Browsing by Subject "Molecular Biology"

Now showing 1 - 9 of 9
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    CRISPR-Cas9-mediated insertion of a short artificial intron for the generation of conditional alleles in mice
    (Elsevier, 2023) Cassidy, Annelise; Pelletier, Stephane; Medical and Molecular Genetics, School of Medicine
    In this protocol, we describe the generation of conditional alleles in mice using the DECAI (DEgradation based on Cre-regulated Artificial Intron) approach. We detail steps for the CRISPR-mediated insertion of the short DECAI cassette within exon 3 of Scyl1 and the functional validation of alleles at genomic, transcriptomic, and protein levels. This strategy simplifies the process of generating mice with conditional alleles.
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    Identification of putative targets of Nkx2-5 in Xenopus laevis using cross-species annotation and microarray gene expression analysis
    (2011-10) Breese, Marcus R.; Edenberg, Howard J.; Hurley, Thomas D., 1961-; Rhodes, Simon J.; Skalnik, David Gordon
    The heart is the first organ to form during development in vertebrates and Nkx2-5 is the first marker of cardiac specification. In Xenopus laevis, Nkx2-5 is essential for heart formation, but early targets of this homeodomain transcription factor have not been fully characterized. In order to discover potential early targets of Nkx2-5, synthetic Nkx2-5 mRNA was injected into eight-cell Xenopus laevis embryos and changes in gene expression measured using microarray analysis. While Xenopus laevis is a commonly used model organism for developmental studies, its genome remains poorly annotated. To compensate for this, a cross-species annotation database called CrossGene was constructed. CrossGene was created by exhaustively comparing UniGene transcripts from Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus, Xenopus laevis, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans using the BLAST family of algorithms. Networks were then assembled by recursively combining reciprocal best matches into groups of orthologous genes. Gene ontology annotation from all organisms could then be applied to all members of the reciprocal group. In this way, the CrossGene database was used to augment the existing genomic annotation of Xenopus laevis. Combining cross-species annotation with differential gene expression analysis of Nkx2-5 overexpression led to the discovery of 99 potential targets of Nkx2-5.
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    Identification of the Pba1 and Pba2 Binding Sites on 20S Core Particle Intermediates
    (2013-07-12) Hammack, Lindsay Jo; Kusmierczyk, Andrew; Malkova, Anna; Randall, Stephen Karl, 1953-; Atkinson, Simon
    The proteasome is responsible for breaking down the majority of the proteins in the cell. However, a complete understanding of how this large multi-subunit protease is assembled is currently lacking. Proper and timely assembly of the proteasome is critical for the functioning of the ubiquitin-proteasome pathway, defects in which have been associated with several different cancers. A recently discovered heterodimeric proteasome assembly chaperone, Pba1p-Pba2p, has been suggested to prevent the assembly process from straying off path. Pba1p-Pba2p associates with proteasomal assembly intermediates via C-terminal HbYX motifs. The HbYX motif is a tri-peptide sequence containing a hydrophobic residue (Hb) followed by a tyrosine (Y), then any amino acid (X). This motif was originally identified in proteasomal activators, and shown to mediate the association of activators with the proteasome by inserting into intersubunit pockets on either end of the proteasome. There are seven unique intersubunit binding pockets, located between neighboring α subunits on the proteasome, to which a HbYX-containing protein can bind; which of these pockets Pba1p-Pba2p binds to remains elusive. I attempted to identify where Pba1p and Pba2p bind via a crosslinking approach. Specific residues were mutagenized to cysteines on Pba1p, Pba2p, and the individual α subunits in order to generate crosslinkable species. By exposing yeast cells expressing these crosslinkable proteins to mild oxidizing conditions, I attempted to trap the Pba1p and Pba2p α intersubunit pocket interactions. In order to optimize crosslinking conditions, the assay was modified several ways. Additionally, measures were taken to increase detection of the crosslinked species via immunoblotting. Despite the efforts to improve the crosslinking and detection, I was unable to successfully detect a crosslinked species. However, crosslinking is a reasonable method to identify the Pba1p and Pba2p proteasomal binding sites, having been successfully used to identify binding sites for other HbYX-motif-containing proteins; further assay optimization should yield Pba1p and Pba2p proteasomal crosslinks.
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    Investigating the Biosynthetic Pathways to Polyacetylenic Natural Products in Fistulina hepatica and Echinacea purpurea
    (2013-08-20) Ransdell, Anthony S.; Minto, Robert; Long, Eric C. (Eric Charles); Li, Lei
    Polyacetylenic natural products, compounds containing multiple carbon-carbon triple bonds, have been found in a large collection of organisms. Radiochemical tracer studies have indicated that these bioactive metabolites are synthesized from fatty acid precursors through a series of uncharacterized desaturation and acetylenation steps. To date, there are three main pathways believed to be involved in acetylenic natural product biosynthesis. However, it is apparent that the crepenynic acid pathway is the origin of a vast majority of the known plant and fungal acetylenic products. This investigation provides concrete evidence that the polyacetylenic natural products found in the fungus Fistulina hepatica and the medicinal plant species Echinacea purpurea are biosynthesized from crepenynic acid. Through heterologous expression in Yarrowia lipolytica, two acetylenases capable of producing crepenynic acid were identified from E. purpurea. Furthermore, heterologous expression of two diverged desaturases isolated from F. hepatica, uncovered a ∆12-acetylenase and the first multifunctional enzyme capable of ∆14-/∆16- desaturation and ∆14-acetylenation.
