Browsing by Subject "Transcription, Genetic"

Now showing 1 - 10 of 10
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    Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation
    (Oxford University Press, 2014-06-01) Zhang, Xinjun; Lin, Hai; Zhao, Huiying; Hao, Yangyang; Mort, Matthew; Cooper, David N.; Zhou, Yaoqi; Liu, Yunlong; Department of Medical & Molecular Genetics, IU School of Medicine
    Small insertions/deletions (INDELs) of ≤21 bp comprise 18% of all recorded mutations causing human inherited disease and are evident in 24% of documented Mendelian diseases. INDELs affect gene function in multiple ways: for example, by introducing premature stop codons that either lead to the production of truncated proteins or affect transcriptional efficiency. However, the means by which they impact post-transcriptional regulation, including alternative splicing, have not been fully evaluated. In this study, we collate disease-causing INDELs from the Human Gene Mutation Database (HGMD) and neutral INDELs from the 1000 Genomes Project. The potential of these two types of INDELs to affect binding-site affinity of RNA-binding proteins (RBPs) was then evaluated. We identified several sequence features that can distinguish disease-causing INDELs from neutral INDELs. Moreover, we built a machine-learning predictor called PinPor (predicting pathogenic small insertions and deletions affecting post-transcriptional regulation, http://watson.compbio.iupui.edu/pinpor/) to ascertain which newly observed INDELs are likely to be pathogenic. Our results show that disease-causing INDELs are more likely to ablate RBP-binding sites and tend to affect more RBP-binding sites than neutral INDELs. Additionally, disease-causing INDELs give rise to greater deviations in binding affinity than neutral INDELs. We also demonstrated that disease-causing INDELs may be distinguished from neutral INDELs by several sequence features, such as their proximity to splice sites and their potential effects on RNA secondary structure. This predictor showed satisfactory performance in identifying numerous pathogenic INDELs, with a Matthews correlation coefficient (MCC) value of 0.51 and an accuracy of 0.75.
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    In vitro transcription of the Shope papilloma virus
    (1971) Kaplan, Lawrence A.
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    Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA Polymerase II CTD
    (Elsevier, 2014-08-12) Hsu, Peter L.; Yang, Fan; Smith-Kinnaman, Whitney; Yang, Wen; Song, Jae-Eun; Mosley, Amber L.; Varani, Gabriele; Department of Biochemistry and Molecular Biology, IU School of Medicine
    The phosphorylation state of heptapeptide repeats within the C-terminal domain (CTD) of the largest subunit of RNA Polymerase II (PolII) controls the transcription cycle and is maintained by the competing action of kinases and phosphatases. Rtr1 was recently proposed to be the enzyme responsible for the transition of PolII into the elongation and termination phases of transcription by removing the phosphate marker on Serine 5, but this attribution was questioned by the apparent lack of enzymatic activity. Here we demonstrate that Rtr1 is a phosphatase of new structure that is auto-inhibited by its own C-terminus. The enzymatic activity of the protein in vitro is functionally important in vivo as well: a single amino acid mutation that reduces activity leads to the same phenotype in vivo as deletion of the protein-coding gene from yeast. Surprisingly, Rtr1 dephosphorylates not only Serine 5 on the CTD, but also the newly described anti-termination Tyrosine 1 marker, supporting the hypothesis that Rtr1 and its homologs promote the transition from transcription to termination.
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    Single-nucleotide polymorphisms interact to affect ADH7 transcription
    (Wiley Blackwell (Blackwell Publishing), 2014-04) Jairam, Sowmya; Edenberg, Howard J.; Department of Biochemistry and Molecular Biology, IU School of Medicine
    BACKGROUND: The class IV alcohol dehydrogenase (ADH7, μ-ADH, σ-ADH) is important in the metabolism of ethanol and retinol. ADH7 is the only ADH not expressed in liver, instead being expressed mainly in the upper gastrointestinal tract. Genome-wide studies have identified significant associations between single-nucleotide polymorphisms in ADH7 and alcoholism and cancer, but the causative variants have not been identified. METHODS: In vitro studies of gene expression by transient transfection into cell lines that express endogenous ADH7 (CP-A cells) and that do not (HepG2 cells). RESULTS: We have identified transcriptional regulatory elements of ADH7 and observed differences in the effects of variants on gene expression in CP-A cells and HepG2 cells. Two haplotypes of the proximal promoter that differ in a single nucleotide at rs2851028, A7P-G and A7P-A, have different transcriptional activities. There is an interaction between variants farther upstream and these proximal variants: Upstream regulatory sequences generally showed a greater increase or smaller reduction in activity when combined with the A7P-A promoter than with the A7P-G promoter. A sequence located 12.5-kb upstream (7P10) can function as an enhancer. In CP-A cells, both haplotypes of 7P10 increased A7P-A activity by 2.5-fold while having only 1.2-fold effect on A7P-G. In HepG2 cells, the 7P10-TTT haplotype had no effect on the A7P-A promoter but decreased A7P-G promoter activity by 50%, whereas the CTT haplotype increased A7P-A activity by 50%, but had no effect on A7P-G. CONCLUSIONS: These complex interactions indicate that the effects of variants in the ADH7 regulatory elements depend on both sequence and cellular context and should be considered in interpretation of the association of variants with alcoholism and cancer.
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