BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: genomics

The epigenome can be effected by pollution

A Thing Floating in the Lake

The epigenome is a lesser known part of the study of genetics. It consists of the parts of the genome which are not part of the DNA, for example transcription factors and the accessibility of different sections of the chromatin. DNA in the cell is wrapped around proteins called histones. The wrapping of DNA around these histones are also a factor which controls which parts of the DNA are read into proteins. Furthermore, DNA methylation is an important regulatory factor. The addition of methane groups to DNA makes it impossible to read, effectively shutting off the gene that is methylating.

The epigenome is unique because it can be changed significantly in response to external stimuli. In a way, it is the body’s way of altering DNA on the fly, without actually altering the genetic code. The epigenome can also plays a role in cell differentiation. In class, we discussed how all cells have identical genetic code, passed down from one cell to another. All cells start the same and eventually change into all the different types. The epigenome helps to control exactly which parts of the genome are expressed. It is the epigenome which controls which parts of the genetic code are expressed.

However, the epigenome is still passed down hereditarily and down cell lines. As cells divide through mitosis or meiosis, the epigenome is passed down to the daughter cells. This combination of constant adaptation and persistence through generations make the epigenome an essential part of the body’s function. The combo also makes the epigenome a key part of how the body can be changed for a significant period of time by negative stimuli. These effects can even span generations and have been shown to effect the course of evolution.

Recently, scientists at the University of Liverpool have demonstrated exposure to pollution in water fleas has effects that last over 15 generations. When exposed to a pollutant for a period of 7 months, which encompasses 15 generations of fleas, scientists observed increased rates of DNA methylation. When transferred back to clean water, the scientists found that DNA methylation remained the same. Thus, the pollution permanently damaged the epigenome of the fleas.

Playing God: New Technology Gives Scientists the Ability to Delete DNA

Since the relatively recent discovery of CRISPR-Cas9, scientists have explored multiple uses of this new technology, from eliminating a patient’s cancer to making super plants, furthering our understanding of DNA and how it works. CRISPR-Cas9 has become the most advanced and efficient gene-editing tool there is. However, thus far, its use has been largely limited to silencing protein-coding genes in the DNA. This leaves out what’s called the DNA “dark matter” — the non-coding DNA that covers about 99 percent of our genetic code. That’s about to change; this article from Futurism explains how a recent study from PLOS Computational Biology is creating a new technique, based on CRISPR, but delving deeper into this unexplored territory.

This brand-new software technology called CRISPETa evolved from a breakthrough tool (which uses CRISPR-Cas9) called DECKO. DECKO was designed for deleting pieces of non-coding DNA using two sgRNAs as molecular scissors. While the concept might seem simple, designing deletion experiments using DECKO was time-consuming due to the lack of software to create the required sgRNAs.

This is where the new tool, CRISPETa, comes in. According to the report, users can tell CRISPETa which region of DNA they wish to delete. The software then generates a pair of optimized sgRNAs that can be used directly for that experiment. Pulido, leader of the research team, stated that “We hope that this new software tool will allow the greatest possible number of researchers to harness the power of CRISPR deletion in their research.”

The software has already demonstrated its efficiency in deleting desired targets in human cells. The research team hopes that its use will go beyond a basic research tool, and be utilized as “a powerful therapeutic to reverse disease-causing mutations,” Johnson added. Herein lies the hidden value of CRISPR-Cas9 and all further developments from it: The more we understand DNA and genomics, the better we will be able to fight diseases and other aspects of human life that cause harm, ultimately leading to a higher quality of life for all.

 

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