Searching journal content for articles similar to Siefert et al. 27 (8): 1406.

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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
....e., computational representations of transcripts depicting their transcription start and termination sites (TSS and TTS) and intron composition (Amarasinghe et al. 2020; Marx 2023). Most lrRNA-seq experiments rely on cDNA libraries, as they provide high sequencing throughput and accuracy. However, reverse...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...to the transcription machinery. As a result, transcription levels can undergo repression leading to a silencing effect of the associated gene. The dominant form of DNA methylation in terminally differentiated human cells occurs proximal to a guanosine residue, and the resulting loci are often referred to as CpG sites...
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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
...that H4K16 modification is dispensable for replication and gene expression.Animal cells duplicate large, complex s by initiating replication at distinct locations within the at different times during S phase. An evolutionarily conserved feature of this regulatory paradigm is a temporal order of DNA...
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Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Joana Sequeira-Mendes,
- Zaida Vergara,
- Ramon Peiró,
- Jordi Morata,
- Irene Aragüez,
- Celina Costas,
- Raul Mendez-Giraldez,
- Josep M. Casacuberta,
- Ugo Bastolla,
- and Crisanto Gutierrez
Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
...states, except state 1 (TSS), state 8 (AT-rich heterochromatin), and state 4 (intergenic, Polycomb, and AT-rich), which are most variable.Interplay between DNA replication origins and transcriptional programsThe relationship between ORI activity and transcriptional programs during development has been...
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Method: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
- Jean Fan,
- Hae-Ock Lee,
- Soohyun Lee,
- Da-eun Ryu,
- Semin Lee,
- Catherine Xue,
- Seok Jin Kim,
- Kihyun Kim,
- Nikolaos Barkas,
- Peter J. Park,
- Woong-Yang Park,
- and Peter V. Kharchenko
Genome Res. August 2018 28: 1217-1227; Published in Advance June 13, 2018, doi:10.1101/gr.228080.117
...transcriptionally distinct subpopulations and genetic subclones. At the same time, simultaneous unbiased assessment of DNA and RNA from an individual cell remains challenging (Dey et al. 2015; Macaulay et al. 2015; Wang et al. 2017).Computational approaches for bulk sequencing data detect copy number variations...
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Research: Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
- Chun-Long Chen,
- Aurélien Rappailles,
- Lauranne Duquenne,
- Maxime Huvet,
- Guillaume Guilbaud,
- Laurent Farinelli,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- Olivier Hyrien,
- and Claude Thermes
Genome Res. April 2010 20: 447-457; Published in Advance January 26, 2010, doi:10.1101/gr.098947.109
...profile of the whole human genome by massively parallel sequencing of nascent BrdU-labeled replicating DNA. These data were compared to the neutral substitution rates along the human genome, obtained by aligning human and chimpanzee genomes using macaque and orangutan as outgroups. All substitution rates...
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Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
- Shaleen Shrestha,
- Jared Allan Sewell,
- Clarissa Stephanie Santoso,
- Elena Forchielli,
- Sebastian Carrasco Pro,
- Melissa Martinez,
- and Juan Ignacio Fuxman Bass
Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
...interaction with an 18-bp indel in the TAL1 superenhancer. Additionally, we identified TFs that bind to three uncharacterized DNA motifs identified in DNase footprinting assays. We anticipate that these enhanced yeast one-hybrid approaches will expand our capabilities to study genetic variation...
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Perspective: Understanding the regulatory and transcriptional complexity of the genome through structure
- Tim R. Mercer and
- John S. Mattick
Genome Res. July 2013 23: 1081-1088; doi:10.1101/gr.156612.113
...and binding motif. (B) Immunoprecipitation of DNA sequence associated with large multiprotein complex results in artifactual indirect enrichments for a wide range of transcription factors. (C ) Active enhancers exhibit a range of ChIP-seq enrichments as a result of a close spatial proximity to histone...
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Next-Generation DNA Sequencing/Review: Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
- Melissa J. Fullwood,
- Chia-Lin Wei,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. April 2009 19: 521-532; doi:10.1101/gr.074906.107
.... Collectively, ChIP-PET and ChIP-seq powered by Illumina and other massively parallel tag sequencing platforms have generated and will continue to generate valuable maps of protein factors interacting with genomic DNA in the genomic landscape. From these analyses, general pictures of transcription factor...
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