Alternative Transcription Initiation Sites in Soybean Genes

 The discovery of DNA's double helix structure occurred more than 70 years ago. Scientists have found a new way to read this structure within genes. Many species of plants and animals have reference genomes which are used by researchers for their own genetic analysis. The soybean genome is used widely in agricultural research for commercial and industrial purposes. While the soybean reference genome may be very advanced, it was missing locations for transcription initiation sites for individual genes within it-- until now.

Transcription initiation sites are locations in DNA that act as the start of transcription, where an mRNA copy of DNA is synthesized to then be translated into a protein. By finding where these sites are within a genome, it allows for a better understanding of how genes are expressed. Normally, transcription initiation sites are located around a TATA box (a thymine and adenine rich DNA sequence), but researcher and major contributor to the soybean reference genome Jianxin Ma disagrees. He and his researchers found that the predicted transcription initiation sites on the reference gene had only about 3% accuracy based on their new study. They identified transcription initiation sites in roughly 40,000 genes. These sites had sequences that varied from what was normally expected. By further completing the database, it improves its effectiveness as a research tool for many geneticists.

https://www.sciencedaily.com/releases/2024/11/241119181836.htm
https://academic.oup.com/plcell/advance-article/doi/10.1093/plcell/koae288/7900478#493737809

Soybean agriculture and genetic transcription

Findings published in The Plant Cell showed recent advancements in genomic research led by researchers from Purdue University. There was a conventional understanding that each gene had a single transcription initiation site. The research led by Jianxin Ma, discovered that over 97% of previously predicted transcription initiation sites are incorrect, and that soybean genes exhibit different transcription initiation sites. These alternative sites allow the transcription factors to bind in different locations, causing different proteins to be produced from the same gene.

The researchers used STRIPE-seq technology which allowed for clear mapping of the initiation sites across the genome. This data will be incorporated into SoyBase, a database that stores genomic information of soybean by many different researchers. Many other researchers share crucial information for the breeding and cultivation of soybeans. A post-doc researcher from Chilvers lab at Michigan State U created a large, free, publicly available database to show plant breeders trends in resistance and gene efficacy in different regions. Austin went as far as using google translate from old surveys from China and South America that were not in English (which is not a monumental task, as the article might lead you to believe), to produce a better and more complete database of phenotypic data and responses to different stressors.

Soybean seams to be a very collaborative field of science that I would have never expected to have such completeness and level of study. I suppose most agricultural companies nowadays benefit from scientific research for the development of crops and soil as farming becomes more and more pressurized for rises and demands in efficiency. Having 97% of pieces of genomic data corrected is, however, an extremely interesting turnover of the previous literature understanding of this variable.

https://m.farms.com/news/new-resource-for-breeding-better-soybeans-219997.aspx

https://phys.org/news/2024-11-advancements-genomic-reveal-alternative-transcription.html

The Impacts Of Adaptive Capacity On Transcriptional Plasticity

 

        With climate change on the horizon, it is important to understand the consequences this will have on our oceans. The marine copepod, Acartia tonsa, was selected as a model organism in a study conducted by Brennen et al. This study aimed to clarify the relationship between adaptation and transcriptional plasticity. The study compared species found in their home environment with that those under experimental future projections. Different groups were kept in either one condition or the other, while others started in one and were kept for 20 generations before transitioning to the alternative. The results revealed that A total of 1876 genes were differentially expressed between control and experimentally evolved replicate lines. These genes are primarily related to stress response, gene expression regulation, actin regulation, developmental processes, and energy production.
        It was revealed that there were faster losses of plasticity during rapid adaptation than theory would predict. The results showed that although plasticity did not impede adaptation, adaptation eroded plasticity. Losing plasticity does not stop organisms from somewhat reverting back to their ancestral conditions; however, it does result in a trade-off of losing adaptive genetic variation.
        The use of experimental evolution is very important to understanding adaptive mechanisms. Since these are going to be the conditions future organisms will exist in, Understanding future mechanisms is just as important as understanding the current mechanisms in order to create comprehensive conservation strategies. These strategies require foresight to ensure their efficacy for the ecosystems of the future. It also revealed possible implications should we cut out emissions and revert back to cooler and less acidic conditions, which can further aid the formulation of such strategies.

