Epigenomics and Synthetic Biology: 2015 in Review

Despite how slow it feels doing it, every year science propels at a startling rate. Here are some paradigm shifts that really impacted my perceptions. Some are a selection of my contributions to EpiGenie and Epibeat, while the rest are written by others from places such as The Scientist and MIT Tech Review.

Epigenomics and Synthetic Biology Breakthroughs:

  1. The labs of Alexander Meissner, J. Keith Joung, and John Rinn brought the non-controversial paper: CRISPR used in human embryonic stem cells to show fundamental difference between mice and men.
  2. Michael Skinner shows that Epigenetics drives genetics straight into evolution
  3. Sperm miRNA Drives Intergenerational Stress Response
  4. A ‘new’ epigenetic mark: 6mA Makes the Grade as a Eukaryotic Epigenetic Mark
  5. DNA Methylation Helps Muscles Remember
  6. The Brain’s Circular RNAs
  7. Epigenome Editing with CRISPR-dCas9, TALEs, and Zinc Fingers
  8. Obesity Alters Sperm Epigenome
  9. CRISPR Gets Creative with Histone Acetylation
  10. Antidepressant Exerts Epigenetic Changes
  11. Move over Optogenetics, here comes Magnetogenetics: Discovery of long-sought biological compass claimed
  12. 5fC is Stable in Mammalian Brains
  13. CRISPR Inversion Untangles How CTCF Controls Chromatin Looping
  14. Epigenetic Clock Goes from Analog to iWatch
  15. New Biotech?! Viral Elements Horizontally Transfer Parasite’s Genes into Non-Standard Host Genomes
  16. RNAi pesticide: ‘Deep inside its labs, Monsanto is learning how to modify crops by spraying them with RNA rather than tinkering with their genes
  17. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function at Protocadherins
  18. CRISPR-Display: For the lncRNA Enthusiast that has Everything
  19. CTCF Tucks Genes Into Their Lamina Associated Beds
  20. Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides
  21. A DNMT1 (protein) and miRNA complex inactivating the catalytic region
  22. For that question you hear a million times: RNA doesn’t correlate with protein? Huh?
  23. Using Synbio to make narcotics: Brewing Bad
  24. Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model
  25. Spray Your Way Free of Cystic Fibrosis with a Gene Editing Nasal Spray
  26. Sex On the Brain: DNA Methylation Defines Gender
  27. New Insights into Puzzling Placental DNA Methylation Domains
  28. 5hmC: a Helping Hand in Drug Addiction
  29. Optogenetic CRISPR/Cas9
  30. Evolving a bigger brain with human DNA
  31. Computed Chromatin Conformation Verfied by CRISPR [Awesome Video]
  32. A Reporter System to Trace Dynamic Changes of DNA Methylation at Single-Cell Resolution

Epigenomic Controversy

Sometimes big ideas need pilots. These pilots need more verification before public exposure but aren’t always uninterpretable, however they should be read with caution in regards to over-interpreting. Small sample sizes aren’t always applicable to a diverse general population and could be noisy but these experiments may start some interesting thoughts and still reveal underlying biology. But sometimes press releases aren’t handled properly.

  1. A paper on Intergenerational Holocaust Effects on Stress Signalling lead to this popular press and then this interesting response.
  2. A talk at ASHG about Epigenomics of Homosexuality got made into popular press and was followed by this critique and subsequent rebuttal.

CRISPR Craze & Crisis

There was  a gene editing summit that called together the leaders of the field. Interestingly it represented a wide variety of the thought spectrum. They came to a conclusion I think most can get behind: don’t start engineering babies clinically, but let the basic research into editing embryos (that don’t go to term) go strong.

Also of interest was the tweeting and blogging of Paul Knoepfler via IPSCell that showed off some of the academic communicative power of social media.

Gene drives have caught my attention as well since they can hijack evolution. They have a lot of potential for disease, with Malaria being the trailblazer. However, they also conjure up images of a dystopia where there’s a new bioterrorism tool in town, capable of specific genocide with just a few genome edited agents needed to ‘infiltrate’ the population.

