Haynes:LitReviewMay2014: Difference between revisions

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=Fall 2013, 11/11/13=
=Spring 2014, 05/08/2014=


<font color="blue">Use the following text format EXACTLY as it is shown below...<br>
<font color="blue">Use the following text format EXACTLY as it is shown below...<br>
Line 34: Line 34:
==ACS Synthetic Biology==
==ACS Synthetic Biology==


# Item
#(2013) '''A Computational Method for Automated Characterization of Genetic Components.''' Boyan Yordanov, Neil Dalchau, Paul K. Grant, ''et. al.'' ACS Synthetic Biology. ePub. [http://pubs.acs.org.ezproxy1.lib.asu.edu/doi/pdf/10.1021/sb400152n Link] <br>'''Summary:''' Developed a computational method for characterizing parts using Lux as an example. Could be used alongside experimental side of quorum sensing project. <br><br>
#(2014) '''Biological 2‑Input Decoder Circuit in Human Cells.''' Michael Guinn and Leonidas Bleris. ACS Synthetic Biology. ePub. [http://pubs.acs.org.ezproxy1.lib.asu.edu/doi/pdf/10.1021/sb4001596 Link] <br>'''Summary:''' Early example of Boolean logic in human cells.<br><br>
#(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. [http://pubs.acs.org.ezproxy1.lib.asu.edu/doi/pdf/10.1021/sb400206c Link] <br>'''Summary:''' Publication from Cold Spring Harbor Synthetic Biology Course.


==Cell==
==Cell==
Line 42: Line 44:
==Frontiers in Microbiotechnology==
==Frontiers in Microbiotechnology==


# Item
# (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. [http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00075/full Link]. <br>'''Summary''': Interesting article on the effects of processing ChIP seq data on the metrics of ChIP-seq quality.<br><br>


==Journal of Biological Engineering==
==Journal of Biological Engineering==


# Item
# (2014) '''Assembly of eukaryotic algal chromosomes in yeast.''' Bogumil Karas, Bhuvan Molparia, Jelena Jablanovic, ''et. al.'' Journal of Biological Engineering. 7:30. [http://www.jbioleng.org/content/pdf/1754-1611-7-30.pdf Link] <br>'''Summary:''' Demonstrate yeast as an organism for assembling exogenous chromosomes. Expressed an algal chromosome in yeast. Did not mention methylation or chromatin structure.<br><br>
# (2013) '''Design and analysis of a tunable synchronized oscillator.''' Brendan Ryback, Dorett Odoni, Ruben van Heck, ''et. al.'' Journal of Biological Engineering. 7:26. [http://www.jbioleng.org/content/pdf/1754-1611-7-26.pdf Link] <br> '''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==
==Journal of Cell Biology==


# Item
:None


==Molecular Biology of the Cell==
==Molecular Biology of the Cell==


# # 2013 '''A short carboxyl-terminal tail is required for single-stranded DNA binding, higher-order structural organization, and stability of the mitochondrial single-stranded annealing protein Mgm101.''' MacMillan Mbantenkhu*, Sara Wierzbicki, Xiaowen Wang, Shangdong Guo, Stephan Wilkens, and Xin Jie Chen. Molecular Biology of the Cell. [http://www.molbiolcell.org/content/24/10/1507.full.pdf+html Link] 24: 1507-1518. Summary: This article goes over the carboxyl-terminal tail on the annealing protein Mgm101. Mgm101 is a single-stranded annealing protein (SSAP) that is required for mitochondrial DNA repair. The c-tail is required for the binding of the protein to DNA, stability of the protein and structural organization. The studies on the c-tail could have better implications for how SSAPs help with DNA repair and maintenance.
# (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. [http://www.molbiolcell.org/content/early/2014/01/14/mbc.E13-10-0628.full.pdf Link]. <br>'''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).<br><br>
 
# (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. [http://www.molbiolcell.org/content/25/8/1374.abstract?sid=39014b33-ddd3-48e3-80ce-2d052e11056e Link]. <br>'''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 .<br><br>


