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  1. Article ; Online: The more the merrier: Simultaneous mapping of multiple chromatin components in a single sample.

    Zentner, Gabriel E

    Molecular cell

    2021  Volume 81, Issue 22, Page(s) 4574–4576

    Abstract: Gopalan et al. (2021) present multi-CUT&Tag, a modification of cleavage under targets and tagmentation (CUT&Tag) that enables simultaneous genome-wide mapping of multiple chromatin-associated targets in a single sample. ...

    Abstract Gopalan et al. (2021) present multi-CUT&Tag, a modification of cleavage under targets and tagmentation (CUT&Tag) that enables simultaneous genome-wide mapping of multiple chromatin-associated targets in a single sample.
    MeSH term(s) Chromatin/genetics ; Chromatin Immunoprecipitation ; Chromosome Mapping
    Chemical Substances Chromatin
    Language English
    Publishing date 2021-11-19
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.10.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genome-Wide Profiling of Transcription Initiation with STRIPE-seq.

    Policastro, Robert A / Zentner, Gabriel E

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2477, Page(s) 21–34

    Abstract: Transcription start site (TSS) usage is a critical factor in the regulation of gene expression. A number of methods for global TSS mapping have been developed, but barriers of expense, technical difficulty, time, and/or cost have limited their broader ... ...

    Abstract Transcription start site (TSS) usage is a critical factor in the regulation of gene expression. A number of methods for global TSS mapping have been developed, but barriers of expense, technical difficulty, time, and/or cost have limited their broader adoption. To address these issues, we developed Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq). Requiring only three enzymatic steps with intervening bead cleanups, a STRIPE-seq library can be prepared from as little as 50 ng total RNA in ~5 h at a cost of ~$12 (US). In addition to profiling TSS usage, STRIPE-seq provides information on transcript levels that can be used for differential expression analysis. Thanks to its simplicity and low cost, we envision that STRIPE-seq could be employed by any molecular biology laboratory interested in profiling transcription initiation.
    MeSH term(s) Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Promoter Regions, Genetic ; Transcription Initiation Site
    Language English
    Publishing date 2022-04-29
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2257-5_2
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  3. Article: The more the merrier: Simultaneous mapping of multiple chromatin components in a single sample

    Zentner, Gabriel E.

    Molecular cell. 2021 Nov. 18, v. 81, no. 22

    2021  

    Abstract: Gopalan et al. (2021) present multi-CUT&Tag, a modification of cleavage under targets and tagmentation (CUT&Tag) that enables simultaneous genome-wide mapping of multiple chromatin-associated targets in a single sample. ...

    Abstract Gopalan et al. (2021) present multi-CUT&Tag, a modification of cleavage under targets and tagmentation (CUT&Tag) that enables simultaneous genome-wide mapping of multiple chromatin-associated targets in a single sample.
    Keywords cells ; chromatin ; sampling
    Language English
    Dates of publication 2021-1118
    Size p. 4574-4576.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.10.019
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  4. Article ; Online: Global approaches for profiling transcription initiation.

    Policastro, Robert A / Zentner, Gabriel E

    Cell reports methods

    2021  Volume 1, Issue 5

    Abstract: Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is ... ...

    Abstract Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
    MeSH term(s) Humans ; Promoter Regions, Genetic ; Gene Expression Regulation ; Protein Isoforms/genetics
    Chemical Substances Protein Isoforms
    Language English
    Publishing date 2021-09-16
    Publishing country United States
    Document type Review ; Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2667-2375
    ISSN (online) 2667-2375
    DOI 10.1016/j.crmeth.2021.100081
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  5. Article ; Online: Sufficient principal component regression for pattern discovery in transcriptomic data.

    Ding, Lei / Zentner, Gabriel E / McDonald, Daniel J

    Bioinformatics advances

    2022  Volume 2, Issue 1, Page(s) vbac033

    Abstract: Motivation: Methods for the global measurement of transcript abundance such as microarrays and RNA-Seq generate datasets in which the number of measured features far exceeds the number of observations. Extracting biologically meaningful and ... ...

