Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability in Saccharomyces cerevisiae.

A critical feature of the intermolecular contacts that bind DNA to the histone octamer is the series of histone arginine residues that insert into the DNA minor groove at each superhelical location where the minor groove faces the histone octamer. One of these "sprocket" arginine residues, histone H4 R45, significantly affects chromatin structure in vivo and is lethal when mutated to alanine or cysteine in Saccharomyces cerevisiae (budding yeast). However, the roles of the remaining sprocket arginine residues (H3 R63, H3 R83, H2A R43, H2B R36, H2A R78, H3 R49) in chromatin structure and other cellular processes have not been well characterized. We have genetically characterized mutations in each of these histone residues when introduced either singly or in combination to yeast cells. We find that pairs of arginine residues that bind DNA adjacent to the DNA exit/entry sites in the nucleosome are lethal in yeast when mutated in combination and cause a defect in histone occupancy. Furthermore, mutations in individual residues compromise repair of UV-induced DNA lesions and affect gene expression and cryptic transcription. This study reveals simple rules for how the location and structural mode of DNA binding influence the biological function of each histone sprocket arginine residue.

Differences in metacognitive regulation in introductory biology students: when prompts are not enough.

Strong metacognition skills are associated with learning outcomes and student performance. Metacognition includes metacognitive knowledge-our awareness of our thinking-and metacognitive regulation-how we control our thinking to facilitate learning. In this study, we targeted metacognitive regulation by guiding students through self-evaluation assignments following the first and second exams in a large introductory biology course (n = 245). We coded these assignments for evidence of three key metacognitive-regulation skills: monitoring, evaluating, and planning. We found that nearly all students were willing to take a different approach to studying but showed varying abilities to monitor, evaluate, and plan their learning strategies. Although many students were able to outline a study plan for the second exam that could effectively address issues they identified in preparing for the first exam, only half reported that they followed their plans. Our data suggest that prompting students to use metacognitive-regulation skills is effective for some students, but others need help with metacognitive knowledge to execute the learning strategies they select. Using these results, we propose a continuum of metacognitive regulation in introductory biology students. By refining this model through further study, we aim to more effectively target metacognitive development in undergraduate biology students.

Novel functional residues in the core domain of histone H2B regulate yeast gene expression and silencing and affect the response to DNA damage.

Previous studies have identified novel modifications in the core fold domain of histone H2B, but relatively little is known about the function of these putative histone modification sites. We have mutated core modifiable residues that are conserved in Saccharomyces cerevisiae histone H2B and characterized the effects of the mutants on yeast silencing, gene expression, and the DNA damage response. We identified three histone H2B core modifiable residues as functionally important. We find that mutating H2B K49 in yeast confers a UV sensitivity phenotype, and we confirm that the homologous residue in human histone H2B is acetylated and methylated in human cells. Our results also indicate that mutating H2B K111 impairs the response to methyl methanesulfonate (MMS)-induced DNA lesions and disrupts telomeric silencing and Sir4 binding. In contrast, mutating H2B R102 enhances silencing at yeast telomeres and the HML silent mating loci and increases Sir4 binding to these regions. The H2B R102A mutant also represses the expression of endogenous genes adjacent to yeast telomeres, which is likely due to the ectopic spreading of the Sir complex in this mutant strain. We propose a structural model by which H2B R102 and K111 regulate the binding of the Sir complex to the nucleosome.