A5014065815- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Estrogen and related hormone effects
- Cancer-related molecular mechanisms research
- Immune Cell Function and Interaction
- Mycobacterium research and diagnosis
- Protein Degradation and Inhibitors
- Molecular Biology Techniques and Applications
- RNA Interference and Gene Delivery
- Infectious Diseases and Mycology
Iowa State University
2021-2024
The interactions between cellular RNAs in MDA-MB-231 triple negative breast cancer cells and a panel of small molecules appended with diazirine cross-linking moiety an alkyne tag were probed transcriptome-wide live cells. allows for facile pull-down bound by each molecule, the enrichment RNA target defines compound's molecular footprint. Among 34 chemically diverse studied, six enriched RNAs. most highly interaction occurs novel RNA-binding compound F1 structured region 5′ untranslated...
A major limiting factor in target discovery for both basic research and therapeutic intervention is the identification of structural and/or functional RNA elements genomes transcriptomes. This was impetus original ScanFold algorithm, which provides maps local stability, evidence sequence-ordered (potentially evolved) structure, unique model structures comprised recurring base pairs with greatest bias. key step quantifying this propensity ordered structure prediction secondary stability...
ABSTRACT In recent years, interest in RNA secondary structure has exploded due to its implications almost all biological functions and newly appreciated capacity as a therapeutic agent/target. This surge of driven the development adaptation many computational biochemical methods discover novel, functional structures across genome/transcriptome. To further enhance efforts study structure, we have integrated prediction tool ScanFold, into IGV. allows users directly perform predictions...
MYC pre-mRNA is spliced with high fidelity to produce the transcription factor known regulate cellular differentiation, proliferation, apoptosis, and alternative splicing. The mechanisms underpinning splicing of , however, remain mostly unexplored. In this study, we examined interaction heterogeneous nuclear ribonucleoprotein C (HNRNPC) intron 2. Building off published eCLIP studies, confirmed poly(U) regions in 2 found that full binding correlated optimal protein production. appears be...
Various approaches have been developed to target RNA and modulate its function with modes of action including binding cleavage. Herein, we explored how small molecule is correlated cleavage induced by heterobifunctional ribonuclease targeting chimeras (RiboTACs), where RNase L recruited cleave the bound target, in a transcriptome-wide, unbiased fashion. Only fraction targets was cleaved L, RiboTAC binding. Global analysis suggested that (i) generally form region stable structure encompasses...
Experimental breakthroughs have provided unprecedented insights into the genes involved in cancer. The identification of such cancer driver is a major step gaining fuller understanding oncogenesis and provides novel lists potential therapeutic targets. A key area that requires additional study posttranscriptional control mechanisms at work genes. This important not only for basic biology cancer, but also to advance new modalities target RNA—an emerging field with great promise toward...
Abstract Epstein–Barr virus (EBV) is a widely prevalent human herpes infecting over 95% of all adults and associated with variety B-cell cancers induction multiple sclerosis. EBV accomplishes this in part by expression coding noncoding RNAs alteration the host cell transcriptome. To better understand structures which are forming viral transcriptomes infected cells, RNA structure probing technique Structure-seq2 was applied to BJAB-B1 line (an lymphoma). This resulted reactivity profiles...
RNA plays vital functional roles in almost every component of biology, and these are often influenced by its folding into secondary tertiary structures. An important role structure is maintaining proper gene regulation; therefore, making accurate predictions the structures involved processes important. In this study, we have expanded on our previous work that led to creation RNAStructuromeDB. Unlike study analyzed human genome at low resolution, now scanned protein-coding transcriptome high...
Abstract The androgen receptor (AR) is a ligand-dependent nuclear transcription factor belonging to the steroid hormone family. Due its roles in regulating cell proliferation and differentiation, AR tightly regulated maintain proper levels of itself many genes it controls. dysregulation driver human diseases including prostate cancer. Though this often occurs at RNA level, there are unknowns surrounding post-transcriptional regulation mRNA, particularly role that secondary structure plays....
Abstract RNA plays vital functional roles in almost every component of biology, and these are often influenced by its folding into secondary tertiary structures. An important role structure is maintaining proper gene regulation; therefore, making accurate predictions the structures involved processes important. In this study, we have expanded on our previous work that led to creation RNAStructuromeDB. Unlike study analyzed human genome at low resolution, now scanned protein-coding...
Buruli Ulcer is a neglected tropical disease that results in disfiguring and dangerous lesions affected persons across wide geographic area, including much of West Africa. The causative agent Mycobacterium ulcerans , relative the bacterium causes tuberculosis leprosy. Few therapeutic options exist for treatment this beyond antibiotics early stages, which are frequently ineffective, surgical removal later stage. In study we analyze six genes have high potential targeting. We focus our...
Abstract Buruli Ulcer is a neglected tropical disease that results in disfiguring and potentially dangerous lesions affected persons across wide geographic area, which includes much of West Africa. The causative agent Mycobacterium ulcerans , relative the bacterium causes tuberculosis leprosy. Few therapeutic options exist for treatment this beyond main approach, surgical removal, frequently ineffective. In study we analyze six genes have high potential targeting. We focus our analysis on...