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  1. Article ; Online: XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells.

    Dror, Iris / Chitiashvili, Tsotne / Tan, Shawn Y X / Cano, Clara T / Sahakyan, Anna / Markaki, Yolanda / Chronis, Constantinos / Collier, Amanda J / Deng, Weixian / Liang, Guohao / Sun, Yu / Afasizheva, Anna / Miller, Jarrett / Xiao, Wen / Black, Douglas L / Ding, Fangyuan / Plath, Kathrin

    Cell

    2024  Volume 187, Issue 1, Page(s) 110–129.e31

    Abstract: X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent ... ...

    Abstract X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
    MeSH term(s) Animals ; Female ; Humans ; Male ; Mice ; Gene Silencing ; Genes, X-Linked ; RNA, Long Noncoding/genetics ; X Chromosome/genetics ; Pluripotent Stem Cells/metabolism
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2024-01-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2023.11.033
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1167: Show issues Location:
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  2. Article ; Online: Metagenome Sequences from Tidal Marsh and Marine Sediment from the Great Bay Estuary of New Hampshire.

    Moore, Brian M / Ní Chadhain, Sinéad M / Miller, Jarrett L / Jones, Stephen H / Launen, Loren A

    Microbiology resource announcements

    2020  Volume 9, Issue 10

    Abstract: Tidal marsh and estuarine marine microbial sediment metagenomes from the Great Bay Estuary of New Hampshire were sequenced and found to be dominated ... ...

    Abstract Tidal marsh and estuarine marine microbial sediment metagenomes from the Great Bay Estuary of New Hampshire were sequenced and found to be dominated by
    Language English
    Publishing date 2020-03-05
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00038-20
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  3. Article ; Online: Metabolic engineering of Yarrowia lipolytica for itaconic acid production.

    Blazeck, John / Hill, Andrew / Jamoussi, Mariam / Pan, Anny / Miller, Jarrett / Alper, Hal S

    Metabolic engineering

    2015  Volume 32, Page(s) 66–73

    Abstract: Itaconic acid is a naturally produced organic acid with diverse applications as a replacement for petroleum derived products. However, its industrial viability as a bio-replacement has been restricted due to limitations with native producers. In this ... ...

    Abstract Itaconic acid is a naturally produced organic acid with diverse applications as a replacement for petroleum derived products. However, its industrial viability as a bio-replacement has been restricted due to limitations with native producers. In this light, Yarrowia lipolytica is an excellent potential candidate for itaconic acid production due to its innate capacity to accumulate citric acid cycle intermediates and tolerance to lower pH. Here, we demonstrate the capacity to produce itaconic acid in Y. lipolytica through heterologous expression of the itaconic acid synthesis enzyme, resulting in an initial titer of 33 mg/L. Further optimizations of this strain via metabolic pathway engineering, enzyme localization, and media optimization strategies enabled 4.6g/L of itaconic acid to be produced in bioreactors, representing a 140-fold improvement over initial titer. Moreover, these fermentation conditions did not require additional nutrient supplementation and utilized a low pH condition that enabled the acid form of itaconic acid to be produced. Overall yields (0.058 g/g yield from glucose) and maximum productivity of 0.045 g/L/h still provide areas for future strain improvement. Nevertheless, this work demonstrates that Y. lipolytica has the potential to serve as an industrially relevant platform for itaconic acid production.
    MeSH term(s) Bioreactors ; Citric Acid Cycle ; Cloning, Molecular ; Culture Media ; Fermentation ; Glucose/metabolism ; Hydrogen-Ion Concentration ; Metabolic Engineering/methods ; Plasmids ; Succinates/metabolism ; Yarrowia/genetics ; Yarrowia/metabolism
    Chemical Substances Culture Media ; Succinates ; Glucose (IY9XDZ35W2) ; itaconic acid (Q4516562YH)
    Language English
    Publishing date 2015-09-16
    Publishing country Belgium
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2015.09.005
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    Zs.A 6288: Show issues Location:
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  4. Article: Metabolic engineering of Saccharomyces cerevisiae for itaconic acid production

    Blazeck, John / Miller, Jarrett / Pan, Anny / Gengler, Jon / Holden, Clinton / Jamoussi, Mariam / Alper, Hal S

    Applied microbiology and biotechnology. 2014 Oct., v. 98, no. 19

    2014  

    Abstract: Renewable alternatives for petroleum-derived chemicals are achievable through biosynthetic production. Here, we utilize Saccharomyces cerevisiae to enable the synthesis of itaconic acid, a molecule with diverse applications as a petrochemical replacement. ...

