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The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student's epistemic beliefs to achieving positive learning outcomes.

Histone acetylation is directly related to gene expression. In yeast, the acetyltransferase general control nonderepressible-5 (GCN5) targets histone H3 and associates with transcriptional co-activators alteration/deficiency in activation-2 (ADA2) and alteration/deficiency in activation-3 (ADA3) in complexes like SAGA. Arabidopsis thaliana has two genes encoding proteins, designated ADA3a and ADA3b, that correspond to yeast ADA3. We investigated the role of ADA3a and ADA3b in regulating gene expression during flowering time. Specifically, we found that knock out mutants ada3a-2 and the double mutant ada3a-2 ada3b-2 lead to early flowering compared to the wild type plants under long day (LD) conditions and after moving plants from short days to LD. Consistent with ADA3a being a repressor of floral initiation, FLOWERING LOCUS T (FT) expression was increased in ada3a mutants. In contrast, other genes involved in multiple pathways leading to floral transition, including FT repressors, players in GA signaling, and members of the SPL transcriptional factors, displayed reduced expression. Chromatin immunoprecipitation analysis revealed that ADA3a affects the histone H3K14 acetylation levels in SPL3, SPL5, RGA, GAI, and SMZ loci. In conclusion, ADA3a is involved in floral induction through a GCN5-containing complex that acetylates histone H3 in the chromatin of flowering related genes.

The histone acetyltransferase GCN5 and associated transcriptional coactivator ADA2b are required to couple endoreduplication and trichome branching. Mutation of ADA2b also disrupts the relationship between ploidy and leaf cell size. Dynamic chromatin structure has been established as a general mechanism by which gene function is temporally and spatially regulated, but specific chromatin modifier function is less well understood. To address this question, we have investigated the role of the histone acetyltransferase GCN5 and the associated coactivator ADA2b in developmental events in Arabidopsis thaliana. Arabidopsis plants with T-DNA insertions in GCN5 (also known as HAG1) or ADA2b (also known as PROPORZ1) display pleiotropic phenotypes including dwarfism and floral defects affecting fertility. We undertook a detailed characterization of gcn5 and ada2b phenotypic effects in rosette leaves and trichomes to establish a role for epigenetic control in these developmental processes. ADA2b and GCN5 play specific roles in leaf tissue, affecting cell growth and division in rosette leaves often in complex and even opposite directions. Leaves of gcn5 plants display overall reduced ploidy levels, while ada2b-1 leaves show increased ploidy. Endoreduplication leading to increased ploidy is also known to contribute to normal trichome morphogenesis. We demonstrate that gcn5 and ada2b mutants display alterations in the number and patterning of trichome branches, with ada2b-1 and gcn5-1 trichomes being significantly less branched, while gcn5-6 trichomes show increased branching. Elongation of the trichome stalk and branches also vary in different mutant backgrounds, with stalk length having an inverse relationship with branch number. Taken together, our data indicate that, in Arabidopsis, leaves and trichomes ADA2b and GCN5 are required to couple nuclear content with cell growth and morphogenesis.

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students., There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.

The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this study, we deliberately integrated bioinformatics instruction at multiple course levels into an existing biology curriculum. Students in an introductory biology course, intermediate lab courses, and advanced project-oriented courses all participated in new course components designed to sequentially introduce bioinformatics skills and knowledge, as well as computational approaches that are common to many bioinformatics applications. In each course, bioinformatics learning was embedded in an existing disciplinary instructional sequence, as opposed to having a single course where all bioinformatics learning occurs. We designed direct and indirect assessment tools to follow student progress through the course sequence. Our data show significant gains in both student confidence and ability in bioinformatics during individual courses and as course level increases. Despite evidence of substantial student learning in both bioinformatics and mathematics, students were skeptical about the link between learning bioinformatics and learning mathematics. While our approach resulted in substantial learning gains, student "buy-in" and engagement might be better in longer project-based activities that demand application of skills to research problems. Nevertheless, in situations where a concentrated focus on project-oriented bioinformatics is not possible or desirable, our approach of integrating multiple smaller components into an existing curriculum provides an alternative.

