the Edge: Programmed Genome Instability in Ciliates. CELL. 152 (3): 406-416

Goldman, Aaron David; Landweber, Laura F. (2012). Oxytricha as a modern analog of ancient genome evolution. TRENDS IN GENETICS. 28 (8): 382-388

Book Chapter

Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F. (2011). RNA-Mediated Epigenetic Programming of Genome Rearrangements. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. Book Series: Annual Review of Genomics and Human Genetics. 12: 367-389

Edited Books

Landweber, L. F. and Winfree, E., eds. (2003) Evolution as Computation. Springer Verlag.

Landweber, L. F. and Dobson, A. P., eds. (1999) Genetics and the Extinction of Species: DNA and the Conservation of Biodiversity. Princeton University Press. PLEASE REQUEST FROM MARKUS LIBRARY.

Landweber, L. and Baum, E., eds. (1998) DNA Based Computers II. American Mathematical Society. PLEASE REQUEST FROM MARKUS LIBRARY.