I’ve also been thinking alot about the designer baby CRISPR CRISIS, it seems that enough of prominet researchers in genomics dismiss the notion of it, since single genes rule very few traits, but I’m still quite worried about myostatin. The condition works in humans, is famous in cows, and has been done in pigssheep, and dogs. It’s just a single gene that can easily make your child athlete of the century or a soldier in a superhuman army. And of course, something about this old Spiderman comic strip reflects on the Stan Lee’s judgement of the current designer baby CRISPR CRISIS:



On one side, yo…

On one side, you have moneyed interests refusing to accept data that might force stronger regulations of their most profitable chemicals. On the other side, you have genetic determinists clinging to an old paradigm.

I’m not a toxicologist, or even an environmentalist. I didn’t come to this as an advocate for or against any particular chemical or policy. I found something in the data, and I pursued it along a logical path, the way any basic researcher would.

Read more: http://www.smithsonianmag.com/ideas-innovations/The-Toxins-That-Affected-Your-Great-Grandparents-Could-Be-In-Your-Genes-231152741.html

Biology of Aging Research Proposal

1) Background:

Although normal aging is characterized by a number changes, none are as central to the identity of a person as their memories1. While there has been a large

amount of research into age related diseases of the brain, there is relatively little known about the molecular mechanisms behind how a healthy brain ages. Currently, aging is viewed as risk factor, rather than a cause, for a number of neurodegenerative diseases1. An understanding of the mechanisms behind why some people show relatively little age-related cognitive decline (ARCD), and others show significant and disabling ARCD, will provide great insight for both the basic and clinical sciences.

Initial studies into normal cognitive aging have shown that as we age gene expression patterns in the brain change; particularly genes involved in synaptic plasticity and vesicular transport show decreased expression after age 402. However, the casual link between aging and gene expression patterns has remained unknown until recently. More recent studies have begun to suggest that epigenetic mechanisms are the missing casual link3, 4. Modern epigenetics can be defined as “a mitotically (or meiotically) inheritable change in gene expression, independent of an alteration in DNA sequence5”. Epigenetic mechanisms encompass a number of molecular marks, such as histone modifications, DNA methylation, and microRNAs.

Epigenetic mechanisms
Epigenetic mechanisms (Photo credit: Wikipedia)

Most molecular research into ARCD has examined mouse models1, 6, 7, which allow for unprecedented observations and interventions, and have focused on the hippocampus, as it is involved in the consolidation of memory from the short-term to the long-term. At this time most studies have chosen to solely examine histone acetylation as the dynamic response to memory consolidation8, 9. These studies have shown that there is an age related failure in establishing histone acetylation in “learning-regulated genes” during memory consolidation. Furthermore, many studies have shown that treatment with histone deacytlase inhibitors (HDACs) can attenuate ARCD and related biomarkers8, 10, 11

While a narrowing of focus into histone acetylation has provided great insight, there is also emerging evidence suggesting that histone modifications act in concert with a number of other epigenetic factors12, 13. Indeed, DNA methyltransferase (DMNT) inhibitors have also been shown to interfere with memory consolidation14. Furthermore, many studies have also narrowed their focus into a relatively small amount candidate genes and/or single pathway being affected as a result of epigenetic modifications8, 15. However, in most cases the epigenome rarely works alone and typically affects gene expression on a much larger scale7, 16. In this research I hypothesize that memory consolidation involves epigenomic changes on a genome-wide scale in the hippocampus and that the dysregulation of these epigenetic marks contributes to ARCD.


2) Specific Objectives:

Specific Objective 1: Evaluate the epigenomic and transcriptomic changes associated with ARCD.

Specific Objective 2: Evaluate the epigenomic and transcriptomic changes associated with interventions that attenuate ARCD.

3) Proposed Research:

Evaluate the epigenomic and transcriptomic changes associated with ARCD.

