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  1. Article ; Online: Correction: Genome-Wide Mapping of 5' Isoforms with 5'-Seq.

    Gvozdenov, Zlata

    Current protocols

    2023  Volume 3, Issue 5, Page(s) e797

    Language English
    Publishing date 2023-05-15
    Publishing country United States
    Document type Published Erratum
    ISSN 2691-1299
    ISSN (online) 2691-1299
    DOI 10.1002/cpz1.797
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genome-Wide Mapping of 5' Isoforms with 5'-Seq.

    Gvozdenov, Zlata

    Current protocols

    2023  Volume 3, Issue 4, Page(s) e750

    Abstract: The transcriptome is far more complex than previously assumed. Transcripts from the same gene can differ in terms of transcription start site, transcription end site, or pattern of splicing, and growing evidence supports the functional importance of ... ...

    Abstract The transcriptome is far more complex than previously assumed. Transcripts from the same gene can differ in terms of transcription start site, transcription end site, or pattern of splicing, and growing evidence supports the functional importance of these distinct transcript isoforms. Easily identifying these isoforms experimentally via library construction and high-throughput sequencing is crucial. Current library construction methods for identifying transcription start sites (5' transcript isoforms) involve large number of steps and (expensive) reagents, utilization of cDNA intermediates for adapter ligation, and are less suitable for studying low-abundance isoforms. Here, I describe a quick protocol for the generation of sequencing libraries to define capped 5' isoforms (5'-Seq) of various abundances in yeast and suggest a 5' isoform data analysis pipeline. The protocol relies on the utilization of a dephosphorylation-decapping method (oligo-capping) to generate a sequencing library from mRNA fragments and is a simplification of previously published 5' isoform protocols in terms of the handling steps, time, and cost. This method is exemplified using Saccharomyces cerevisiae mRNA, but it can be applied to various cellular conditions to study the effects of 5' transcript isoforms on transcriptional and/or translational regulation. © 2023 Wiley Periodicals LLC. Basic Protocol: Construction of a DNA sequencing library from capped 5' isoforms Support Protocol: Sequencing data analysis.
    MeSH term(s) Sequence Analysis, RNA/methods ; RNA, Messenger/genetics ; Protein Isoforms/genetics ; Transcriptome ; Software
    Chemical Substances RNA, Messenger ; Protein Isoforms
    Language English
    Publishing date 2023-04-21
    Publishing country United States
    Document type Journal Article
    ISSN 2691-1299
    ISSN (online) 2691-1299
    DOI 10.1002/cpz1.750
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.

    Gvozdenov, Zlata / Barcutean, Zeno / Struhl, Kevin

    Molecular cell

    2023  Volume 83, Issue 11, Page(s) 1786–1797.e5

    Abstract: We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much ... ...

    Abstract We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of random-sequence RNAs are comparable to yeast mRNAs, although transcription and decay rates are higher. Transcriptional initiation from random-sequence DNA occurs at numerous sites, indicating very low intrinsic specificity of the RNA Pol II machinery. In contrast, poly(A) profiles of random-sequence RNAs are roughly comparable to those of yeast mRNAs, suggesting limited evolutionary restraints on poly(A) site choice. Random-sequence RNAs show higher cell-to-cell variability than yeast mRNAs, suggesting that functional elements limit variability. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.
    MeSH term(s) Nucleosomes/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Chromatin/genetics ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Transcription, Genetic
    Chemical Substances Nucleosomes ; Chromatin ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2023-05-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2023.04.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5055: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells

    Gvozdenov, Zlata / Barcutean, Zeno / Struhl, Kevin

    Molecular Cell. 20232023 June 02, May 02, v. 83, no. 11 p.1786-1797.e5

    2023  

    Abstract: We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much ... ...

    Abstract We measure transcriptional noise in yeast by analyzing chromatin structure and transcription of an 18-kb region of DNA whose sequence was randomly generated. Nucleosomes fully occupy random-sequence DNA, but nucleosome-depleted regions (NDRs) are much less frequent, and there are fewer well-positioned nucleosomes and shorter nucleosome arrays. Steady-state levels of random-sequence RNAs are comparable to yeast mRNAs, although transcription and decay rates are higher. Transcriptional initiation from random-sequence DNA occurs at numerous sites, indicating very low intrinsic specificity of the RNA Pol II machinery. In contrast, poly(A) profiles of random-sequence RNAs are roughly comparable to those of yeast mRNAs, suggesting limited evolutionary restraints on poly(A) site choice. Random-sequence RNAs show higher cell-to-cell variability than yeast mRNAs, suggesting that functional elements limit variability. These observations indicate that transcriptional noise occurs at high levels in yeast, and they provide insight into how chromatin and transcription patterns arise from the evolved yeast genome.
    Keywords DNA ; RNA ; genome ; nucleosomes ; transcription (genetics) ; yeasts ; transcription ; chromatin ; polyadenylation ; biological function ; biological noise
    Language English
    Dates of publication 2023-0502
    Size p. 1786-1797.e5.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2023.04.010
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2005/501: Show issues

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  5. Article ; Online: The Nuclear and DNA-Associated Molecular Chaperone Network.

