Spt6 is a highly conserved histone chaperone that interacts directly with both RNA polymerase II and histones to regulate gene expression. To gain a comprehensive understanding of the roles of Spt6, we performed genome-wide analyses of transcription, chromatin structure, and histone modifications in a Schizosaccharomyces pombe spt6 mutant. Our results demonstrate dramatic changes to transcription and chromatin structure in the mutant, including elevated antisense transcripts at >70% of all genes and general loss of the ؉1 nucleosome. Furthermore, Spt6 is required for marks associated with active transcription, including trimethylation of histone H3 on lysine 4, previously observed in humans but not Saccharomyces cerevisiae, and lysine 36. Taken together, our results indicate that Spt6 is critical for the accuracy of transcription and the integrity of chromatin, likely via its direct interactions with RNA polymerase II and histones. Studies over the last few years have revealed that transcription across eukaryotic genomes is much more widespread and complex than previously believed (1). Although it was once thought that transcription occurs primarily across protein-coding regions, genome-wide studies have now shown that transcription is also prevalent in intergenic regions and on antisense strands, in organisms ranging from yeast to humans (2, 3). Although roles for a small amount of this transcription have been established, for most, we have little understanding of its biological functions. Furthermore, while some factors have been shown to control the level of noncoding and antisense transcripts, many questions remain regarding the regulation of their synthesis and stability.One factor that plays a prominent role in the genome-wide control of transcription is Spt6. Originally identified in Saccharomyces cerevisiae (4, 5), Spt6 is conserved throughout eukaryotes and also has homology to the prokaryotic activator Tex (6). Spt6 interacts directly with several important factors, including RNA polymerase II (RNAPII) (7-11), histones (12, 13), and the transcription factor Iws1/Spn1 (7,14,15), suggesting that it is multifunctional. Recent studies in mammalian cells show that Spt6 also interacts directly with other chromatin related factors, including H3K27 demethylases (16, 17). Several gene-specific studies have demonstrated roles for Spt6 in transcription initiation (18)(19)(20), elongation (21, 22), and termination (23, 24). In addition, Spt6 is required for H3K36 methylation (25-28) and regulates nucleosome positioning and occupancy, particularly over highly expressed genes (12,19,29). Finally, Spt6 can assemble nucleosomes in vitro in an ATP-independent fashion (12). These results suggest that Spt6 acts as a histone chaperone by restoring nucleosomes in the wake of RNAPII transcription (30,31).In vivo, Spt6 is critical for normal growth and transcription. It is either essential or nearly essential for viability in all organisms tested, and viable spt6 mutations cause severe defects. In S. cerevisiae spt6 mutants,...

Iron-sulfur clusters (ISCs) are important prosthetic groups that define the functions of many proteins. Proteins with ISCs (called iron-sulfur or Fe-S proteins) are present in mitochondria, the cytosol, the endoplasmic reticulum and the nucleus. They participate in various biological pathways including oxidative phosphorylation (OXPHOS), the citric acid cycle, iron homeostasis, heme biosynthesis and DNA repair. Here, we report a homozygous mutation in LYRM4 in two patients with combined OXPHOS deficiency. LYRM4 encodes the ISD11 protein, which forms a complex with, and stabilizes, the sulfur donor NFS1. The homozygous mutation (c.203G>T, p.R68L) was identified via massively parallel sequencing of >1000 mitochondrial genes (MitoExome sequencing) in a patient with deficiency of complexes I, II and III in muscle and liver. These three complexes contain ISCs. Sanger sequencing identified the same mutation in his similarly affected cousin, who had a more severe phenotype and died while a neonate. Complex IV was also deficient in her skeletal muscle. Several other Fe-S proteins were also affected in both patients, including the aconitases and ferrochelatase. Mutant ISD11 only partially complemented for an ISD11 deletion in yeast. Our in vitro studies showed that the l-cysteine desulfurase activity of NFS1 was barely present when co-expressed with mutant ISD11. Our findings are consistent with a defect in the early step of ISC assembly affecting a broad variety of Fe-S proteins. The differences in biochemical and clinical features between the two patients may relate to limited availability of cysteine in the newborn period and suggest a potential approach to therapy.

Metabolism underlies many important cellular decisions, such as the decisions to proliferate and differentiate, and defects in metabolic signaling can lead to disease and aging. In addition, metabolic heterogeneity can have biological consequences, such as differences in outcomes and drug susceptibilities in cancer and antibiotic treatments. Many approaches exist for characterizing the metabolic state of a population of cells, but technologies for measuring metabolism at the single cell level are in the preliminary stages and are limited. Here, we describe novel analysis methodologies that can be applied to established experimental methods to measure metabolic variability within a population. We use mass spectrometry to analyze amino acid composition in cells grown in a mixture of 12C- and 13C-labeled sugars; these measurements allow us to quantify the variability in sugar usage and thereby infer information about the behavior of cells within the population. The methodologies described here can be applied to a large range of metabolites and macromolecules and therefore have the potential for broad applications.

The early stages of medical school involve education in a number of foundational biomedical sciences including genetics, immunology, and physiology. However, students entering medical school may have widely varying levels of background in these areas due to differences in the availability and quality of prior education on these topics. Even students who have recently taken formal courses in these subjects may not feel confident in their level of preparation, leading to anxiety for early-stage medical students. These differences can make it difficult for instructors to create meaningful learning experiences that are appropriate for all students. Additionally, actual or perceived differences in preparation may lead fewer students from diverse backgrounds to apply to medical school. Therefore, creating an efficient and scalable way to increase students’ knowledge and confidence in these topics addresses an important need for many medical schools. We recorded pre- and post-course quiz scores for 9790 individuals who completed HMX online courses, developed in accordance with evidence-based learning practices and covering the fundamentals of biochemistry, genetics, immunology, pharmacology, and physiology. Each question was accompanied by a Likert scale question to assess the learner’s confidence in their answer. Learners’ median post-course quiz performance and self-assessed confidence significantly increased relative to pre-course quiz performance for each course. Improvements were consistent across US-based medical schools, non-US medical schools, and course runs open to the public. This indicates that online courses created using evidence-based learning practices can lead to significant increases in knowledge and confidence for many learners, helping prepare them for further medical education. Supplementary Information The online version contains supplementary material available at 10.1007/s40670-022-01660-4.

Recently, our lab found that the canonical glucose/galactose regulation pathway in yeast makes the decision to metabolize galactose based on the ratio of glucose to galactose concentrations in the external medium. This led to the question of where and how the ratio-sensing is achieved. Here, we consider the possibilities of an intracellular, extracellular, or membrane bound ratio sensing mechanisms. We show that hexose transporters in the plasma membrane are mainly responsible for glucose/galactose ratio-sensing in yeast. Further, while the glucose sensors Gpr1, Snf3, and Rgt2 are not required for ratio sensing, they help modulate the ratio sensing phenotype by regulating the expression of individual transporters in different environments. Our study provides an example of an unexpected, but potentially widespread, mechanism for making essential decisions.