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  1. Article ; Online: A fluorescence-based protocol to quantitatively titrate CUT&RUN buffer components.

    Katznelson, Andrew / Zaret, Kenneth

    STAR protocols

    2024  Volume 5, Issue 1, Page(s) 102866

    Abstract: Cleavage under targets & release using nuclease (CUT&RUN) is a technique for identifying genomic sites where proteins or histone modifications are present in chromatin in permeabilized cells. Here, we present a fluorescence-based protocol to ... ...

    Abstract Cleavage under targets & release using nuclease (CUT&RUN) is a technique for identifying genomic sites where proteins or histone modifications are present in chromatin in permeabilized cells. Here, we present a fluorescence-based protocol to quantitatively titrate CUT&RUN buffer components, for efficient cell permeabilization and retention of target epitopes on chromatin. We describe steps for capturing cells on concanavalin A beads and using a fluorescently labeled secondary antibody to titrate concentrations of digitonin and NaCl in CUT&RUN buffers. We then detail procedures for fluorescence imaging to identify optimal conditions. For complete details on the use and execution of this protocol, please refer to Lerner et al.
    MeSH term(s) Chromatin ; Antibodies ; Endonucleases ; Epitopes ; Genomics
    Chemical Substances Chromatin ; Antibodies ; Endonucleases (EC 3.1.-) ; Epitopes
    Language English
    Publishing date 2024-02-07
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2024.102866
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2.

    Lerner, Jonathan / Katznelson, Andrew / Zhang, Jingchao / Zaret, Kenneth S

    Cell reports

    2023  Volume 42, Issue 7, Page(s) 112748

    Abstract: Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription ... ...

    Abstract Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. To better understand nucleosome targeting in vivo, we assess whether pioneer factors FoxA1 and Sox2 target stable or unstable nucleosomes and find that they target DNase-resistant, stable nucleosomes, whereas HNF4A, a non-nucleosome binding factor, targets open, DNase-sensitive chromatin. Despite FOXA1 and SOX2 targeting similar proportions of DNase-resistant chromatin, using single-molecule tracking, we find that FOXA1 uses lower nucleoplasmic diffusion and longer residence times while SOX2 uses higher nucleoplasmic diffusion and shorter residence times to scan compact chromatin, while HNF4 scans compact chromatin much less efficiently. Thus, pioneer factors target compact chromatin through distinct processes.
    MeSH term(s) Chromatin ; Deoxyribonucleases/metabolism ; Nucleosomes ; Protein Binding ; Transcription Factors/metabolism ; Hepatocyte Nuclear Factor 3-alpha/metabolism ; SOXB1 Transcription Factors/metabolism
    Chemical Substances Chromatin ; Deoxyribonucleases (EC 3.1.-) ; Nucleosomes ; Transcription Factors ; Hepatocyte Nuclear Factor 3-alpha ; SOXB1 Transcription Factors
    Language English
    Publishing date 2023-07-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2023.112748
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Why

    Turelli, Michael / Katznelson, Andrew / Ginsberg, Paul S

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 47, Page(s) e2211637119

    Abstract: Cytoplasmic incompatibility (CI) is the most common reproductive manipulation produced ... ...

    Abstract Cytoplasmic incompatibility (CI) is the most common reproductive manipulation produced by
    MeSH term(s) Female ; Humans ; Wolbachia/genetics ; Fertility ; Cytoplasm/metabolism ; Reproduction ; Selection, Genetic ; Symbiosis
    Language English
    Publishing date 2022-11-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2211637119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  4. Article ; Online: Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity.

    Katsuda, Takeshi / Sussman, Jonathan H / Ito, Kenji / Katznelson, Andrew / Yuan, Salina / Takenaka, Naomi / Li, Jinyang / Merrell, Allyson J / Cure, Hector / Li, Qinglan / Rasool, Reyaz Ur / Asangani, Irfan A / Zaret, Kenneth S / Stanger, Ben Z

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1761

    Abstract: Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate " ... ...

    Abstract Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cell's enhancers. Here we report that SOX4 is sufficient to initiate hepatobiliary metaplasia in the adult mouse liver, closely mimicking metaplasia initiated by toxic damage to the liver. In lineage-traced cells, we assessed the timing of SOX4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, SOX4 directly binds to and closes hepatocyte regulatory sequences via an overlapping motif with HNF4A, a hepatocyte master regulatory transcription factor. Subsequently, SOX4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.
    MeSH term(s) Animals ; Mice ; Cell Differentiation/genetics ; Cellular Reprogramming/genetics ; Chromatin ; Metaplasia ; Transcription Factors/metabolism
    Chemical Substances Chromatin ; Transcription Factors ; Sox4 protein, mouse
    Language English
    Publishing date 2024-02-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45939-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Physiological reprogramming

    Katsuda, Takeshi / Sussman, Jonathan / Ito, Kenji / Katznelson, Andrew / Yuan, Salina / Li, Jinyang / Merrell, Allyson J / Takenaka, Naomi / Cure, Hector / Li, Qinglan / Rasool, Reyaz Ur / Asangani, Irfan A / Zaret, Kenneth S / Stanger, Ben Z

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate " ... ...

