Over the last funding period, we have made a paradigm-shifting observation: that the information contained in the promoter dictates the fate of the mRNA in the cytoplasm. Hence mRNA fate in the cytoplasm can be determined at the time of its birth. This remote control regulation of the mRNA outcome appears to apply to genes with time dependent expression patterns, such as cell cycle, metabolic product or stress induced genes. We propose to uniquely integrate biochemical, genetic and imaging approaches to identify the hierarchy of factors imprinted co-transcriptionally in the mRNA as well as to define the regulatory DNA sequences that dictate this mRNA behavior. The use of innovative technology, combining the use of microscopy with fluorescent tagging of mRNA is directed toward elucidating the coordination of transcription and downstream events of the RNA life; events that likely create an autoregulatory loop. We envision a tight coupling from transcription through decay and back, mediated by specific factors that would be released from the mRNA upon its degradation, to signal the gene to make more. We hypothesize that cell cycle and stress-regulated genes require a robust coordination between transcription, translation and decay. We expect that factors imprinted by the promoter regulate the strength of the transcriptional response. Taken together, these observations suggest a shuttling of factors between the nucleus and the cytoplasm important for fine-tuning the response of the cell.
The Aims of this project chart a straightforward path to investigate the mechanisms regulating the fate of an mRNA during transcription and how the cells achieve precise gene expression patterns by coordinating mRNA transcription, translation and decay. In order to do this, we will develop and use tools specifically reporting each of the steps in mRNA metabolism and identify factors that coordinate these steps. 1. Impact of promoter sequence on transcription and mRNA localization 2. Purification of factors regulating transcription and mRNA fate 3. Visualization of proteins loaded on the nuclear transcripts and followed into the cytoplasm 4. Kinetics of translation and decay and factors

Public Health Relevance

PROJECT RELEVANCE Despite years of research, we still do not understand how the cell regulates the appearance and disappearance of messenger RNAs (mRNA) and proteins necessary for the cycles of cell growth and division. We have discovered that correct regulation relies on tagging the mRNAs responsible for cell division proteins with the seeds of its own destruction at the moment of its birth. These tags then destroy the mRNA at the exact moment its job is finished, so that the cell can progress to the next part of the cycle by making new proteins. We have developed new imaging tools that will let us see this happen in living cells in real time in order to understand how the cell orchestrates this synchrony. Cell growth and division are the bases of all biological processes, normal and diseased and this understanding will provide information for addressing runaway cell growth such as in cancer, or flaws in cell division that may lead to birth defects or susceptibility to infections.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
6R01GM057071-22
Application #
9860643
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Flicker, Paula F
Project Start
1998-01-01
Project End
2019-11-30
Budget Start
2019-01-01
Budget End
2019-11-30
Support Year
22
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Albert Einstein College of Medicine
Department
Type
DUNS #
081266487
City
Bronx
State
NY
Country
United States
Zip Code
10461
Tutucci, Evelina; Vera, Maria; Biswas, Jeetayu et al. (2018) An improved MS2 system for accurate reporting of the mRNA life cycle. Nat Methods 15:81-89
Zhang, Qianjun; Meng, Xiuhua; Li, Delin et al. (2017) Binding of DEAD-box helicase Dhh1 to the 5'-untranslated region of ASH1 mRNA represses localized translation of ASH1 in yeast cells. J Biol Chem 292:9787-9800
Wang, Guangli; Zeng, Yao; Chen, Shaoying et al. (2017) Localization of TFPI-2 in the nucleus modulates MMP-2 gene expression in breast cancer cells. Sci Rep 7:13575
Brickner, Donna Garvey; Sood, Varun; Tutucci, Evelina et al. (2016) Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms. Mol Biol Cell 27:2980-93
Vera, Maria; Biswas, Jeetayu; Senecal, Adrien et al. (2016) Single-Cell and Single-Molecule Analysis of Gene Expression Regulation. Annu Rev Genet 50:267-291
Smith, Carlas S; Preibisch, Stephan; Joseph, Aviva et al. (2015) Nuclear accessibility of ?-actin mRNA is measured by 3D single-molecule real-time tracking. J Cell Biol 209:609-19
Smith, Carlas; Lari, Azra; Derrer, Carina Patrizia et al. (2015) In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol 211:1121-30
Grimm, Jonathan B; English, Brian P; Chen, Jiji et al. (2015) A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat Methods 12:244-50, 3 p following 250
Hocine, Sami; Vera, Maria; Zenklusen, Daniel et al. (2015) Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH. Sci Rep 5:9934
Buxbaum, Adina R; Haimovich, Gal; Singer, Robert H (2015) In the right place at the right time: visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 16:95-109

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