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Regulation Of Translation And Alternative Splicing By The Drosophila Rna Binding Protein Sister Of Sex Lethal
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Book Synopsis Regulation of Translation and Alternative Splicing by the Drosophila RNA-binding Protein Sister-of-Sex-lethal by : Rebecca Moschall
Download or read book Regulation of Translation and Alternative Splicing by the Drosophila RNA-binding Protein Sister-of-Sex-lethal written by Rebecca Moschall and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Functional Analysis of the Drosophila RNA-binding Protein Sister-of-sex-lethal by : Philipp Julian Dexheimer
Download or read book Functional Analysis of the Drosophila RNA-binding Protein Sister-of-sex-lethal written by Philipp Julian Dexheimer and published by . This book was released on 2014 with total page 74 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Regulation of Alternative Splicing in Drosophila Melanogaster by : Jefferson Matthew Taliaferro
Download or read book Regulation of Alternative Splicing in Drosophila Melanogaster written by Jefferson Matthew Taliaferro and published by . This book was released on 2012 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: The patterns and mechanisms by which eukaryotic cells regulate the expression of their genetic information are highly complex and intricate. The transmittance of this information from nuclear repository to cytoplasmic translation contains within it several steps, including the selective removal and concomitant joining of pieces of information in a process called alternative splicing. The projects detailed within this document describe the regulation of alternative splicing through the interaction of specific proteins with specific pre-mRNA transcripts. The Rio lab has studied PSI, a protein involved in the regulation of the P element transposase transcript, for many years. It has since been shown to regulate the splicing of hundreds of other transcripts. The experiments described here look at the organization of PSI and other proteins on the P element transcript by site-specific labeling of the transcript using radioactive 32P. We also investigate two phosphorylation events of PSI, identifying the kinases responsible and demonstrate that these events may change the protein-protein interaction partners of PSI. It has become increasingly apparent that alternative splicing may not only be regulated by protein/RNA interactions, but also by RNA/RNA interactions. To probe this, we designed experiments to test if some well-known small RNA-associated proteins are regulating alternative splicing. Using splice junction microarrays, we determined that Argonaute-2 (Ago-2) regulated the splicing of over 100 splice junctions, and further experiments using ChIP-seq and mRNA-seq of Ago-2 mutants revealed that Ago-2 also has a role in transcriptional repression, possibly through being incorporating in complexes composed of polycomb-group genes. We also used CLIP-seq to determine the RNA binding profile and preferences of Ago-2 in Drosophila tissue culture cells. Finally, we characterized the functions of a Drosophila specific splicing factor called LS2. LS2 is orthologous to the highly conserved splicing factor dU2AF50, but its origin through retroduplication and subsequent divergence to acquire distinct sequence specificity, expression pattern, and function show it to be an interesting case in the evolution of alternative splicing regulation. This may be a mechanism that underlies the existence of some members of the large families of splicing factors, including hnRNP proteins and SR proteins. That is, by duplicating functional copies of genes, cellular systems create new proteins to tinker with and acquire new functions while keeping the former functionality and stability of the parent protein. While these projects are essentially independent of each other, they all fall under the umbrella of protein regulation of RNA metabolism and hopefully contribute to a more complete understanding of the regulation of gene expression.