A central question in biology is to understand how gene expression is precisely regulated to give rise to a variety of forms during the process of development. Epigenetic effects such as DNA methylation or histone modification have been increasingly shown to play a critical role in regulation of genome function. GCN5 is a prototypical histone acetyltransferase that participates in regulating developmental gene expression in several metazoan species. In Arabidopsis thaliana, plants with T-DNA insertions in GCN5 (also known as HAG1) display a variety of pleiotropic effects including dwarfism, loss of apical dominance, and floral defects affecting fertility. We sought to determine when during early development floral abnormalities first arise. Using scanning electron microscopy, we demonstrate that gcn5-1/hag1-1 and gcn5-5/hag1-5 mutants display overproliferation of young buds and development of abnormal structures around the inflorescence meristem. gcn5 mutants also display defects in stamen number and arrangement at later stages. This analysis provides temporal and spatial information to aid in the identification of GCN5 target genes in the developing flower. Preliminary studies of putative targets using reverse transcriptase PCR suggest that the floral meristem identity gene LEAFY is among factors upregulated in gcn5-1 mutants.

The Insulin-like growth factor 2 (Igf2) and H19 genes are imprinted, resulting in silencing of the maternal and paternal alleles, respectively. This event is dependent upon an imprinted-control region two kilobases upstream of H19 (refs 1, 2). On the paternal chromosome this element is methylated and required for the silencing of H19 (refs 2-4). On the maternal chromosome the region is unmethylated and required for silencing of the Igf2 gene 90 kilobases upstream. We have proposed that the unmethylated imprinted-control region acts as a chromatin boundary that blocks the interaction of Igf2 with enhancers that lie 3' of H19 (refs 5, 6). This enhancer-blocking activity would then be lost when the region was methylated, thereby allowing expression of Igf2 paternally. Here we show, using transgenic mice and tissue culture, that the unmethylated imprinted-control regions from mouse and human H19 exhibit enhancer-blocking activity. Furthermore, we show that CTCF, a zinc finger protein implicated in vertebrate boundary function, binds to several sites in the unmethylated imprinted-control region that are essential for enhancer blocking. Consistent with our model, CTCF binding is abolished by DNA methylation. This is the first example, to our knowledge, of a regulated chromatin boundary in vertebrates.

Genomic imprinting in mammals is an epigenetic process that results in differential expression of the two parental alleles. The tightly linked murine H19 and Igf2 genes are reciprocally imprinted: H19 is expressed from the maternal chromosome while Igf2 is expressed from the paternal chromosome. A single regulatory region in the 5' flank of the H19 gene has been implicated in silencing both genes. On the paternal chromosome, this region is heavily methylated at CpG residues, leading to repression of the H19 gene. The mechanism by which the same region in an unmethylated state on the maternal chromosome silences Igf2 is less well understood. We have probed the chromatin structure of the region by assessing its sensitivity to nuclease digestion. Two regions of nuclease hypersensitivity that are specific to the maternal chromosome were identified. These coincide with the region that is most heavily methylated on the paternal chromosome. As is the case with paternal methylation, hypersensitivity is present in all tissues surveyed, irrespective of H19 expression. We suggest that the chromatin structure of the maternal 5' flank of the H19 gene may represent an epigenetic mark involved in the silencing of Igf2.

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles., In their 2012 report, the President's Council of Advisors on Science and Technology advocated “replacing standard science laboratory courses with discovery-based research courses”—a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates.

The importance of engaging students in science and helping them to become informed citizens has been highlighted by many groups invested in science education. This report describes a project that furthers both academic and civic goals through the integration of a service learning component into an undergraduate course. This nonmajors class covers the biology underlying the use of genetic information in today's society and provides students with the opportunity to discuss related ethical and political issues. The service learning project itself involved the creation of instructional materials dealing with the above topics and issues for use in local secondary school classrooms. Students developed materials in a digital media format to allow for revision in response to peer and community feedback. Outcomes of this pilot project suggest benefits to undergraduates as well as high school educators and students. Interdisciplinary collaborations and local educational partnerships have also been developed and strengthened through this work.

