Haynes:LitReviewMay2014

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JOURNAL ASSIGNMENTS:

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

INSTRUCTIONS: Please search for lab-relevant articles dated November 11, 2013 up to today.

Spring 2014, 05/08/2014

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 list 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. (2013) A Computational Method for Automated Characterization of Genetic Components. Boyan Yordanov, Neil Dalchau, Paul K. Grant, et. al. ACS Synthetic Biology. ePub. Link
   Summary: Developed a computational method for characterizing parts using Lux as an example. Could be used alongside experimental side of quorum sensing project.
   
   
2. (2014) Biological 2‑Input Decoder Circuit in Human Cells. Michael Guinn and Leonidas Bleris. ACS Synthetic Biology. ePub. Link
   Summary: Early example of Boolean logic in human cells.
   
   
3. (2013) Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription−Translation (TX-TL) Systems. Melissa K. Takahashi, James Chappell, Clarmyra A. Hayes, et. al. ACS Synthetic Biology. ePub. Link
   Summary: Publication from Cold Spring Harbor Synthetic Biology Course.

Cell

1. Item

Frontiers in Microbiotechnology

1. (2014) Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data. Thomas Carroll, Ziwei Liang, and Rafik Salama et al. Frontiers in Genetics. 5:75. Link.
   Summary: Interesting article on the effects of processing ChIP seq data on the metrics of ChIP-seq quality.
   
   

Journal of Biological Engineering

1. (2014) Assembly of eukaryotic algal chromosomes in yeast. Bogumil Karas, Bhuvan Molparia, Jelena Jablanovic, et. al. Journal of Biological Engineering. 7:30. Link
   Summary: Demonstrate yeast as an organism for assembling exogenous chromosomes. Expressed an algal chromosome in yeast. Did not mention methylation or chromatin structure.
   
   
2. (2013) Design and analysis of a tunable synchronized oscillator. Brendan Ryback, Dorett Odoni, Ruben van Heck, et. al. Journal of Biological Engineering. 7:26. Link
   Summary: Example of using Lux system to build gene circuits. Built a synchronized transcriptional feedback loop using LuxI and LuxR. Used a positive feedback loop with plus pushing LuxI and negative feedback with an AHL lactonase.

Journal of Cell Biology

None

Molecular Biology of the Cell

1. (2014) An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation. Pierangela Sabbattini, Marcela Sjoberg, and Svetlana Nikic et al. Molecular Biology of the Cell. 25:904-915. Link.
   Summary: Identified a methyl-phospho switch at H3K9/S10 that increased binding of methyltransferase to H3K27 in embryonic stem cells. Identifies interesting methylation mark at H3K9me, which is a repressor. It is bound by Heterochromatin Protein 1 (HP1).
   
   
2. (2014) Transcription of the Geminin gene is regulated bya negative-feedback loop. Yoshinori Ohno, Keita Saeki, and Shin'ichiro Yasunga et al. Molecular Biology of the Cell. 25:1374-1383. Link.
   Summary: Describes the process of a Gene called Geminin, which has the effect of enhancing trimethylation of H3K27. Found Geminin negatively regulated by inhibition of chromatin remodeling .
   
   

Molecular and Cellular Biology

1. (2013) Elements of the Polycomb Repressor SU(Z)12 Needed for Histone H3-K27 Methylation, the Interface with E(Z), and In Vivo Function. Aswathy N. Rai, Marcus L. Vargas, Liangjun Wang, et. al. Molecular and cellular biology 33: 4844-56. Link
   Summary: Identified function of a subdomain VEFS of SU(Z) in facilitating SU(Z)12-E(Z) assembly and PRC2 binding.

Nature

1. Item

Nature Biotechnology

1. (2014) Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Richard I Sherwood, Tatsunori Hashimoto, and Charles W O’Donnel et al. Nature Biotech. 32:171-179. Link.
   Summary: Researchers at Harvard have developed a technique known as "Protein Interaction Quantification" that can analyze genome-wide DNAse hypersensitivity data. This technique is a high-throughput version of CHIP-Seq that compares DNAse-seq data to a reference genome. Using machine-learning algorithms that factor the shape of all known transcription factors into the calculations, protein interaction quantification predicts the probability that a specific transcription factor occupies a specific section of the genome. This technique is directly relevant to the Haynes lab as a high-throughput method of probing changes in chromatin architecture.Commentary on the article: Link
   
   

Nature Methods

1. (2014) CRISPR transcriptional repression devices and layered circuits in mammalian cells. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. Nature Methods, E-pub ahead of print. Link.
   Summary: The Weiss group at MIT designed CRISPR-based gene repressors and demonstrated that these could be used to build layered circuits (where the product of one gene controls the expression of another) in mammalian cells. Noteworthy: expression of guide RNAs from synthetic introns.
   
   
2. (2014) Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, Wang L, Hodgkins A, Iyer V, Huang X, Skarnes WC. Nature Methods, 11:399-402. Link.
   Summary: This group used nicking CRISPR to create mutations in mice (embryonic cells, used to create engineered mouse lines). Mutations were insertions and/or deletions (indels) of 22–138 bp.