Book Synopsis RNA Splicing Regulation in Drosophila Melanogaster by : Angela Norie Brooks
Download or read book RNA Splicing Regulation in Drosophila Melanogaster written by Angela Norie Brooks and published by . This book was released on 2011 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt: A majority of metazoan genes contain introns in their primary transcripts (pre-mRNA) that require removal by the spliceosome--a cellular complex composed of protein and RNA. Upon removal of introns from the primary transcript, the remaining exonic portion of the transcript is spliced together. It is essential to remove the correct intronic portion of a primary transcript in order to produce the desired product, typically a protein-coding mRNA. Pre-mRNAs are alternatively spliced when different intron boundaries are used by the spliceosome, thus creating different mRNA products. Alternative splicing allows for an additional step of gene regulation by producing transcript isoforms that can be differentially processed in a particular tissue or developmental time point. Alternative splicing is primarily regulated by RNA binding proteins that bind to pre-mRNA and act to recruit or inhibit the spliceosome at specific splice sites. A central aim of this work is to gain a better understanding of splicing regulation by the identification and characterization of protein regulators of splicing and cis-acting splicing regulatory sequences in the model organism, Drosophila melanogaster. To identify splicing regulatory elements, many previous studies in vertebrate genomes have used computational methods. In collaboration with Anna I. Podgornaia, I applied such an approach to predict splicing regulatory elements in Drosophila melanogaster and compared them with elements found in vertebrates. I identified 330 putative splicing enhancer sequences enriched near weak 5' and 3' splice sites of constitutively spliced introns. I found that a significant proportion (58%) of D. melanogaster enhancers were previously reported as splicing enhancers in vertebrates. To provide additional evidence for the function of the intronic splicing enhancers (ISEs), I identified intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. This analysis uncovered 73 putative ISEs that are also enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter by Julie L. Aspden, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and highlight those regulatory sequences that are present in distant metazoan genomes. To identify and characterize splicing regulators, collaborators and I have combined RNAi and RNA-Seq to identify exons that are regulated by 58 known or putative splicing regulators. To identify and quantify alternative splicing events from RNA-Seq data, I developed the JuncBASE (Junction Based Analysis of Splicing Events) software package. For a pilot study, I identified 404 splicing events significantly affected upon depletion of pasilla. Preliminary analysis showed 879 splicing events affected by at least one of the 57 other proteins. The sequence regions upstream and within Pasilla-repressed exons and downstream of Pasilla-activated exons are enriched for YCAY repeats, which is consistent with the location of these motifs near regulated exons of the mammalian ortholog, Nova. Thus, the RNA regulatory map of Pasilla and Nova is highly conserved between insects and mammals despite the fact that the pre-mRNAs that are regulated by Pasilla and Nova are almost entirely non-overlapping. This observation strongly suggests that the regulatory codes of individual RNA binding proteins are nearly immutable, yet the regulatory modules controlled by these proteins are highly evolvable. I also present RNA regulatory maps for the four hnRNP proteins: hrp36, hrp38, hrp40, and hrp48. Lastly, I examine splicing regulation throughout the life cycle of D. melanogaster. Using transcriptome data from 30 developmental time points produced by collaborators from the modENCODE Consortium, I identified a total of 23,859 alternative splicing events in Drosophila, taking into account all transcript information from D. melanogaster annotations, short sequenced reads (Illumina RNA-Seq), sequenced cDNA, long RNA-Seq reads (454 RNA-Seq) from adult flies, and short read sequences of rRNA-depleted RNA from embryonic time points. I observed that 60.7% of intron-containing genes in D. melanogaster are alternatively spliced. Using only the Illumina RNA-Seq reads throughout development, 21,216 splicing events were expressed and 13,951 events were differentially spliced in at least one time point. I also observed exons with similar patterns of splicing changes throughout development as well as sex-biased alternative splicing. Integrating information from our pasilla study, I also observed correlations of pasilla gene expression with alternative splicing changes of its target exons throughout development.
Book Synopsis Regulation of Alternative Splicing in Drosophila by : Jenny Marie Kreahling
Download or read book Regulation of Alternative Splicing in Drosophila written by Jenny Marie Kreahling and published by . This book was released on 2005 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Regulation of Alternative Splicing in Drosophila by 56 RNA Binding Proteins by :
Download or read book Regulation of Alternative Splicing in Drosophila by 56 RNA Binding Proteins written by and published by . This book was released on 2015 with total page 10 pages. Available in PDF, EPUB and Kindle. Book excerpt: Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA sequence elements and activate or repress adjacent exons. Here, we used RNA interference and RNA-seq to identify splicing events regulated by 56 Drosophila proteins, some previously unknown to regulate splicing. Nearly all proteins affected alternative first exons, suggesting that RBPs play important roles in first exon choice. Half of the splicing events were regulated by multiple proteins, demonstrating extensive combinatorial regulation. We observed that SR and hnRNP proteins tend to act coordinately with each other, not antagonistically. We also identified a cross-regulatory network where splicing regulators affected the splicing of pre-mRNAs encoding other splicing regulators. In conclusion, this large-scale study substantially enhances our understanding of recent models of splicing regulation and provides a resource of thousands of exons that are regulated by 56 diverse RBPs.
