RNA stress response to insufficient transcription
Transcription of DNA into mRNA is the initial and essential step in the gene expression process. As such, this process is tightly regulated at multiple levels. Moreover, transcription was shown to regulate numerous other processes, such as splicing, translation, and mRNA stability. Transcription constantly creates new transcripts of various sizes, types, and flavors, fueling all cellular activities. But what happens when the process of transcription is slowed down or inhibited? If the transcription of a single gene is reduced, probably the cell can compensate for it by inducing the expression of other genes with similar functions. But what happens when the transcription of numerous genes is inhibited? What the cell does when it is unable to produce mRNAs at the rate necessary to support cellular processes? We term this condition “transcriptional insufficiency” and suggest it is integral to multiple conditions. For example, transcriptional insufficiency can be observed when there are not enough nutrients, upon DNA damage, or when transcription is pharmacologically targeted, such as by anti-cancer drugs. What does the cell do to alleviate this condition? How does it survive? Could it survive at all? And if does, how do the cellular dynamics change? We address these and other questions by studying human cells and inducing transcriptional insufficiency in various ways. Then, we are measuring multiple cellular parameters and try to understand the strategies that cells employ to survive conditions that interfere with efficient gene expression.
Cap-independent initiation of translation
Translating the information encoded in the mRNA molecule to a sequence of amino acids that create proteins is a critical process that enables the flow of genetic information. Naturally, such an important process is tightly regulated at multiple levels. The beginning of translation, also termed initiation, is a highly complicated step regulated by multiple factors. Typically, identification of the 5’cap structure present on every mRNA molecule is the initial step of translation initiation. However, there are also alternative ways to initiate translation. The best-known "tricks" to initiate translation without the 5'cap structure include the use of IRES elements (IRES stands for Internal Ribosome Entry Site) and methylated adenosines (m6A). We previously showed that SARS-CoV-2 employs cap-independent modes of translation initiation. While it is widely accepted that certain viruses employ cap-independent IRES-mediated initiation of translation, it is still poorly understood how frequently this mode of translation initiation is employed in mammalian cells and under which stimuli. We aim to contribute to this field by studying the ability of mammalian cells to initiate cap-independent translation in different situations.
Trans-regulation within the gene expression cascade
Gene expression is an intricate cascade of events enabling the flow of information from the DNA to the protein level. Francis Crick, one of the greatest scientists of all time, was the first to describe the basics of gene expression and define the central dogma of molecular biology back in 1970. Since then, multiple additional steps of the gene expression process have been discovered. Naturally, each process possesses its own regulation, making the whole process of gene expression one of the most complicated and versatile. We aim to contribute to the research of the gene expression process by identifying trans-regulation between the different processes within the cascade of events. For example, we previously reported the ability of transcription to regulate the efficiency of translation and stability of mRNAs. More recently, we helped establish the connection between splicing and m6A deposition, which profoundly affects mRNA stability. Our vision of gene expression suggests cross-regulation between its multiple steps, which contributes to the synchronization and high responsiveness of the whole process. We aim to identify previously unknown ties between the different steps and describe the underlying molecular mechanisms.