What to read next: 

Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism

RNA Polymerase Fixes Faulty RNA

RNA polymerase is responsible for transcribing DNA into mRNA. Mutations or changes during transcription may lead to health risks as well as aging. During this transcription step, RNA polymerase is able to find the miscoded DNA and can back track to fix it. Researchers at Hong Kong University of Science and Technology show the dynamics of how backtracking works during transcription. The discovered the RNA polymerase occurs in stepwise mode where RNA moves away from the active site and reaches of “frayed state” before the enzyme can reach the backtracked state. They found that an amino acid serves as a sensing probe to detect faulty RNA chains. These results will provide insight into the fundamental mechanisms of transcription. Their goal for the future is to be able to backtrack the mechanisms for more than one RNA molecule.

http://www.biologynews.net/archives/2016/05/03/scientists_reveal_how_cell_corrects_errors_made_in_gene_transcription.html

http://www.ust.hk/

Cells Compact DNA When Oxygen Starved

In a recent study, researchers and scientists from the Institute of Molecular Biology at Johannes Gutenberg University Mainz in Germany have discovered that when a cell suffers from hypoxia or lack of nutrients, the DNA in the nucleus packs tightly together and forms clumps instead of being loose when the cell is not being starved of these. If this happens and blood flow is restricted like in cases such as a heart attack or stroke, the gene-reading molecules will not be able to access the genetic code which will then cause the cell to stop working.

These scientists used a new technique, called single-molecule localization microscopy, in order to look inside mammal cells to see their chromatin complexes in order to find locations of each DNA molecule in the cell. This is done by using blinking dyes that bind to DNA. The chromatin complexes are looked at since chromatin tightly packs together DNA and proteins. When the chromatin becomes restricted and compacted when there is low oxygen and nutrient levels, transcription is reduced. Along with transcription being reduced, the mobility of linker histone H1 is also reduced. By looking at the results of this technique, different ways in which to stop the DNA from compacting can be more easily found.

The two articles that deal with this study that I found were very interesting, seeing as though a heart attack or stroke victim can still deal with more things detrimental to their health even though they survived the event. Knowing that the DNA compacts when oxygen and nutrient deprived, scientists and researchers can now work to prevent it from happening. These events happen every day to people around the world and to know something now that we did not know years or even months before the study was completed is a huge step forward in the right direction in making the long-term damage as short as possible.

Click here for the original article

An enzyme that fixes broken DNA sometimes destroys it instead

The research team at Stanford University School of Medicine has a remarkable insight that the enzymes inside cells that would repair damaged DNA sometimes can wrecked it. With this information, it can lead to better understanding of he causes of some types of cancer and neurodegenerative disease. The paper that is to be published explains how the mechanism of DNA damage occurs when genetic transcript, composed of RNA, stick to the DNA instead of detaching from it. Enzymes like endonuclease are attached to DNA/RNA hybrids that form when the gene transcription goes the wrong way and the enzyme ends up cutting the DNA like scissors to damage it.

The research was conducted with human cells in culture using molecular biology techniques to turn off specific genes. By using this way, the researchers are able to induce cells to form hybrids and to see what would happen if different enzyme were inhibited. There is evidence of same enzyme helping to repair DNA lesions from sunlight and certain chemicals; also that same enzyme has same structure that is similar to those formed in cells damaged by ultraviolet light. The next step for the researchers is to try to understand why some of the enzymes are that control the transcription car causing DNA damage. This is a very interesting find in the DNA transcription.

http://www.medicalnewstoday.com/releases/286147.php

Mice, Humans, and the ENCODE Project

The purpose of this article was to depict the similarities and differences between the human and mouse genomes, and it intended to illuminate the fact that mice may be used to study human biology only to an extent. Researchers have determined that the ways in which humans and mice regulate their genes has been around for a long time; in other words, the gene regulation is evolutionary. The ENCODE project (the Encyclopedia of DNA Elements) is currently keeping track of the similarities between the two genomes, such as which genes are activated at what time and the DNA sequences of each. The ENCODE project has proven to be an effective database for genetic biologists nationwide, allowing professionals to use the mouse genome to assist in treatments for diseases.

However, the genome of mice can't be used to aid in the treatment in human disease in all cases. Two examples of systems that can't be compared between the two genomes is the immune system and response to stress. Environmental factors may have contributed to the differences between the mouse and human genomes. However, the ways in which genes are regulated are extremely similar; gene transcription and chromatin modification are two examples of gene regulation. Despite the similarities in these processes, they differed from one type of cell to the next. In one project, an author of Nature found several statistics that demonstrate the difference and similarities between the genomes. For example, after studying over one million locations of DNase 1, he found that approximately 35% of the information was the same in mice and humans.

