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Research: Genome-wide activities of Polycomb complexes control pervasive transcription
- Hun-Goo Lee,
- Tatyana G. Kahn,
- Amanda Simcox,
- Yuri B. Schwartz,
- and Vincenzo Pirrotta
Genome Res. August 2015 25: 1170-1181; Published in Advance May 18, 2015, doi:10.1101/gr.188920.114
...activation and a positive role to H3K27me1 in productive transcription.Here we characterize the distribution and evaluate the effects of pervasive H3K27 methylation in the Drosophila . H3K27me2 is found ubiquitously except in actively transcribed regions or in PcG target regions, which contain H3K27me3. We...
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Research: Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2
- Jacob M. Garrigues,
- Simone Sidoli,
- Benjamin A. Garcia,
- and Susan Strome
Genome Res. January 2015 25: 76-88; Published in Advance December 2, 2014, doi:10.1101/gr.180489.114
...of heterochromatin protein 1 (HP1), a highly conserved, small nonhistone protein first identified in Drosophila (James and Elgin 1986). Heterochromatin is typically concentrated at pericentric and subtelomeric regions. How heterochromatin is distributed in an organismwithnumerous centromeres distributed along...
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Research: CBX3 regulates efficient RNA processing genome-wide
- Andrea Smallwood,
- Gary C. Hon,
- Fulai Jin,
- Ryan E. Henry,
- Joaquín M. Espinosa,
- and Bing Ren
Genome Res. August 2012 22: 1426-1436; Published in Advance June 8, 2012, doi:10.1101/gr.124818.111
...to gene bodies. However, we were not able to detect significant H3K9me2/3 at CBX3 target genes (data not shown). This is in agreementwithHP1 and SU(VAR)3-9 localizing together at pericentric regions but independently atmanyother regions inDrosophila (Greil et al. 2003). Next, we tested the possibility...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
.... For example, the 2009 identification of the mutation that causes SCA31 was achieved solely by “traditional” methods: bacterial artificial chromosome (BAC)-based cloning, Sanger sequencing, and Southern blot, with targeted shotgun resequencing (Sato et al. 2009).The techniques employed by the Human Genome...
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Research: Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome
- Michaela Schwaiger,
- Hubertus Kohler,
- Edward J. Oakeley,
- Michael B. Stadler,
- and Dirk Schübeler
Genome Res. June 2010 20: 771-780; Published in Advance April 30, 2010, doi:10.1101/gr.101790.109
...Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome Michaela Schwaiger 1 , Hubertus Kohler , Edward J. Oakeley 2 , Michael B. Stadler and Dirk Schübeler 3 Friedrich Miescher Institute...
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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
...Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin Nicole C. Riddle 1 , 9 , Aki Minoda 2 , 9 , Peter V. Kharchenko 3 , 9 , Artyom A. Alekseyenko 4 , Yuri B. Schwartz 5 , 6...
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Research: Developmental control of gene copy number by repression of replication initiation and fork progression
- Noa Sher,
- George W. Bell,
- Sharon Li,
- Jared Nordman,
- Thomas Eng,
- Matthew L. Eaton,
- David M. MacAlpine,
- and Terry L. Orr-Weaver
Genome Res. January 2012 22: 64-75; Published in Advance November 16, 2011, doi:10.1101/gr.126003.111
...length 25). ChIP peak calling The ChIP-seq reads were mapped back to the Drosophila melanogaster (FlyBase version 5.2) using MAQ (version 0.7.1) Developmental control of origins and fork movement Genome Research 73 www..org (Li et al. 2008) with a maximum of three mismatches per read. For the salivary...
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LETTER: The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide
- Rituparna Mukhopadhyay,
- WenQiang Yu,
- Joanne Whitehead,
- JunWang Xu,
- Magda Lezcano,
- Svetlana Pack,
- Chandrasekhar Kanduri,
- Meena Kanduri,
- Vasudeva Ginjala,
- Alexander Vostrov,
- Wolfgang Quitschke,
- Igor Chernukhin,
- Elena Klenova,
- Victor Lobanenkov,
- and Rolf Ohlsson
Genome Res. August 2004 14: 1594-1602; Published in Advance July 15, 2004, doi:10.1101/gr.2408304
...in Drosophila melanogaster and its gene. Mol. Cell Biol. 6 : 3862 –3872. ↵ Kanduri, C., Holmgren, C., Franklin, G., Pilartz, M., Ullerås, E., Kanduri, M., Liu, L., Ginjala, V., Ulleras, E., Mattsson, R., et al. 2000a . The 5'-flank of the murine H19 gene in an unusual chromatin conformation unidirectionally...
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Research: Developmental control of the DNA replication and transcription programs
- Jared Nordman,
- Sharon Li,
- Thomas Eng,
- David MacAlpine,
- and Terry L. Orr-Weaver
Genome Res. February 2011 21: 175-181; Published in Advance December 22, 2010, doi:10.1101/gr.114611.110
...–213. Pindyurin AV, Moorman C, de Wit E, Belyakin SN, Belyaeva ES, Christophides GK, Kafatos FC, van Steensel B, Zhimulev IF. 2007. SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila. J Cell Sci 120: 2344–2351. Rodman TC. 1967. DNA replication in salivary gland nuclei of Drosophila...
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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
...) (see Fig. 3B,C). This is consistent with the known mechanism of dosage compensation in Drosophila, whereby the MSL complex targets actively transcribed genes along the X chromosome by recognizing H3K36me3 and then inducing H4K16 acetylation Sex-specific chromatin landscape of Drosophila Genome Research...

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