Intellectual Merit: In unicellular eukaryotes like yeast, genes are expressed in a cell cycle specific manner and in response to specific environmental cues during growth, development and homeostasis. Regulation of gene expression at the level of transcription (RNA synthesis) is controlled by a variety of mechanisms. One such mechanism involves formation of a looped architecture due to the interaction of the gene promoter with the terminator region. This interaction of the distal ends of a gene during transcription is referred to as gene looping. Research in this lab has further shown that gene looping accompanies activated transcription. First reported in yeast, gene looping is now emerging as a universal feature of RNA polymerase II-transcribed genes in eukaryotes. The ubiquity of gene looping and how it leads to increased transcriptional efficiency, however, remains unclear. The overall objective of this research is to define the molecular basis of loop formation and to determine the extent of gene looping on a genomewide scale in yeast. The successful completion of this project will reveal the general scope of gene looping in yeast. The protein-protein interactions that facilitate gene looping will also be defined. The findings of this project will serve as a paradigm for understanding the role of gene looping in higher eukaryotes like plants and mammals.
Broader Impacts: The project will be carried out at Wayne State University, which is located in the city of Detroit, Michigan. Many Wayne State students are residents of Detroit and thus represent the ethnic and economically diverse population. This project will provide a unique educational opportunity for training students, particularly those from underrepresented and economically disadvantaged groups. The ultimate goal is to enable undergraduate and graduate students to contemplate a scientific career. Simultaneously, this project will (i) provide opportunities for critical thinking and analysis of data; (ii) add value to student's educational experience by translating their excitement of knowledge into discovery; (iii) show how research in basic sciences is beneficial for the human society; (iv) exemplify that scientific progress requires a multidisciplinary approach; (v) inculcate team spirit and a sense of scientific cooperation among students; and (vi) provide training in oral and written presentation of the scientific work as well as mentoring experience to senior students.
Normal 0 false false false false EN-US X-NONE X-NONE This project contributed both in terms of the ‘intellectual merit’ and the ‘broader impact’ criteria as described in NSF guidelines. The following are the outcomes of the project during the entire funding period in terms of these two criteria. Intellectual Merit Genes are the master regulators of our cells. Because of this fundamental importance, a disease may result if a gene does not function properly. Genes perform their function by coding for proteins. Transcription creates a message (mRNA) from the gene and the message is then translated to make proteins. Genes are transcribed in a highly coordinated manner in cells. The mechanisms exist in the cell to regulate the coordinated transcription of genes during development and in response to a hormonal or an environmental signal. Misregulation of transcription is often the cause of diseases like cancer. Transcription starts at a DNA site on a gene called the ‘promoter’ and terminates at the other end of the gene called the ‘terminator’ (Fig. 1). The start of transcription requires a group of factors called ‘initiation factors’, which binds to the promoter site on DNA. Similarly, termination of mRNA synthesis requires a group of factors collectively called ‘termination factors’, which bind to the other end of a gene (Fig. 1). The initiation and the termination factors are believed to have dedicated roles in the starting and ending of transcription. The latest results from our laboratory, however, suggest that this may not be the case. We found that TFIIB and Mediator complex, which are initiation factors, occupy the promoter as well as the terminator regions of genes during transcription. Similarly, we found that a number of termination factors, which are believed to operate at the terminator end of the gene, localize to the promoter region during expression of the gene. Furthermore, the promoter and terminator regions of a gene are juxtaposed forming a looped gene architecture during transcription of a gene (Fig. 2). The looped gene architecture is formed by the interaction of promoter-bound initiation factors with the termination factors occupying the other end of the gene. Thus, the transcription enzyme RNA polymerase II transcribes a circular rather than a linear template. We found that this structure is essential for termination of transcription. Due to gene looping, RNAP II is released from the terminator in the vicinity of the promoter, thereby facilitating reinitiation of transcription. Thus, the ending and beginning of a transcription cycle, which were thought to occur independently, integrate with each other through gene looping to enhance the transcription of a gene. These results have made us rethink the way the process of transcription is regulated in cells. Our findings will have implications in understanding transcription of genes in healthy and diseased cells. Broader Impact Wayne State University is located in the city of Detroit which has an ethnically diverse community with many underrepresented groups. The city is facing a severe crisis due to loss of manufacturing jobs in the auto industry. Many of our students come from economically struggling families whose earning members have lost their jobs. A fairly large number of our students are the first in their families to attend college. It is therefore critical to prepare every student to meet the challenges they are going to face and help them succeed in the future. This NSF grant provided a unique educational opportunity for training students in research, particularly those from underrepresented and economically weaker groups. Four graduate students working in the PI’s laboratory for a PhD degree benefitted from this grant. Three of these graduate students have completed and defended their PhD theses during the duration of this project. One of these students, Scott Medler, is a local student, while another student Nadra belongs to an under-represented minority group. All three students who graduated with a PhD are continuing research at other universities. The training and development opportunities provided by this grant proposal played a crucial role in shaping the careers of these graduate students. In addition, this grant provided training opportunities for undergraduate students. At least fifteen undergrads worked with me under ‘directed study research program’ during the period of this grant. These students worked in the laboratory for at least two semesters; attended lab meetings and journal club, and presented their work in lab meeting. Six of these students also performed their research within the ‘Honors Thesis Program’. Two of these undergrads also received authorships in publications. Two more of these undergrads are now graduate students in our department. The training opportunities provided by this grant exposed these students to the intricacies of research and motivated them to contemplate a career in scientific research. This grant resulted in five journal articles, three PhD theses and seven undergraduate dissertations.
