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  1. Article: Back to the origin: reconsidering replication, transcription, epigenetics, and cell cycle control.

    Evertts, Adam G / Coller, Hilary A

    Genes & cancer

    2013  Volume 3, Issue 11-12, Page(s) 678–696

    Abstract: In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and ... ...

    Abstract In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and transcription. In metazoans, the organization of replication is more enigmatic. The lack of a specific sequence that defines origins of replication has, until recently, severely limited our ability to define the organizing principles of DNA replication. This question is of particular importance as emerging data suggest that replication stress is an important contributor to inherited genetic damage and the genomic instability in tumors. We consider here the replication program in several different organisms including recent genome-wide analyses of replication origins in humans. We review recent studies on the role of cytosine methylation in replication origins, the role of transcriptional looping and gene gating in DNA replication, and the role of chromatin's 3-dimensional structure in DNA replication. We use these new findings to consider several questions surrounding DNA replication in metazoans: How are origins selected? What is the relationship between replication and transcription? How do checkpoints inhibit origin firing? Why are there early and late firing origins? We then discuss whether oncogenes promote cancer through a role in DNA replication and whether errors in DNA replication are important contributors to the genomic alterations and gene fusion events observed in cancer. We conclude with some important areas for future experimentation.
    Language English
    Publishing date 2013-04-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2538519-7
    ISSN 1947-6027 ; 1947-6019
    ISSN (online) 1947-6027
    ISSN 1947-6019
    DOI 10.1177/1947601912474891
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Modern approaches for investigating epigenetic signaling pathways.

    Evertts, Adam G / Zee, Barry M / Garcia, Benjamin A

    Journal of applied physiology (Bethesda, Md. : 1985)

    2010  Volume 109, Issue 3, Page(s) 927–933

    Abstract: Epigenetics is increasingly being recognized as a central component of physiological processes as diverse as obesity and circadian rhythms. Primarily acting through DNA methylation and histone posttranslational modifications, epigenetic pathways enable ... ...

    Abstract Epigenetics is increasingly being recognized as a central component of physiological processes as diverse as obesity and circadian rhythms. Primarily acting through DNA methylation and histone posttranslational modifications, epigenetic pathways enable both short- and long-term transcriptional activation and silencing, independently of the underlying genetic sequence. To more quantitatively study the molecular basis of epigenetic regulation in physiological processes, the present review informs the latest techniques to identify and compare novel DNA methylation marks and combinatorial histone modifications across different experimental conditions, and to localize both DNA methylation and histone modifications over specific genomic regions.
    MeSH term(s) Animals ; Chromatin Assembly and Disassembly ; Chromatin Immunoprecipitation ; DNA Methylation ; Epigenesis, Genetic ; Genomics/methods ; Histones/metabolism ; Humans ; Mass Spectrometry ; Protein Processing, Post-Translational ; Sequence Analysis, Protein ; Signal Transduction/genetics
    Chemical Substances Histones
    Language English
    Publishing date 2010-01-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 219139-8
    ISSN 1522-1601 ; 0021-8987 ; 0161-7567 ; 8750-7587
    ISSN (online) 1522-1601
    ISSN 0021-8987 ; 0161-7567 ; 8750-7587
    DOI 10.1152/japplphysiol.00007.2010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The Hermes transposon of Musca domestica and its use as a mutagen of Schizosaccharomyces pombe.

    Park, Jung M / Evertts, Adam G / Levin, Henry L

    Methods (San Diego, Calif.)

    2009  Volume 49, Issue 3, Page(s) 243–247

    Abstract: Transposon mutagenesis allows for the discovery and characterization of genes by creating mutations that can be easily mapped and sequenced. Moreover, this method allows for a relatively unbiased approach to isolating genes of interest. Recently, a ... ...

    Abstract Transposon mutagenesis allows for the discovery and characterization of genes by creating mutations that can be easily mapped and sequenced. Moreover, this method allows for a relatively unbiased approach to isolating genes of interest. Recently, a system of transposon based mutagenesis for Schizosaccharomyces pombe became available. This mutagenesis relies on Hermes, a DNA transposon from the house fly that readily integrates into the chromosomes of S. pombe. The Hermes system is distinct from the retrotransposons of S. pombe because it efficiently integrates into open reading frames. To mutagenize S. pombe, cells are transformed with a plasmid that contains a drug resistance marker flanked by the terminal inverted repeats of Hermes. The Hermes transposase expressed from a second plasmid excises the resistance marker with the inverted repeats and inserts this DNA into chromosomal sites. After S. pombe with these two plasmids grow 25 generations, approximately 2% of the cells contain insertions. Of the cells with insertions, 68% contain single integration events. The protocols listed here provide the detailed information necessary to mutagenize a strain of interest, screen for specific phenotypes, and sequence the positions of insertion.
    MeSH term(s) Animals ; DNA Transposable Elements ; Houseflies/genetics ; Mutagenesis, Insertional/methods ; Plasmids ; Schizosaccharomyces/genetics
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2009-05-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2009.05.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3239: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  4. Article: The hermes transposon of Musca domestica is an efficient tool for the mutagenesis of Schizosaccharomyces pombe.

