Bowdoin Science Journal

Lia Scharnau

Uncovering Our Inner Overlord: How DEADbox ATPases Built Their Empire Off Regulating RNA Maturation

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Do you remember the simple days? Recall your fond memories of learning about organelles in introductory biology. This is where we learned our favorite biology fact, that the mitochondria is the powerhouse of the cell. Sigh, those were the days. Well, recently the field of biology has discovered a new type of organelles in the cell; membraneless organelles! They are formed through liquid-liquid phase separation (LLPS). If you imagine the droplets formed when you combined oil and water, that’s a form of LLPS. Membraneless organelles rely on LLPS for rapid and reversible cell compartmentalization.

In 2019, researcher Maria Hondele and her team took particular interest in investigating membraneless organelles, focusing specifically on DEAD-box ATPases (DDX) and their role in regulating them. DEAD-box ATPases keep ribonucleoprotein complexes from misfolding or building up over time. The role of DDX-mediated phase separation in compartmentalizing RNA processing is a rare cellular organization conserved across prokaryotes and eukaryotes over time (Hondele 2022). Highly conserved proteins have withstood the test of evolution and have continued to be passed down through generations without significant mutation. Hondele looked specifically at RNA-dependent DEAD-box ATPases because they regulate the RNA movement in and out of the membraneless organelles.

This investigation focused on  Dhh1, which is a DEAD-box ATPase specific to Saccharomyces cerevisiae (yeast). A wide range of assays were run to systematically determine the conditions required for the in vitro formation of Dhh1 liquid droplets. Liquid droplets are formed through LLPs and are indicators of membraneless organelles. Hondele found that liquid droplet formation is a fickle process that requires specific amounts of RNA and ATP to be added to the system and the cell environment to be at a low pH and salt concentration (Hondele 2019). Additionally from a DNA standpoint, the DDX itself must have low-complexity domain tails which means the ends of the proteins do not consist of a large variety of amino acids (Hondele 2019). 

After the initial investigation of the DDX ATPase and how it runs controls Dhh1 droplet formation, Hondele, and her team investigated DDX ATPase’s role in the regulation of RNA. Through a series of experiments, they found that DDX ATPases have played an extensive role in RNA regulation. The DDX ATPases can actually control the RNA maturation steps so they become spatially and temporally separated in distinct membraneless organelles (Hondele 2019). This means that each membraneless organelle may specialize in one step of the RNA maturation process so that the RNA must move between different organelles throughout the process. Of course, the release and transfer of RNA is regulated by ATPase activity, confirming DDX ATPase’s role as the omnipotent overlord of RNA. The DDXs derive their power from the low-complexity domains. These domains give DDXs the intrinsic ability to set up distinct compartments and when teamed up with the ATPases, they can influence the partitioning of RNA molecules between compartments (Hondele 2019).

Hondele and her team managed to uncover a complex and extensive dictatorship that has been operating for years under our very noses and in our very cells. The well-established and conserved cellular network of DEAD-box ATPases allows the RNA processing steps to be regulated, leading to DEAD-box ATPase control over maturation state, RNP composition, and ultimately RNA fate.

Unfortunately, we are still in the investigation phase and are yet to decide on how best to manipulate this dictatorship to benefit us. Current intelligence indicates that the dysregulation of DDXs could have pathological consequences that could contribute to the development of aggregation diseases, such as Parkinson’s, Alzheimer’s, Amyotrophic lateral sclerosis, and Frontotemporal Dementia (Gomes 2018). Luckily liquid-liquid phase separation has provided a mechanistic link between normal cellular function and disease phenotypes. Over time, these liquid droplets become more static and aggregated, likely leading these protein aggregates to be an end-stage phenotype after aberrant phase separation has overwhelmed cellular machinery that ordinarily reverses these altered phases (Gomes 2018). Through further study and comprehension of how DDXs contribute to these diseases, new treatments could be developed.

 

Literature Cited:

Gomes, E,. Shorter, J. The molecular language of membraneless organelles. J. Biol Chem. 2018; 294(18):7115-7127. 10.1074/jbc.TM118.001192

Hondele, M.,  Sachdev, R., Heinrich, S., Wang, J., Vallotton, P., Fontoura, B.M.A., Weis, K. DEAD-box ATPases are global regulators of phase-separated organelles. Nature. 2019; 573(7772):144-148. 10.1038/s41586-019-1502-y.

Hondele, M., Weis, K. The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA-Protein Condensates. Annu Rev Biochem. 2022;  91:197-219. 10.1146/annurev-biochem-032620-105429. 