Chromatin Structure and Gene Expression, Second Edition Edited by Sarah C.R. Elgin and Jerry L. Workman Oxford: Oxford University Press (2001). 328 pp. $60.00Few active scientists can legitimately claim to remember the days when conventional wisdom held that deoxyribonucleic acid was far too simple a chemical to embody genetic information. We now smile knowingly at the quaint arguments that the four “letters” in the DNA alphabet could hardly suffice to encode the vast range of genetic characteristics inherent in any individual organism, in the differences between organisms of a species, and among the myriad species of our biotic world. The successful modeling of the structure of DNA led to the solution of the coding problem and eventually to the unraveling of the mechanisms of replication, transcription, and translation that accomplish the copying and reading of the genetic code.Not so rare are scientists who can recall a similar opprobrium being laid to chromatin. Even in early days, it was recognized that something had to package some 2 meters of linear DNA to fit within the 10 μm diameter of a human cell nucleus. The obviously redundant structure of the nucleosome (and the higher orders of chromatin structure, up to the compacted mitotic chromosomes) might certainly help to accomplish this packaging. But the genetic regulatory role of this packaging has at times been viewed as no more than an obvious steric hindrance to those elegant processes noted above.In another sense, we've known better for a long time, and so over the years most conferences on eukaryotic replication or transcriptional mechanisms included at least a few token talks on chromatin (sometimes relegated to the morning session after the closing banquet). No longer. In current discussions of the control of eukaryotic gene expression, chromatin is considered not so much a static barrier to transcription as an active participant in the delicate dance in time and space that results in the appropriate turning on and off of the right genes in the right cells at the right times in response to the right signals.Within the last five years, our knowledge and understanding of chromatin structure and its function in gene regulation has dramatically expanded. This emerging understanding has resulted from a marriage of genetic, biochemical, and molecular approaches. For example, we now have a very clear picture of the structure of the nucleosome, although the higher-order structures of chromatin remain clouded in mystery. Also, we now recognize several classes of proteins (or protein complexes) that actively modify chromatin structure. These include histone acetyltransferases (HATs) and deacetylases (HDACs), as well as ATP-dependent remodeling activities (involving SWI/SNFs and ISWIs). Interestingly, many of these proteins had been previously described with respect to their effects on transcription, thereby strengthening the link between chromatin and gene regulation. Not only have these modifying activities and the factors responsible for them been characterized, but it has also become clear that these proteins function in complexes. Many of these complexes contain a large number of (sometimes overlapping) members, suggesting a web of functional interactions that might be viewed as either elegantly integrated or hopelessly tangled.This expansion of knowledge and understanding is highlighted in the second edition of Chromatin Structure and Gene Expression, edited by Sarah C.R. Elgin and Jerry L. Workman. This text examines the effects of chromatin on transcription through a wide range of structural levels from the nucleosome to nuclear organization. Because of this breadth, laboratories focused on one particular aspect of chromatin and gene regulation may find that this book will serve as a useful reference text for information on other subfields. The book is targeted to a fairly broad audience, including beginning graduate students and scientists established in distinct research areas. However, the novice should be forewarned; whereas the first edition (published in 1995) offered a very readable summary of the major concepts in this field at that time, this new volume packs a wealth of information much more densely.The book begins with a chapter on chromatin structure, highlighting information gleaned from the crystal structure of the nucleosome and noting the continuing dearth of detail for higher-order structures. The next few chapters discuss the effects on chromatin and its assembly during replication of DNA and begin to discuss its role in transcription, setting the stage for future chapters. Apparent throughout these first chapters is a continuing discussion of nucleosomal and chromatin dynamics. The reader is introduced to chromatin proteins themselves and their variations and modifications, as well as the proteins and complexes that are responsible for nucleosome assembly and chromatin modification.Four full chapters explore chromatin-modifying activities (including the chromatin remodeling ATPase families and the acetylation and deacetylation enzymes) and their effects on gene regulation, reflecting the current research focus in these areas and the vast increase in our knowledge of these processes since the publication of the first edition. The book then addresses chromatin regulation of gene function at several higher organization levels. Three chapters discuss different forms of epigenetic regulation in yeast, Drosophila, and mammals. A chapter added to this new edition illustrates chromatin effects on the developmental regulation of genes using two examples, control of gene expression by the thyroid hormone receptor and the regulation of the β-globin locus. A chapter on chromatin boundaries discusses the role of these elements in preventing misregulation of neighboring genes as well as possible roles in organization of genomes. This concept leads very nicely into the final chapter, another new addition that deals with large-scale chromatin structure and nuclear organization and highlights many new areas of research.While the text is quite comprehensive in accommodating a wide range of biological systems, genetic pathways, and experimental approaches, one notable omission is the role of chromatin in regulation of gene expression in plants. Work in Arabidopsis is mentioned briefly in chapters on modifying complexes, an area of current investigation that will likely reveal both important similarities and differences when compared with extensive studies in yeast and other higher eukaryotes. Plants are also notable for having a higher degree of methylation throughout their genomes, and this and other epigenetic effects on gene expression (i.e., posttranscriptional gene silencing, paramutation, etc.) warrant some attention in a text such as this. The scant attention given in this text to the roles of histone variants reflects their unappreciated status in the field generally, a deficit that some might hope will be remedied in the near future.Accompanying illustrations found in each of the chapters are of excellent quality, and many appear to be original to this publication. The figures typically provide a summary of information or a model, which can be helpful either as a quick reference or as a point of clarification for the beginner. This latter notion is particularly true for tables included in the chapters on chromatin modifying activities, which help one to keep track of the various complexes.Each chapter was written by investigators from at least two different laboratories, a strategy that helps balance the depth and breadth of material. The editors are commended for the remarkable consistency throughout the book in the detail to which each topic is covered. In addition to a dialog between chapter authors, the book is further enhanced by discussions with authors of other sections, which are often reflected in the “Final Comments” at the end of each chapter. One of many positive aspects of the book is the highlighting of unanswered questions and future directions, perhaps especially critical in such a fast-changing field.Overall, this text provides a detailed introduction to various research areas concerning the interaction between chromatin function and gene regulation. At this point, these fields have not completely merged. For example, we don't fully understand how the effects of various chromatin-modifying activities on the transcriptional machinery may result in epigenetic phenomena that affect a single locus or an entire chromosome. However, the question is no longer whether chromatin structure plays an active and dynamic role in regulating gene expression, but how the complexities and intricacies of this role are accomplished. By the time we see a third edition of this useful volume, it is likely that at least some of these mechanisms will be more clearly defined.

