Author: Juan Ramón Tejedor Vaquero
Publisher:
ISBN:
Category :
Languages : en
Pages : 233
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Book Description
Alternative splicing is an essential regulatory layer of gene expression that expands the coding potential of the genome in multicellular organisms. The spliceosome -the sophisticated machinery involved in intron removal- allows versatile regulation of gene expression programs. The splicing process relies on the dynamic interplay between hundreds of components of the spliceosome, and the steps at which the complex process of the splicing reaction can be regulated remain largely unknown. The main objective of this thesis has been to develop high- throughput approaches to systematically identify novel regulators of alternative splicing, as well as to study the mechanisms by which they modulate splice site choice. We have identified a variety of regulators of Fas/CD95 alternative splicing within and outside of the splicing machinery and provide novel insights into connections between iron homeostasis and alternative splicing regulation. Using computational networks, we carried out a systematic functional analysis of the spliceosome components and their regulatory potential. Our results reveal the extensive regulatory plasticity of core spliceosome components throughout its assembly process. They also identified links between alternative splicing and iron homeostasis, providing a mechanism by which iron modulates alternative splicing through regulation of the RNA binding properties of a Zinc knuckle domain in the SR regulatory protein SRSF7. The results of this thesis highlight the value of high throughput technologies and network analyses to study complex molecular mechanisms, and unveils novel functional connections between the splicing machinery and other cellular processes.
Author: Philippe Jeanteur
Publisher: Springer Science & Business Media
ISBN: 3662097281
Category : Science
Languages : en
Pages : 254
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Book Description
The discovery in 1977 that genes are split into exons and introns has done away with the one gene - one protein dogma. Indeed, the removal of introns from the primary RNA transcript is not necessarily straightforward since there may be optional pathways leading to different messenger RNAs and consequently to different proteins. Examples of such an alternative splicing mechanism cover all fields of biology. Moreover, there are plenty of occurrences where deviant splicing can have pathological effects. Despite the high number of specific cases of alternative splicing, it was not until recently that the generality and extent of this phenomenon was fully appreciated. A superficial reading of the preliminary sequence of the human genome published in 2001 led to the surprising, and even deceiving to many scientists, low number of genes (around 32,000) which contrasted with the much higher figure around 150,000 which was previously envisioned. Attempts to make a global assessment of the use of alternative splicing are recent and rely essentially on the comparison of genomic mRNA and EST sequences as reviewed by Thanaraj and Stamm in the first chapter of this volume. Most recent estimates suggest that 40-60% of human genes might be alternatively spliced, as opposed to about 22% for C. elegans.
Author: Manishi Pandey
Publisher:
ISBN:
Category : Electronic dissertations
Languages : en
Pages : 109
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Book Description
Splicing is a crucial step of processing pre-mRNA molecules for precise flow of genetic information from DNA to proteins, where introns are removed and exons of pre-mRNA are joined together to form mature mRNA. The variability in splicing pattern generate a wide array of mature mRNAs from a limited set of genes enabling greater protein diversity with different functions. This process is carried out by a megadalton complex called the spliceosome that consists of more than 200 proteins and snRNA molecules. Previous studies have shown that alterations to a DNA sequence of spliceosome proteins introduce errors in the splicing process that leads to incorrect splicing. Many spliceosome proteins have been implicated in diseases like neurodegenerative disorders, retinitis pigmentosa, cancer and spinal muscular atrophy. Thus, it is important to understand the role of individual spliceosome proteins in the splicing process and their effect on splicing fidelity.The spliceosome undergoes a series of transitions from a pre-catalytic state (complex A) to catalytically active state (complex C) during the splicing process. A subset of spliceosome proteins forms the core component of the spliceosome that are present throughout the splicing process, while other proteins are transient that bind and leave the complex at different points during the splicing process. Our lab previously characterized loss-of-function mutations in four different spliceosome