Periodic Reporting for period 4 - TranslationRegCode (Cracking the Translation Regulatory Code)
Periodo di rendicontazione: 2020-09-01 al 2022-08-31
Regulation of gene expression is central for understanding how the human body works. Regulation of gene expression underlies major changes that occur in our cells in response to numerous physiological and environmental signals. Furthermore, it is often deregulated in numerous diseases. Thus, a deep understanding of the molecular mechanisms underlying regulation of gene expression is essential for understanding disease, and future therapy.
Regulation of transcription, the first step of gene expression, i.e. the synthesis of RNA from DNA, has been widely studies for decades. More recently, the scientific community is becoming increasingly aware of the great complexity of regulation at the level of RNA, and more specifically, RNA translation, the process of protein synthesis from RNA. With emerging new RNA therapies and RNA-based drugs, such as the recent drug treatment for the fatal SMA disease, that manipulates post-transcriptional RNA processing, it is becoming more and more important to get a high resolution understanding of post-transcriptional regulatory processes.
This project aimed to get a genome-wide, high resolution mapping and understanding of regulation at the level of mRNA, from transcription, through post-transcriptional regulation, to translation. The project has made several novel discoveries of new regulatory phenomena governing gene expression regulation in the mammalian stress response. Furthermore, our work has revealed failed components of gene expression responses in aging and neurodegeneration.
Regulation of transcription, the first step of gene expression, i.e. the synthesis of RNA from DNA, has been widely studies for decades. More recently, the scientific community is becoming increasingly aware of the great complexity of regulation at the level of RNA, and more specifically, RNA translation, the process of protein synthesis from RNA. With emerging new RNA therapies and RNA-based drugs, such as the recent drug treatment for the fatal SMA disease, that manipulates post-transcriptional RNA processing, it is becoming more and more important to get a high resolution understanding of post-transcriptional regulatory processes.
This project aimed to get a genome-wide, high resolution mapping and understanding of regulation at the level of mRNA, from transcription, through post-transcriptional regulation, to translation. The project has made several novel discoveries of new regulatory phenomena governing gene expression regulation in the mammalian stress response. Furthermore, our work has revealed failed components of gene expression responses in aging and neurodegeneration.
While studying mRNA regulation in a genome-wide scale, we have identified several novel key phenomena which play a major role in the regulatory response to stress in mammalian cells. These were centered around three main themes:
(1) Gene expression regulation in cellular stress responses, such as oxidative stress, heat stress, ER stress, and others, which cells undergo all the time as part of normal physiology, (2) cellular aging, and how stress responses are altered in the aged cells, and (3) protein aggregation, that occur and underlie many types of neurodegenerative diseases.
(1) During the project we uncovered and characterized several novel regulatory modes which take place in response to cellular stress. The first, includes naturally-occurring stress-induced transcriptional readthrough, which we found to be a hallmark of acute proteotoxic (i.e. stresses that affect protein folding state) stress responses. We found that there is a broad, yet regulated, defect in transcription termination, leading to the generation of thousands of long transcripts spanning gene ends. We developed a new tool for their identification, which is freely available to the community. We further uncovered that one of the consequences of this phenomenon is continuous transcription into downstream neighboring genes, which generate gene chimeras. Importantly, this affects the incomplete splicing of the downstream gene, acting as an evolutionarily conserved QC mechanism to keep these chimeras in the nucleus. These findings were published in a series of three papers along the grant period, Vilborg et al. 2017, Wiesel et al. 2018, and Hadar et al. 2022. In addition, our work has revealed two regulatory modes that take place as part of the UPR, namely the Unfolded protein response, which affects the Endoplasmic Reticulum (the ER, also known as ER stress), the organelle responsible for synthesis and processing of all secreted and membrane proteins. The first describes the preferential repression of translation of ER targeted proteins in response to ER stress. Furthermore, we found a novel mode of translational regulation, in which rewiring of amino acid metabolism is coupled to protein synthesis demands, which change in response to ER stress. These two works were described in two publications, Gonen et al. 2019 and Gonen, Meller et al, 2019.
