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Research: Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin
- Kirsty Jamieson,
- Elizabeth T. Wiles,
- Kevin J. McNaught,
- Simone Sidoli,
- Neena Leggett,
- Yanchun Shao,
- Benjamin A. Garcia,
- and Eric U. Selker
Genome Res. January 2016 26: 97-107; Published in Advance November 4, 2015, doi:10.1101/gr.194555.115
...relationships between marks of constitutive and facultative heterochromatin. Specifically, we used the filamentous fungus Neurospora crassa, which unlike many other simple model eukaryotes (e.g., budding and fission yeasts,Drosophila and Caenorhabditis elegans) has both DNA methylation and H3K27me (Aramayo...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...) enzymes SUV39H1 and SUV39H2. This H3K9me3 histone mark is then recognized by chromobox 5 (Cbx5; also known as heterochromatin protein 1 [HP1]) corepressor reader molecules that self-oligomerize to impart gene silencing and facilitate the tethering of heterochromatin domains to the nuclear lamina...
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Research: Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila
- Robin L. Armstrong,
- Taylor J.R. Penke,
- Brian D. Strahl,
- A. Gregory Matera,
- Daniel J. McKay,
- David M. MacAlpine,
- and Robert J. Duronio
Genome Res. November 2018 28: 1688-1700; Published in Advance October 2, 2018, doi:10.1101/gr.239913.118
...-poor, inaccessible heterochromatin, a causal relationship between chromatin structure and replication initiation remains elusive. Here, we combined histone gene engineering and whole- sequencing in Drosophila to determine how perturbing chromatin structure affects replication initiation. We found that most...
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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
..., Schizosaccharomyces pombe, Drosophila menlanogaster, Homo sapiens). A window of 300 kb is shown for each chromosome in a browser. (B) Summary of genomic features of the same organisms named in A. For details on collected data, see Methods. (C) Detection of histone modifications in vegetative Paramecium nuclei...
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Research: Chromatin signatures of the Drosophila replication program
- Matthew L. Eaton,
- Joseph A. Prinz,
- Heather K. MacAlpine,
- George Tretyakov,
- Peter V. Kharchenko,
- and David M. MacAlpine
Genome Res. February 2011 21: 164-174; Published in Advance December 22, 2010, doi:10.1101/gr.116038.110
...the relative time of replication for all unique sequences in the Drosophila (Fig. 1A, top),map early activating origins of replication (Fig. 1A, middle), and identify, at near nucleotide resolution, the locations of ORC binding by using high-throughput sequencing (Fig. 1A, bottom). Genomic tiling arrays were...
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Research: Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome
- Masako Suzuki,
- Mayumi Oda,
- María-Paz Ramos,
- Marién Pascual,
- Kevin Lau,
- Edyta Stasiek,
- Frederick Agyiri,
- Reid F. Thompson,
- Jacob L. Glass,
- Qiang Jing,
- Richard Sandstrom,
- Melissa J. Fazzari,
- R. Scott Hansen,
- John A. Stamatoyannopoulos,
- Andrew S. McLellan,
- and John M. Greally
Genome Res. November 2011 21: 1833-1840; Published in Advance September 28, 2011, doi:10.1101/gr.116509.110
...chromatid cohesion (Gartenberg 2009). Decades of cytological studies have also characterized heterochromatin by its late-replication timing within the cell cycle (Gilbert 2002). From amolecular point of view, certain proteins (e.g., HP1) (Fanti and Pimpinelli 2008) or post-translational variants (e.g., H3K9...
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Research: Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- Nicole C. Riddle,
- Aki Minoda,
- Peter V. Kharchenko,
- Artyom A. Alekseyenko,
- Yuri B. Schwartz,
- Michael Y. Tolstorukov,
- Andrey A. Gorchakov,
- Jacob D. Jaffe,
- Cameron Kennedy,
- Daniela Linder-Basso,
- Sally E. Peach,
- Gregory Shanower,
- Haiyan Zheng,
- Mitzi I. Kuroda,
- Vincenzo Pirrotta,
- Peter J. Park,
- Sarah C.R. Elgin,
- and Gary H. Karpen
Genome Res. February 2011 21: 147-163; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110
...↵ 9 These authors contributed equally to this work. Abstract Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis...
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Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
- Christelle Cayrou,
- Philippe Coulombe,
- Alice Vigneron,
- Slavica Stanojcic,
- Olivier Ganier,
- Isabelle Peiffer,
- Eric Rivals,
- Aurore Puy,
- Sabine Laurent-Chabalier,
- Romain Desprat,
- and Marcel Méchali
Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
...at the initiation site, and the analysis reveals specificGC-rich motifs in bothmouse andDrosophilaOris at initiation sites. A strong correlation between HP1 binding sites and Oris was found at Drosophila chromosome 4, which is mainly constituted of heterochromatin. In combination with DNA combing data, our scale...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...positioning (Kornberg and Stryer 1988). Third, a broad class of regulatory factors, the ATP-dependent nucleosome remodelers, plays a key role in assembling, displacing, and evicting nucleosomes (Clapier and Cairns 2009). Finally, additional structural elements such as Heterochromatin Protein 1 (HP1...
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Research: The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes
- Emily J. Brown and
- Doris Bachtrog
Genome Res. July 2014 24: 1125-1137; Published in Advance May 19, 2014, doi:10.1101/gr.172155.114
...), and RNAi knockdownof the heterochromatin protein HP1 preferentially reduces male viability (Liu et al. 2005). Position-effect variegation (PEV), the partial silencing of reporter genes in some cells that normally express a gene resulting in mosaic expression patterns, is often used as an indicator...

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