    Abstract Motivation: Methods for the global measurement of transcript abundance such as microarrays and RNA-Seq generate datasets in which the number of measured features far exceeds the number of observations. Extracting biologically meaningful and experimentally tractable insights from such data therefore requires high-dimensional prediction. Existing sparse linear approaches to this challenge have been stunningly successful, but some important issues remain. These methods can fail to select the correct features, predict poorly relative to non-sparse alternatives or ignore any unknown grouping structures for the features.
    Results: We propose a method called SuffPCR that yields improved predictions in high-dimensional tasks including regression and classification, especially in the typical context of omics with correlated features. SuffPCR first estimates sparse principal components and then estimates a linear model on the recovered subspace. Because the estimated subspace is sparse in the features, the resulting predictions will depend on only a small subset of genes. SuffPCR works well on a variety of simulated and experimental transcriptomic data, performing nearly optimally when the model assumptions are satisfied. We also demonstrate near-optimal theoretical guarantees.
    Availability and implementation: Code and raw data are freely available at https://github.com/dajmcdon/suffpcr. Package documentation may be viewed at https://dajmcdon.github.io/suffpcr.
    Contact: daniel@stat.ubc.ca.
    Supplementary information: Supplementary data are available at
    Language English
    Publishing date 2022-05-14
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbac033
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Involvement of the SAGA and TFIID coactivator complexes in transcriptional dysregulation caused by the separation of core and tail Mediator modules.

    Saleh, Moustafa M / Hundley, Heather A / Zentner, Gabriel E

    G3 (Bethesda, Md.)

    2022  Volume 12, Issue 12

    Abstract: Regulation of RNA polymerase II transcription requires the concerted efforts of several multisubunit coactivator complexes, which interact with the RNA polymerase II preinitiation complex to stimulate transcription. We previously showed that separation ... ...

    Abstract Regulation of RNA polymerase II transcription requires the concerted efforts of several multisubunit coactivator complexes, which interact with the RNA polymerase II preinitiation complex to stimulate transcription. We previously showed that separation of the Mediator core from Mediator's tail module results in modest overactivation of genes annotated as highly dependent on TFIID for expression. However, it is unclear if other coactivators are involved in this phenomenon. Here, we show that the overactivation of certain genes by Mediator core/tail separation is blunted by disruption of the Spt-Ada-Gcn5-Acetyl transferase complex through the removal of its structural Spt20 subunit, though this downregulation does not appear to completely depend on reduced Spt-Ada-Gcn5-Acetyl transferase association with the genome. Consistent with the enrichment of TFIID-dependent genes among genes overactivated by Mediator core/tail separation, depletion of the essential TFIID subunit Taf13 suppressed the overactivation of these genes when Med16 was simultaneously removed. As with Spt-Ada-Gcn5-Acetyl transferase, this effect did not appear to be fully dependent on the reduced genomic association of TFIID. Given that the observed changes in gene expression could not be clearly linked to alterations in Spt-Ada-Gcn5-Acetyl transferase or TFIID occupancy, our data may suggest that the Mediator core/tail connection is important for the modulation of Spt-Ada-Gcn5-Acetyl transferase and/or TFIID conformation and/or function at target genes.
    MeSH term(s) Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Gene Expression Regulation, Fungal ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Trans-Activators/metabolism ; Transcription Factor TFIID/genetics ; Transcription Factor TFIID/metabolism ; Transcription, Genetic
    Chemical Substances Saccharomyces cerevisiae Proteins ; RNA Polymerase II (EC 2.7.7.-) ; Trans-Activators ; Transcription Factor TFIID
    Language English
    Publishing date 2022-09-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkac290
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  7. Article ; Online: Genome-Wide Profiling of Protein-DNA Interactions with Chromatin Endogenous Cleavage and High-Throughput Sequencing (ChEC-Seq ).

    Saleh, Moustafa M / Tourigny, Jason P / Zentner, Gabriel E

    Methods in molecular biology (Clifton, N.J.)

    2021  Volume 2351, Page(s) 289–303

    Abstract: Interactions between regulatory proteins and specific genomic regions are critical for all chromatin-based processes, including transcription, DNA replication, and DNA repair. Genome-wide mapping of such interactions is most commonly performed with ... ...