Article: http://www.sciencedaily.com/releases/2014/11/141119132703.htm
Supporting Article: https://www.broadinstitute.org/scientific-community/science/projects/mammals-models/mouse/mouse-genome-project

Gene activity: spacial orientation vs. quantity of transcript molecules

Today, gene activity is studied and measured by analyzing the amount of transcript molecules within a cell. For the first time, it has been found that the spatial organization of the gene transcript molecules is more helpful in determining gene activity than is the amount of these highly specified molecules. When genes are activated within a cell, transcript molecules are produced to make the gene able to perform its specific function. These transcript molecules are also known as mRNA. There are many different types of mRNA, or transcript molecules, that can bring the information from the activated gene inside the nucleus to the cytoplasm of the cell so that the specific protein can be made. This protein is made so that the function specific to the activated gene can be completed. This breakthrough, made by the biologists from the University of Zurich under Professor Lucas Pelkmans, will help us in the comprehension of the gene activity in single cancerous tumor cells.

This project was made possible through the assistance of robots, an automated fluorescence microscope, and a supercomputer named Brutus. The robots are used to stain the transcript molecules while the fluorescent microscope causes these molecules to glow. The supercomputer, Brutus (in this case) is then used to analyze these glowing molecules. This process makes it possible to study the spatial organization of one thousand genes in ten thousand different cells at once. Being able to study the spatial organization of these transcript molecules was not possible until this point in time. With this project, it was also found that certain cells act differently depending on the gene activity and ultimately the spatial orientation within that particular cell. These biologists had expected to have seen more of an impact in the gene activity by the quantity of transcript molecules that existed but instead, they found that the spatial organization of the transcript molecules varied much more. This concept can apply to a single cell or multiple cells.

This realization was crucial because now, the individual function of genes can be determined based on the specific mRNA, or transcript molecule's spatial orientation. This can furthermore be important in cancer research because it is easier to target the genes that are malfunctioning and causing cancer to persist.

I found this experiment extremely important and interesting. For so long researchers were focused on the wrong concept of specialized transcript cells. This might have been one of the reasons why cancer research is constantly at such a stand still. Maybe with the realization that the transcript molecule's spatial orientation being more vital than the quantity of these molecules, it will be easier to find a cure for cancer. I am very hopeful that this finding will ultimately aid to ending the eternal struggle with this deadly disease as well as others.

http://www.sciencedaily.com/releases/2013/10/131006161357.htm
http://www.nature.com/scitable/topicpage/gene-expression-14121669

Research finds role for gene silencing protein

The article talks about how important it is to pay attention to the tail end of a gene as well as the front. They talk about the dicer-like 4 and how it helps go in and clean up and form the gene product and produces tiny RNA's in cells.   Scientists at the John Innes Centre on Norwich Research Park found that DICER-LIKE 4 steps in when effective termination through normal mechanisms has not occured.  DCL 4 plays a role in transcription termination and gene silencing.  When termination fails DCL 4 is a great back up for gene expression and gene silencing. 

To article: http://www.sciencedaily.com/releases/2012/03/120329141923.htm

Research on Dicer protein:

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028548

New function of DICER protein found in plant

An article in Science Daily recently stated that researchers found the function of DICER protein DCL4, in Arabidopsis thaliana, a type of flowering plant. The protein, which is known to produce tiny RNAs, previously had no known function besides producing RNAs.  Scientists now know that the DICER protein is also involved in the termination processes of transcription. DCL4 plays a part in gene silencing at the end of the termination process of transcription. Scientists say that gene silencing is just as important as the formation of gene product. So, paying more attention to the end of the termination processes is crucial, says Professor Caroline Dean from JIC, which is strategically funded by BBSRC. “When termination fails a lot of aberrant RNA is made -- this is degraded as part of a cell's quality control mechanism. This can have consequences for other sequences in the genome that match the aberrant RNA.” "If a gene ends badly, aberrant RNA will trigger silencing pathways," said Dean. This shows that if the there is an error in termination, DCL4 will step in and try to correct the mistakes taken place.

The Genetics of a Cell's Natural Defense

For years there has been debate and question over just exactly how cells in our bodies fight off disease and infections. The "Immune System" is a broad range of mechanisms and devices within the human body that keep us healthy. However, in a study conducted UC San Diego, the immune defense of intestinal cells was studied. Using the roundworm  C. elegans, scientists were able to study the exact mechanisms of how infection was fought. The worm was ideal for the study because of its physical transparency, and similarity to human cells.

[caption id="" align="alignleft" width="360" caption="A Cell's Immune System at Work"][/caption]

It was found that the cell's defense depended on the availability of certain transcription factors. Since the "infection" would inhibit the normal activity of the roundworms cells, once proteins stopped being synthesized, antibiotic defense factors were released by the cell. It was determined by this study that the inhibition of protein synthesis in the roundworm directly expresses the cell's defense genes. Scientists and experts estimate that many other similar chemical pathways exist, and that certain toxins, nutrients, and other materials may express certain genes.