Haynes:LitReviewNov2016

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JOURNAL ASSIGNMENTS:

JOURNAL WEBSITE Assigned to…
ACS Synthetic Biology http://pubs.acs.org/journal/asbcd6 Cassandra B.
BioRxiv http://biorxiv.org/ Daniel V.
Cell http://www.cell.com Ben N.
EMBO Molecular Systems Biology http://msb.embopress.org Daniel V.
Journal of Biological Engineering http://www.jbioleng.org Ben N.
Journal of Cell Biology http://jcb.rupress.org Daniel V.
Molecular Biology of the Cell http://www.molbiolcell.org Rene D.
Molecular and Cellular Biology http://mcb.asm.org Rene D.
Nature http://www.nature.com/nature/index.html Cassandra B.
Nature Biotechnology http://www.nature.com/nbt/index.html Stefan T.
Nature Methods http://www.nature.com/nmeth/index.html Daniel V.
Public Library of Science (PLoS): Biology http://journals.plos.org/plosbiology/ Rene D.
Public Library of Science (PLoS) One: Synthetic Biology http://journals.plos.org/plosone/browse/synthetic_biology Ben N.
Proceedings of the National Academy of Sciences http://www.pnas.org Stefan T.
Science http://www.sciencemag.org/journals Stefan T.
Miscellaneous Reviews and Media N/A Dr. Haynes


INSTRUCTIONS

  • Search for lab-relevant articles dated May 2016 up to today. You can use PubMed or go directly to the journal's website.
  • Be prepared to give a 3-minute summary of why the article should be read by the group.
  • Use the following text format EXACTLY as it is shown in the example below...

# (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 THEN copy the template that is shown below. Do not use keyboard line returns to space out the numbered list, or else each item will start with the number 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.


SPRING 2016, 05/16/2015

ACS Synthetic Biology

  1. (2016) Joseph K Cheng and Hal S. Alper. Transcriptomics-Guided Design of Synthetic Promoters for a Mammalian System. ACS Synbio. Article ASAP. Link.
    Summary: The authors used an “omics” approach that included profiling the transcriptome of a specific cell line under desired conditions, bioinformatically identifying promoter motifs, and building/testing synthetic reporters to establish a framework for the identification/construction of novel mammalian promoters. This work aimed to broaden the limited, often virally based toolkit that is currently in use.
  2. (2016) Tina Lebar and Roman Jeraia. Benchmarking of TALE- and CRISPR/dCas9-Based Transcriptional Regulators in Mammalian Cells for the Construction of Synthetic Genetic Circuits. ACS Synbio.10:1050-1058. Link.
    Summary: This paper compares the TALE and CRISPR/Cas9-based systems of transcriptional regulation (both activation and repression). They optimized strand targeting for Cas9-based repressors and activators and constructed NOR gates as a proof of concept. They concluded that although Cas9 may be easier to use for new sites, TALE-based systems showed better activation and were more suited to complex logical designs.
  3. (2016) Spencer R. Scott and Jeff Hasty. Quorum Sensing Communication Modules for Microbial. ACS Synbio. 9:969-977. Link.
    Summary: This paper aims to improve the quorum sensing toolkit by characterizing the rpa and tra systems, to accompany the widely used lux system. They tested signal and promoter crosstalk to develop orthogonal systems for the construction of genetic circuits.

BioRxiv

  1. 1 (2016) Characterizing the Non-Normal Distribution of Flow Cytometry measurements from transiently expressed constructs in mammalian cells. Peter F McLean, Christina D Smolke, Marc Salit et al. BioRxiv [1].

Authors argue that the current flow cytometry protocol is too biased and give inaccurate results that can't be compared between experiments. They uploaded FCS files into R and processed these using several flow based packages in R. This allowed them to look at the different means (geometric mean, gated geometric mean, bimodal mean and a right tail gauss mean) which is supposed to give a more reproducible mean and allow comparison of fluorescent signals.

  1. 2 (2016) The impact of chromatin dynamics on Cas9-mediated genome editing in human cells. René M. Daer, Josh P. Cutts, David A. Brafman, and Karmella A. Haynes. Biorix. Link.
    Summary: This paper was extremely relevant and interesting because our lab produced this article yay. .


Cell

  1. (2016) Two Conserved Histone Demethylases Regulate Mitochondrial Stress-Induced Longevity. Carsten Merkwirth, Virginija Jovaisaite, and Jenni Durieux et al. Cell. 165:1209–1223. Link.
    Summary: Two H3K27 demethylases, both jumonjiC-domain-containing proteins, play a role in activating unfolded protein response (UPR) mitochondrial stress pathway. Knockout of these demethylases results in shortened lifespan in C elegans and mice, whereas gain-of-function mutations increases lifespan. (My take: targeted delivery of PcTF to the mitochondria could replicate these findings. Could be an additional area of study for epigenome engineering.)
  2. (2016) Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells. Author One, Author Two, and Author Three et al. Cell. 165:1389–1400. Link.
    Summary: Researchers compared gene expression & H3K27me3 presence in mouse intestinal stem cells vs differentiated villus cells. Very similar methodology to our recent PcTF paper. They found that PRC2 plays important role in determining transcriptional fate at bivalent promoters in ISCs.

