AP Biology class blog for discussing current research in Biology

Tag: transcription

Cracking the Code one Gene at a Time

Cells are one of the most important objects in the human body, yet scientists still have yet to truly understand the underlying mechanics. Recently researchers have observed how RNA transcription occurs in real, live cells. For the longest time scientists have observed RNA transcription extracellularly. Until now they have only been able to observe how RNA polymerase 2, a DNA copying enzyme, and other enzymes “by breaking cells apart and measuring the activity… outside the cellular environment.”


The molecules involved in RNA transcription have been studied profusely, but only frozen in time. Now we can use “a highly specialized optical microscope” to watch how RNA polymerase copies DNA into mRNA. Researchers then labeled certain molecules with a tag so that they glowed when looked at. An issue with this method, though, is that there are so many of these molecules in the nucleus that if we were just to examine the reactions after adding the fluorescent tag, we would just have a glowing nucleus. The scientists have combated this by suppressing the signals from other reactions. This, along with the ultra-sensitive microscope allows us to focus on one gene and transcription occurs for it.

Through this new technique, we now have a much more detailed and intricate picture of how DNA, RNA, and enzymes function in transcription. This process can be replicated for many more reactions and will help us understand bounds more about ourselves and how we truly work.

I am personally very excited to see what new concepts and techniques will be discovered from this breakthrough. Genetics is the future of biology and using this to crack the code is one step closer to curing many genetic diseases. Combining this with other genetic breakthroughs like CRISPR is a cause for excitement in the future of biology. If you have any other ideas about why this could be useful please comment below.


Why Don´t We Grow Ears on Our Arms?

The Miracle of DNA Regulation

Now, the question posed is why we don’t grow ears on our arms. May I introduce to you: gene regulation. That’s right. Even though every single cell in your body has the same DNA, the body is able to ‘turn off’ different genes so that only ones that are necessary are read. This is why you do not grow ears on your arms, because those ear-making genes are ‘turned off’.

But… How?

This question has been plaguing scientists for quite a while, as we have discovered genes in the human genome that are ‘turned off’ but could potentially be quite useful such as the regeneration of limbs (same as a starfish or a crab). Now there has been a new breakthrough in how we understand gene regulation thanks to some researchers in Cambridge, Massachusetts. The binding domain’s function in gene regulation has been known for quite some time already. The mystery lied within the activation domain. It has now been discovered that the activation domain sort of acts as a net, capturing the molecules for gene regulation and anchoring the transcription ‘machinery’ by the gene that is to be transcribed.

But… How? What Does This Mean?

Well, the activation domain creates little droplets by mingling with transcription proteins that attract the transcription machinery stuff. It’s kind of like creating oil droplets in vinegar. This process is now called phase separation. This has grand implications for even more research on gene regulation and can even give more insight into diseases such as cancer. When do you think the next breakthrough will come? Do you think this is the key to unlocking how to turn genes on and off for good or is there much more work to be done?


The Gene Switch

Researchers at the Stowers Institute for Medical Research have created a high-resolution mechanism to “precisely and reliably map individual transcription factor binding sites in the genome.” This new technique, published in Nature Biology today, has proven to be more efficient and successful than those previously studied.

All of the cells in an organism carry DNA; however different cells in the body express different portions of it to function properly. For instance, nerve cells express genes that facilitate them carrying messages to other nerve cells. This process is known as gene expression and is responsible for making our bodies function the way we do. Despite our limited knowledge on gene expression, researchers are aware that it is is controlled by proteins called transcription factors that bind to specific sites around a gene and,  in the right order, allow the gene’s sequence to be read.

Transcription factor binding sites in DNA are extremely difficult to locate but, thanks to new technology, it is becoming easier to track their location. “The transcription factor binding sites that are likely functional leave behind clear footprints, indicating that transcription factors consistently land on very specific sequences. In contrast, questionable binding sites that were previously detected as bound showed a more scattered unspecific pattern that was no longer considered bound.”

These techniques are implemented through a method called chromatin immunoprecipitation or ChIP, a tool that determines the relativity of the proteins to their positions on the DNA, cuts the DNA into reasonable sizes, and then isolates the sections that are bound by the proteins. While the research is largely preliminary, scientist Zeitlinger attests to the significance of this creation; ”If we do this kind of analysis for lots of transcription factors, we will gather information needed to better understand gene expression.”


chIP mechanism

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