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  1. Article ; Online: Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors.

    Hannon, Colleen E / Eisen, Michael B

    eLife

    2024  Volume 12

    Abstract: Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of ... ...

    Abstract Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early
    MeSH term(s) Animals ; Transcription Factors/genetics ; Protein Conformation ; Proteome ; Amino Acid Sequence ; Drosophila/metabolism ; Intrinsically Disordered Proteins/metabolism
    Chemical Substances Transcription Factors ; Proteome ; Intrinsically Disordered Proteins
    Language English
    Publishing date 2024-01-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.88221
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  2. Article ; Online: Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation.

    Singleton, Marc D / Eisen, Michael B

    PLoS computational biology

    2024  Volume 20, Issue 4, Page(s) e1012028

    Abstract: Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite ... ...

    Abstract Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite the prevalence and importance of IDRs in eukaryotic proteomes and various biological processes, associating them with specific molecular functions remains a significant challenge due to their high rates of sequence evolution. However, by comparing the observed values of various IDR-associated properties against those generated under a simulated model of evolution, a recent study found most IDRs across the entire yeast proteome contain conserved features. Furthermore, it showed clusters of IDRs with common "evolutionary signatures," i.e. patterns of conserved features, were associated with specific biological functions. To determine if similar patterns of conservation are found in the IDRs of other systems, in this work we applied a series of phylogenetic models to over 7,500 orthologous IDRs identified in the Drosophila genome to dissect the forces driving their evolution. By comparing models of constrained and unconstrained continuous trait evolution using the Brownian motion and Ornstein-Uhlenbeck models, respectively, we identified signals of widespread constraint, indicating conservation of distributed features is mechanism of IDR evolution common to multiple biological systems. In contrast to the previous study in yeast, however, we observed limited evidence of IDR clusters with specific biological functions, which suggests a more complex relationship between evolutionary constraints and function in the IDRs of multicellular organisms.
    Language English
    Publishing date 2024-04-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1012028
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  3. Article ; Online: We need to act now.

    Eisen, Michael B

    eLife

    2020  Volume 9

    Abstract: eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists. ...

    Abstract eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists.
    MeSH term(s) African Americans ; Human Rights ; Humans ; Leadership ; Models, Organizational ; Publishing/organization & administration ; Publishing/standards ; Racism/prevention & control ; Science/organization & administration ; Science/standards ; Social Justice
    Language English
    Publishing date 2020-06-05
    Publishing country England
    Document type Editorial
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.59636
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  4. Article ; Online: Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos.

    Albright, Ashley R / Stadler, Michael R / Eisen, Michael B

    PloS one

    2022  Volume 17, Issue 6, Page(s) e0270471

    Abstract: Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to ... ...

    Abstract Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the use of single-nucleus RNA sequencing in Drosophila embryos prior to cellularization, here we look at gene expression in control and insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we provide a resource of candidate differentially expressed genes that might show local changes in gene expression between control and maternal dCTCF null nuclei with no detectable differential expression in bulk. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.
    MeSH term(s) Animals ; Drosophila/genetics ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/metabolism ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation, Developmental ; Morphogenesis/genetics ; RNA/metabolism ; Sequence Analysis, RNA
    Chemical Substances Drosophila Proteins ; RNA (63231-63-0)
    Language English
    Publishing date 2022-06-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0270471
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  5. Article: Unified bursting strategies in ectopic and endogenous

    Berrocal, Augusto / Lammers, Nicholas C / Garcia, Hernan G / Eisen, Michael B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or amplitude. ... ...

    Abstract Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or amplitude. Previous studies observed that different enhancers can achieve a wide range of transcriptional outputs through the same strategies of bursting control. For example, despite responding to different transcription factors, all
    Language English
    Publishing date 2023-02-10
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.09.527927
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  6. Article ; Online: We need to act now

    Michael B Eisen

    eLife, Vol

    2020  Volume 9

    Abstract: eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists. ...

    Abstract eLife, like the rest of science, must tackle the many inequalities experienced by Black scientists.
    Keywords racism in science ; equality ; diversity and inclusion ; scientific publishing ; eLife ; careers in science ; discrimination ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos.

    Ashley R Albright / Michael R Stadler / Michael B Eisen

    PLoS ONE, Vol 17, Iss 6, p e

    2022  Volume 0270471

    Abstract: Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to ... ...

    Abstract Our current understanding of the regulation of gene expression in the early Drosophila melanogaster embryo comes from observations of a few genes at a time, as with in situ hybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the use of single-nucleus RNA sequencing in Drosophila embryos prior to cellularization, here we look at gene expression in control and insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and published in situ hybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we provide a resource of candidate differentially expressed genes that might show local changes in gene expression between control and maternal dCTCF null nuclei with no detectable differential expression in bulk. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the early Drosophila melanogaster embryo.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612 ; 570
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  8. Article ; Online: Atlas…t, patterns from every cell.

    Stadler, Michael R / Eisen, Michael B

    Science (New York, N.Y.)

    2017  Volume 358, Issue 6360, Page(s) 172–173

    MeSH term(s) Animals ; DNA ; Drosophila melanogaster/embryology ; Gene Expression Regulation, Developmental ; RNA
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2017--13
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.aap8493
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 27: 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)
    Zs.MG 77: Show issues

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  9. Article: Genome-wide measurement of spatial expression in patterning mutants of

    Combs, Peter A / Eisen, Michael B

    F1000Research

    2017  Volume 6, Page(s) 41

    Abstract: Patterning in ... ...

    Abstract Patterning in the
    Language English
    Publishing date 2017
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.9720.1
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  10. Article ; Online: Whole Genome Sequences of 23 Species from the

    Bronski, Michael J / Martinez, Ciera C / Weld, Holli A / Eisen, Michael B

    G3 (Bethesda, Md.)

    2020  Volume 10, Issue 5, Page(s) 1443–1455

    Abstract: Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species- ... ...

    Abstract Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich
    MeSH term(s) Animals ; Drosophila/genetics ; Drosophila melanogaster/genetics ; Genome ; Genomics ; Phylogeny
    Language English
    Publishing date 2020-05-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1534/g3.119.400959
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