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.

 Professor

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.

 

Recommended Readings: Joan A. Steitz, Ph.D. Friday January 5th, 2018

Friday Lectures

Friday, January 5, 2018  3:45 p.m.

Caspary Auditorium

Joan A. Steitz, Ph.D.

Sterling Professor

Molecular Biophysics and Biochemistry

Yale University

RNA Triple Helices in Cellular and Viral Biology

 

Recommended Readings:

Science News

Michael White. Oct 17, 2017. The Women Who Should Win the Nobel Prize—but Haven’t. PacificStandard

Empirical Articles

Brown, Jessica A.; Kinzig, Charles G.; DeGregorio, Suzanne J.; et al. (2016). Methyltransferase-like protein 16 binds the 3 ‘-terminal triple helix of MALAT1 long noncoding RNA. PNAS. 113 (49): 14013-14018

Brown, Jessica A.; Kinzig, Charles G.; Degregorio, Suzanne J.; et al. (2016). Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix. RNA. 22 (5): 743-749

Brown, Jessica A.; Bulkley, David; Wang, Jimin; et al. (2014). Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 21 (7): 633-640

Guo, Yang Eric; Riley, Kasandra J.; Iwasaki, Akiko; et al. (2014). Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function. MOLECULAR CELL. 54 (1): 67-79

Brown, Jessica A.; Valenstein, Max L.; Yario, Therese A.; et al. (2012). Formation of triple-helical structures by the 3 ‘-end sequences of MALAT1 and MEN beta noncoding RNAs. PNAS. 109 (47): 19202-19207

Borah, Sumit; Darricarrere, Nicole; Darnell, Alicia; et al. (2011). A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLOS PATHOGENS. 7 (10)

Mitton-Fry, Rachel M.; DeGregorio, Suzanne J.; Wang, Jimin; et al. (2010). Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix. SCIENCE. 330 (6008): 1244-1247

Review Papers

Tycowski, Kazimierz T.; Guo, Yang Eric; Lee, Nara; et al. (2015). Viral noncoding RNAs: more surprises. GENES & DEVELOPMENT. 29 (6): 567-584

Cech, Thomas R.; Steitz, Joan A. (2014). The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones. CELL. 157 (1): 77-94