Rivka Dikstein Lab

Decoding Gene Regulatory Information

Research

Regulation of gene expression at the transcriptional and translational levels is fundamental to all biological activities and is frequently altered in disease states. Our broad research interest is to elucidate the basic regulatory mechanisms of transcription and mRNA translation. We focus on several key issues:

How do transcription and translation processes control the response to extracellular stimuli?
The connections between transcription, mRNA processing and translation.
The mechanism underlying unique mechanisms of translation initiation.
Developing chemical and genetic research tools for transcription and translation.

By integrating molecular, biochemical, bioinformatics, and chemical approaches, our studies have led to novel insights related to transcription initiation and elongation, mRNA processing and stability, and translation initiation, as well as the connections between them. We address these issues utilizing several biological systems:

Spt4/Spt5 (DSIF), a transcription elongation factor involved in stress responses and a prime target for inherited neurodegenerative diseases
Regulation of translation initiation: (i) the role translation initiation factors (eIFs); (ii) specialized translation driven by ribosome intrinsic mRNA binding (iii) cellular and viral ribosome binding proteins (iv) Stress and mitogenic signals
Identification of mammalian and viral translation regulatory elements and their potential use in RNA therapeutics
Mediators of the crosstalk between gene expression stages

Research page

The role of DSIF in inherent neurodegenerative diseases

Transcription-translation and transcription-mRNA fates links

Translation initiation regulatory mechanisms

Selected Publications

Unraveling the landscapes and regulation of scanning, leaky scanning, and 48S initiation complex conformations

Weiss B. & Dikstein R. (2024) Cell Reports. 43, 5, 114126.

Scanning and initiation are critical steps in translation. Here, we utilized translation complex profiling (TCP-seq) to investigate 48S organization and eIF4G1-eIF1 inhibition impact. We provide global views of scanning and leaky scanning, uncovering a central role of eIF4G1-eIF1 in their regulation. We confirm AUG context importance, with non-leaky genes featuring a Kozak context and cytosine at positions −1 and +5. Capturing 48S complexes associated with eIF1, eIF4G1, eIF3, and eIF2 through selective TCP-seq revealed that the eIF3-scanning ribosome is highly vulnerable to eIF4G1-eIF1 inhibition, and eIF1 tends to dissociate upon AUG recognition. Initiation-site footprint analysis revealed a class spanning −12 to +18/19 from the AUG, representing the entire 48S and enriched with eIF2, eIF1, and eIF4G1, indicative of early initiation. Another eIF3-dependent class extends up to +26 and exhibits reduced eIF2 and eIF4G1 association, suggesting a late/alternative initiation complex. Our analysis provides an overview of scanning, initiation, and evidence for conformational rearrangements in vivo.

Lowering mutant huntingtin by small molecules relieves Huntingtons disease symptoms and progression

Bahat A., Itzhaki E., Weiss B., Tolmasov M., Tsoory M., Kuperman Y., Brandis A., Shurrush K. A. & Dikstein R. (2024) EMBO Molecular Medicine. 16, 3, p. 523-546

Huntingtons disease (HD) is an incurable inherited disorder caused by a repeated expansion of glutamines in the huntingtin gene (Htt). The mutant protein causes neuronal degeneration leading to severe motor and psychological symptoms. Selective downregulation of the mutant Htt gene expression is considered the most promising therapeutic approach for HD. We report the identification of small molecule inhibitors of Spt5-Pol II, SPI-24 and SPI-77, which selectively lower mutant Htt mRNA and protein levels in HD cells. In the BACHD mouse model, their direct delivery to the striatum diminished mutant Htt levels, ameliorated mitochondrial dysfunction, restored BDNF expression, and improved motor and anxiety-like phenotypes. Pharmacokinetic studies revealed that these SPIs pass the blood-brain-barrier. Prolonged subcutaneous injection or oral administration to early-stage mice significantly delayed disease deterioration. SPI-24 long-term treatment had no side effects or global changes in gene expression. Thus, lowering mutant Htt levels by small molecules can be an effective therapeutic strategy for HD.

Selective translational control of cellular and viral mRNAs by RPS3 mRNA binding

Havkin-Solomon T., Itzhaki E., Joffe N., Reuven N., Shaul Y. & Dikstein R. (2023) Nucleic Acids Research. 51, 9, p. 4208-4222

RPS3, a universal core component of the 40S ribosomal subunit, interacts with mRNA at the entry channel. Whether RPS3 mRNA-binding contributes to specific mRNA translation and ribosome specialization in mammalian cells is unknown. Here we mutated RPS3 mRNA-contacting residues R116, R146 and K148 and report their impact on cellular and viral translation. R116D weakened cap-proximal initiation and promoted leaky scanning, while R146D had the opposite effect. Additionally, R146D and K148D displayed contrasting effects on start-codon fidelity. Translatome analysis uncovered common differentially translated genes of which the downregulated set bears long 5'UTR and weak AUG context, suggesting a stabilizing role during scanning and AUG selection. We identified an RPS3-dependent regulatory sequence (RPS3RS) in the sub-genomic 5'UTR of SARS-CoV-2 consisting of a CUG initiation codon and a downstream element that is also the viral transcription regulatory sequence (TRS). Furthermore, RPS3 mRNA-binding residues are essential for SARS-CoV-2 NSP1-mediated inhibition of host translation and for its ribosomal binding. Intriguingly, NSP1-induced mRNA degradation was also reduced in R116D cells, indicating that mRNA decay occurs in the ribosome context. Thus, RPS3 mRNA-binding residues have multiple translation regulatory functions and are exploited by SARS-CoV-2 in various ways to influence host and viral mRNA translation and stability.

All Publications