To evaluate the epigenomic and transcriptomic changes associated with ARCD, I will use a C57BL/6J mouse model6. This model will allow for the collection of a

Workflow overview of the MeDIP procedure. MeDI...
Workflow overview of the MeDIP procedure. MeDIP procedure is followed by array-hybridization (A) or high-throughput/next generation sequencing (B) (Photo credit: Wikipedia)

significant amount (n=10) of hippocampal samples (CA1, CA3, and Dentate Gyrus). These samples will be collected from mice at the ages of 3, 8, and 16 months, which represent young, middle-aged, and old mice respectively6. The use of these 3 age groups will be sufficient for experimentation, as previous research has shown significant memory impairment in 16 month-old mice, with the 8 month-old mice showing an intermediate phenotype8. Samples will be obtained both before and at multiple time points during memory consolidation as initiated by fear conditioning17 (10 min, 30 min, 60 min, and 1d after)8. The different regions of the hippocampus will then be sequenced using next-generation sequencing technologies, including methylated DNA immunoprecipitation paired with sequencing (MeDIP-seq), chromatin immunoprecipitation paired with sequencing (ChIP-Seq), and RNA-Seq methodologies. These technologies will allow for an assessment of repressive epigenetics marks, such as DNA methylation (5-methylcytosine) and H4 lysine-27 trimethylation (H4K27me3). Additional Chip-Seq will also examine the activating marks of H4 lysine-12 acetylation (H4K12ac) and H4 lysine-3 tri-methylation (H4K3me3). Finally, micoRNA and gene expression patterns can also be assessed at a genome wide level by RNA-seq. Bioinformatic analysis will then be done to examine regions of the genome that show overlapping and unique responses of the (epi)genome upon memory consolidation across all age groups (Figure 1). Results from top candidates will be confirmed via sodium bisulfite sequencing, respective qPCR technologies (immunoprecipitation or reverse transcription based), and western blotting to confirm whether the observed alterations in gene expression and/or epigenetic marks translate to the protein level.

It should be noted that the histone modifications chosen only represent a fraction of those that occur, and while the ones chosen are the most extensively studied in this context, it is possible that there are more informative marks. If any of the marks are found to be non-informative in the preliminary experiments, alternative histone modifications will then be examined in a large-scale screening assay based off western blotting.

Evaluate the epigenomic and transcriptomic changes associated with interventions that affect ARCD.

The evaluation of epigenomic and transcriptomic changes associated with interventions that attenuate ARCD will be done using a similar experimental design to

English: Schematic showing how antisense DNA p...
English: Schematic showing how antisense DNA prevents protein translation. (Photo credit: Wikipedia)

the previous objective, but will focus on time points and regions of interest. The main difference will be the addition of two new groups; mice that serve as a matched-control for the methodology of intervention (i.e: vehicle injection) and those that have received the intervention (Figure 1). The interventions used will include HDAC2 inhibitors, which have received much attention in prior research11. Furthermore, given that DMNT inhibitors interfere with memory consolidation14, methyl-donor rich diets, such as those with choline18, will also be examined. Novel interventions, such as RNAi for transcripts of interest and environmental enrichment19 will also be examined.

It should be noted that there is a large amount of variation in the methodologies of the interventions mentioned. If during preliminary experiments an intervention does not attenuate ARCD, additional experiments will be carried out to optimize the conditions for each intervention (i.e.: dosage and timing of exposure).