    Evertts, Adam G / Plymire, Christopher / Craig, Nancy L / Levin, Henry L

    Genetics

    2007  Volume 177, Issue 4, Page(s) 2519–2523

    Abstract: Currently, no transposon-based method for the mutagenesis of Schizosaccharomyces pombe exists. We have developed such a system based on the introduction of the hermes transposon from the housefly into S. pombe. This system efficiently disrupts open ... ...

    Abstract Currently, no transposon-based method for the mutagenesis of Schizosaccharomyces pombe exists. We have developed such a system based on the introduction of the hermes transposon from the housefly into S. pombe. This system efficiently disrupts open reading frames and allows the insertion sites to be readily identified.
    MeSH term(s) Animals ; Binding Sites ; DNA Transposable Elements ; Houseflies/genetics ; Mutagenesis, Insertional/methods ; Open Reading Frames ; Schizosaccharomyces/genetics
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2007-10-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 2167-2
    ISSN 1943-2631 ; 0016-6731
    ISSN (online) 1943-2631
    ISSN 0016-6731
    DOI 10.1534/genetics.107.081075
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.B 767: Show issues Location:
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  5. Article ; Online: Quantitative dynamics of the link between cellular metabolism and histone acetylation.

    Evertts, Adam G / Zee, Barry M / Dimaggio, Peter A / Gonzales-Cope, Michelle / Coller, Hilary A / Garcia, Benjamin A

    The Journal of biological chemistry

    2013  Volume 288, Issue 17, Page(s) 12142–12151

    Abstract: Acetylation on the tails of histones plays an important role in controlling transcription initiation. Although the steady-state abundances of histone acetyl groups have been reported, the rate at which histones are acetylated and deacetylated on a ... ...

    Abstract Acetylation on the tails of histones plays an important role in controlling transcription initiation. Although the steady-state abundances of histone acetyl groups have been reported, the rate at which histones are acetylated and deacetylated on a residue-specific basis has not been quantitatively established. We added [(13)C]glucose to human cells and monitored the dynamic incorporation of (13)C-labeled acetyl groups onto specific histone lysines with quantitative mass spectrometry. We determined the turnover of acetylation to be generally slower than phosphorylation, but fast relative to methylation, and that the rate varied depending on the histone, the residue modified, and also the neighboring modifications. Cells were also treated with a deacetylase inhibitor to determine the rate due to histone acetyltransferase activity alone and in the absence of deacetylase activity. Introduction of (13)C-labeled glucose also resulted in the incorporation of (13)C into alanine, which allowed us to partition histones into existing and newly synthesized protein categories. Newly synthesized histones were slower to accumulate histone modifications, especially modifications associated with silent chromatin. Finally, we applied our new approaches to find that quiescent fibroblasts exhibited lower levels of labeled acetyl accumulation compared with proliferating fibroblasts. This suggests that acetylation rates can be modulated in cells in different biological states and that these changes can be detected with the approach presented here. The methods we describe can be broadly applied to defining the turnover of histone acetylation in other cell states such as during cellular reprogramming and to quantify non-histone protein acetylation dynamics.
    MeSH term(s) Acetylation ; Alanine/metabolism ; Glucose/metabolism ; HEK293 Cells ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational/physiology
    Chemical Substances Histones ; Glucose (IY9XDZ35W2) ; Alanine (OF5P57N2ZX)
    Language English
    Publishing date 2013-03-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M112.428318
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  6. Article ; Online: H4K20 methylation regulates quiescence and chromatin compaction.

    Evertts, Adam G / Manning, Amity L / Wang, Xin / Dyson, Nicholas J / Garcia, Benjamin A / Coller, Hilary A

    Molecular biology of the cell

    2013  Volume 24, Issue 19, Page(s) 3025–3037

    Abstract: The transition between proliferation and quiescence is frequently associated with changes in gene expression, extent of chromatin compaction, and histone modifications, but whether changes in chromatin state actually regulate cell cycle exit with ... ...