==Molecular and Cellular Biology==
==Molecular and Cellular Biology==


#(2013) '''Expression of Polycomb Targets Predicts Breast Cancer Prognosis.''' Alba Jene-Sanz, Renáta Váraljai, Alexandra V. Vilkova, ''et. al.''. Molecular and Cellular Biology. 33:3951-3961. [http://www.ncbi.nlm.nih.gov/pubmed/23918806 Link]. <br>'''Mix of analysis of human tissue samples, publicly available ChIP-seq and microarray data, and cell culture experiments to understand how EZH2 expression, a protein subunit of PRC2, can modify cancer cell behavior and predict patient outcomes. They conclude high expression of EZH2 predicts aggressive phenotype, high expression of PRC2 predicts better patient outcome, low expression of PRC2 predicts metastasis.'''.<br><br>
#(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. [http://mcb.asm.org.ezproxy1.lib.asu.edu/content/33/24/4844.full.pdf Link] <br> '''Summary:''' Identified function of a subdomain VEFS of SU(Z) in facilitating SU(Z)12-E(Z) assembly and PRC2 binding.
#(2013) '''Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters.''' Woo CJ, Kharchenko PV, Daheron L, ''et. al.'' Molecular and Cellular Biology. 33:3274-3285. [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/23775117 Link]. <br>'''Found new target sites from HOXB and HOXC that recruit PcG by using a reporter construct. Experiments done in mesenchymal stem cells. Discovered two DNA-binding proteins, JARID2 and YY1, possibly regulate PcG.'''<br><br>


==Nature==
==Nature==


# (2013) '''Effect of natural genetic variation on enhancer selection and function.''' S. Heinz, C. Benner, and E. Romanoski et al. Nature. Epub ahead of print. [http://www.nature.com.ezproxy1.lib.asu.edu/nature/journal/vaop/ncurrent/full/nature12615.html Link]. <br>'''Summary''':  The study found Inter-individual genetic variation was highly defined by the functioning of lineage determining transcription factors signal-specific binding to enhancer-like regions of the genome. This helps define epigentic and transcriptomic states and prioritizing regulator variants. <br><br>
# Item


==Nature Biotechnology==
==Nature Biotechnology==


#(2013) '''Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions'''. Joshua N Burton, Andrew Adey, Rupali P Patwardhan, et al. Nature Biotechnology. advance online publication: 1-7. [http://www.nature.com/nbt/journal/vaop/ncurrent/pdf/nbt.2727.pdf Link] <br> '''Group from University of Washington developed improved method of generating contiguous sequencing results by aligning chromosome conformation capture with shotgun sequencing results.'''
# (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. [http://www.nature.com/nbt/journal/v32/n2/pdf/nbt.2798.pdf Link]. <br>'''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: [http://www.nature.com.ezproxy1.lib.asu.edu/nbt/journal/v32/n2/pdf/nbt.2824.pdf Link] <br><br>


==Nature Methods==
==Nature Methods==


# (2013) '''A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA''' Strack RL, Disney MD, Jaffrey SR. Nature Methods. [Epub ahead of print]. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/vaop/ncurrent/full/nmeth.2701.html Link]. <br>'''Summary''': The Jaffrey group was the first to develop and test an RNA that folds into a structure that produces green fluorescence ("Spinach"). In this paper, they report a more stable version, '''Spinach2''', with shows a brighter signal. They used the tag to study the dynamics of "toxic RNA" that is associated with FragileX syndrome.<br><br>
# (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. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/vaop/ncurrent/full/nmeth.2969.html Link]. <br>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.<br><br>
# (2013) '''Cas9 as a versatile tool for engineering biology''' Mali P, Esvelt KM, Church GM. Nature Methods. 10:957-63. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/v10/n10/full/nmeth.2649.html Link]. <br>'''Summary''': This article is a perspective piece on the Cas9-guide-RNA methodology.<br><br>
# (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. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/v11/n4/full/nmeth.2857.html Link]. <br>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.
# (2013) '''ExpressionBlast: mining large, unstructured expression databases''' Zinman GE, Naiman S, Kanfi Y, Cohen H, Bar-Joseph Z. 10:925-6. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/v10/n10/full/nmeth.2630.html Link]. <br>'''Summary''': This article is a correspondence piece that describes a convenient tool for finding out how your gene of interest is expressed. The data are extracted from the NCBI Gene Expression Omnibus (which is usually very difficult to navigate).<br><br>