Your DNA Remembers: Correlating Epigenetics and Early Childhood Trauma through DNA Methylation

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What’s your earliest memory? Can you remember everything that happened between the ages of three to five? No? Me neither. Despite the gaps in your memory, your body—specifically your DNA—knows what happened to you. It shouldn’t be surprising that DNA has such a good memory. After all, it stores genetic information tracing back thousands of years. This of course prompts several questions, namely the following; how does DNA store my memories and how does that affect me?

Let’s start from the beginning. Epigenetics encompasses all heritable changes in gene activity that do not stem from a change in DNA sequences (Moore et al, 2013). DNA methylation introduces a particularly salient new epigenetic mechanism for gene regulation and cell differentiation. The key to DNA methylation lies within the special enzymes that modify the cytosine DNA base by adding a methyl group (Moore et al, 2013; Suelves, 2016). Interestingly, cell differentiation is partly driven by differing levels of DNA methylation. An overall increase in DNA methylation occurs during the differentiation process, while a decrease in it at cell-specific loci helps define cellular identity (Suelves et al, 2016). Additionally, the progressive decrease in overall DNA methylation can contribute to physiological aging and the development of cancer (Suelves et al, 2016). Overall, these altered cytosines play key roles in human development and health issues (Moore et al, 2013).  

This brings us to the second question: how does my DNA’s photographic memory affect me? Well, it turns out that choices such as diet, drinking, exercise, illness, and environmental conditions can all have an impact on genomic stability and gene-specific DNA methylation (Lim et al, 2012). So while you might not remember what happened as a kid, your DNA may already be internalizing those experiences. The Avon Longitudinal Study of Parents and Children patiently waited for years so they could specifically study how childhood experiences affect epigenetic markers in adolescence. A cohort of 13,988 children with due dates between April 1991 and 1992 were monitored for exposure to childhood adversity from birth to the age of eleven. Using changes in DNA methylation at the age of fifteen, researchers investigated whether the timing of adversity has epigenetic consequences across childhood and adolescence (Lussier et al, 2023). 

Each mother reported whether their child faced any of the following seven types of childhood adversity; caregiver physical or emotional abuse, sexual or physical abuse, maternal psychopathology, one-adult households, family instability, and neighborhood disadvantage as well as the timing that the adversity was present. Out of the 13,988 children, 609-665 showed signs of both adversity and a decrease in DNA methylation at 15 years old (Lussier et al, 2023). 

Within this sample from the original cohort, further DNA analysis identified twenty-two loci that showed significant associations between exposure to adversity and altered DNA methylation at the age of 15 (Lussier et al, 2023). Of the loci identified to be associated with decreased DNA methylation, the highest percent of loci were correlated with growing up in one-adult households (Lussier et al, 2023). None of the identified loci indicated that adversity may alter DNA methylation at birth or the age of seven, but instead only emerged in adolescence (Lussier et al, 2023).  

Researchers concluded that the ages between three and five years old are when children are vulnerable to adversity and the consequences of this adversity may biologically embed itself and later manifest itself in adolescence (Lussier et al, 2023). Additionally, the adversity-associated decrease in DNA methylation is correlated to have effects on the central nervous system (Lussier et al, 2023). Of course, it’s great timing that the altered DNA methylation becomes an issue during puberty. Especially since it’s associated with poor self-esteem and increased depressive symptoms. 

What’s the upside? There has to be a silver lining or else this article is just a doomsday proclamation. The ability to finally trace health complications back to epigenetic mechanisms due to latent childhood trauma provides an important piece of the puzzle of understanding complex diseases. However, the puzzle is far from solved. The cohort in this study was predominantly of European descent and further research into how the complexities of race factor into DNA methylation and childhood adversity is the next step in this journey.

Literature Cited:

Lim , U., & Song, M. (2012). Dietary and Lifestyle Factors of DNA Methylation. In Cancer Epigenetics (Vol. 863, pp. 359–376). Humana Press.

 Lussier, A. A., Zhu, Y., Smith B. J., Cerutti J., Fisher J., Melton P. E., Wood N. M., Cohen-Woods S., Huang R., Mitchell C., et al. (2023). Association between the timing of childhood adversity and epigenetic patterns across childhood and adolescence: findings from the Avon Longitudinal Study of Parents and Children (ALSPAC) prospective cohort. Lancet Child Adolesc Health. 7(8), 532-43. https://doi.org/10.1016/S2352-4642(23)00127-X

Moore, L. D., Le, T., & Fan, G. (2013). DNA methylation and its basic function. Neuropsychopharmacology, 38(1), 23–38. https://doi.org/10.1038/npp.2012.112

Suelves, M., Carrió, E., Núñez-Álvarez, Y., & Peinado, M. A. (2016). DNA methylation dynamics in cellular commitment and differentiation. Briefings in Functional Genomics, elw017. https://doi.org/10.1093/bfgp/elw017