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, 04/21/2015

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: The data analysis and presentation in this paper is relevant to the quorum sensing project. They expressed many TetR homologs in mammalian cells and measured the efficacy as well as their orthogonality with each other.
   
   

1. (2014) Modularized CRISPR/dCas9 Effector Toolkit for Target-Specific Gene Regulation. Michael Agne, Ilona Blank, and Alicia J. Emhardt et. al. ACS Synthetic Biology. 3(12): 986-989. Link
   Summary: They fused protein domains to dCas9 (a mutated version of Cas9 that does not have nuclease functions) to regulate transcription. This paper discusses the fusion of 3 effector domains: transcriptional transactivation domain VP16, transcriptional repressor domain KRAB, and histone methyltransferase G9a-SD. The latter is known to induce heterochromatin formation. There may be potential in applying this paper's methods by using dCas9 to regulate chromatin in our projects.
   
   

1. (2014) Enhanced MyoD-Induced Transdifferentiation to a Myogenic Lineage by Fusion to a Potent Transactivation Domain. Ami Kabadi, Patiksha Thakore, Christopher Vockley, et al. ACS Synthetic Biology. (ePub ahead of print) Link
   Summary: This paper has a similar motivation as our lab’s project using PcTF to push alpha cells to beta cells. They built three MyoD-activator domain fusion proteins and demonstrate that their globally-regulating fusion proteins are stronger and faster at inducing myotube formation than overexpression of wtMyoD as well as targeted upregulation of specific differentiation markers. The experimental design and paper layout are relevant to multiple PcTF projects in the lab.
   
   

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

1. (2015) Can the natural diversity of quorum-sensing advance synthetic biology? Rene Davis, Ryan Muller, Karmella Haynes. Front. Bioeng. Biotechnol. 3:30. Link.
   Summary: Very familiar review of Quorum-Sensing networks. Discusses the need, problems and strategies in making diverse, orthogonal quorum-sensing pathways for synthetic gene circuits.
   
   
2. (2015) How the cell cycle impacts chromatin architecture and influences cell fate Yiqin Ma, Kiriaki Kanakousaki, Laura Buttitta. Front. Genet. 6:19. Link.
   Summary: Hard to find related articles. Closest article. Discusses histone biogenesis after cell replication. Some interesting review on how post-translational modifications of histones take place during the cell cycle.
   
   

Journal of Biological Engineering

• No new relevant articles.
  
  

Journal of Cell Biology

• No new relevant articles

Molecular Biology of the Cell

• No new relevant articles

Molecular and Cellular Biology

1. (2015) USP7 Cooperates with SCML2 To Regulate the Activity of PRC1 Emilio Locona, Varun Narendra, and Danny Reinberg. Molecular and Cellular Biology, 35.7:1157-1168. Link Summary: Relevant to anyone interested in the complexity of polycomb regulation. This paper proposes the role of USP7 in PRC1 stabilization and activity. They show USP7 maintains PRC1 activity and ubiqutination of H2A. Ubiquitination of H2A is required to keep ES cells from differentiating.

Nature

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 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

1. (2015) Quantifying cellular capacity identifies gene expression designs with reduced burden. Francesca Ceroni, Rhys Algar, Guy-Bart Stan & Tom Ellis. Nature Methods 10.1038/nmeth.3339. Link.
   Summary: Researchers in the UK designed a monitor to measure the changes in the cell capacity of E. coli caused by bacterial transformation, and identified construct designs that were less burdensome on the cells than others.
   

Nature Molecular Systems Biology

1. (2015) A high‐throughput ChIP‐Seq for large‐scale chromatin studies. Christophe D Chabbert, Sophie H Adjalley, Bernd Klaus et al. Nature Molecular Systems Biology. 11: 777. Link.
   Summary: Researchers from Stanford and Heidelberg developed a modified ChIP protocol. By ligating barcodes to chromatin fragments, the researchers were able to perform experimental scale up, allowing 90 ChIP-seq data sets without robotic instrumentation. Researchers chose to probe several chromatin-associated mechanisms including the role of H3K4 trimethylation in cryptic transcription within SET2 mutant.
   
   

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

1. (2015) Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. Maxence Vieux-Rochasa, Pierre J. Fabrea, Marion Leleua, Denis Duboulea, and Daan Noordermeera. PNAS 112:15 pp. 4672-4677. Link
   Summary: Researchers in Switzerland found that genes, including HoxD, inactivated by Polycomb group proteins with the H3K27me3 marker, cluster together in a noncooperative manner with other nearby and distant PcG or H3K27me3-rich loci.
   
2. (2015) SOX2 primes the epigenetic landscape in neural precursors enabling proper gene activation during hippocampal neurogenesis. Alejandro Amador-Arjonaa, Flavio Cimadamorea et al. PNAS 112:15 pp. 1936-1945. Link.
   Summary: Researchers at the Whitehead Institute in Cambridge, MA found that SOX2 protein binds to marked promoters of proneural genes in neural progenitor stem cells, preventing activity of PRC2 and excessive H3K27me3 marking, maintaining an unrepressed epigenetic state.
   

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

1. (2015) Chromatin regulation at the frontier of synthetic biology. Keung, A. J., Joung, J. K., Khalil, A. S., & Collins, J. J. Nature Reviews Genetics. 16:159-171. Link.
   Summary: Extremely comprehensive piece on work that has been done to manipulate chromatin.
   
   
2. (2015) Synthetic epigenetics-towards intelligent control of epigenetic states and cell identity. Jurkowski, T. P., Ravichandran, M., & Stepper, P. Clinical epigenetics, 7:18. Link.
   Summary: Recent review on efforts to manipulate he genome. Good material for placing our work in context of other work.

News

1. 04/15/15. RNA Constructs Thread Translational Needle. Genetic Engineering News (GEN). Link
   Summary: Article about a Gordon Conference on RNA Nanotechnology. Mentions RNA-based nanoparticles that can be used to deliver drugs (including proteins) into tissues/ cells.
   
   
2. 04/15/15. Sperm with Specific Epigenetic Tags Linked to Autism. Genetic Engineering News (GEN). Link
   Summary: Scientists from Johns Hopkins (A Feinberg et al.) say they have found that DNA from the sperm of some men whose children had early signs of autism shows distinct patterns of regulatory tags that could contribute to the condition..
   
   
3. 04/07/15. Sperm with Specific Epigenetic Tags Linked to Autism. Genetic Engineering News (GEN). Link
   Summary: Researchers from Duke University used a p300 (HAT) core peptide tethered to dCas9 to epigenetically regulate genes. The fusion was functional when targeted to promoters an enhancers. The article is published in Nature Biotechnology (4/06/15).