| 1. |
- Davids, Wagied, et al.
(författare)
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Loss of gene function : Clues from expressed gene fragments in Rickettsia
- 2002
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Ingår i: Trends in Genetics. - 0168-9525 .- 1362-4555. ; 18:7, s. 331-334
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Tidskriftsartikel (refereegranskat)abstract
- Many obligate intracellular pathogens have small genomes with high fractions of pseudogenes. A recent analysis of gene expression patterns in Rickettsia conorii shows that short open reading frames inside deteriorating genes are occasionally transcribed into RNA. Here, we show that substitution frequencies at nonsynonymous sites are similar for expressed and unexpressed parts of the fragmented genes. We conclude that the observed expression is a temporary stage in the gene degradation process, suggesting that the expressed gene fragments are not functional.
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| 2. |
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| 3. |
- Behm, Mikaela, et al.
(författare)
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RNA Editing : A Contributor to Neuronal Dynamics in the Mammalian Brain
- 2016
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 32:3, s. 165-175
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Forskningsöversikt (refereegranskat)abstract
- Post-transcriptional RNA modification by adenosine to inosine (A-to-I) editing expands the functional output of many important neuronally expressed genes. The mechanism provides flexibility in the proteome by expanding the variety of isoforms, and is a requisite for neuronal function. Indeed, targets for editing include key mediators of synaptic transmission with an overall significant effect on neuronal signaling. In addition, editing influences splice-site choice and miRNA targeting capacity, and thereby regulates neuronal gene expression. Editing efficiency at most of these sites increases during neuronal differentiation and brain maturation in a spatiotemporal manner. This editing-induced dynamics in the transcriptome is essential for normal brain development, and we are only beginning to understand its role in neuronal function. In this review we discuss the impact of RNA editing in the brain, with special emphasis on the physiological consequences for neuronal development and plasticity.
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| 4. |
- Chen, Dan, et al.
(författare)
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Lessons and implications from association studies and post-GWAS analyses of cervical cancer
- 2015
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 31:1, s. 41-54
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Forskningsöversikt (refereegranskat)abstract
- Cervical cancer has a heritable genetic component. A large number of genetic associations with cervical cancer have been reported in hypothesis-driven candidate gene studies, but many of these results are either inconsistent or have failed to be independently replicated. Genome-wide association studies (GWAS) have identified additional susceptibility loci previously not implicated in cervical cancer development, highlighting the power of genome-wide unbiased association analyses. Post-GWAS analyses including pathway-based analysis and functional characterization of associated variants have provided new insights into the pathogenesis of cervical cancer. In this review we summarize findings from candidate gene association studies, GWAS, and post-GWAS analyses of cervical cancer. We also discuss gaps in our understanding, possible clinical implications of the findings, and lessons for studies of other complex diseases.
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| 5. |
- Darby, Alistair C., et al.
(författare)
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Intracellular pathogens go extreme: genome evolution in the Rickettsiales
- 2007
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 23:10, s. 511-520
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Forskningsöversikt (refereegranskat)abstract
- The Rickettsiales, a genetically diverse group of the α-Proteobacteria, include major mammalian pathogens, such as the agents of epidemic typhus, scrub typhus, ehrlichioses and heartwater disease. Sequenced genomes of this bacterial order have provided exciting insights into reductive genome evolution, antigenic variation and host cell manipulation. Recent results suggest that human pathogens emerged relatively late in the evolution of the Rickettsiales. Surprisingly, there is no association between pathogenicity and the acquisition of novel virulence genes. Here, we explore the genomic differences between members of the Rickettsiales and ask what are the changes that enable infectious agents to emerge from seemingly harmless bacteria.
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| 6. |
- Dussex, Nicolas, et al.
(författare)
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The kākāpō (Strigops habroptilus)
- 2022
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Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 38:8
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Ekwall, Karl
(författare)
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Genome-wide analysis of HDAC function
- 2005
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 21:11, s. 608-615
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Tidskriftsartikel (refereegranskat)abstract
- This article focuses on new developments in the genome-wide analysis of histone deacetylase (HDAC) function in yeast. HDACs are highly conserved in many organisms; therefore, their basic functions can be investigated using experimentally tractable model organisms, such as the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. New microarray techniques have enabled the systematic study of HDACs by identifying their direct and indirect gene targets in addition to their physiological functions and enzymatic specificity. These new approaches have already provided new surprising insights into the basic function of HDACs.
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| 8. |
- Ellegren, Hans
(författare)
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The different levels of genetic diversity in sex chromosomes and autosomes
- 2009
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 25:6, s. 278-284
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Forskningsöversikt (refereegranskat)abstract
- Sex chromosomes and autosomes differ in their effective population size, mutation and demography, all of which affect the relative level of genetic diversity within the genome. Moreover, natural selection acts differentially on the two chromosomal categories, for example, because recessive mutations are directly exposed to selection on the single X chromosome of males. Recent genome analyses reveal a heterogeneous picture of the sex-chromosome-to-autosome diversity ratio in different organisms. Reduced X chromosome diversity has been interpreted to reflect demographic features such as bottlenecks and male-biased dispersal, whereas more equal diversity in sex chromosomes and autosomes has been explained by polygynous mating systems.
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| 9. |
- Fortes-Lima, Cesar A., et al.
(författare)
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Closing the Gaps in Genomic Research
- 2021
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Ingår i: Trends in Genetics. - : Cell Press. - 0168-9525 .- 1362-4555. ; 37:2, s. 104-106
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Despite Africa's central role in the origin of our species, our knowledge of the genomic diversity in Africa is remarkably sparse. A recent publication by Choudhury et al. underscores the scientific imperative for a broader characterisation of African genomic diversity to better understand demographic history and improve global human health.
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| 10. |
- Fouché, Simone, et al.
(författare)
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A devil's bargain with transposable elements in plant pathogens
- 2022
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Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 38:3, s. 222-230
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Forskningsöversikt (refereegranskat)abstract
- Transposable elements (TEs) spread in genomes through self-copying mecha-nisms and are a major cause of genome expansions. Plant pathogens have finely tuned the expression of virulence factors to rely on epigenetic control targeted at nearby TEs. Stress experienced during the plant infection process leads to de -repression of TEs and concurrently allows the expression of virulence factors. We argue that the derepression of TEs elements causes an evolutionary conflict by favoring TEs that can be reactivated. Active TEs and recent genome size expansions indicate that plant pathogens could face long-term consequences from the short-term benefit of fine-tuning the infection process. Hence, encoding key virulence factors close to TEs under epigenetic control constitutes a devil's bargain for pathogens.
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