Searching journal content for articles similar to Strobino et al. 30 (12): 1740.

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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...devised new methods to map DNA supercoiling and single-stranded DNA in Caenorhabditis elegans embryos and diapause larvae. To map supercoiling, we quantified the incorporation of biotinylated psoralen into DNA using high-throughput sequencing. To map single-stranded DNA, we combined permanganate treatment...
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Method: RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases
- László Halász,
- Zsolt Karányi,
- Beáta Boros-Oláh,
- Tímea Kuik-Rózsa,
- Éva Sipos,
- Éva Nagy,
- Ágnes Mosolygó-L,
- Anett Mázló,
- Éva Rajnavölgyi,
- Gábor Halmos,
- and Lóránt Székvölgyi
Genome Res. June 2017 27: 1063-1073; Published in Advance March 24, 2017, doi:10.1101/gr.219394.116
...(experiments 17–24)In comparison to the original DRIP protocol, classical chromatin immunoprecipitation (ChIP) involves the capture of RNA-DNA hybrids by immunoprecipitation from cross-linked and sonicated chromatin (rather than naked DNA) followed by phenol/chloroform purification (Fig. 1C). Since sonication...
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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
.... Initially defined based on histological staining patterns in interphase cells (Heitz 1928), these subtypes are now known to represent distinct genomic and nuclear domains distinguished by a variety of properties including DNA sequence composition, gene density, replication timing, nuclear localization...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...among different tissue types, cell types, and individuals, potentially underscoring divergent epigenetic regulation at different scales of phenotypic diversity. We find that differential DNA methylation at enhancer elements, with concurrent changes in histone modifications and transcription factor...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...cells to re-enter the cell cycle partially restores a youthful H3K27me3 landscape, suggesting that DNA replication may rejuvenate chromatin structure (Yang et al. 2023). However, even mitotically active somatic stem cells display age-related increases in Polycomb repression: Aged Drosophila intestinal...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
.... elegans were sampled from the cleavage stage until hatching (but not after). First, while analyzing mtDNA and nuclear DNA-encoded OXPHOS gene expression, we found that, unlike mammals and chicken, CMNGE elevation occurred in X. tropicalis before hatching (Fig. 6A; Supplemental Figs. S46–S48). In replicate...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
..., and consistent with this, DNA breaks in human centromeres during the G1 phase of the cell cycle are actively repaired using RAD51, despite the absence of a replicated sister chromatid (Yilmaz et al. 2021).Because of the observed high levels of satellite structural polymorphism, it has been proposed that unequal...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...GenomiPhi Kit was used for cell lysis and multiple displacement amplification. Sequencing was performed using Illumina sequencing methodology (Bentley et al. 2008). In detail, 2 µg of amplified DNA was introduced into Illumina's TruSeq DNA PCR-free library preparation. Paired-end sequencing was conducted...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...-capped extremities composed of sequences originating from more internal genomic regions were associated with high DNA methylation, suggesting that de novo heterochromatin formation contributes to the restoration of chromosome end stability in C. reinhardtii. The diversity of alternative strategies present...
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Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Stephen G. Landt,
- Georgi K. Marinov,
- Anshul Kundaje,
- Pouya Kheradpour,
- Florencia Pauli,
- Serafim Batzoglou,
- Bradley E. Bernstein,
- Peter Bickel,
- James B. Brown,
- Philip Cayting,
- Yiwen Chen,
- Gilberto DeSalvo,
- Charles Epstein,
- Katherine I. Fisher-Aylor,
- Ghia Euskirchen,
- Mark Gerstein,
- Jason Gertz,
- Alexander J. Hartemink,
- Michael M. Hoffman,
- Vishwanath R. Iyer,
- Youngsook L. Jung,
- Subhradip Karmakar,
- Manolis Kellis,
- Peter V. Kharchenko,
- Qunhua Li,
- Tao Liu,
- X. Shirley Liu,
- Lijia Ma,
- Aleksandar Milosavljevic,
- Richard M. Myers,
- Peter J. Park,
- Michael J. Pazin,
- Marc D. Perry,
- Debasish Raha,
- Timothy E. Reddy,
- Joel Rozowsky,
- Noam Shoresh,
- Arend Sidow,
- Matthew Slattery,
- John A. Stamatoyannopoulos,
- Michael Y. Tolstorukov,
- Kevin P. White,
- Simon Xi,
- Peggy J. Farnham,
- Jason D. Lieb,
- Barbara J. Wold,
- and Michael Snyder
Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
...IP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments...
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