Epigenetics: An Unconventional Take on Cancer

Written By: Christine Lu

Edited By: Christina Del Greco, Peijin Han, and Emily Glass

When you think about cancer, what pops into mind? Likely pain, disease, death, or even a family member who has been affected by cancer. In terms of the cause of cancer, we most likely think of genetic mutations. Very few of us will think about epigenetics. Yet, this does not diminish the fact that epigenetics takes on an equally important role in cancer progression. To understand the role of epigenetics in cancer, we must first appreciate what epigenetics is.

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Dr. Brenda Bass: Distinguishing self and non-self dsRNA in vertebrates and invertebrates

This piece was written live during the 5th annual RNA Symposium: Processing RNA. Follow us on Twitter or the tag #umichrna

Live Blogger: Chloe Rybicki-Kler

Editor: Emily Glass

Welcome to Dr. Brenda Bass, a senior professor of Biochemistry at the University of Utah. Dr. Bass worked with Dr. Cheque on enzymatic binding sites during her PhD and will be talking to us about self- and non-self detection of mRNA.

When Dr. Brenda Bass began studying long double-stranded RNA (ldsRNA) during her post-doc, it was known that the only time that cells contain dsRNA was after viral infection. After infection, binding proteins attach to viral dsRNA, forming an “SOS”-like signal that initiates an immune response.

Dr. Bass and others had stumbled on some but not all dsRNAs, and thus began compiling the LONG dsRNAome. The self-sequences were found primarily in introns and UTRs (untranslated regions) of protein-coding genes.

Three -omes were considered in the thinking through of the self/non-self identification question – mouse, human, and C. elegans. Later, Drosophila would replace C. elegans as the invertebrate model due to difficulties transitioning from in vivo to in vitro studies of invertebrate dsRNA detection machinery.

Even now, we don’t know the function of many of these ldsRNAs, but we do know that if cells don’t pay attention to these sequences there are consequences for the immune response to viral infection.

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Dr. Tracy Johnson: RNA Splicing, Chromatin Modification, and the Coordinated Control of Gene Expression

This piece was written live during the 5th annual RNA Symposium: Processing RNA. Follow us on Twitter or the tag #umichrna

Live Blogger: Emily Glass

Editor: Zoe Yeoh

Tracy Johnson, Ph.D., a researcher at the University of California – Los Angeles, uses yeast (S. cerevisiae) to study gene regulation and expression with a focus on the spliceosome. The spliceosome is a dynamic cellular machine made up of 5 ribonucleoprotein subunits that is responsible for creating mature messenger RNA (mRNA). During precursor mRNA (pre-mRNA) splicing, the spliceosome removes the many non-coding sequences (introns) that eukaryotic DNA produces in protein-encoding genes during transcription and splices together the coding sequences (exons) to allow for mature mRNA production. 

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Dr. Christopher Lima: Control of RNA degradation in the exosome

This piece was written LIVE during the 5th annual RNA Symposium: Processing RNA. Follow us on Twitter or the tag #umichrna!

Live blogger: Logan Walker

Editor: Alyse Krausz

Over the last two days, we have heard talks all about how RNA is a key building block in myriad biochemical processes, both natural and artificial. But, with all of this RNA floating around, we are left with a simple question: what happens to the RNA molecules once our cells are “done” with them? The answer turns out to be a constellation of proteins that work together to detect incorrect sequences, turnover old RNA molecules, perform post-translational modifications, and remove invasive sequences, such as viral RNA molecules. In the case of RNA turnover, much of this processing is performed by the RNA exosome complex, making it an important target of study for diseases where it is dysregulated, such as multiple myeloma, pulmonary fibrosis, and many subtypes of cancer.

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Dr. Feng Zhang: Harnessing Biological Diversity for COVID-19 Diagnostics

Coming to you LIVE from the 5th annual RNA Symposium: Processing RNA. Follow us on Twitter or the tag #umichrna!