proteins that act as suppressors of splice site mutations in Chlamydomonas reinhardtii. Interestingly, three out of four proteins are part of the small group of proteins that joins the catalytically active spliceosome complex C late in the splicing process. This dissertation focuses on understanding the role of two of these spliceosome proteins, DGCR14 and FRA10AC1. I analyzed the splicing patterns in dgr14 and fra10 mutants in a wild-type background and in double mutants with a mutation that affects nonsense mediated decay (NMD) to capture the breadth of global splicing changes incurred by the spliceosome mutants. The study demonstrates that NMD is an active pathway in C. reinhardtii and degrades non-functional transcripts as shown by analyzing a nonsense mutation in the SMG1 gene, which disrupts the NMD pathway. Next, I show that the two splicing factors affect the 3' and 5' splice site choice and their absence specifically weakens the selectivity of weak 3' splice site. Also, the newly formed alternate 3' splice site demonstrate significant decrease in the splicing fidelity at 3' end. This suggests that the two splicing factors affect the splicing fidelity even though they join the spliceosome complex at late stage, pointing towards a potential proof-reading mechanism in splicing. Further work to investigate the interaction of these factors with other spliceosome proteins and 5' and 3' splice site is warranted.To capture the extent to which alternative splicing is active and functional in C. reinhardtii, I analyzed the existing RNA-seq data from Zones et al., 2015 study, obtained during the diurnal cell cycle of C. reinhardtii. The analysis shows that alternative splicing events are temporally regulated during the cell cycle and identified a subset of events that show periodic changes during the diurnal cell cycle. Many of these events introduce premature termination codon (PTC) in the transcript that potentially makes them NMD targets. This study also demonstrates a potential AS mediated regulation of ODC1 gene which encodes for ornithine decarboxylase enzyme, during light to dark transition during the diurnal cell cycle. Our findings are concordant with previous studies that show light-mediated activation of the ODC1 activity in C. reinhardtii and tobacco plants.Together my research work in this dissertation reveals new insights into the post-transcriptional regulation of genes by alternative splicing in C. reinhardtii and highlights the role of non-core spliceosome proteins in maintaining the splicing fidelity and selection of weak splice sites.
Author: Justin William Mabin
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Intron removal is a key step in the maturation of eukaryotic messenger RNAs (mRNAs), and theprocess of alternative splicing generates multiple transcript isoforms leading to an expanded proteome. Human pre-mRNA splicing is primarily catalyzed by the major spliceosome, consisting of five small nuclear ribonucleoprotein complexes, U1, U2, U4, U5, and U6 snRNPs, each containing a U-rich small nuclear RNA (snRNA) as well as shared and snRNA-specific proteins. The major snRNAs are encoded by multicopy gene families, comprising expressed snRNA sequence variants and putatively untranscribed retrotransposon-like pseudogenes. However, since their discovery decades ago, it remained largely unknown which snRNA genes were expressed and what the functional significance of snRNA sequence variants might be. Gene duplication and variation are powerful mechanisms of evolutionary adaptation; therefore, I hypothesized that the sequence variants that are incorporated into spliceosomes could have distinct functions in pre-mRNA splicing, such as the ability to recognize different premRNA splice sites. To determine which snRNA variants are potentially functional, I systematically profiled human U1, U2, U4 and U5 snRNA variant gene transcripts. I identified 55 variants that are detectably expressed in human cells, 38 of which incorporate into snRNPs and spliceosomes in human HEK293T cells. All U1 snRNA variants are more than 1000-fold less abundant in spliceosomes than the canonical U1, and less than 1% of spliceosomes contain a variant U2 or U4. In contrast, eight U5 snRNA sequence variants occupy spliceosomes at levels of 1 to 46%, indicating the absence of a canonical U5 gene. Furthermore, snRNA variants display distinct expression patterns across five human cell lines and adult and fetal tissues. From our findings I hypothesize that variant spliceosomes containing non-canonical snRNAs may contribute to different tissue- and cell-type specific alternative splicing patterns. To determine if U5 snRNA variants have distinct functions in splicing, I created individual homozygous knock-out 293T cell lines for each of the eight most highly expressed U5 genes and performed RNA-sequencing. I identified alternative splicing changes in each U5 knockout line by mRNA-Seq, which revealed that the loss of individual U5 