Histone acetylation is an example of covalent modification of chromatin structure that has the potential to regulate gene expression. Gcn5 is a prototypical histone acetyltransferase that associates with the transcriptional coactivator Ada2. In Arabidopsis, two genes encode proteins that resemble yeast ADA2 and share approximately 45% amino acid sequence identity. We previously reported that plants harboring a T-DNA insertion in the ADA2b gene display a dwarf phenotype with developmental defects in several organs. Here we describe T-DNA insertion alleles in the ADA2a gene, which result in no dramatic growth or developmental phenotype. Both ADA2a and ADA2b are expressed in a variety of plant tissues; moreover, expression of ADA2a from a constitutive promoter fails to complement the ada2b-1 mutant phenotype, consistent with the hypothesis that the two proteins have distinct biochemical roles. To further probe the cellular roles of ADA2a and ADA2b, we studied the response of the transcriptional coactivator mutants to abiotic stress. Although ada2b seedlings display hypersensitivity to salt and abscisic acid and altered responses to low temperature stress, the responses of ada2a seedlings to abiotic stress generally parallel those of wildtype plants. Intriguingly, ada2a;ada2b double mutant plants display an intermediate, gcn5-like phenotype, suggesting that ADA2a and ADA2b each work independently with GCN5 to affect genome function in Arabidopsis.