Haynes:LitReviewOct2014

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JOURNAL ASSIGNMENTS:

• ACS Synthetic Biology - Rene
• Cell - Meli'sa
• Frontiers in Microbiotechnology – David
• Journal of Biological Engineering - Meli'sa
• Journal of Cell Biology - Jonah
• Molecular Biology of the Cell - David
• Molecular and Cellular Biology - Rene
• Nature - Jonah
• 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 May 9, 2014 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 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) Conditional control of mammalian gene expression by tetracycline- dependent hammerhead ribozymes. Kim Beilstein, Alexander Wittmann, Manuel Grez, et al. ACS Synthetic Biology. Published online ahead of print. Link.
   Summary: The authors demonstrated the functionality of a 3'-UTR rybozyme that results in correct folding of the mRNA after addition of tet. Important because the mammalian synthetic biology toolbox is limited so more parts are valuable (even though this want can't really be used with the well-characterized TetR system), eliminates basal pTet expression, and it removes an integration step for building a transgenic inducible system.
   
   
2. (2014) Environmental Sensing of Heavy Metals Through Whole Cell Microbial Biosensors: A Synthetic Biology Approach Lara Bereza-Malcolm, Gulay Mann, and Ashley Edwin Franks. ACS Synthetic Biology, Published online ahead of print. Link.
   Summary: People use quorum sensing to build microbial biosensors. Good resource for QS review.
   
   

Cell

1. (2014) Ruled by Ubiquitylation: A New Order for Polycomb Recruitment. Yuri B Schwartz, Vincenzo Pirrotta et al. Cell, 8.2:321-325. Link
   Summary: This paper provides a new way of thinking about Polycomb complexes and how they play a role in gene regulation! Everything we currently know about polycomb complex recruitment is going to be challenged. The recruitment of polycomb complexes have always been studied in two steps. First, the PRC2 produces histone H3K27 trimethylation at a specific gene, then, the PRC1 complex is recruited by its ability to bind to H3k27me3. However, there have been articles that contradict this process by focusing on a variant of the PRC1 complex and H2A ubiquitylation of surrounding chromatin in the recruitment of PRC2 and H3k27.
   
   
2. (2014) Generation of Functional Human Pancreatic β Cells in Vitro. Felicia W. Paglicua, Jeffery R. Millman, Mads Gurtler et al. Cell, 159:2, 428-439. [1]
   Summary: Attn. David; This research focused on generating glucose responsive β cells from hPSC with limited genetic differences. This, of course, could play a very important role in diabetes treatment.

Frontiers in Microbiotechnology

None. Closest was an article on tools for designing synthetic genes.

1. (2014) Computational tools and algorithms for designing customized synthetic genes. Nathan Gould, Oliver Hendy, and Dimitris Papamichail. Frontiers in Bioengineering and Biotechnology. 2:41.Link.
   Summary: Large summary of software tools for the design of synthetic genes. Tools include DNAWorks, Jcat, Synthetic Gene Designer etc. Also examines criteria for optimizing gene expression in created synthetic genes.

However, I did find a few cool articles from PLoS ONE and PLoS Genetics

1. (2014) The Epigenetic Bivalency of Core Pancreatic β-Cell Transcription Factor Genes within Mouse Pluripotent Embryonic Stem Cells Is Not Affected by Knockdown of the Polycomb Repressive Complex 2, SUZ12. Jennfier C.Y. Wong, Michelle Jack, Yan Li, Christopher O'Neill. 9:5. link.
   Summary: Found that a part of the histone methylase PRC2, SUZ12 knockout was not enough to reduce the level of H3K27me3 at beta cell transcription factors in embryonic stem cells. Suggests that the regulation of bivalency at histone modifications near transcription factor genes require levels of regulation than just changes in level of PcG activity (PRC2). Also a good paper to reference for genes to use to find differentiation from alpha to beta.
2. (2014) Histone H3 Lysine 27 Methylation Asymmetry on Developmentally-Regulated Promoters Distinguish the First Two Lineages in Mouse Preimplantation Embryos. John Arne Dahl, Andrew H. Reiner, Arne Klungland, Teruhiko Wakayama, Philippe Collas. 5:2 Link
   Summmary: Might be a good paper for Jan's research. References differences in distribution of H3K27me3 on promoters between two developmental lineages in mouse embryos and suggests an epigenetic skewing with embryonic stem cell derivation. Probably things we already know in terms of histone methylation differences before and after differentiation events.