==Nature Molecular Systems Biology==
==Nature Molecular Systems Biology==


# (2013) '''Design of orthogonal genetic switches based on a crosstalk map of sigma s, anti-sigma s, and promoters.''' Virgil A Rhodius, Thomas H Segall-Shapiro, Brian D Sharon, et al. Nature Molecular Systems Biology. 9.702:1-13 [http://www.nature.com/msb/journal/v9/n1/pdf/msb201358.pdf Link] <br> '''A group from the University of California, San Francisco tested 86 extracytoplasmic function sigma factors and 62 anti sigma factors and identified a subset of 20 sigma factors and promoters highly orthogonal to each other.'''
# (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. [http://onlinelibrary.wiley.com/doi/10.1002/msb.134859/pdf Link]. <br>'''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.<br><br>
# (2013) '''Temporal control of self-organized pattern formation without morphogen gradients in bacteria.''' Stephen Payne, Bochong Li, Yangxiaolu Cao, et al. Nature Molecular Systems Biology. 9.697:1-10 [http://www.nature.com/msb/journal/v9/n1/pdf/msb201355.pdf Link] <br> '''The majority of biological pattern formation requires morphogens as a spatial cue. A group at Duke University programmed E.coli to instead create a self-organized ring pattern, using the morphogen as a timing cue.'''


==Public Library of Science Biology (PLoS Biology)==
==Public Library of Science Biology (PLoS Biology)==


# (2013) '''Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites'''. Sarah D. Diermeier, Attila Németh, Michael Rehli,Ingrid Grummt, Gernot Längst. PLoS Genetics 9:9: 1-12. [http://www.plosgenetics.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1003786&representation=PDF Link]
 
Determined that clustered binding sites increase the binding affinity of transcription factors in chromatin.
# (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: [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001737 Link]. <br>'''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. <br><br>
#(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) [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/23940458 Link]<br>'''Summary:''' Stochastic gene expression in yeast chromosomes.


==Proceedings of the National Academy of Sciences==
==Proceedings of the National Academy of Sciences==
#(2013) '''Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells'''. Patrick Murphy et. al. Proceedings of the National Academy of Sciences. 110: 19: 7772-7777. [http://www.pnas.org/content/110/19/7772.full Link]
# Item


==Science==
==Science==


#(2013) '''Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma'''. Peter W. Lewis, Manuel M. Müller, Matthew S. Koletsky, ''et. al.''. Science 340:857-61. [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/23539183 Link]<br>'''Summary:''' Found that Lys27Met mutations in histone tails inhibit PRC2 activity in a specific child cancer. Somewhat novel application of therapies being explored in our lab.<br><br>
# (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. [http://www.sciencemag.org/content/343/6166/77.short Link]. <br>'''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).<br><br>
# (2014) '''Total Synthesis of a Functional Designer Eukaryotic Chromosome.''' Narayana Annaluru, Héloïse Muller, Leslie A. Mitchell et al. Science. 344:55-58. [https://www.sciencemag.org/content/344/6179/55.abstract Link]. <br>'''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.<br><br>
# (2013) '''Genetics Driving Epigenetics.''' Terrence S. Furey, Praveen Sethupathy. Science. 342:705-706. [http://www.sciencemag.org.ezproxy1.lib.asu.edu/content/342/6159/705.long Link]. <br>'''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! ''' <br><br>


==Miscellaneous Reviews and Media==
==Miscellaneous Reviews and Media==


'''2013 iGEM World Championship - Projects of Interest'''
'''Reviews'''