Book Synopsis Alternative Splicing in Brain Function by : Kif Liakath-Ali
Download or read book Alternative Splicing in Brain Function written by Kif Liakath-Ali and published by Frontiers Media SA. This book was released on 2023-12-13 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Functional and structural intricacies of biological systems emerge from the complex nature of the genome. A key aspect of genome complexity can be attributed to the process of alternative splicing of precursor mRNA (or pre-mRNA), during which introns are removed and exons are selectively spliced together. This highly regulated process generates different mature mRNA transcripts from a single gene and is widespread throughout the eukaryotic evolution. The majority of the genes expressed in the mammalian central nervous system undergo extensive alternative splicing. Some genes can generate more than a thousand isoforms resulting in diverse proteoforms that can differ in their function, binding preference, catalytic activity, and localization. Perturbation in alternative splicing has been linked to many neurological disorders. Despite its significance, we still lack a comprehensive understanding of its role in neuronal function. Recent studies suggest that alternative splicing is a regulator of tissue identity and development. This is particularly relevant to the brain where developmental regulation and heterogenous cell population play a crucial role in shaping its function. For a long time, technological limitations in detecting and measuring alternatively spliced transcripts hindered the progress in understanding the biology of alternative splicing. Recent advances in long-read and native mRNA sequencing and robust computational tools allow us to capture and quantify in their full-length form. Public transcriptomics datasets can be utilized for the meta-analysis of alternative splicing landscapes of various experimental conditions and disease samples. In addition, protein isoform detection complements mRNA isoform levels. Given its biological significance and recent advances, the objective of this Research Topic is to assemble current knowledge, views, and challenges in the studies of alternative splicing in brain function.
Download or read book Entomology Abstracts written by and published by . This book was released on 1994 with total page 836 pages. Available in PDF, EPUB and Kindle. Book excerpt: Monthly, with annual author and subject indexes. Abstracts from about 2750 primary journals dealing with the subject of insects. Arranged in classified order. Entries include titles given or translated into English, authors, addresses offirst authors, and abstracts; all insects cited in the abstracts are identified by scientific family names. Each monthly issue has Index to classes and orders, Author index.
Download or read book Genetics Abstracts written by and published by . This book was released on 1990 with total page 970 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cumulated Index Medicus written by and published by . This book was released on 1987 with total page 1252 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Cambridge Scientific Biochemistry Abstracts by :
Download or read book Cambridge Scientific Biochemistry Abstracts written by and published by . This book was released on 1991-04 with total page 738 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Bibliography of Agriculture written by and published by . This book was released on 1998 with total page 1960 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RUNX Proteins in Development and Cancer by : Yoram Groner
Download or read book RUNX Proteins in Development and Cancer written by Yoram Groner and published by Springer. This book was released on 2017-03-15 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides the reader with an overview of the diverse functions of the RUNX family of genes. As highlighted in the introduction and several of the 29 chapters, humans and other mammals have three RUNX genes that are known to play specific roles in blood, bone and neuronal development. However, their evolutionary history has recently been traced back to unicellular organisms and their involvement in many well-known signaling pathways (Wnt, TGFb, Notch, Hippo) is indicative of a more general function in cell biology. Their documented roles in cell fate decisions include control of proliferation, differentiation, survival, senescence and autophagy. The pleiotropic effects of RUNX in development are mirrored in cancer, where RUNX genes can function as oncogenes that collaborate strongly with Myc family oncogenes or as tumour suppressor genes. In the latter role, they display hallmarks of both ‘gatekeepers’ that modulate p53 responses and ‘caretakers’ that protect the genome from DNA damage. Several chapters focus on the importance of these genes in leukemia research, where RUNX1 and CBFB are frequently affected by chromosomal translocations that generate fusion oncoproteins, while recent studies suggest wider roles for RUNX modulation in solid cancers. Moreover, RUNX genes are intimately involved in the development and regulation of the immune system, while emerging evidence suggests a role in innate immunity to infectious agents, including HIV. At the biochemical level, the RUNX family can serve as activators or repressors of transcription and as stable mediators of epigenetic memory through mitosis. Not surprisingly, RUNX activity is controlled at multiple levels, this includes miRNAs and a plethora of post-translational modifications. Several chapters highlight the interplay between the three mammalian RUNX genes, where cross-talk and partial functional redundancies are evident. Finally, structural analysis of the RUNX/CBFB interaction has led to the development of small molecule inhibitors that provide exciting new tools to decipher the roles of RUNX in development and as targets for therapy. This volume provides a compendium and reference source that will be of broad interest to cancer researchers, developmental biologists and immunologists.