    Abstract Renewable alternatives for petroleum-derived chemicals are achievable through biosynthetic production. Here, we utilize Saccharomyces cerevisiae to enable the synthesis of itaconic acid, a molecule with diverse applications as a petrochemical replacement. We first optimize pathway expression within S. cerevisiae through the use of a hybrid promoter. Next, we utilize sequential, in silico computational genome-scanning to identify beneficial genetic perturbations that are metabolically distant from the itaconic acid synthesis pathway. In this manner, we successfully identify three non-obvious genetic targets (∆ade3 ∆bna2 ∆tes1) that successively improve itaconic acid titer. We establish that focused manipulations of upstream pathway enzymes (localized refactoring) and enzyme re-localization to both mitochondria and cytosol fail to improve itaconic acid titers. Finally, we establish a higher cell density fermentation that ultimately achieves itaconic acid titer of 168� mg/L, a sevenfold improvement over initial conditions. This work represents an attempt to increase itaconic acid production in yeast and demonstrates the successful utilization of computationally guided genetic manipulation to increase metabolic capacity.
    Keywords Saccharomyces cerevisiae ; cytosol ; enzymes ; fermentation ; genetic engineering ; metabolic engineering ; mitochondria ; yeasts
    Language English
    Dates of publication 2014-10
    Size p. 8155-8164.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-014-5895-0
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  5. Article ; Online: Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production.

    Blazeck, John / Hill, Andrew / Liu, Leqian / Knight, Rebecca / Miller, Jarrett / Pan, Anny / Otoupal, Peter / Alper, Hal S

    Nature communications

    2014  Volume 5, Page(s) 3131

    Abstract: Economic feasibility of biosynthetic fuel and chemical production hinges upon harnessing metabolism to achieve high titre and yield. Here we report a thorough genotypic and phenotypic optimization of an oleaginous organism to create a strain with ... ...

    Abstract Economic feasibility of biosynthetic fuel and chemical production hinges upon harnessing metabolism to achieve high titre and yield. Here we report a thorough genotypic and phenotypic optimization of an oleaginous organism to create a strain with significant lipogenesis capability. Specifically, we rewire Yarrowia lipolytica's native metabolism for superior de novo lipogenesis by coupling combinatorial multiplexing of lipogenesis targets with phenotypic induction. We further complete direct conversion of lipid content into biodiesel. Tri-level metabolic control results in saturated cells containing upwards of 90% lipid content and titres exceeding 25 g l(-1) lipids, which represents a 60-fold improvement over parental strain and conditions. Through this rewiring effort, we advance fundamental understanding of lipogenesis, demonstrate non-canonical environmental and intracellular stimuli and uncouple lipogenesis from nitrogen starvation. The high titres and carbon-source independent nature of this lipogenesis in Y. lipolytica highlight the potential of this organism as a platform for efficient oleochemical production.
    MeSH term(s) Biofuels/microbiology ; Carbon/pharmacology ; Fatty Acids/metabolism ; Fermentation/drug effects ; Fluorescence ; Genes, Fungal ; Genetic Engineering ; Genomics ; Genotype ; Isoleucine/pharmacology ; Leucine/pharmacology ; Lipids/biosynthesis ; Lipogenesis/drug effects ; Phenotype ; Glycine max/chemistry ; Time Factors ; Yarrowia/drug effects ; Yarrowia/metabolism
    Chemical Substances Biofuels ; Fatty Acids ; Lipids ; Isoleucine (04Y7590D77) ; Carbon (7440-44-0) ; Leucine (GMW67QNF9C)
    Language English
    Publishing date 2014-01-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/ncomms4131
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  6. Article ; Online: Metabolic engineering of Saccharomyces cerevisiae for itaconic acid production.

    Blazeck, John / Miller, Jarrett / Pan, Anny / Gengler, Jon / Holden, Clinton / Jamoussi, Mariam / Alper, Hal S

    Applied microbiology and biotechnology

    2014  Volume 98, Issue 19, Page(s) 8155–8164

    Abstract: Renewable alternatives for petroleum-derived chemicals are achievable through biosynthetic production. Here, we utilize Saccharomyces cerevisiae to enable the synthesis of itaconic acid, a molecule with diverse applications as a petrochemical replacement. ...

    Abstract Renewable alternatives for petroleum-derived chemicals are achievable through biosynthetic production. Here, we utilize Saccharomyces cerevisiae to enable the synthesis of itaconic acid, a molecule with diverse applications as a petrochemical replacement. We first optimize pathway expression within S. cerevisiae through the use of a hybrid promoter. Next, we utilize sequential, in silico computational genome-scanning to identify beneficial genetic perturbations that are metabolically distant from the itaconic acid synthesis pathway. In this manner, we successfully identify three non-obvious genetic targets (∆ade3 ∆bna2 ∆tes1) that successively improve itaconic acid titer. We establish that focused manipulations of upstream pathway enzymes (localized refactoring) and enzyme re-localization to both mitochondria and cytosol fail to improve itaconic acid titers. Finally, we establish a higher cell density fermentation that ultimately achieves itaconic acid titer of 168 mg/L, a sevenfold improvement over initial conditions. This work represents an attempt to increase itaconic acid production in yeast and demonstrates the successful utilization of computationally guided genetic manipulation to increase metabolic capacity.
    MeSH term(s) Biosynthetic Pathways ; Fermentation ; Metabolic Engineering ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Succinates/metabolism
    Chemical Substances Saccharomyces cerevisiae Proteins ; Succinates ; itaconic acid (Q4516562YH)
    Language English
    Publishing date 2014-10
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-014-5895-0
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2229: Show issues Location:
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