Stephen M. Mount - US grants

Our objective is a better understanding of both the conditions that lead to insertional mutations and the molecular basis of those mutations. The specific aims are: 1) To understand the mechanism of action of genetic modifiers of white-apricot (wa), a mutation caused by the insertion of thee transposable element copia, at the molecular level. New modifiers of wa will be isolated, and the effects of modifiers of wa on the expression of wa and copia itself will be assessed by examination of the RNA and protein products of gene fusions. Specific promoter or polyadenylation sequence elements through which these genes might affect copia expression will be identified by examining the effects of in vitro mutations. 2) To identify the genetic and environmental factors which influence the transposition of copia. The transposition of a marked copia element will be assayed by a novel test; these experiments are designed to be the first to assign a rate to copia transposition. Genetic suppression in Drosophila is fundamentally different from suppression in prokaryotes, which usually involves the suppression of point mutations within coding regions by second-site mutations in tRNAs. In contrast, suppressible alleles in Drosophila are generally of spontaneous origin and are associated with the insertion of transposable elements into noncoding DNA. Available information indicates that suppression in Drosophila involves the alteration of factors which act in either transcription or RNA processing, and that the study of suppression in Drosophila will identify the products of suppressor loci as trans-acting factors which act at these stages of gene expression. The transposable element copia is a member of the broad class of structurally homologous genetic elements that includes thee transposable Ty elements of yeast, vertebrate retrovirus proviruses, and a number of distinct Drosophila transposable elements. Many spontaneous mutations in Drosophila are caused by the insertion of transposable elements, and many of these are suppressible. The apricot allele of the white locus (which affects eye pigmentation) has been chosen for this study of suppression in Drosophila. wa is associated with the presence of copia within an intron of white. A major advantage of wa is that small deviations from its intermediate level of pigmentation are readily discerned by inspection. The mutant phenotype of wa is enhanced (pigmentation is further reduced) by En(wa) and su(f)), but suppressed by su(wa).

This project is directed towards an understanding of the rules which govern the expression of genes, particularly those rules concerned with the formation of mature messenger RNAs from primary transcripts. One area of emphasis is on the mechanism by which transposable element insertions within the transcribed regions of genes affect the production of messenger RNAs from those genes. The importance of this problem is underscored by the observation that insertion mutations account for the majority of spontaneous mutations in the fruit fly Drosophila and are responsible for at least some human genetic disease. The mutant allele white-apricot has been chosen as the focus for this study because of the relative ease with which second-site modifiers of the expression of white-apricot can be obtained and studied. The product of this research on white-apricot, attainable within the five year period, should be a mechanistic description at the molecular level of the suppression and enhancement of white-apricot by second-site modifiers. Current indications are that modifiers of white-apricot are genes that encode proteins with roles in the processing of messenger RNAS. Specific sequences that are essential for the response of white-apricot to suppressors and enhancers will be identified by testing the effects of mutations in these sequences. This will be done by analyzing phenotype (eye color and RNA products) in transformed flies as a function of genetic modifiers, and by in vitro splicing experiments. In addition, we will continue to identify and characterize modifier loci by genetic analysis and molecular cloning. A second, related, area of emphasis is the Ul small nuclear ribonucleoprotein particle (snRNP), a component of the higher eukaryotic splicing apparatus which functions in the selection of splice sites at the 5' ends of introns. We will carry out a genetic analysis of components of the Ul snRNP. One protein of the UlsnRNP, the so-called 70K protein, contains a region of sequence similar to portions of three genetically identified splicing regulators in Drosophila, including suppressor-of-white-apricot. Specific hypotheses for the function of this domain will be tested by transforming a strain bearing a mutation in the wild type 70K gene with altered forms of this gene, and by complementary biochemical analysis.