    Abstract Interactions between regulatory proteins and specific genomic regions are critical for all chromatin-based processes, including transcription, DNA replication, and DNA repair. Genome-wide mapping of such interactions is most commonly performed with chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), but a number of orthogonal methods employing targeted enzymatic activity have also been introduced. We previously described a genome-wide implementation of chromatin endogenous cleavage (ChEC-Seq), wherein a protein of interest is fused to micrococcal nuclease (MNase) to enable targeted, calcium-dependent genomic cleavage. Here, we describe the ChEC-Seq protocol for use in budding yeast though it can be used in other organisms in conjunction with appropriate methods for introduction of an MNase fusion protein.
    MeSH term(s) Chromatin/genetics ; Chromatin/metabolism ; Chromatin Immunoprecipitation Sequencing/methods ; DNA-Binding Proteins/metabolism ; Genome-Wide Association Study/methods ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomycetales/genetics ; Saccharomycetales/metabolism
    Chemical Substances Chromatin ; DNA-Binding Proteins
    Language English
    Publishing date 2021-08-11
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1597-3_16
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  8. Article ; Online: Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters.

    Saleh, Moustafa M / Jeronimo, Célia / Robert, François / Zentner, Gabriel E

    PLoS genetics

    2021  Volume 17, Issue 8, Page(s) e1009529

    Abstract: The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the ... ...

    Abstract The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We propose that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.
    MeSH term(s) Adenosine Triphosphatases/genetics ; Gene Expression Profiling/methods ; Gene Expression Regulation, Fungal ; Mediator Complex/genetics ; Mutation ; Promoter Regions, Genetic ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Analysis, RNA ; TATA-Binding Protein Associated Factors/genetics ; TATA-Box Binding Protein/metabolism ; Trans-Activators ; Transcription, Genetic
    Chemical Substances Mediator Complex ; SIN4 protein, S cerevisiae ; SPT15 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; TATA-Binding Protein Associated Factors ; TATA-Box Binding Protein ; Trans-Activators ; Adenosine Triphosphatases (EC 3.6.1.-) ; MOT1 protein, S cerevisiae (EC 3.6.1.-)
    Language English
    Publishing date 2021-08-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1009529
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Genome-wide characterization of Mediator recruitment, function, and regulation.

    Grünberg, Sebastian / Zentner, Gabriel E

    Transcription

    2017  Volume 8, Issue 3, Page(s) 169–174

    Abstract: Mediator is a conserved and essential coactivator complex broadly required for RNA polymerase II (RNAPII) transcription. Recent genome-wide studies of Mediator binding in budding yeast have revealed new insights into the functions of this critical ... ...

    Abstract Mediator is a conserved and essential coactivator complex broadly required for RNA polymerase II (RNAPII) transcription. Recent genome-wide studies of Mediator binding in budding yeast have revealed new insights into the functions of this critical complex and raised new questions about its role in the regulation of gene expression.
    Language English
    Publishing date 2017-05-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2646974-1
    ISSN 2154-1272 ; 2154-1264
    ISSN (online) 2154-1272
    ISSN 2154-1264
    DOI 10.1080/21541264.2017.1291082
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The promise and peril of CRISPR gene drives: Genetic variation and inbreeding may impede the propagation of gene drives based on the CRISPR genome editing technology.

    Zentner, Gabriel E / Wade, Michael J

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2017  Volume 39, Issue 10

    Abstract: Gene drives are selfish genetic elements that use a variety of mechanisms to ensure they are transmitted to subsequent generations at greater than expected frequencies. Synthetic gene drives based on the clustered regularly interspersed palindromic ... ...

    Abstract Gene drives are selfish genetic elements that use a variety of mechanisms to ensure they are transmitted to subsequent generations at greater than expected frequencies. Synthetic gene drives based on the clustered regularly interspersed palindromic repeats (CRISPR) genome editing system have been proposed as a way to alter the genetic characteristics of natural populations of organisms relevant to the goals of public health, conservation, and agriculture. Here, we review the principles and potential applications of CRISPR drives, as well as means proposed to prevent their uncontrolled spread. We also focus on recent work suggesting that factors such as natural genetic variation and inbreeding may represent substantial impediments to the propagation of CRISPR drives.
    MeSH term(s) Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Endonucleases/metabolism ; Gene Editing/methods ; Genetic Engineering/methods ; Genetic Therapy
    Chemical Substances Endonucleases (EC 3.1.-)
    Language English
    Publishing date 2017-09-01
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.201700109
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    In stock of ZB MED Cologne/Königswinter

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