MADE FROM SCRATCH

Foundational Genetic Mechanisms for Biological Developement

You’ve set out to bake the perfect cake. For the last hour, you’ve flipped through numerous recipes in your cookbook, with each cake recipe unique in its own way. Just as there are different recipes for cake, a similar diversity exists in your own genome. Each part of your genome serves a particular purpose, such as cellular functions or protein construction, all of which come together to form the most complex and interesting cake of all–you!

To identify all the processes that create organisms like yourself, it’s important to understand the central dogma of biology. As the basis of genetic expression, it allows the conversion of endless streams of DNA into the physiology, development, and functionality of your body’s genome, formulating the basis of evolution at the species level.

READING THE RECIPE: GENE EXPRESSION BASICS

But how do these fundamental components and processes lead to the expression of genes, or sequences of DNA, that form the basic units of inheritance? In the Kadonaga Lab at UC San Diego, research associate and recent graduate Torrey Rhyne studies the DNA core promoter in eukaryotic organisms in order to better understand its role in gene expression. The core promoter is a stretch of DNA that directs the initiation of gene transcription by acting as a recognition site for binding of RNA polymerase to DNA. RNA polymerase transcribes, or converts, the DNA into messenger RNA (mRNA), providing the body with readable templates to make functional proteins that are important to the structure, function, and regulation of the body.

Within the core promoter of some genes, a short DNA sequence containing many thymine and adenine nucleotides, known as the TATA box, further guides the initiation of transcription, indicating where DNA can be read and decoded. However, the TATA box is found in less than 25% of the core promoters within the human genome, leaving many scientists puzzled as to how human cells direct transcription.

At the Kadonaga Lab, Rhyne and her colleagues generated and examined a vast database of core promoters across the human species, each containing differing sequences in the region where the TATA box is primarily located. Upon inserting the promoter sequences into HeLa cells, human cells that can be rapidly cultured and used for in-vitro experimental models, these promoters then helped drive the transcription of stretches of DNA, called downstream core promoter regions (DPRs). Using machine learning techniques, the researchers assigned transcription scores to each DPR sequence by comparing the scores they obtained experimentally to known values stored in the computer database. These transcription scores quantify DNA transcription and thus gene expression by measuring the mRNA levels within each cell. Analyzing this data, they concluded that DPRs containing vast repetitions of guanine, a specific nucleotide base, had higher transcription scores than those without guanine nucleotides. In other words, the DPRs containing these specific guanine sequences exhibited a higher frequency of transcription, and thus a greater likelihood of gene expression to occur, compared to DPRs of differing nucleotide sequences. Likewise, RNA polymerase appeared to have a higher affinity toward these DPRs, therefore increasing the likelihood for transcription initiation to occur. With this information, the Kadonaga Lab was unable to discover universal core promoter elements. While the TATA box may function as a core promoter element in one organism, the DPR may act as a critical core promoter element in another, as commonly seen in humans.

Condensation Elongation Segmentation Differentiation

The digit development in mammalian limbs, starting from the initial paddle formation and progressing into separated digits through the processes of controlled expression of BMP4 through MSX2 regulation.

Central Dogma

Overall, identifying core promoter elements such as the DPR helps scientists understand the transformation of DNA to functional proteins. Applying their research to modernday issues, the Kadonaga Lab hopes that their contributions to understanding gene expression will advance theory behind the molecular mechanisms of complex genetic conditions, allowing researchers to trace its pathology back to the DNA level.

BAKING THE CAKE: THE ACTIVATION OF GENE REGULATION

Just as a cookbook provides the basic instructions and ingredients for a cake, the central dogma of biology lays the foundation for the transformation of the information coded in DNA into the structures and functions needed to construct an organism.

The transcriptional process of reading DNA to form biological structures is as essential as understanding the recipe when baking. Like altering the amount of ingredients that can transform the cake, changes to the regulation of transcription can impact how the DNA is read and the organism is formed. Discovering its intricacies is essential to many areas of research, including the mechanisms of mammalian development. UC San Diego’s Cooper Lab studies a specific instance of this phenomenon, where Ph.D candidate and student researcher Alex Weitzel contributed to studying the interdependent MSX2 and BMP4 genes that enable the growth and positioning of limbs and digits.

During fetal development, the body starts from scratch and differentiates cells into features such as limbs. To direct this growth the body applies particular mechanisms, one of which is the gene regulation studied by Weitzel which allows for digit construction. Initially, a “paddle” formation is created, where digits are connected by lines of cells. He found that to achieve the ideal separated digits, the BMP4 gene is expressed in a specific pattern between future digits. The BMP4 gene is responsible for apoptosis, or cell death, allowing it to remove the excess cells between digits. A second gene, MSX2, is also required to ensure this process happens correctly. MSX2 is an upstream activating sequence which enhances the transcription of surrounding genes such as BMP4. The expression of MSX2 along the same patterns between digits also increases BMP4 expression in those areas, making sure only necessary cells are removed.

PERFECTING THE RECIPE: EVOLUTION FROM MODIFICATIONS

The Cooper Lab recognized that the MSX2 and BMP4 mechanisms were not always part of mammalian development, since our ancestors had paddled limbs, yet their role has evolved as most mammals today have separated digits. Genetic evolution occurs over time through accumulated changes in a species’ collective genome, like generations of bakers adding unique flairs to their recipes. The Cooper Lab identified a method to delve into this aspect of evolution: the jerboa animal model. Jerboas have radically different front and hind limbs. Their hind limbs are much larger and skinnier than the front limbs, which have standard rodent anatomy. The animal model allows researchers to compare the genetic evolutionary changes that have led the jerboa to form different front and hind limbs, while also eliminating confounding factors that arise between different species. The front limbs undergo standard limb development, as the Cooper Lab expected, but the hind limbs modify this process to better suit their unique structure. Studying the evolution of genes and their function can help us better decipher the complex processes that construct diverse structures, a prime example being the separation of digits and the formation of different limb structures. Grasping genetic evolutionary developments will help scientists understand the significance of each individual recipe within the overall cookbook of mammalian development.

Conclusion

The multifaceted role of genetics begins with DNA transcription, aided by core promoters, eliciting the first step in gene expression: using information from a gene to synthesize proteins or aid in cellular processes. The following interactions between different genes are essential to the body’s function, such as limb development, and evolutionary changes, as evidenced by the jerboa. Everywhere you look, genetics holds a considerable influence. Interactions between your genome and the world is what makes you, you — and that is as perfect as any slice of cake.