Ten biologists from the Departments of Zoology and Psychology of the University of Maryland, College Park are requesting funds to purchase a laser-scanning confocal microscope and image analysis workstation to support and enhance their research. Drs. Mount, Payne, Popper and Rivas will be the primary users of the instrument. Within our multidisciplinary group, the uses of confocal microscopy include investigations of neuronal polarity in cerebellar granule neurons (Dr. Rivas, Co-PI on this grant), regeneration of sensory hair cells in the ear (Drs. Dooling and Popper), the role of calcium ions in phototransduction (Dr. Payne), the development of central auditory projections in the CNS (Drs. Brauth, Carr, and Hall), how the correct processing of RNA from protein-coding genes is specified in higher organisms (Dr. Mount), homology of invertebrate auditory neurons (Yager), and investigations of stream meiofauna (Dr. Palmer). These laboratories have a large number of postdoctoral, graduate and advanced undergraduate students who will use the confocal microscope during their research training. We are requesting a Bio-Rad MRC 1024 confocal imaging system coupled to a Nikon 300 inverted epi-fluorescence microscope, and a Silicon Graphics "Indy." image analysis workstation for quantitative image analysis and three-dimensional image reconstruction. The confocal system will include a krypton-argon laser (with emission lines at 488, 568, and 647 nm), triple dichroic beamsplitter, four detection channels (three PMT-based detector channels and one detector for transmitted light), and high resolution 24-bit acquisition software. This system will allow us to image up to three separate fluorescent channels for multi-label applications. An inverted configuration with DIC optics is needed so that the epi-fluorescence Nikon microscope can be used for cell cultures, and to provide ample access for micromanipulation, as is required by several of our users. Confocal micr oscopy will significantly enhance the research programs of each of the core investigators, and will allow them to pursue areas of research that have heretofore been extremely difficult or impossible to examine with conventional microscopy. In contrast to conventional fluorescence microscopy, in confocal microscopy out-of-focus structures do not contribute to background because they receive little or no illumination, and any fluorescent signal produced by them is rejected by the instrument. Unlike conventional microscopy, where one must physically cut a thick tissue into extremely thin sections for imaging, the extremely shallow depth-of-field of confocal microscopy allows the optical sectioning of either intact cells or thick specimens (such as embryos or brain slices). Optical sections taken at successive focal planes can be re-combined using computer-generated techniques to produce a highly informative three-dimensional reconstruction of an entire tissue or cellular structure. These characteristics make this technique essential for our multi-disciplinary studies, all of which require optical sectioning through thick biological specimens with elimination of out-of-focus fluorescence. Each of the investigators in this proposal will use the optical sectioning and quantitative capabilities of the confocal imaging system. For example, Dr. Rivas will use the confocal to study the development of fluorescently-labeled neurons that were implanted into the brain. Using conventional fluorescence microscopy, out-of-focus fluorescence from thousands of implanted neurons masks the structure of any particular cell. Indeed, individual neurons extend through many focal planes, allowing sharp focusing only on particular portions of the cell. Drs. Brauth, Carr, Dooling, Hall, Popper, and Yager face similar methodological problems as they attempt to study the complex structure of neurons in the auditory nervous system. Dr. Mount will use the confocal to make optical sections th rough thick Drosophila embryos, and Dr. Palmer will use the confocal to section through invertebrate whole mounts. Dr. Payne will extend our use of the confocal into the area of neuronal cell physiology. Dr. Payne will investigate a localized light-induced elevation of intracellular calcium that is co-incident with the electrical response of photoreceptors to light. Drs. Rivas and Yager will also use the confocal for live neuronal imaging, using the optical sectioning capabilities of the confocal to image fluorescently-labeled neurons in thick brain slices or embryos. Thus, in each area of our research, the confocal will greatly improve our ability to study correlated structure and function.