Journal of Biological Engineering

No relevant articles.

Journal of Cell Biology

1. (2014) Translational Control in Germline Stem Cell Development. Maija Slaidina and Ruth Lehmann. Link
   Summary: The unique set of RNA regulatory proteins in primordial germ cells (PGCs) are conserved and play an essential role in gene expression regulation and the protection of the genome against foreign RNAs. Studies have revealed evidence that supports the idea that germline stem cells (GSCs) act like PGCs when transplanted back into an embryo; GSCs are less programmed than other stem cell lines due to their involvement of in the development of new embryos. This article is focused on the study of the mechanisms for the GSC self-renewal, stem cell maintenance, and stem cell differentiation, in pursuit of understanding the requirements and demands placed on germline stem cells in the generation of completely new organisms. It was discovered that the switch from a GSC program to an oocyte differentiation program is controlled by specific interactions between self-renewal and differentiation factors. These interactions and networks are based on mutual translational repression through feedback loops (which can be referenced in the paper, Fig. 4B). In addition to this translational repression, the article suggests that protein stability and chromatin modifications affect the GSC cytoblast’s (CB) decision to initiate differentiation by undergoing cellular division with incomplete cytokinesis.

Molecular Biology of the Cell

1. (2014) Cbx2 stably associates with mitotic chromosomes via a PRC2 or PRC1-independent mechanism and is needed for recruiting PRC1 complex to mitotic chromosomes. Chao Yu Zhen, Huy Nguyen Duc, Marko Kokotovic, Christopher J. Phiel and Xiaojun Ren. Link
   Summary: Finds that Cbx2 stably binds to mitotic chromosomes and is independent of the PcG proteins. Also shows that PRC1 rapidly exchanges with interphasic chromatin. Could be useful due to the rapid PRC1 exchanges as well as the insight into the mechanism of epigenetic inheritance related to H3K27me3.

Molecular and Cellular Biology

1. (2014) Polycomb Repressive Complex 2 and H3K27me3 Cooperate with H3K9 Methylation To Maintain Heterochromatin Protein 1α at Chromatin. Joanna Borosa, Nausica Arnoulta, Vincent Stroobant, et al. Molecular and Cellular Biology. 34:3662-3674. Link.
   Summary: This paper investigates the crosstalk between PRC2 and H3K9me2/3 with H3K9me2/3 and heterochomatin protein 1 (HP1). Interesting for our work that involves identifying promoters with H3K27me and measuring up regulation of downstream genes. Based on this paper, we might expect that bivalent promoters with both H3K9me3 and H3K27me3 may not be unregulated by our fusion protein because H3K27me3 and PCR2 can stabilize HP1 binding.
2. (2014) CTCF Controls HOXA Cluster Silencing and Mediates PRC2-Repressive Higher-Order Chromatin Structure in NT2/D1 Cells. Miao Xu, Guang-Nian Zhao, Xiang Lv, et al. Molecular and Cellular Biology. 34:3867-3879. Link.
   Summary: Hox gene silencing during development and differentiation results in higher order chromatin structures. CCCTC-binding factor (CTCF) is important to higher order structure silent chromatin structure and was shown to protect / stabilize H3K27me3 marks at HOXA gene clusters. Important for chromatin sensor projects because, while the sensors can tell us a lot, we should know that some things might be missed when taking small regulatory sections out of a large, higher dimensional cluster.
   
   

Nature

1. (2014) Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system. Tetsushi Sakuma, Ayami Nishikawa, Satoshi Kume, Kazuaki Chayama, and Takashi Yamamoto. Link.
   Summary: In this study, researchers developed a system for multiplex genome engineering using a CRISPR/Cas9 vector that contained multiple guide RNAs that allowed for mutagenesis at up to 7 genomic loci in cultured human cells. It is believed that this system could make the delivery of multiple guide RNA cassettes more efficient and lead to profound advancements in epigenetic research and CRISPR based technologies.
   
   

Nature Biotechnology

1. (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Xuebing Wu, David A Scott, and Andrea J Kriz, et al. Nature Biotechnology. 32:670–676. Link.
   Summary: In this study, four different sgRNAs and hemaglutinin-tagged dCas9 were used to target sequences in mouse embryonic stem cells. Sequence and genomic loci data of the off-target sites, acquired by hemaglutinin-iP-seq, suggests Cas9 requires PAM motif and 5 nucleotide seed for initial binding, but needs additional recognition for cleavage. Chromatin inhibits Cas9 binding, resulting in 70% off target effects occurring in gene-coding regions.
   
