Haynes:LitReviewApr2015

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JOURNAL ASSIGNMENTS:

• ACS Synthetic Biology - Rene
• Cell - Ben
• Frontiers in Microbiotechnology – David Barclay
• Journal of Biological Engineering - Ben
• Journal of Cell Biology - David Tze
• Molecular Biology of the Cell - David
• Molecular and Cellular Biology - Rene
• Nature - Theodore K.
• Nature Biotechnology - Ryan
• Nature Methods - Jan
• Nature Molecular Systems Biology - Ryan
• Public Library of Science Biology (PLoS Biology) - Cameron
• Proceedings of the National Academy of Sciences - Jan
• Science - Cameron
• Miscellaneous Reviews and Media - Dr. Haynes

INSTRUCTIONS: Please search for lab-relevant articles dated October 2014 up to today.

Spring 2015, 05/21/2015

Use the following text format EXACTLY as it is shown below...

1. (year) Title. Author One, Author Two, and Author Three et al. Journal. Volume:pages. Link.
   Summary: Very short explanation of why this paper is relevant/ interesting.
   
   
2. (2011) Engineering a Photoactivated Caspase-7 for Rapid Induction of Apoptosis. Evan Mills, Xi Chen, Elizabeth Pham, Stanley Wong, and Kevin Truong et al. ACS Synthetic Biology, 1.3:75-82. Link.
   Summary: A group from University of Toronto developed a protein that causes rapid apotosis (cell death) of targeted cells.
   
   

Open edit mode and copy the example above. Do not erase the <br><br> tags!!! Do not use keyboard line returns to space out the numbered list, or else each item will start with the number 1.

ACS Synthetic Biology

1. (2014) Systematic transfer of prokaryotic sensors and circuits to mammalian cells. Brynne Stanton, Velia Sicilian, and Amar Ghodasara et al. ACS Synthetic Biology, 3.12: 880-891. Link
   Summary: Applying what is known about bacterial cell-cell communication to the development of mammalian genetic sensors and circuits. -JW

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Cell

1. (2015) Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds. Jesse G. Zalatan, Michael E. Lee, and Ricardo Almeida et al. Cell. 160:339-350. Link.
   Summary: By modifying guide RNAs used in CRISPR to contain sites for recruiting effector proteins, the authors are able to target specific regions of the genome with different actions (such as activation or repression of the gene) mediated through the effector proteins.
   
   
2. (2015) Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming. Abdenour Soufi, Meilin Fernandez Garcia, and Artur Jaroszewicz et al. Journal. 160:1-14. Link.
   Summary: The 'pioneer' transcription factors are able to recognize sequences partially occluded by nucleosomes. Partial motif recognition occurs through coordinate binding between factors.
   
   

Frontiers in Microbiotechnology

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Journal of Biological Engineering

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Journal of Cell Biology

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Molecular Biology of the Cell

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Molecular and Cellular Biology

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Nature

1. (2015) PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells. Syuzo Kaneko,Jinsook Son, Steven S Shen,Danny Reinberg, Roberto Bonasio et. al Nature Structural & Molecular Biology 1258–1264 Link.
   Summary: Explains PRC2 effects, especially the effects of nascent ezRNA on PRC2. PCR cell first samples the DNA strand independent from the transcriptional state their in.Then when PRC2 binds to a dna strand if a nascent ezRNA is present, it stops the tri-methylation on H3K27.
   
   

1. (2015) Ezh2 mediated H3K27me3 activity facilitates somatic transition during human pluripotent reprogramming. Radhika Arasala Rao,Narendra Dhele,Sabna Cheemadan,Alhad Ketkar, Giridhara R. Jayandharan,Dasaradhi Palakodeti,Shravanti Rampalli et. al Scientific Reports 2045-2322 http://www.nature.com/srep/2015/150204/srep08229/full/srep08229.html Link
   Summary: EZH2, the enzyme in PrC2 that methylates H3K27 and its effects on converting cells back into pluripotent cells.
   
   

Nature Biotechnology

1. (2015) Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Isaac B Hilton, Anthony M D'Ippolito, and Christopher M Vockley et al. Nature Biotechnology. Advanced online print. Link.
   Summary: Researchers from Duke fused dCas9 to catalytic core of acetyltransferase p300. The construct demonstrated site-specific gene activation by acetylation at H3K27. The p300 catalytic core can also be fused to other DNA-binding proteins for similar programmable effects.
   
   
2. (2015) ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Qiye He, Jeff Johnston, and Julia Zeitlinger. Nature Biotechnology, 33:395–401. Link.
   Summary: A group from Stowers Institute for Medical Research developed a new ChIP-exo protocol called ChIP nexus, (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation) which affords higher nucleotide resolution of transcription factor binding by using a circularization step in the library preparation.
   
   

Nature Methods

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Nature Molecular Systems Biology

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Public Library of Science Biology (PLoS Biology)

Nothing very relevant.

1. (2015) Cell Cycle-Dependent Differentiation Dynamics Balances Growth and Endocrine Differentiation in the Pancreas Yung Hae Kim, Hjalte List LArsen, Anne Grapin-BOtton, et. al. PLoS Bio. 10.1371:1002111. Link.
   Summary: Investigation of differentiation of pancreatic progenitor cells with a focus on differentiating into beta cells for diabetes therapy. Found that endocrine differentiation is largely stochastic. Proposed a model in which the production of a progenitor and a differentiated cell in the pancreas results from the stochastic induction of differentiation in one daughter after cell division, rather than the unequal partitioning of molecules between two daughters at the time of division, as observed in the nervous system
   
   

Proceedings of the National Academy of Sciences

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Science

1. (2015) Epigenetic inheritance uncoupled from sequence-specific recruitment Kaushik Ragunathan, Gloria Jih, and Danesh Moazed. Science. 348:6230. Link.
   Summary: Shows that epigenetic inheritable changes in gene expression are not dependent on DNA-specific transcription factors (focuses on H3K9). Constructed a chromatin inducible cell-line similar to the one used in lab.
   
   
2. (2015) Combinatorial labeling of single cells for gene expression cytometry H. Christina Fan, Glenn K. Fu, Stephen P.A. Fodor. Science. 347:6222. Link.
   Summary: New method for gene expression profiling of thousands of single cells across an arbitrary number of genes without using robotics or automation.
   
   
3. (2014) Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Fahim Farzadfard and Timothy K. Lu. Science. 346:6211. Link.
   Summary: Synthetic Cellular Recorders Integrating Biological Events (SCRIBE) is a new system with uses genomic DNA for analog, rewritable, and flexible memory distributed across living cell populations. SCRIBE enables the recording of analog information such as the magnitude and time span of exposure to an input, SCRIBE-induced mutations can be written and erased and can be used to record multiple inputs across the distributed genomic DNA of bacterial populations. SCRIBE memory can be decomposed into independent input, write, and read operations and used to create genetic logic-and-memory circuits as well as sample-and-hold circuits..
   
   

Review

1. (2014) The new frontier of genome engineering with CRISPR-Cas9 Jennifer A. Doudna and Emmanuelle Charpentier. Science. 346:6213. Link.
   Summary: A good review on using the CRISPR-Cas9 system for genome engineering.
   
   

Miscellaneous Reviews and Media

Reviews

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News

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