Live blogger: Alyse Krausz

Editor: Logan Walker

CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) is well-known as “molecular scissors” that enables scientists to edit DNA. But there’s more to CRISPR technology than just cutting and pasting DNA! In bacteria, the many CRISPR-Cas systems provide a defense system against viral infections, and viruses use DNA or RNA as their genetic material. Nature has evolved some CRISPR-Cas systems that target DNA, such as CRISPR-Cas9, and others that target RNA, such as CRISPR-Cas13. Dr. Feng Zhang, a Professor of Brain and Cognitive Sciences and of Biological Engineering at MIT, and his lab have discovered and developed the CRISPR-Cas13a system for use as a diagnostic tool. Their lab has harnessed CRISPR-Cas13a as a biotechnology to create a molecular detection platform called SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) capable of detecting RNA or DNA with high sensitivity and specificity.   

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Dr. Kevin Weeks: a MaP of RNA structural landscapes

Coming to you LIVE from the 5th annual RNA Symposium: Processing RNA. Follow us on Twitter or the tag #umichrna!

Live blogger: Zoe Yeoh

Editor: Alyse Krausz

Recently, RNA has risen to the forefront of nucleic acid research due to its newly characterized, integral roles in cellular regulation. Many of the secrets in RNA regulation lie in its ability to form complex secondary and tertiary structures that relate to its function. However, many of these structure-function relationships are poorly characterized due to a lack of rigorous tools used to study them. Dr. Kevin Weeks and his group at University of North Carolina-Chapel Hill have developed “novel chemical microscopes that reveal quantitative structure and function interrelationships for RNA” to study these complex RNA structures and answer important biological questions.

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Undoing the Damage of ‘America-First’ on Scientific Progress

Written by: Elana Goldenkoff

Editors: Jacob Flaherty, Genesis Rodriguez, and Emily Glass

The coronavirus pandemic is the most immediate crisis that President Joe Biden is facing and, because of the global impact of the virus, it is not a fight the United States can win alone. Managing the effects of the virus requires concerted international efforts to address.  However, in recent years the U.S. has disengaged from the political affairs of other countries. Unfortunately, the increased American isolationism and ‘America First’ policy of the previous administration hindered foreign relationship-building and limited the connections and resources that the U.S. has at its disposal.

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The Right Technology at the Right Time: The backstory of Moderna’s COVID-19 vaccine

This piece was written LIVE during the University of Michigan RNA Seminar featuring Dr. Melissa Moore of Moderna Therapeutics.

Live blogger: Alyse Krausz

Editor: Emily Glass

The saying goes that when something is too good to be true, it typically is. So when the FDA authorized the use of Moderna’s COVID-19 vaccine less than a year into the SARS-CoV-2 pandemic, many people were skeptical. Is the vaccine safe? Is it effective? How was this vaccine developed so quickly when others have taken years?

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What did Rev-Erbβ say to heme? ‘Never let go. Your chemistry drives my biology.’

Written by: Anindita Sarkar

Edited by: Isabel Colon-Bernal, Christina Del Greco, & Alyse Krausz


My pet dog would be scratching and pawing me at roughly the same time every day without fail. My mother believes that he had a better sense of time than me and my sister. I would always convince my mom that the credit for his sense of time should be given to his internal biological clock. This internal biological clock, better known as the circadian rhythm, tunes different physiological processes in not just my dog but also other living beings, to a 24-hour cycle. That is why we tend to feel sleepy or hungry at almost the same time every day. Needless to say, this biological time-tracking system functions as a result of an intricate interplay of several genes and proteins. In fact, I work on one important member of this family of proteins, Rev-Erbβ, which is responsible for the proper upkeep of the circadian rhythm.

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With experiments, comes waste: Scientific waste and where it ends up

Written by: Lirong Shi and Manaswini Sarangi

Editor: Sarah Kearns and Alyse Krausz

Introduction

As a scientist working around scientists, we may not realize how much scientific waste we and our colleagues produce every day, just like everyone else who may not pay attention to how much household waste we produce in our kitchen. We are so used to the waste in the lab, and compared to the large garbage bin outside, we might think the small plastic bucket in the lab should be negligible. But that is not true. Accounting for only 0.1% of the population, scientists create approximately 5.5 million tons of plastic waste annually in life science alone, which accounts for approximately 2% of the plastic waste produced worldwide [1]. The large amount of plastic waste wandering around the oceans can disrupt carbon balance, poison fish, and end up on humans’ tables. Through experiments, scientists are attempting to improve everyone’s life while also literally contributing to the detriment of the world.

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