Nature Molecular Systems Biology

1. (2014) A chromatin structure‐based model accurately predicts DNA replication timing in human cells. Yevgeniy Gindin, Manuel S Valenzuela, and Mirit I Aladjem et al. Mol Syst Biol. 10:722. Link.
   Summary: Researchers generated an in-silico, time-stochastic model that used chromatin structure data to predict DNA replication timing in human cells. The model rivaled repeated wet lab experiments.
   
   

Public Library of Science Biology (PLoS Biology)

1. (2013) Polycomb Protein SCML2 Regulates the Cell Cycle by Binding and Modulating CDK/CYCLIN/p21 Complexes. Emilio Lecona, Luis Alejandro Rojas, Roberto Bonasio et al. Public Library of Science Biology (PLoS Biology). 11(12): e1001737: Link.
   Summary: While most work with the Polycomb group of proteins has involved using chromatin modifications to influence the transcriptional status of cell cycle regulators, this study has discovered a transcription-independent function for human Polycomb group proteins in regulating the cell cycle (being the modulation of the progression of cells from G1 into S phase through interacting with p21 to repress CDK2/CYCE complexes during early G1; this does not interact with the Polycomb complex and highlights a relationship between Polycomb's cellular memory and cell-cycle machinery in mammals). The Haynes lab studies the involvement of Polycomb in maintaining chromatin silencing, so although this is not super relevant to our research, it was the most relevant thing I could find in PLoS and is interesting regardless.
   
   
2. (2013) Linking stochastic fluctuations in chromatin structure and gene expression. Brown CR, Mao C, Falkovskaia W, Jurica MS, Boeger H. Public Library of Science Biology (PLoS Biology) Link
   Summary: Stochastic gene expression in yeast chromosomes.

Proceedings of the National Academy of Sciences

1. Item

Science

1. (2014) A Cascade of Histone Modifications Induces Chromatin Condensation in Mitosis. Bryan J. Wilkins, Nils A. Rall1, Yogesh Ostwal et al. Science. 343:77-80. Link.
   Summary: Examined the driving forces of chromatin hypercondensation during mitosis by inserting ultraviolet light inducible cross-linker amino acids in histone proteins of living yeast to trace interactions of proteins along the cell cycle. Found that H3 S10 phosphorylation leads to recruitment of the histone deacetylase Hst2p which removes an acetyl group from histone H4 lysine 16, allowsing the H4 tail to promote fiber condensation on the surface of neighboring nucleosomes. This series of reactions yields a condensin-independent driving force of chromatin hypercondenation during mitosis (where previously it was thought that metaphase chromosome condensation required the condensin complex to remain undisrupted). Although the chromatin marker being researched in this article is H3S10 rather than our marker of interest in the Haynes lab (H3K27me3) I thought the use of ultra violet light could be relevant to Branden's project (although I'm unsure of the details of his work so this may not be the case).
   
   
2. (2014) Total Synthesis of a Functional Designer Eukaryotic Chromosome. Narayana Annaluru, Héloïse Muller, Leslie A. Mitchell et al. Science. 344:55-58. Link.
   Summary: Designer eukaryotic chromosome synthesized based on native Saccharomyces cerevisiae chromosome III. This chromosome is functional in S.cerevisiae. All nonessential genes were made to be flanked by loxPsym sites which enabled inducible evolution and genome reduction; this allows for direct evolutionary testing (e.g. max number of nonessential genes that can be modified or deleted without a catastrophic loss of fitness). This chromosome synthesis is a major and exciting step forward in synthetic biology. Authors postulate that it will soon be feasible to engineer new eukaryotic genomes with synthetic chromosomes encoding desired function and phenotypic properties. Another very exciting component of this breakthrough is that it was accomplished by undergraduate students, demonstrating the significant power of open sourced work and brain pooling.
   
   
3. (2013) Genetics Driving Epigenetics. Terrence S. Furey, Praveen Sethupathy. Science. 342:705-706. Link.
   Summary: I don't think this article needs to be discussed in the meeting, however I thought it was a good (and very short) background on how DNA sequence variation influences epigentics through transcription factor modulated histone tail modificatons and epigenetic mechanisms in general. I would recommend lab members not already familiar with this topic to read it!
   
   

Miscellaneous Reviews and Media

Reviews

1. (2014) Programming biological operating systems: genome design, assembly and activation. Gibson DG. Nature Methods, 11:521-6. Link
   Summary: REVIEW - Dan Gibson (inventor of Gibson Assembly) published a very nice review on genome building.
   
   
2. (2014) Principles of genetic circuit design. Brophy JA, Voigt CA. Nature Methods, 11:508-20. Link
   Summary: REVIEW - A very nice review from the Voigt lab exploring the requirements and challenges of building genetic circuits. This review is important and timely because it emphasizes the "circuit-building" aspect of synthetic biology, which sets it apart from traditional genetic engineering.

News

1. (2014) A Giant Leap for Synthetic Genes. Haynes Lab Blog, ASU. http://haynes.lab.asu.edu/uncategorized/a-giant-leap-for-synthetic-genes/