    Abstract The transition between proliferation and quiescence is frequently associated with changes in gene expression, extent of chromatin compaction, and histone modifications, but whether changes in chromatin state actually regulate cell cycle exit with quiescence is unclear. We find that primary human fibroblasts induced into quiescence exhibit tighter chromatin compaction. Mass spectrometry analysis of histone modifications reveals that H4K20me2 and H4K20me3 increase in quiescence and other histone modifications are present at similar levels in proliferating and quiescent cells. Analysis of cells in S, G2/M, and G1 phases shows that H4K20me1 increases after S phase and is converted to H4K20me2 and H4K20me3 in quiescence. Knockdown of the enzyme that creates H4K20me3 results in an increased fraction of cells in S phase, a defect in exiting the cell cycle, and decreased chromatin compaction. Overexpression of Suv4-20h1, the enzyme that creates H4K20me2 from H4K20me1, results in G2 arrest, consistent with a role for H4K20me1 in mitosis. The results suggest that the same lysine on H4K20 may, in its different methylation states, facilitate mitotic functions in M phase and promote chromatin compaction and cell cycle exit in quiescent cells.
    MeSH term(s) Cell Cycle/genetics ; Cell Proliferation ; Chromatin/genetics ; DNA Replication/genetics ; Fibroblasts/cytology ; Gene Knockdown Techniques ; Histone-Lysine N-Methyltransferase/genetics ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/genetics ; Histones/metabolism ; Humans ; Lysine/genetics ; Lysine/metabolism ; Methylation ; Mitosis ; Primary Cell Culture
    Chemical Substances Chromatin ; Histones ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2013-08-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1098979-1
    ISSN 1939-4586 ; 1059-1524
    ISSN (online) 1939-4586
    ISSN 1059-1524
    DOI 10.1091/mbc.E12-07-0529
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    Zs.A 2853: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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    Zs.MO 410: Show issues

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  7. Article ; Online: H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence.

    Chicas, Agustin / Kapoor, Avnish / Wang, Xiaowo / Aksoy, Ozlem / Evertts, Adam G / Zhang, Michael Q / Garcia, Benjamin A / Bernstein, Emily / Lowe, Scott W

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

    2012  Volume 109, Issue 23, Page(s) 8971–8976

    Abstract: Cellular senescence is a tumor-suppressive program that involves chromatin reorganization and specific changes in gene expression that trigger an irreversible cell-cycle arrest. Here we combine quantitative mass spectrometry, ChIP deep-sequencing, and ... ...

    Abstract Cellular senescence is a tumor-suppressive program that involves chromatin reorganization and specific changes in gene expression that trigger an irreversible cell-cycle arrest. Here we combine quantitative mass spectrometry, ChIP deep-sequencing, and functional studies to determine the role of histone modifications on chromatin structure and gene-expression alterations associated with senescence in primary human cells. We uncover distinct senescence-associated changes in histone-modification patterns consistent with a repressive chromatin environment and link the establishment of one of these patterns--loss of H3K4 methylation--to the retinoblastoma tumor suppressor and the H3K4 demethylases Jarid1a and Jarid1b. Our results show that Jarid1a/b-mediated H3K4 demethylation contributes to silencing of retinoblastoma target genes in senescent cells, suggesting a mechanism by which retinoblastoma triggers gene silencing. Therefore, we link the Jarid1a and Jarid1b demethylases to a tumor-suppressor network controlling cellular senescence.
    MeSH term(s) Cell Line ; Cellular Senescence/physiology ; Chromatin/metabolism ; Chromatin Immunoprecipitation ; Gene Expression Regulation/genetics ; Gene Silencing/physiology ; Genetic Vectors ; High-Throughput Nucleotide Sequencing ; Histones/metabolism ; Humans ; Immunoblotting ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Mass Spectrometry ; Methylation ; Nuclear Proteins/metabolism ; Repressor Proteins/metabolism ; Retinoblastoma-Binding Protein 2/metabolism ; Retroviridae ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA
    Chemical Substances Chromatin ; Histones ; Nuclear Proteins ; Repressor Proteins ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; KDM5A protein, human (EC 1.14.11.-) ; KDM5B protein, human (EC 1.14.11.-) ; Retinoblastoma-Binding Protein 2 (EC 1.14.11.27)
    Language English
    Publishing date 2012-05-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1119836109
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