# (2013) '''COLISWEEPER: The world's first bacterial minesweeper game.''' ETH Zurich iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:ETH_Zurich Link]. <br>'''Summary''': Biological version of the Minesweeper game. Bacterial spot-cultures (spaced on a grid on agar) represented either mines or number clues (via expression of some combination of colorimetric enzymes). '''Quorum sensing (Lux)''' was used to enable the number clue spots to create a certain color depending upon their positioning near one, two, or more mines. Their data included a nice demonstration of AHL-concentration-dependent gene induction.<br><br>
# (2014) '''Programming biological operating systems: genome design, assembly and activation.''' Gibson DG. Nature Methods, 11:521-6. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/v11/n5/full/nmeth.2894.html Link]<br>Summary: '''REVIEW''' - Dan Gibson (inventor of Gibson Assembly) published a very nice review on genome building.<br><br>
# (2013) '''E. teamwork: Engineering a synthetic microbial consortium.''' Braunschweig iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:Braunschweig Link]. <br>'''Summary''': '''Quroum sensing (Las and Rhl)''' was used to cross-induce ampicillin resistance in cells so that the survival of each relied on eachother. Cell types were "tagged" with pigment expression (blue and pink) in order to quantify the proportion of each in co-culture. The team reported a third strain (labeled yellow) but I only saw data for a two-strain blue/ pink co-culture on their poster.<br><br>
# (2014) '''Principles of genetic circuit design.''' Brophy JA, Voigt CA. Nature Methods, 11:508-20. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/v11/n5/full/nmeth.2926.html Link]<br>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.
# (2013) '''Exosome mediated mammalian cell-cell communication.''' MIT iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:MIT Link]. <br>'''Summary''': The Acyl-TyA peptide tag was used to incorporate proteins into '''mammalian exosomes''', which are vesicles that carry "cargo" from one mammalian cell to another. There is data that suggests that cell membrane localization worked, but no data for actual protein delivery (just tests to see if the tag disrupted protein function).<br><br>
# (2013) '''The uniCAS toolkit for gene regulation.''' Freiburg iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:Freiburg Link]. <br>'''Summary''': The team used the Cas9 protein/ guide-RNA system to target various transcriptional regulators to genes in mammalian cells. One very cool, straight-forward application was a split transcription activator: Cas9+CRY2 binds DNA, and CIB1+VP16 is required to activate transcription. Blue light stimulates CRY2-CIB1 interaction; as a result, VP16 recruitment to a gene is controlled by light. Note: the Cas9+Vp16 has been published recently.<br><br>


'''News'''
'''News'''


# November 6, 2013. '''BBSRC Invests $16M in Synthetic Biology Startup Fund.''' GenomeWeb Staff Reporter. GenomeWeb Daily News. [http://www.genomeweb.com/bbsrc-invests-16m-synthetic-biology-startup-fund Link]. <br>'''Summary''': Biotechnology and Biological Science Research Council (BBRC) said today that it has provided £10 million ($16.1 million USD) to launch an investment fund that will fund early-stage companies in the '''United Kingdom''' that are focused on commercializing synthetic biology technologies<br><br>
# (2014) A Giant Leap for Synthetic Genes. Haynes Lab Blog, ASU. http://haynes.lab.asu.edu/uncategorized/a-giant-leap-for-synthetic-genes/
# October 24, 2013. '''SRC launches synthetic biology research effort at six universities.''' Semiconductor Research Corp. R&D Magazine. [http://www.rdmag.com/news/2013/10/src-launches-synthetic-biology-research-effort-six-universities Link]. <br>'''Summary''': Semiconductor Research Corporation (SRC) launched the Semiconductor Synthetic Biology (SSB) research program on hybrid bio-semiconductor systems. The program will initially fund research at six universities: Massachusetts Institute of Technology, the Univ. of Massachusetts at Amherst, Yale, Georgia Tech, Brigham Young, and the Univ. of Washington.<br><br>

Latest revision as of 14:12, 9 May 2014

<- Back to Publications

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/
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