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    Lrp4 Mediates Bone Homeostasis and Mechanotransduction through Interaction with Sclerostin In Vivo
    (Elsevier, 2019-10-25) Bullock, Whitney A.; Hoggatt, April M.; Horan, Daniel J.; Elmendorf, Andrew J.; Sato, Amy Y.; Bellido, Teresita; Loots, Gabriela G.; Pavalko, Fredrick M.; Robling, Alexander G.; Anatomy and Cell Biology, School of Medicine
    Wnt signaling plays a key role in regulating bone remodeling. In vitro studies suggest that sclerostin's inhibitory action on Lrp5 is facilitated by the membrane-associated receptor Lrp4. We generated an Lrp4 R1170W knockin mouse model (Lrp4KI), based on a published mutation in patients with high bone mass (HBM). Lrp4KI mice have an HBM phenotype (assessed radiographically), including increased bone strength and formation. Overexpression of a Sost transgene had osteopenic effects in Lrp4-WT but not Lrp4KI mice. Conversely, sclerostin inhibition had blunted osteoanabolic effects in Lrp4KI mice. In a disuse-induced bone wasting model, Lrp4KI mice exhibit significantly less bone loss than wild-type (WT) mice. In summary, mice harboring the Lrp4-R1170W missense mutation recapitulate the human HBM phenotype, are less sensitive to altered sclerostin levels, and are protected from disuse-induced bone loss. Lrp4 is an attractive target for pharmacological targeting aimed at increasing bone mass and preventing bone loss due to disuse.
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    PRMT5 Cooperates with pICln to Function as a Master Epigenetic Activator of DNA Double-Strand Break Repair Genes
    (Elsevier, 2020-01-24) Owens, Jake L.; Beketova, Elena; Liu, Sheng; Tinsley, Samantha L.; Asberry, Andrew M.; Deng, Xuehong; Huang, Jiaoti; Li, Chenglong; Wan, Jun; Hu, Chang-Deng; Medical and Molecular Genetics, School of Medicine
    DNA double-strand break (DSB) repair is critical for cell survival and genome integrity. Upon recognition of DSBs, repair proteins are transiently upregulated to facilitate repair through homologous recombination (HR) or non-homologous end joining (NHEJ). We present evidence that PRMT5 cooperates with pICln to function as a master epigenetic activator of DNA damage response (DDR) genes involved in HR, NHEJ, and G2 arrest (including RAD51, BRCA1, and BRCA2) to upregulate gene expression upon DNA damage. Contrary to the predominant role of PRMT5 as an epigenetic repressor, our results demonstrate that PRMT5 and pICln can activate gene expression, potentially independent of PRMT5's obligate cofactor MEP50. Targeting PRMT5 or pICln hinders repair of DSBs in multiple cancer cell lines, and both PRMT5 and pICln expression positively correlates with DDR genes across 32 clinical cancer datasets. Thus, targeting PRMT5 or pICln may be explored in combination with radiation or chemotherapy for cancer treatment.
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    A Read/Write Mechanism Connects p300 Bromodomain Function to H2A.Z Acetylation
    (Elsevier, 2019-11-22) Colino-Sanguino, Yolanda; Cornett, Evan M.; Moulder, David; Smith, Grady C.; Hrit, Joel; Cordeiro-Spinetti, Eric; Vaughan, Robert M.; Krajewski, Krzysztof; Rothbart, Scott B.; Clark, Susan J.; Valdés-Mora, Fátima; Biochemistry and Molecular Biology, School of Medicine
    Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active regulatory regions associated with gene expression. Although the Tip60 complex is proposed to acetylate H2A.Z, functional studies suggest additional enzymes are involved. Here, we show that p300 acetylates H2A.Z at multiple lysines. In contrast, we found that although Tip60 does not efficiently acetylate H2A.Z in vitro, genetic inhibition of Tip60 reduces H2A.Zac in cells. Importantly, we found that interaction between the p300-bromodomain and H4 acetylation (H4ac) enhances p300-driven H2A.Zac. Indeed, H2A.Zac and H4ac show high genomic overlap, especially at active promoters. We also reveal unique chromatin features and transcriptional states at enhancers correlating with co-occurrence or exclusivity of H4ac and H2A.Zac. We propose that differential H4 and H2A.Z acetylation signatures can also define the enhancer state. In conclusion, we show both Tip60 and p300 contribute to H2A.Zac and reveal molecular mechanisms of writer/reader crosstalk between H2A.Z and H4 acetylation through p300.