DESCRIPTION: This proposal aims to use genetic, in vivo and in vitro approaches to investigate the role of individual SR type "basal" splicing factors in regulated splicing events. The proposal focuses largely on the activities of two proteins, B52 and U1 70K. Both proteins contain RRM regions and Ser/Arg rich regions. B52 is a member of the group of SR proteins that can be both necessary for basal splice site function and which can alter splice site choice in a concentration dependent manner. U1 70K is a protein which binds to the first loop of the U1snRNA. Both proteins have functional homologs in vertebrates and loss of function mutations exist for both in Drosophila. In addition, biochemical work in other systems has shown that different SR proteins are differentially effective in activating particular splice sites. The B52 protein is chosen for study as a representative of the SR proteins, and also because a specific dominant allele seems to alter the splicing of a number of loci (eg w, dsx, Ubx) in which alternative splicing can lead to phenotypically notable consequences. Studies on B52 first catalogue the tissue and temporal expression of two alternative splice variants of the RNA which encode proteins differing by 5 aa in the spacer region between the two RRMs. In vitro experiments are then envisioned to determine the preferred RNA bindng specificity for the wild type and mutant forms of the protein using either SELEX techniques or characterization of binding sites on possible in vivo targets suchs as w, dsx or Ubx. This is particularly important since the cause of the dominant mutant phenotypes is not clearly understood and since only the dominant allele seems to interact in two (w and dsx) of the genetic tests described in the proposal. Additional tests of the dominant B52 allele will involve testing its ability to function as a basal splicing factor in complementation of S100 extracts from Drosophila or Hela cells and tests of its ability to alter 5' splice site choice in appropriate globin constructs (the canonical SR protein as splice site regulator assay). To attempt to assay differences between specific and non-specific activities of the dominant allele, mutations will be made in the B52 binding sites of some or all of the potential target genes and then assayed for changes in binding and for changes in assembly of splicing complexes. These experiments will (I think) be carried out in vitro without corresponding in vivo functional tests. The possibility of interactions between variants of B52 and other splicing proteins will be analyzed by far-western analysis. These include tests of interaction with the U1 70K protein. Various in vivo studies will be attempted using loss of function or variant dominant alleles of B52. Some will involve looking at mutant transgenes in clones of cells which have lost wild type function. Tests will be made of wild type and dominant sequences altered in their RRM or SR domiains. A related set of experiments will be performed with the U1 70K gene involving production of total loss of function alleles and tests of the relative importance of the RRM and SR domains for function in vitro and in vivo. In addition, since preliminary work suggests that U1 70K, like another U1 associated protein, is necessary to establish appropriate female function of Sxl, tests will be done to determine the effects of 70K mutations on Sxl splicing and to see if 70K is regulated in the female germline. Finally, it is proposed to do a screen of existing lethal P- element insertions to identify genes which fail to complement the B52 dominant/+. The rationale is that the B52 dominant mutation interferes with at least some aspects of normal splicing and sensitizes the system such that loss of half the dose of any other near limiting splicing component will be revealed in a detectable phenotype. Previous results show that such an interaction can be seen in animals the are also tra-2/+; tra/+ in the dominant background. Additionally, at least one potential spontaineous mutation which enhances the dominant B52 phenotype has been found, although it remains unmapped.

A Fluorescence Image Deconvolution-Reconstruction Microscope will be used for a variety of different applications with living cells. Use will be restricted to observations of living cells that are present singly, or in thin specimens. This microscope generates a stack of fluorescent images at different focal planes, and then employs a set of sophisticated algorithms to determine point-spread functions for sources of fluorescence in the specimen. Out-of focus noise is subtracted from the signals in the image slices, and the slices are restacked to generate a three-dimensional reconstruction of the object at high resolution. Since small, bright objects placed against a dark background are detected as spots, it is possible to image fluorescence sources that are smaller than the theoretical limit of resolution for the microscope.

During the last twenty years, developments in the design of novel indicator fluorescent probes have enabled biologists to attack formerly intractable problems in cell biology and cell physiology. The cellular processes that have been amenable to this kind of analysis include photoreception, neuronal transmission, animal development, hormonal signaling, triggered gene expression, mitotic regulation, and chemotaxis. The developments in fluorescent dye design have moved in parallel with improvements in our ability to visualize and measure low light intensity signals from small numbers of molecules in living cells, with newly-designed optical microscopes and large pixel array CCD camera detectors. It is reasonable to expect that a significant expansion of analysis of processes in living cells will result from combined developments of reporter molecules and digital imaging technologies. It seems clear that the convergence of developments in photochemistry, biochemistry, cell biology, physiology and microscopy are all about to intersect within the living cell, and when accurate assessments of changing abundance and activity of a variety of molecules can be made in vivo and through time.

This microscope will be placed in an imaging facility that provides faculty, postdocs, graduate and undergraduate students with access to several high performance microscopes equipped with the capacity to view small quantities of fluorescent reporter molecules in living cells.

Existing genefinders use information about splice sites and differences
between exons and introns, but do not explicitly incorporate information
about sequences known as splicing enhancers, which promote incorporation
of exons into mRNA. This is a project to characterize exonic splicing
enhancers in Arabidopsis. Although splicing enhancers likely function in
splice site selection in many plant genes, and contribute to the
regulation of alternative splicing, plant splicing enhancers have not
yet been described in detail. Computational analysis of a database of
Arabidopsis exons and introns will be used to identify candidate
splicing enhancer sequences. The role of these sequences, and sequences
from genes that are known to be alternatively spliced, will be tested in
transgenic Arabidopsis using a splicing reporter construct. The activity
of these enhancers will be examined in transgenes that depend on exon
inclusion for expression. This will include analysis of the
tissue-specificity of splicing enhancer activity and should provide an
extensive database of information about the role of particular sequences
in promoting splicing. This project will generate:

1) 2,000 publicly available transgenic lines, available through the
ABRC, carrying splicing reporter genes with defined candidate splicing
enhancer sequences

2) A description of marker gene expression for each splicing enhancer
candidate. This will consist of a description of all expression patterns
and images of typical and selected patterns, available through the
internet (http://www.tigr.org/2010-splicing/) and linked to the seed stocks

3) Improved genefinding and gene annotation available as improvements to
the existing GlimmerM server (http://www.tigr.org/softlab/glimmerm/).