   
2. (2014) Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation. John G Doench, Ella Hartenian, and Daniel B Graham et al. Nature Biotechnology, advanced online. Link.
   Summary: In this study, researchers examined six endogenous mouse and three endogenous human genes and made a pool of 1841 sgRNAs corresponding all the possible target sites in these nine genes. Using antibody staining and flow cytometry, the researchers quantitatively determined key features of highly-active sgRNAs and developed an online tool for targeting any gene of interest.
   
   

Nature Methods

1. Chemically defined generation of human cardiomyocytes

Summary: The researchers looked at a commonly used supplement in cell culture, B27, which has 27 different components, and identified only two that had any impact on cardiomyocyte differentiation: L-ascorbic acid 2-phosphate (a form of Vitamin C) and rice-derived recombinant human albumin. They used these two supplements in base RPMI medium to grow up TNNT2-positive cardiomyocytes with reported 95% efficency.

Nature Molecular Systems Biology

1. (2014) The functional diversity of protein lysine methylation. Sylvain Lanouette, Vanessa Mongeon, and Daniel Figeys et al. Nature Molecular systems Biology. 10:724. Link.
   Summary: Review article on diversity of protein lysine methylation. Begin review with focus on histone methylation, including H3K27 trimethylation.
   
   
2. (2014) Specificity, propagation, and memory of pericentric heterochromatin. Katharina Müller‐Ott, Fabian Erdel, and Anna Matveeva et al. Nature Molecular Systems Biology, 10:746. Link.
   Summary: Researchers developed a mathematical model from CHiP-seq data of 16 pericentric heterochromatin factors. Experimental data and model supports a "nucleation and looping" mechanism that explains inheritance of epigenetic marks.
   
   

Public Library of Science Biology (PLoS Biology)

Nothing super relevant.
Perhaps a bit relevant to Jan/David

1. (2014) Mitosis Gives a Brief Window of Opportunity for a Change in Gene Transcription Richard P. Halley-Stott, Jerome Jullien, Vincent Pasque et al. PLoSBio. 12(7). Link.
   Summary: Found that mitotic chromatin (which has most transcription factors temporarily displaced) is reprogrammed 100 times faster than interphase nuclei in post-nuclear transfer to amphibian oocytes. Genes pass through a transient phase of high responsiveness to reprogramming factors during mitosis which alters cell fates and is an opportunity for reprogramming to pluripotency. This may be a result of histone H2A deubiquitination.
   
   

Proceedings of the National Academy of Sciences

1. Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation
   Summary: The researchers used genome editing to identify small DNA sequences capable of recruiting Polycomb proteins. They inserted 28 different DNA elements and looked at how well the elements were able to promote H3K27me3 deposition, and found that sequences as short as 220 bp could model DNA methylation of much longer sequences. The researchers concluded that their data support the model whereby PRC2 recruitment at specific targets in mammals is positively regulated by local CpG density yet obstructed by transcriptional activity or DNA methylation.
   
   

1. Bacterial quorum sensing and metabolic slowing in a cooperative population
   Summary: Proteobacteria use Acyl-homoserine lactone-mediated quorum sensing to control the production of numerous intra- and extracellular products. Although the controls on production may hinder individuals, they are helpful to the group. The researchers looked at a particular species, Burkholderia glumae, and found that quorum sensing down-regulates glucose uptake, substrate level and oxidative phosphorylation. The researchers concluded that quorum sensing acted as a brake to prevent individual bacteria from growing too rapidly when the colony began to increase in size, and may have evolved to ensure homeostasis of the metabolism of individual bacteria under crowded conditions.
   
   

1. Reversal of hyperglycemia in diabetic mouse models using induced-pluripotent stem (iPS)-derived pancreatic β-like cells
   Summary: Using induced pluripotent stem (iPS) cells, researchers were able to derive β-like cells that were functionally similar to the innate insulin-secreting cells in mice. These β-like cells secreted insulin in response to glucose and corrected a hyperglycemic phenotype in two mouse models of type 1 and 2 diabetes via an iPS cell transplant. Long-term correction of hyperglycemia was achieved, as determined by blood glucose and hemoglobin A1c levels. Researchers concluded that this proof-of-principle study showed that reprogrammed somatic cells could be used clinically to treat diabetes.