Book Synopsis Molecular Biology of The Cell by : Bruce Alberts
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Reproductive and Developmental Strategies by : Kazuya Kobayashi
Download or read book Reproductive and Developmental Strategies written by Kazuya Kobayashi and published by Springer. This book was released on 2018-06-01 with total page 783 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides new insights into the universality of biological systems in animal reproduction and development by a comparative study of a variety of mechanisms in animals ranging from basal invertebrates to vertebrates, including mammals. Animals accomplish genetic diversity through meiosis and fertilization, and during embryogenesis animals must produce specialized cell types, including germ cells, in accordance with their individual body plan. This series of phenomena is essential to the continuity of life in the animal kingdom, and animals show various reproductive and developmental strategies. This volume, comprising four parts, reviews animal kingdom diversity, including reproductive strategies and germ cell differentiation mechanisms (Part 1), sex determination and differentiation (Part2), the mechanisms of fertilization (Part 3), and body axis formation (Part 4). Readers will find descriptions of the reproduction or development of 180 species, 13 phyla, 35 classes, 74 orders, 117 families, and 151 genera in this book. Of particular interest is the diversity of molecules and mechanisms used to achieve the same biological purpose in different animals. Undergraduates, graduate students, and professional scientists who want a deeper understanding of animal reproductive and developmental mechanisms will find this book to be of great value.
Book Synopsis Introduction to Epigenetics by : Renato Paro
Download or read book Introduction to Epigenetics written by Renato Paro and published by Springer Nature. This book was released on 2021-03-23 with total page 215 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access textbook leads the reader from basic concepts of chromatin structure and function and RNA mechanisms to the understanding of epigenetics, imprinting, regeneration and reprogramming. The textbook treats epigenetic phenomena in animals, as well as plants. Written by four internationally known experts and senior lecturers in this field, it provides a valuable tool for Master- and PhD- students who need to comprehend the principles of epigenetics, or wish to gain a deeper knowledge in this field. After reading this book, the student will: Have an understanding of the basic toolbox of epigenetic regulation Know how genetic and epigenetic information layers are interconnected Be able to explain complex epigenetic phenomena by understanding the structures and principles of the underlying molecular mechanisms Understand how misregulated epigenetic mechanisms can lead to disease
Book Synopsis Area-Wide Control of Insect Pests by : M.J.B. Vreysen
Download or read book Area-Wide Control of Insect Pests written by M.J.B. Vreysen and published by Springer Science & Business Media. This book was released on 2007-10-30 with total page 758 pages. Available in PDF, EPUB and Kindle. Book excerpt: Insect pests are becoming a problem of ever-more biblical proportions. This new textbook collates a series of selected papers that attempt to address various fundamental components of area-wide insect pest control. Of special interest are the numerous papers on pilot and operational programs that pay special attention to practical problems encountered during program implementation. It’s a compilation of more than 60 papers authored by experts from more than 30 countries.