Effective use of the complete nucleotide sequence of Arabidopsis
requires improved gene annotation. Information about the messenger RNA
products of genes is incomplete. This project will provide to the
scientific community both experimental data on splicing enhancers that
will improve gene annotation, and genetic material for further study.

This award supports the acquisition of eight plant growth chambers and computerized monitoring system that will provide the foundation of a new multi-user plant growth facility in the Department of Cell Biology and Molecular Genetics at the University of Maryland. The facility will be used by investigators whose work with the model plant Arabidopsis thaliana, but address diverse problems. These include the function of vacuolar ion pumps and ethylene receptors, the control and function of genes encoding gluconases used in cell-wall formation and remodeling, and splicing of messenger RNA. Arabidopsis has been increasingly adopted as the experimental material of choice for studies of basic plant biology because of the knowledge of the complete genomic sequence and the availability of large mutant collections, extensive databases and powerful new molecular genetic tools. These chambers will increase the growth area available to these researchers by 3 to 4-fold, and will provide precise control of day-length, light and temperature, all of which can affect the outcome of experiments intended to increase knowledge of plant development, physiology and genetics.

Alternative RNA splicing is used by diverse organisms, including plants, to produce multiple proteins per gene. This project will develop information about the global regulation of alternative RNA splicing, using the model plant Arabidopsis thaliana to elaborate a "splicing code" that describes how DNA sequences specify splicing outcomes in plant species. First, a large number of short sequences will be systematically tested to see how they affect splicing. Then, a microarray platform for studying the alternative splicing of many genes in Arabidopsis will be developed. A relatively small set of developmental and environmental variables will be used to validate the platform. Then, data on alternative splicing from the microarray platform will be used to predict defined discrete regulatory splicing signals that will then be tested using the in planta assay.

Systematic studies of gene expression in Arabidopsis, like those in other organisms, have focused on the overall abundance of RNA without regard to the relative abundance of alternatively spliced isoforms that may encode distinct protein isoforms. The Arabidopsis research community as a whole will benefit from the availability of a microarray platform for studying alternative splicing, and it is likely that the existence of this alternative splicing platform will promote the discovery of regulation at the level of RNA processing that would have otherwise gone without notice. Similarly, continued development of the SEE ESE web server (http://www.tigr.org/software/SeeEse/eseF.html), which identifies sequences involved in the regulation of splicing, will provide the Arabidopsis community with a resource for evaluating the potential impact of specific mutations on splicing. Students working on this project will be exposed to research and will have a valuable hands-on laboratory experience. The University of Maryland is a large state University that serves a diverse population and undergraduates who were exposed to research in the Mount laboratory have gone on to Ph.D. programs at top research universities.

The long-term goal of the proposed research is to uncover fundamental principles governing plant and animal development. The superb molecular genetic and genomic tools available in the flowering plant Arabidopsis thaliana combined with two previously well characterized flower development genes LEUNIG and SEUSS, provide a unprecedented opportunity to investigate transcription repression mechanisms in higher plant development. The proposed experiments will elucidate how the Arabidopsis LEUNIG and SEUSS genes repress their target gene expression, will determine what the identities of their target genes and pathways are, and will identify other factors that aid LEUNIG and SEUSS in selecting their specific targets. A combination of molecular, genetic and biochemical approaches will be used to address these questions. As LEUNIG/SEUSS is the first transcription co-repressor complex discovered in higher plants, the proposed work on this co-repressor complex will help pioneer the analyses of transcriptional networks in higher plants. Due to the conservation of genetic mechanisms between Arabidopsis and other flowering plants, the proposed work will advance research and application in important crop plants. DNA and research materials developed for transcription repression assays will be freely distributed to the research community. The research will involve undergraduate students particularly minority undergraduate students as well as graduate students and postdoctoral fellows.

