These files include source datasets for the article "Multipartite stabilization of the C. beijerincki pfl ZTP aptamer disfavors terminator hairpin folding by gating strand invasion". RELATED ARTICLE: Strobel, E.J., Cheng, L., Berman, K.E. et al. A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control. Nat Chem Biol 15, 1067–1076...
Prostate cancer (PCa) is the most common non-cutaneous cancer among U.S. men. Lack of effective treatments for advanced disease make it a significant public health concern. However, PCa’s long natural history makes it an excellent target for prevention approaches that reduce overtreatment of indolent disease, treatment related morbidity, and mortality....
NSD2, a histone methyltransferase specific for methylation of histone 3 lysine 36 (H3K36), exhibits a glutamic acid to lysine mutation at residue 1099 (E1099K) in childhood acute lymphocytic leukemia (ALL). Cells harboring this mutation can become the predominant clone in relapsing disease. We studied the effects of this mutant enzyme...
Transcription is tightly regulated to ensure genes are appropriately expressed both temporally and spatially. This tight regulation governs various processes within the cell, such as differentiation and cell identity, cellular maintenance, and dynamic responses to external signals. Transcription factors (TFs) coordinate these various gene programs and in particular, are key...
Oocyte meiosis is a specialized, but error prone, form of cell division that is poorly understood. Errors during meiosis often result in aneuploidy, or abnormal chromosome number, that impacts human health and fertility. Aneuploidy is the leading cause of miscarriages and birth defects, such as Down's syndrome in which cells...
Type I interferon (IFN) is the primary antiviral cytokine establishing a broad and potent antiviral response to protect mammalian cells from virus infection. The functional repertoire of IFN extends to innate and adaptive immunity, neoplastic transformation, resistance and cancer immunotherapy. IFN functions are primarily mediated through the Janus kinase (JAK)...
The cellular innate immune response to viruses is a defense mechanism executed by most cells in the human body to form the initial barrier to virus replication. Detection of viral nucleic acids initiates widespread gene expression changes that combine to establish an antiviral state and stimulate professional immune cell activation....
Proper size control of organs and tissues is critical to their function, and it is necessary for the millions of precisely sized tubes that make up those organs— for example, excessive cell growth can lead to devastating diseases such as Polycystic Kidney Disease. The regulation of tube growth is therefore...
Neural crest cells are a population of multipotent stem cells that are unique to vertebrates and give rise to a wide range of derivatives in the developing embryo, including elements of the craniofacial skeleton, pigmentation of the skin and peripheral nervous system. Although these cells reside in the ectoderm, they...
Splicing factor 3B1 (SF3B1) is a core splicing protein that stabilizes the interaction between the U2 snRNA and the branch point (BP) in the RNA target during splicing. SF3B1 is heavily phosphorylated at its N terminus and a substrate of cyclin-dependent kinases (CDKs). Although SF3B1 phosphorylation coincides with splicing catalysis,...
Many transcription factors (TFs) regulate oncogenic processes and are therefore desirable targets for drug intervention. However, few TF inhibitors have been developed to date due to a lack of specificity and few TF binding pockets. The Meade Lab has overcome these challenges by using cobalt-based complexes that disrupt Cys2His2 zinc...
Epigenetics is the study of chromatin-based events that regulate gene expression without the change of DNA sequence, including DNA methylation, histone modification and chromatin remodeling. Epigenetic regulators are encoded to modify chromatin in a highly regulated and dynamic manner. A growing number of studies have suggested the dysregulation of epigenetic...
RNA repair pathways exist in all three domains of life. In eukaryotes, they play key roles in fundamental biological processes such as tRNA splicing and endoplasmic reticulum (ER) stress induced noncanonical splicing of a master transcription factor mRNA (named XBP1 in mammalian cells). Even though most living organisms contain an...
The apolipoprotein E (APOE) E4 isoform is the strongest genetic risk factor for sporadic Alzheimer’s disease (AD). While APOE is predominantly expressed by astrocytes in the central nervous system, neuronal expression of APOE is of increasing interest in age-related cognitive impairment, neurological injury, and neurodegeneration. Here we show that endogenous...
The blueprint of life is contained within the sequence of an organism’s genome. While virtually all cells of an individual multicellular eukaryotic organism contain a near identical code of nucleic acid sequences, an organism must give rise to and maintain a varied set of cells and phenotypes. As such, sequence...
Promyelocytic leukemia (PML) nuclear bodies act as quality control centers in the nucleus, participating in a plethora of nuclear functions. As such, PML bodies are a signature model for functional nuclear organization. PML bodies have a dynamic protein composition that responds to changing conditions of the cell. Many of the...
The literature has established glucokinase (GCK) to be the principal hexokinase (HK) in the liver, operating as a glucose sensor to regulate glucose metabolism and lipid homeostasis. We have recently proposed Hexokinase Domain Containing-1 (HKDC1) to be a novel 5th HK with expression in the liver. Here, we reveal HKDC1...
Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS) are two devastating neurodegenerative diseases that affect 100,000s of people globally. They have a severe adverse impact on society, yet there are currently no early diagnostic tools or disease-modifying therapies available. Despite their clinical heterogeneity, evidence points to these diseases being on...
Many human diseases are chronic and ultimately fatal because they damage organs and tissues beyond the body’s normal repair mechanisms. Therefore, there is significant medical interest in developing pharmaceuticals that enhance the body’s natural injury repair mechanisms and engineering organs in the lab for transplantation. However, comparatively little is known...
Contactin associated protein like 2 (CNTNAP2) has emerged as a prominent susceptibility gene implicated in multiple complex neurodevelopmental disorders, including autism spectrum disorders (ASD), intellectual disability (ID), and schizophrenia (SCZ). The presence of seizure comorbidity in many of these cases, as well as inhibitory neuron dysfunction in Cntnap2 knockout (KO)...