    Gvozdenov, Zlata / Kolhe, Janhavi / Freeman, Brian C

    Cold Spring Harbor perspectives in biology

    2019  Volume 11, Issue 10

    Abstract: Maintenance of a healthy and functional proteome in all cellular compartments is critical to cell and organismal homeostasis. Yet, our understanding of the proteostasis process within the nucleus is limited. Here, we discuss the identified roles of the ... ...

    Abstract Maintenance of a healthy and functional proteome in all cellular compartments is critical to cell and organismal homeostasis. Yet, our understanding of the proteostasis process within the nucleus is limited. Here, we discuss the identified roles of the major molecular chaperones Hsp90, Hsp70, and Hsp60 with client proteins working in diverse DNA-associated pathways. The unique challenges facing proteins in the nucleus are considered as well as the conserved features of the molecular chaperone system in facilitating DNA-linked processes. As nuclear protein inclusions are a common feature of protein-aggregation diseases (e.g., neurodegeneration), a better understanding of nuclear proteostasis is warranted.
    MeSH term(s) Cell Nucleus/metabolism ; DNA/metabolism ; Humans ; Molecular Chaperones/metabolism ; Nuclear Proteins/metabolism
    Chemical Substances Molecular Chaperones ; Nuclear Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2019-10-01
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1943-0264
    ISSN (online) 1943-0264
    DOI 10.1101/cshperspect.a034009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility.

    Gvozdenov, Zlata / Bendix, Lindsey D / Kolhe, Janhavi / Freeman, Brian C

    Journal of molecular biology

    2019  Volume 431, Issue 24, Page(s) 4993–5003

    Abstract: Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family. Our studies identified a biphasic use of ... ...

    Abstract Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor protein family. Our studies identified a biphasic use of Hsp90 in which early inactivation (15 min) of the chaperone triggered a wide reduction of DNA binding events along the genome with concurrent changes to chromatin structure. Long-term loss (6 h) of Hsp90 resulted in a decline of a divergent yet overlaying pool of transcription factors that produced a distinct chromatin pattern. Although both phases involve protein folding, the early point correlated with Hsp90 acting in a late folding step that is critical for DNA binding function, whereas prolonged Hsp90 inactivation led to a significant decrease in the steady-state transcription factor protein levels. Intriguingly, despite the broad chaperone impact on a variety of transcription factors, the operational influence of Hsp90 was at the level of chromatin with only a mild effect on gene regulation. Thus, Hsp90 selectively governs the transcription factor process overseeing local chromatin structure.
    MeSH term(s) Chromatin/genetics ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Fungal Proteins ; Gene Expression Regulation ; HSP90 Heat-Shock Proteins/genetics ; HSP90 Heat-Shock Proteins/metabolism ; Molecular Chaperones/metabolism ; Mutation ; Protein Binding ; Protein Stability ; Transcription Factors/metabolism
    Chemical Substances Chromatin ; Fungal Proteins ; HSP90 Heat-Shock Proteins ; Molecular Chaperones ; Transcription Factors
    Language English
    Publishing date 2019-10-16
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2019.09.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 867: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: Hsp90 and p23 Molecular Chaperones Control Chromatin Architecture by Maintaining the Functional Pool of the RSC Chromatin Remodeler.

    Echtenkamp, Frank J / Gvozdenov, Zlata / Adkins, Nicholas L / Zhang, Yang / Lynch-Day, Melinda / Watanabe, Shinya / Peterson, Craig L / Freeman, Brian C

    Molecular cell

    2016  Volume 64, Issue 5, Page(s) 888–899

    Abstract: Molecular chaperones govern protein homeostasis, being allied to the beginning (folding) and ending (degradation) of the protein life cycle. Yet, the Hsp90 system primarily associates with native factors, including fully assembled complexes. The ... ...

    Abstract Molecular chaperones govern protein homeostasis, being allied to the beginning (folding) and ending (degradation) of the protein life cycle. Yet, the Hsp90 system primarily associates with native factors, including fully assembled complexes. The significance of these connections is poorly understood. To delineate why Hsp90 and its cochaperone p23 interact with a mature structure, we focused on the RSC chromatin remodeler. Both Hsp90 and p23 triggered the release of RSC from DNA or a nucleosome. Although Hsp90 only freed bound RSC, p23 enhanced nucleosome remodeling prior to discharging the complex. In vivo, RSC mobility and remodeling function were chaperone dependent. Our results suggest Hsp90 and p23 contribute to proteostasis by chaperoning mature factors through energetically unfavorable events, thereby maintaining the cellular pool of active native proteins. In the case of RSC, p23 and Hsp90 promote a dynamic action, allowing a limited number of remodelers to effectively maintain chromatin in a pliable state.
    MeSH term(s) Animals ; Chromatin Assembly and Disassembly ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Gene Deletion ; HSP90 Heat-Shock Proteins/genetics ; HSP90 Heat-Shock Proteins/metabolism ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Nucleosomes/metabolism ; Protein Conformation ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances DNA-Binding Proteins ; HSP90 Heat-Shock Proteins ; Molecular Chaperones ; Nucleosomes ; RSC complex, S cerevisiae ; SBA1 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Transcription Factors
    Language English
    Publishing date 2016-11-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2016.09.040
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5055: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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