EMBO Molecular Systems Biology

  1. tba

Journal of Biological Engineering

No relevant articles.

Journal of Cell Biology

  1. tba

Molecular Biology of the Cell

  1. (2016) Nuclear constriction segregates mobile nuclear proteins away from chromatin. Jerome Irianto, Charlotte R. Pfeifer, Rachel R. Bennett, Yuntao Xia, Irena L. Ivanovska, et al. Molecular Biology of the Cell, online preprint. Link
    Summary: Cancer and other cells squeeze themselves through tight spots sometimes. When they do this, they compact their genomes with chromatin, reducing accessibility to Fok1. Could potentially decrease access by Cas9.

Molecular and Cellular Biology

No relevant articles.

Nature

No relevant articles found in the last five months.

Nature Biotechnology

  1. (2016) Oakes et al. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch Link
    Summary: This paper discusses the screening and characterization of an allosterically controlled Cas9 domain that selectively binds only when a small molecule is present. They show it is highly specific for the small molecule, as well as for its target. The construct was shown to work in prokaryotic and eukaryotic cells, as well as inducible and reversible activation.
  2. (2016) Weiner et al. Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution Link.
    Summary: This paper describes a method for mapping combinations of histone marks using ChIP and sequencing.
  3. (2016) Morita et al. Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions Link.
    Summary: First of all, I can't believe this paper made it into NBT... This paper demonstrated targeted DNA demethylation and subsequent upregulation of genes in cell cultures, cancer cell lines, neural cells, and mouse fetuses by a two part fusion protein. One fusion consisted of a dCas9 and GCN4 peptide used to target the DNA. The other fusion consisted of an anti-GCN4 scFv fused to a TET1 hydroxylase. The Cas9 proteins targets the demethylase to a specific locus, activating nearby genes and doing something that our lab could totally do with histone modifying proteins.

Nature Methods

  1. tba

Nature Molecular Systems Biology

  1. tba

Public Library of Science (PLoS): Biology

  1. (2016) Protocols.io: Virtual Communities for Protocol Development and Discussion. Leonid Teytelman, Alexei Stoliartchouk, Lori Kindler, and Bonnie L. Hurwitz. PLOS Biology, 14(8): e1002538. Link
    Summary: Phone app for sharing and discussing protocols. Allows you to follow a step by step protocol as you do each step, can add notes/variations there. Similar to using Benchling in publications: can include a link to the protocol so if you make updates to the protocol, anyone who accesses it will see the changes.
  2. (2016) Differences in Collaboration Patterns across Discipline, Career Stage, and Gender. Xiao Han T. Zeng, Jordi Duch, Marta Sales-Pardo, João A. G. Moreira, Filippo Radicchi, Haroldo V. Ribeiro, Teresa K. Woodruff, Luís A. Nunes Amaral. PLOS Biology, 14(11): e1002573. Link
    Summary: Collaboration patterns vary between genders. Lots of possible reasons listed but important for us to keep in mind for our own careers as collaboration is key for success.

Public Library of Science (PLoS) One: Synthetic Biology

  1. (2016) The Polycomb Group Protein Pcgf1 Is Dispensable in Zebrafish but Involved in Early Growth and Aging.. Dupret B, Völkel P, Le Bourhis X et al. PLoS ONE. 11(7): e0158700. Link.
    Summary: Remember that paper about how different PCGFs colocalize in different parts of the genome with different components of PRC1? These researchers created a vertebrate model (zebrafish) that's missing PCGF1. They found that although the fish were viable, they were susceptible to early development defects and premature aging.

Proceedings of the National Academy of Sciences

Lots of cool protein engineering papers, but nothing relevant to synthetic epigenetics

Science

  1. (2016) Piunti and Shilatfard Epigenetic balance of gene expression by Polycomb and COMPASS families Link
    Summary: This review discusses recent research regarding polycomb and COMPASS proteins and how they control epigenetics.

Miscellaneous Reviews and Media

Reviews

  1. (2016) The Multiple Facets of PRC2 Alterations in Cancers. J of Mol Biol. Link.
    Summary: This review summarizes and distinguishes Polycomb alterations that characterize different types of cancers (different tissues/ organs including breast carcinoma).
  2. (2016) MLL3/MLL4/COMPASS Family on Epigenetic Regulation of Enhancer Function and Cancer. Cold Spring Harb Perspect Med. Link.
    Summary: A recent review of COMPASS, a complex that has the 'opposite' function of Polycomb. Highly relevant for epigenetic reactivation projects in the lab.


New Databases

  1. (2016) Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res. Link. Summary: A new database reported by Mei et al. from Harvard might be more comprehensive than the UCSC genome browser, since it also pulls data from GEO (which UCSC does not always do). The focus is on human and mouse.


News

  1. (11/2016) Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription. Epigenetics News. Link.
    Summary: David Allis' lab showed in macrophage cells simultaneous modification (phosphorylation) of both histones (H3S28) and a transcription factor protein (p65) upon induced activation. The proteins that generate the phosphorylation marks are mitogen- and stress-activated protein kinases (MSK's). Paper: Josefowicz, S.J. et al: Mol. Cell 2016 Oct 20;64(2):347-361. doi: 10.1016/j.molcel.2016.09.026. Link
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