4) Expected Findings and Overall Significance of Proposed Research:

The proposed research will provide an unprecedented resolution of the dynamic and transient epigenetic and transcriptomic changes occurring upon memory consolidation. The results are expected to reveal a large number of previously unobserved interactions between the epigenome, genome, and transcriptome due to the relatively unbiased nature of sequencing technologies. The use of mice at different ages will allow for the identification of novel regions that become deregulated with age and contribute to ARCD. The integration of multiple data sets by bioinformatic analysis will also provide novel insight into how epigenetic mechanisms co-regulate changes in gene expression and allow for cross-communication between relatively distinct regions of the genome and/or pathways during memory consolidation. Furthermore, the examination of interventions that attenuate ARCD will also provide a number of novel insights into clinical treatment for ARCD. The use of HDAC inhibitors will allow for an examination of the most commonly used intervention11, and has the potential to reveal the mechanisms behind many of the potential negative side effects associated with a drug of such global nature.  The use of RNAi will allow for assessment of the effect in changes the dosage of individual candidate genes. Finally dietary choline supplementation and environmental enrichment serve as noninvasive interventions, with the potential for positive global epigenetic changes18, 19. These interventions, both established and novel, will confirm and reveal much about the inner workings of the aging brain and also further our understanding of the effectiveness of treatments for ARCD.

5) References:

1. Barnes, C. A. Secrets of aging: What does a normally aging brain look like? F1000 Biol. Rep. 3, 22-22. Epub 2011 Oct 3 (2011).

2. Lu, T. et al. Gene regulation and DNA damage in the ageing human brain. Nature 429, 883-891 (2004).

3. Fischer, A., Sananbenesi, F., Wang, X., Dobbin, M. & Tsai, L. H. Recovery of learning and memory is associated with chromatin remodelling. Nature 447, 178-182 (2007).

4. Graff, J. & Tsai, L. H. Histone acetylation: molecular mnemonics on the chromatin. Nat. Rev. Neurosci. 14, 97-111 (2013).

5. Berger, S. L., Kouzarides, T., Shiekhattar, R. & Shilatifard, A. An operational definition of epigenetics. Genes Dev. 23, 781-783 (2009).

6. Jucker, M. & Ingram, D. K. Murine models of brain aging and age-related neurodegenerative diseases. Behav. Brain Res. 85, 1-26 (1997).

7. Sweatt, J. D. Neuroscience. Epigenetics and cognitive aging. Science 328, 701-702 (2010).

8. Peleg, S. et al. Altered histone acetylation is associated with age-dependent memory impairment in mice. Science 328, 753-756 (2010).

9. Bousiges, O. et al. Detection of Histone Acetylation Levels in the Dorsal Hippocampus Reveals Early Tagging on Specific Residues of H2B and H4 Histones in Response to Learning. PLoS One 8, e57816 (2013).

10. Graff, J. et al. An epigenetic blockade of cognitive functions in the neurodegenerating brain. Nature 483, 222-226 (2012).

11. Day, J. J. & Sweatt, J. D. Epigenetic treatments for cognitive impairments. Neuropsychopharmacology 37, 247-260 (2012).

12. Miller, C. A., Campbell, S. L. & Sweatt, J. D. DNA methylation and histone acetylation work in concert to regulate memory formation and synaptic plasticity. Neurobiol. Learn. Mem. 89, 599-603 (2008).

13. Castellano, J. F. et al. Age-related memory impairment is associated with disrupted multivariate epigenetic coordination in the hippocampus. PLoS One 7, e33249 (2012).

14. Miller, C. A. & Sweatt, J. D. Covalent modification of DNA regulates memory formation. Neuron 53, 857-869 (2007).

15. Salih, D. A. et al. FoxO6 regulates memory consolidation and synaptic function. Genes Dev. 26, 2780-2801 (2012).

16. Bird, A. Perceptions of epigenetics. Nature 447, 396-398 (2007).

17. Fischer, A., Sananbenesi, F., Wang, X., Dobbin, M. & Tsai, L. H. Recovery of learning and memory is associated with chromatin remodelling. Nature 447, 178-182 (2007).

18. Zeisel, S. H. & da Costa, K. A. Choline: an essential nutrient for public health. Nutr. Rev. 67, 615-623 (2009).

19. Pang, T. Y. & Hannan, A. J. Enhancement of cognitive function in models of brain disease through environmental enrichment and physical activity. Neuropharmacology 64, 515-528 (2013).