During the embryonic and postembryonic development of plants and animals, cell proliferation and cell differentiation must be coordinated to achieve final organ size, shape and function. It appears that plants and animals utilize distinct strategies to achieve this coordinated cell growth. Plant cells are particularly flexible in that they can be easily cultured in medium and regenerated into an entirely new plant. It was proposed that certain coordination genes, which function differently in plants, might underlie this distinct property of plant cells. Previous genetic analyses of an Arabidopsis thaliana mutant tso1 showed a failure of cell differentiation in the mutant flowers, suggesting that the TSO1 gene might encode such an important coordinator gene. The sequence similarity between the Arabidopsis TSO1 protein and the Drosophila Mip120 protein suggested that TSO1 might function as a crucial component of a chromatin complex. This oneyear pilot project is aimed at establishing several essential tools and reagents necessary for the characterization of TSO1 and testing the hypothesis that TSO1 is a component of a novel plant chromatin complex. These studies may shed light on the unique properties of plant cells in tissue and whole plant regeneration. Due to the conservation of genetic mechanisms between Arabidopsis and other plants, the work will also advance research and application in important crop plants. The project will involve and train Ph.D. students, undergraduate students, and postdoctoral fellows. Efforts will be placed on recruiting students from under representative groups at the University of Maryland and nearby universities.

Proteins are one of the basic building blocks of living organisms. Each tissue carefully regulates the set of proteins that it produces, both of the types of protein made and the amounts of each. For instance, the proteins that make up the structure and enable the function of the heart are different from those defining the lungs or brain. A deep understanding of the processes that control what proteins are made and how this is timed is of fundamental scientific importance, with implications throughout biology. This project focuses on two critical points in protein regulation: the step in which genes are read off of the genomic DNA to make the intermediate mRNA (called transcription), and the step in which some pieces of the mRNA are removed and the ends reconnected (called splicing), so that translation to protein will result in versions with distinct properties. Complete profiling of mRNA produced by tissues is possible but results in very large, complex data sets. This project will create software tools to facilitate efficient analyses of these data sets, making sense of the two processes described above. The results can be applied to investigate a wide variety of biological questions. Besides the scientific contributions, several educational and outreach activities are aimed at students at the high school and undergraduate levels. In particular, a summer workshop will be organized to provide hands-on bioinformatics experiences to local high school teachers and representative students. Students in the University of Maryland Terrapin Teacher program will be mentored to create lesson plans in Bioinformatics; the lessons will subsequently be delivered at local high schools. In addition, high school students will be invited to participate in summer research experiences under the mentorship of the PIs.

Cellular morphology and function is determined by precise regulation of gene activity. A long-term goal of biological research is to fully decipher the mechanisms of gene regulation. Spatial and temporal regulation of final gene products is primarily executed when genes are transcribed and the resulting RNA is processed. In turn, transcriptional regulation is mediated by regulatory elements, such as enhancers and promoters, which are characterized by diffuse clusters of short degenerate DNA motifs. An important task in the analysis of the transcriptional regulation involves comparison of regulatory regions, both within and across genomes. With regards to post-transcriptional processing events, critical first steps are identification, characterization and quantification of alternatively processed variants of a gene. Increasingly, sequence data are available that hold the answers to these questions, but which must be mined in order to extract their secrets. The scale of the task of incorporating the massive amounts of next generation sequencing data render conventional solutions inefficient and thus presents a major computational bottleneck. The proposed research will develop efficient algorithms and tools for the analysis of gene expression at both transcriptional and post-transcriptional levels by exploiting recently developed ultrafast data structures for DNA words or k-mers. The proposed solutions to two related but different fundamental problems - quantification of regulatory region similarity, and quantification of alternative isoforms of a gene, provide an alternative to traditional approaches by reformulating the problems in terms of k-mer similarity searches, for which extremely efficient solutions have been recently developed and exploited for related problems, including transcript quantification (e.g. Sailfish). The proposed tools will enable investigation of certain fundamental mechanistic and evolutionary questions pertaining to transcriptional regulation and analysis of splice isoform variants at an unprecedented scale.
The research goals will be tied to several STEM educational activities focused on local high school students, both in terms of early research involvement and classroom education. Some of these activities will be organized at the Center for Bioinformatics and Computational Biology (CBCB), thereby encouraging the close interaction between the students and the center faculty.
The link to the results will be provided at PI's lab page at cbcb.umd.edu/~sridhar/software.html