Engineering REST-Specific Synthetic PUF Proteins to Control Neuronal Gene Expression: A Combined Experimental and Computational Study

REST Is Not Resting: REST/NRSF in Health and Disease

Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.

Mechanisms and Strategies for Determining m6 A RNA Modification Sites by Natural and Engineered m6 A Effector Proteins

N⁶ -Methyladenosine (m⁶ A) is the most common internal RNA modification in the consensus sequence of 5'-RRACH-3'. The methyl mark is added by writer proteins (METTL3/METTL14 metyltransferase complex) and removed by eraser proteins (m⁶ A demethylases; FTO and ALKBH5). Recognition of this methyl mark by m⁶ A reader proteins leads to changes in RNA metabolism. How the writer and eraser proteins determine their targets is not well-understood, despite the importance of this information in understanding the regulatory mechanisms and physiological roles of m⁶ A. However, approaches for targeted manipulation of the methylation state at specific sites are being developed. In this review, I summarize the recent findings on the mechanisms of target identification of m⁶ A regulatory proteins, as well as recent approaches for targeted m⁶ A modifications.

RNA binding protein PUM1 promotes colon cancer cell proliferation and migration

Colon cancer is the third leading cause of death worldwide and sixth in India, where it is the cause of 5.8% of the total deaths. Pumilio-1 (PUM1) is an RNA binding protein whose regulatory role is by binding to the consensus 5'UGUANAUA3' sequence on the 3'UTR of the mRNA targets and post-transcriptionally repressing their expression. This study is the first of its kind to report the expression or function of PUM1 in colon cancer. We found that PUM1 mRNA expression is high in primary and metastatic colon cancer cell lines when compared to the normal colon cell line. Immunohistochemistry analysis showed similar trend wherein compared to the normal colon tissue, PUM1 was found to be overexpressed in both adenocarcinoma and in metastatic carcinoma. This confirms the role of PUM1 in colon cancer progression. PUM1 overexpression study in HCT116 revealed that cells transfected with PUM1 plasmid show an increased rate of proliferation, migration and colony formation. Overexpressing PUM1 increases the number and size of spheroids indicating the role of PUM1 in maintaining cancer stem cells. Overall, this is the first study that has shown the role of PUM1 in colon cancer development.

Effective RNA Regulation by Combination of Multiple Programmable RNA-Binding Proteins

RNAs play important roles in gene expression through translation and RNA splicing. Regulation of specific RNAs is useful to understand and manipulate specific transcripts. Pumilio and fem-3 mRNA-binding factor (PUF) proteins, programmable RNA-binding proteins, are promising tools for regulating specific RNAs by fusing them with various functional domains. The key question is: How can PUF-based molecular tools efficiently regulate RNA functions? Here, we show that the combination of multiple PUF proteins, compared to using a single PUF protein, targeting independent RNA sequences at the 3′ untranslated region (UTR) of a target transcript caused cooperative effects to regulate the function of the target RNA by luciferase reporter assays. It is worth noting that a higher efficacy was achieved with smaller amounts of each PUF expression vector introduced into the cells compared to using a single PUF protein. This strategy not only efficiently regulates target RNA functions but would also be effective in reducing off-target effects due to the low doses of each expression vector.