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Sökning: WFRF:(Feuk Lars) > Annan publikation

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  • Wetterbom, Anna, et al. (författare)
  • Deep sequencing of the chimpanzee transcriptome identifies numerous novel transcribed regions in frontal cortex and liver
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • We have performed the first global profiling of the chimpanzee transcriptome by using deep sequencing of cDNA from brain and liver. This enabled us to quantify expression of RefSeq transcripts, identify novel transcribed regions with no previous annotations in databases and additionally search for transcribed regions with no support in the human genome. Using stringent criteria for transcription, we identified 9,061 expressed RefSeq transcripts and 5,532 novel transcribed regions., of which the vast majority were found intronically in RefSeq transcripts and ~ 15 % mapped intergenically. In addition,  a little less than 150 novel transcribed regions in the chimpanzee appeared to be absent from the human reference sequence. Novel transcribed regions may represent new coding regions, untranslated regions unspliced mRNAs or diferent types of non-coding transcripts. The transcriptional profile of the brain stands out in several ways: a higher number of RefSeq transcripts were expressed in brain than in liver and novel transcribed regions were also more abundant in brain. Furthermore, we identified an interesting subset of RefSeq genes with a high density of novel transcribed regions scattered across the introns. These genes clustered in central pathways of the nervous system, with an overrepresentation of genes acting in the synapse and many of which have been associated to cognitive disorders in the human. Our results support the prevailing view of wide-spread transcription in mammalian genomes and further highlight the vast, mostly uncharacterized, transcript variability in the primate brain.  
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  • Wetterbom, Anna, 1977-, et al. (författare)
  • Global comparison of the human and chimpanzee transcriptomes using Affymetrix exon arrays
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • We have used high-density exon arrays to study the human and chimpanzee transcriptome in cerebellum, heart and liver excluding probesets with mismatches to the chimpanzee. A total of 6281 RefSeq genes were expressed in our samples, the majority being expressed in two or more tissues, while ~ 6 % lacked expression in one of the species. A total of 923 RefSeq genes showed differences in expression between human and chimpanzes. More genes were differentially expressed in cerebellum (8.4 %) than in liver (6.9 %) and heart (4.5 %). Genes showing differential expression between species to a large extent also showed strong tissue-specific expression within species. Of the differentially expressed genes, more were upregulated in human versus chimpanzee, than the other way around. Liver had the highest proportion of genes with spliced genes (50 %), followed by cerebellum (40 %) and heart (30 %). Differentially expressed genes were often detected also as spliced (66-78 %). As one type of splice variation, we identified 26 genes with cassette exons, i.e. the exon is only included in one species. Cassette exon usage was tissue specific to a large extent and for the majority of cassette exons we observed expression in both human and chimpanzee in the other tissues. Taken together, our results indicate that splicing differences represents an extensive and important source of variation between species.
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  • Zaghlool, Ammar, et al. (författare)
  • Mutation in the chromatin-remodeling factor BAZ1A is associated with intellectual disability
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Exome sequencing has led to the identification of mutations in several genes involved in chromatin remodeling in syndromic forms of intellectual disability. Here, we used exome sequencing to identify a single non-synonymous de novo mutation in BAZ1A, encoding the ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), in a patient with unexplained intellectual disability. ACF1 has been previously reported to bind to the promoter of vitamin D receptor (VDR) regulated genes and suppress their expression in the absence of vitamin D. We found that the mutation in BAZ1A affects the expression of many genes, mainly involved in extra cellular matrix organization, synaptic function and vitamin D3 metabolism. The differential expression of CYP24A, SYNGAP1 and COL1A2 correlates with the clinical diagnosis of the patient. We therefore propose that BAZ1A represents yet another chromatin remodeling gene involved in causing an intellectual disability syndrome.
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  • Resultat 1-9 av 9

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