    Abstract Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cell's enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.
    Language English
    Publishing date 2023-02-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.14.528556
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Different factors limit early- and late-season windows of opportunity for monarch development.

    Yang, Louie H / Swan, Karen / Bastin, Eric / Aguilar, Jessica / Cenzer, Meredith / Codd, Andrew / Gonzalez, Natalie / Hayes, Tracie / Higgins, August / Lor, Xang / Macharaga, Chido / McMunn, Marshall / Oto, Kenya / Winarto, Nicholas / Wong, Darren / Yang, Tabatha / Afridi, Numan / Aguilar, Sarah / Allison, Amelia /
    Ambrose-Winters, Arden / Amescua, Edwin / Apse, Mattias / Avoce, Nancy / Bastin, Kirstin / Bolander, Emily / Burroughs, Jessica / Cabrera, Cristian / Candy, Madeline / Cavett, Ariana / Cavett, Melina / Chang, Lemuel / Claret, Miles / Coleman, Delaney / Concha, Jacob / Danzer, Paxson / DaRosa, Joe / Dufresne, Audrey / Duisenberg, Claire / Earl, Allyson / Eckey, Emily / English, Maddie / Espejo, Alexander / Faith, Erika / Fang, Amy / Gamez, Alejandro / Garcini, Jackelin / Garcini, Julie / Gilbert-Igelsrud, Giancarlo / Goedde-Matthews, Kelly / Grahn, Sarah / Guerra, Paloma / Guerra, Vanessa / Hagedorn, Madison / Hall, Katie / Hall, Griffin / Hammond, Jake / Hargadon, Cody / Henley, Victoria / Hinesley, Sarah / Jacobs, Celeste / Johnson, Camille / Johnson, Tattiana / Johnson, Zachary / Juchau, Emma / Kaplan, Celeste / Katznelson, Andrew / Keeley, Ronja / Kubik, Tatum / Lam, Theodore / Lansing, Chalinee / Lara, Andrea / Le, Vivian / Lee, Breana / Lee, Kyra / Lemmo, Maddy / Lucio, Scott / Luo, Angela / Malakzay, Salman / Mangney, Luke / Martin, Joseph / Matern, Wade / McConnell, Byron / McHale, Maya / McIsaac, Giulia / McLennan, Carolanne / Milbrodt, Stephanie / Mohammed, Mohammed / Mooney-McCarthy, Morgan / Morgan, Laura / Mullin, Clare / Needles, Sarah / Nunes, Kayla / O'Keeffe, Fiona / O'Keeffe, Olivia / Osgood, Geoffrey / Padilla, Jessica / Padilla, Sabina / Palacio, Isabella / Panelli, Verio / Paulson, Kendal / Pearson, Jace / Perez, Tate / Phrakonekham, Brenda / Pitsillides, Iason / Preisler, Alex / Preisler, Nicholas / Ramirez, Hailey / Ransom, Sylvan / Renaud, Camille / Rocha, Tracy / Saris, Haley / Schemrich, Ryan / Schoenig, Lyla / Sears, Sophia / Sharma, Anand / Siu, Jessica / Spangler, Maddie / Standefer, Shaili / Strickland, Kelly / Stritzel, Makaila / Talbert, Emily / Taylor, Sage / Thomsen, Emma / Toups, Katrina / Tran, Kyle / Tran, Hong / Tuqiri, Maraia / Valdes, Sara / VanVorhis, George / Vue, Sandy / Wallace, Shauna / Whipple, Johnna / Yang, Paja / Ye, Meg / Yo, David / Zeng, Yichao

    Ecology and evolution

    2022  Volume 12, Issue 7, Page(s) e9039

    Abstract: Seasonal windows of opportunity are intervals within a year that provide improved prospects for growth, survival, or reproduction. However, few studies have sufficient temporal resolution to examine how multiple factors combine to constrain the seasonal ... ...

    Abstract Seasonal windows of opportunity are intervals within a year that provide improved prospects for growth, survival, or reproduction. However, few studies have sufficient temporal resolution to examine how multiple factors combine to constrain the seasonal timing and extent of developmental opportunities. Here, we document seasonal changes in milkweed (
    Language English
    Publishing date 2022-07-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2635675-2
    ISSN 2045-7758
    ISSN 2045-7758
    DOI 10.1002/ece3.9039
    Database MEDical Literature Analysis and Retrieval System OnLINE

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