(2) During the project, asking how cellular aging affects the gene expression response to stress, we uncovered a multi-level deterioration in gene expression programs, centered on nuclear transcription and splicing, which fail to properly respond to stress in aging cells. These findings, including a high resolution characterization of the gene expression programs that deteriorate and the decoupling of the regulation of transcription and translation that occurs in cellular aging, were published in Sabath et al. 2020, and reviewed in Meller & Shalgi 2021.
(3) Finally, studies of cellular models of pathological aggregation in two neurodegenerative diseases, Huntington’s disease and ALS, have characterized the differences in the cellular detection of these two different types of aggregates, and unraveled that the cellular response to both types is different, yet always maladaptive. These findings, made in the course of the project, have led to a much broader functional study of these two aggregate types, including the discovery of novel ALS disease modifiers which substantially protect from ALS-associated aggregation. These findings were published in Rozales et al. 2022.
(1) Gene expression regulation in cellular stress responses, such as oxidative stress, heat stress, ER stress, and others, which cells undergo all the time as part of normal physiology, (2) cellular aging, and how stress responses are altered in the aged cells, and (3) protein aggregation, that occur and underlie many types of neurodegenerative diseases.
(1) During the project we uncovered and characterized several novel regulatory modes which take place in response to cellular stress. The first, includes naturally-occurring stress-induced transcriptional readthrough, which we found to be a hallmark of acute proteotoxic (i.e. stresses that affect protein folding state) stress responses. We found that there is a broad, yet regulated, defect in transcription termination, leading to the generation of thousands of long transcripts spanning gene ends. We developed a new tool for their identification, which is freely available to the community. We further uncovered that one of the consequences of this phenomenon is continuous transcription into downstream neighboring genes, which generate gene chimeras. Importantly, this affects the incomplete splicing of the downstream gene, acting as an evolutionarily conserved QC mechanism to keep these chimeras in the nucleus. These findings were published in a series of three papers along the grant period, Vilborg et al. 2017, Wiesel et al. 2018, and Hadar et al. 2022. In addition, our work has revealed two regulatory modes that take place as part of the UPR, namely the Unfolded protein response, which affects the Endoplasmic Reticulum (the ER, also known as ER stress), the organelle responsible for synthesis and processing of all secreted and membrane proteins. The first describes the preferential repression of translation of ER targeted proteins in response to ER stress. Furthermore, we found a novel mode of translational regulation, in which rewiring of amino acid metabolism is coupled to protein synthesis demands, which change in response to ER stress. These two works were described in two publications, Gonen et al. 2019 and Gonen, Meller et al, 2019.
(2) During the project, asking how cellular aging affects the gene expression response to stress, we uncovered a multi-level deterioration in gene expression programs, centered on nuclear transcription and splicing, which fail to properly respond to stress in aging cells. These findings, including a high resolution characterization of the gene expression programs that deteriorate and the decoupling of the regulation of transcription and translation that occurs in cellular aging, were published in Sabath et al. 2020, and reviewed in Meller & Shalgi 2021.
(3) Finally, studies of cellular models of pathological aggregation in two neurodegenerative diseases, Huntington’s disease and ALS, have characterized the differences in the cellular detection of these two different types of aggregates, and unraveled that the cellular response to both types is different, yet always maladaptive. These findings, made in the course of the project, have led to a much broader functional study of these two aggregate types, including the discovery of novel ALS disease modifiers which substantially protect from ALS-associated aggregation. These findings were published in Rozales et al. 2022.
In summary, the project has yielded significant discoveries of multiple regulatory phenomena related to the mammalian stress response, which broadly span from acute cellular responses, through cellular aging and how aging cells fail, to underlying cellular mechanisms of neurodegeneration. The outcomes of the project have shed new light on the breadth and the novel types of regulatory processes that affect and dictate the cellular gene expression programs and shape the landscape of RNA and its different fates in cells subject to transient or sustained stress, aging or neurodegeneration.