variants primarily induces intron retention events. The majority of altered splicing events appeared to be unique to each variant. Differential gene expression analysis found that, despite the unique changes in splicing, three lower abundance U5 snRNAs had similar gene expression profiles. RT-PCR analysis validated a few of the alternative splicing events shared by these three U5 snRNAs and revealed an additive effect of their gene deletions. Interestingly, the loss of these three snRNAs appears to cause missplicing and dysregulation of tumor suppressor p53 pathway genes. Splicing mis-regulation plays an important role in disease and cancer, as exemplified by both protein splicing factors and U1 snRNA mutations. For instance, in a specific subtype of medulloblastoma tumors, mutations in U1 were found to drive cryptic splicing in tumor suppressor- and onco-genes. My thesis research highlights the need to interrogate the mechanism of splicing regulation by these newly characterized variant snRNAs. My results demonstrate that the RNA components of the spliceosome are variably expressed in a cell-type dependent manner and can generate functionally distinct variant spliceosomes. This is a previously uncharacterized layer of alternative splicing regulation that has implications in shaping the transcriptome. Furthermore, my studies add to emerging evidence that perturbations to snRNA and snRNA variant genes may elicit specific alternative splicing defects underlying human diseases.
Author: Philippe Jeanteur
Publisher: Springer Science & Business Media
ISBN: 3540344497
Category : Science
Languages : en
Pages : 265
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Book Description
Splicing of primary RNA transcript is a quasi-systematic step of gene expression in higher organisms. This is the first book to highlight the medical implications, i.e. diseases, caused by alternative splicing. Alternative splicing not only vastly increases protein diversity but also offers numerous opportunities for aberrant splicing events with pathological consequences. The book also outlines possible targets for therapy.
Author: B. D. Hames
Publisher: Oxford University Press, USA
ISBN:
Category : Music
Languages : en
Pages : 238
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Book Description
This book gives a co-ordinated review of our present knowledge of eukaryotic RNA synthesis.
Author: Ezequiel Petrillo
Publisher: Frontiers Media SA
ISBN: 2889639746
Category : Nature
Languages : en
Pages : 175
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Book Description
This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Author: Rosanna Asselta
Publisher: Frontiers Media SA
ISBN: 2889662357
Category : Science
Languages : en
Pages : 197
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Book Description
This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Author: Peter Gunning
Publisher: Springer Science & Business Media
ISBN: 0387857664
Category : Medical
Languages : en
Pages : 323
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Book Description
A recent review of one of my grant applications commented on the ‘rediscovery of tropomyosin’. I was tempted to write back in my rebuttal to the reviewer that I didn’t realise it had been lost. Uncharacteristic maturity prevailed and I resisted the temptation, but I was struck by the underlying observation that research on the str- ture and function of tropomyosin has been somewhat invisible, particularly in terms of the cytoskeleton isoforms. So, how can it be that one of the two major components of the actin filament has been so thoroughly overlooked? I suspect that the answer is disappointingly pedestrian. Whereas the biochemistry of the 1980s revealed the potential of tropomyosin isoforms to diversify the function of actin filaments, the subsequent disenchantment with isoform biology in general in the 1990s inhibited growth of this field. With the development of more sophisticated experimental - proaches we are now seeing a growing realisation of the importance of tropomyosin in regulating actin filaments beyond its pivotal role in muscle contraction. The opportunity to edit this book came at a time when we had written several reviews on different aspects of tropomyosin function and I had just finished the background reading for a comprehensive review of tropomyosin biology. I realised that the field was simply beyond the capacity of any one person to do the field j- tice.
Author: Winslow R. Briggs
Publisher: John Wiley & Sons
ISBN: 3527604855
Category : Science
Languages : en
Pages : 496
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Book Description
This first complete resource on photosensory receptors from bacteria, plants and animals compiles the data on all known classes of photoreceptors, creating a must-have reference for students and researchers for many years to come. Among the editors are the current and a former president of the American Society for Photobiology.