Science

1. (2014) H3K27me and PRC2 transmit a memory of repression across generations and during development. Laura J. Gaydos, Wenchao Wang2, Susan Strome. Science. 345 no. 6203 pp. 1515-1518 . Link.
   Summary: Attn. Jonah; Studied gene repression via methylation of H3K27me by PRC2. Generated embryos containing chromosomes with and without H3K27me. Without PRC2, H3K27me was transmitted to daughter chromatids through several rounds of cell division rather than the mosaic H3K27 pattern through embrygensis present in embryos with PRC2. Suggests that PRC2 represses X chromosomes in Caenorhabditis elegans germ cells. Shows that H3K27me and PRC2 both contribute to transmitting memory of repression across generations epigenetically.
   
   
2. (2014) Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling. Hans-Martin Herz, Marc Morgan, Xin Gao et al. Science. Vol. 345 no. 6200 pp. 1065-1070. Link.
   Summary: Established pathogenic histone H3K27M mutation in Drosophila. Noticed overexpression resembles PRC2 loss-of-function phenotypes. Examine other histone mutations in chromatin signaling pathways.
   
   
3. (2014) Chromatin state dynamics during blood formation. David Lara-Astiaso1, Assaf Weiner, Erika Lorenzo-Vivas et al. Journal. Vol. 345 no. 6199 pp. 943-949. Link.
   Summary: Attn. Meli'sa; High-sensitivity indexing-first chromatin immunoprecipitation approach to profile the dynamics of four chromatin modifications across 16 stages of hematopoietic differentiation developed. Paired with enhancer region studies to predict transcription factor network controlling chromatin dynamics programs in hematopoiesis.
   
   
4. (2014) Sequential histone-modifying activities determine the robustness of transdifferentiation. Steven Zuryn1, Arnaud Ahier, Manuela Portoso et al. Journal. Vol. 345 no. 6198 pp. 826-829 . Link.
   Summary: Attn. David; Explored efficiency of reprogramming events for cell conversion in vitro. Found conversion requires stepwise histone-modifying activities partitioned into fragmented phases of transdifferentiation through nuclear degradation of JMJD-3.1 and interactions with transcription factors at particular phases relevant in fate selection. Studied H3K27me3.
   
   

Miscellaneous Reviews and Media

Reviews

1. (2014) Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis. Burton A, Torres-Padilla ME. Nat Rev Mol Cell Biol. doi: 10.1038/nrm3885. [Epub ahead of print] Link
   Summary: Good review for understanding how chromatin changes after one fertilized egg gives rise to many cells, and as subpopulations of these cells differentiate.
   
   
2. (2014) Synthetic biology in mammalian cells: next generation research tools and therapeutics. Lienert F, Lohmueller JJ, Garg A, Silver PA. Nat Rev Mol Cell Biol. 15:95-107. Link
   Summary: Attn. Dr. Haynes, Jonah; Pretty comprehensive teview on mammalian cel synthetic bio from the Silver lab. Includes chromatin engineering approaches (targeting of chromatin proteins fused with DNA binding domains). Good for figuring out what has not been explored yet & outstanding questions.
   
   
3. (2014) Synthetic therapeutic gene circuits in mammalian cells. Ye H, Fussenegger M. FEBS Letters. 588:2537-44. Link
   Summary: (another) review on mammalian synthetic circuits from the Fussenegger lab.
   
   
4. (2014) The Controversial Role of the Polycomb Group Proteins in Transcription and Cancer: How Much Do We Not Understand Polycomb Proteins? Scelfo A, Piunti A, Pasini D. FEBS J. doi: 10.1111/febs.13112. [Epub ahead of print]. Link
   Summary: Potentially game-changing information!
   
   
5. (2014) Epigenetic therapy of cancer with histone deacetylase inhibitors. Lakshmaiah KC, Jacob LA, Aparna S1, Lokanatha D, Saldanha SC. J Cancer Res Ther. 10:469-78. Link
   Summary: Useful for catching up on the state of the art in chromatin modification for cancer therapy. Also highlights adverse effects of HDAC therapy.
   
   

News

1. (2014) No One Should be Afraid of Synthetic Biology-Produced Vanilla. Haynes KA. Slate.com. Link
   
   
2. (2014) So Häagen-Dazs ‘says no to synbio’? Watson E. Food Navigator-USA.com. Link