Searching journal content for articles similar to Weil et al. 14 (7): 1374.

Displaying results 1-10 of 170

For checked items

view abstracts
download to citation manager

Select this article
Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...these two states has not been accessible to simultaneous measurement. To this end, we developed KAS-ATAC, a combination of the kethoxal-assisted ssDNA sequencing (KAS-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) methods for mapping single-stranded DNA (and thus active...
Select this article
Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...in novel genetic interactions with unlinked genes. We validated a novel genetic interaction between different CNVs and BMH1 that was common to multiple strains. We also analyzed global gene expression and found that transcriptional dosage compensation does not affect most genes amplified by CNVs, although...
OPEN ACCESS ARTICLE
Select this article
Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...), which may be important for the clearance of serum DNA/chromatin complexes (Sisirak et al. 2016). Indeed, loss of function in Dnase1l3 or Dnase1 is associated with systemic lupus erythematosus (SLE) in humans and mice (Napirei et al. 2000; Al-Mayouf et al. 2011).Using genetically modified mice in which...
OPEN ACCESS ARTICLE
Select this article
Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
- Veronica Astro,
- Kelly Yojanna Cardona-Londoño,
- Lorena Viridiana Cortés-Medina,
- Rawan Alghamdi,
- Gustavo Ramírez-Calderón,
- Fotios Kefalas,
- Jair Dilmé-Capó,
- Santiago Radío,
- and Antonio Adamo
Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
...genes with dosage sensitivity to the Y number are shown. Pearson's correlation coefficient (R), P-value, and FDR are indicated.The presence of an extra Y Chromosome results in subtle changes in DNA methylationTo understand the impact of an extra Y Chromosome on global DNA methylation, we performed...
OPEN ACCESS ARTICLE
Select this article
Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...-quadruplexes (Wells 2007), which can have functional impacts on the (Mao et al. 2018; Georgakopoulos-Soares et al. 2022a,b). Furthermore, variation of the length of STRs can result in changes at both DNA and chromatin level. For instance, GAA expansions that underlie Friedreich's ataxia (FRDA) [MIM: 229300] (Hannan...
Select this article
Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...to explore the chromatin landscape, surveying the occupancy of all DNA-binding factors across the , without regard to their identities. It provides an alternative to ChIP-based approaches which use an antibody to ensure the identity of a single factor whose occupancy is being surveyed. Because thousands...
Select this article
Research: DNA replication and transcription programs respond to the same chromatin cues
- Yoav Lubelsky,
- Joseph A. Prinz,
- Leyna DeNapoli,
- Yulong Li,
- Jason A. Belsky,
- and David M. MacAlpine
Genome Res. July 2014 24: 1102-1114; Published in Advance July 1, 2014, doi:10.1101/gr.160010.113
...replicating domains were defined at the level of origin selection (ORC binding) and likely mediated by chromatin accessibility. In contrast, dynamic domains exhibited low ORC densities in both cell types, suggesting that origin activation and not origin selection governs the plasticity of the DNA replication...
OPEN ACCESS ARTICLE
Select this article
Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
...-primate differences in regulatory mechanisms and phenotypes other than gene expression levels, such as DNA methylation levels, chromatin modifications and accessibility, and protein expression levels (Cain et al. 2011; Pai et al. 2011; Hernando-Herraez et al. 2013, 2015a,b; Ward et al. 2013; Stergachis et al. 2014...
OPEN ACCESS ARTICLE
Select this article
Research: Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns
- Elisheva Javasky,
- Inbal Shamir,
- Shashi Gandhi,
- Shawn Egri,
- Oded Sandler,
- Scott B. Rothbart,
- Noam Kaplan,
- Jacob D. Jaffe,
- Alon Goren,
- and Itamar Simon
Genome Res. October 2018 28: 1455-1466; Published in Advance August 30, 2018, doi:10.1101/gr.230300.117
...that although mitotic chromatin is highly condensed, global levels of histone methylation is mostly maintained. In contrast, histone acetylation abundance was reduced in mitotic samples as seen by measuring both global protein levels (via proteomics and immunofluorescence) and DNA association (via Ch...
Select this article
Research: Global survey of escape from X inactivation by RNA-sequencing in mouse
- Fan Yang,
- Tomas Babak,
- Jay Shendure,
- and Christine M. Disteche
Genome Res. May 2010 20: 614-622; Published in Advance April 2, 2010, doi:10.1101/gr.103200.109
...by pull-down using protein A–Sepharose beads (Amersham). Controls included ChIP carried out without antibody (no antibody fraction) and the input fraction. After incubation with the antibody overnight, protein A–Sepharose beads were added to pull down the chromatin. DNA was purified from the Ch...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Weil et al. 14 (7): 1374.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: