Author: Young-Joon Kim
Publisher:
ISBN:
Category :
Languages : en
Pages : 412
Book Description
Studies on the RRM-type RNA Binding Protein Gene Family in Drosophila Melanogaster
Author: Young-Joon Kim
Publisher:
ISBN:
Category :
Languages : en
Pages : 412
Book Description
Publisher:
ISBN:
Category :
Languages : en
Pages : 412
Book Description
Genetic and Molecular Studies of the Drosophila Splicing Factor B52
Author: Huijun Zhou Ring
Publisher:
ISBN:
Category :
Languages : en
Pages : 294
Book Description
Publisher:
ISBN:
Category :
Languages : en
Pages : 294
Book Description
Development of Novel Techniques to Study RNA Binding Proteins and Their Domains in Drosophila Melanogaster
Author: Amol Panhale
Publisher:
ISBN:
Category :
Languages : en
Pages : 146
Book Description
Publisher:
ISBN:
Category :
Languages : en
Pages : 146
Book Description
RNA-protein Interactions
Author: Kiyoshi Nagai
Publisher: Oxford University Press, USA
ISBN:
Category : Medical
Languages : en
Pages : 302
Book Description
The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Publisher: Oxford University Press, USA
ISBN:
Category : Medical
Languages : en
Pages : 302
Book Description
The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Structures of Large RNA Molecules and Their Complexes
Author:
Publisher: Academic Press
ISBN: 0128019360
Category : Science
Languages : en
Pages : 675
Book Description
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs. - Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes
Publisher: Academic Press
ISBN: 0128019360
Category : Science
Languages : en
Pages : 675
Book Description
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs. - Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes
The Elav Gene of Drosophila Melanogaster Encodes a Neuron-specific RNA Binding Protein which is Required for the Development and Maintenance of the Nervous System
Author: Steven Neal Robinow
Publisher:
ISBN:
Category : Drosophila melanogaster
Languages : en
Pages : 250
Book Description
Publisher:
ISBN:
Category : Drosophila melanogaster
Languages : en
Pages : 250
Book Description
A Molecular and Genetic Analysis of Two Related Chromosome Binding Proteins in Drosophila Melanogaster
Author: Edward Janin Sharp
Publisher:
ISBN:
Category :
Languages : en
Pages : 330
Book Description
Publisher:
ISBN:
Category :
Languages : en
Pages : 330
Book Description
Cumulated Index Medicus
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1844
Book Description
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1844
Book Description
RNA Splicing Regulation in Drosophila Melanogaster
Author: Angela Norie Brooks
Publisher:
ISBN:
Category :
Languages : en
Pages : 236
Book Description
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.
Publisher:
ISBN:
Category :
Languages : en
Pages : 236
Book Description
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.
RNA Polymerase III Transcription
Author: Robert J. White
Publisher: Springer Science & Business Media
ISBN: 3662035189
Category : Science
Languages : en
Pages : 274
Book Description
This monograph reviews and summarizes the substantial body of work that has been published on the transcription by polymerase III over the past 5 years. Progress in this field has been very rapid since 1993, and this new edition incorporates all the recent developments and offers the reader a highly detailed analysis of the current state of research on this largest and most complex of the eukaryotic RNA polymerases.
Publisher: Springer Science & Business Media
ISBN: 3662035189
Category : Science
Languages : en
Pages : 274
Book Description
This monograph reviews and summarizes the substantial body of work that has been published on the transcription by polymerase III over the past 5 years. Progress in this field has been very rapid since 1993, and this new edition incorporates all the recent developments and offers the reader a highly detailed analysis of the current state of research on this largest and most complex of the eukaryotic RNA polymerases.