Searching journal content for articles similar to Castaño et al. 13 (5): 905.

Displaying results 1-10 of 5371

For checked items

view abstracts
download to citation manager

Select this article
Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...is a critical mechanism in XCI, a dosage compensation process ensuring a single active X Chromosome in both XY and XX individuals (Lyon 1962). In typical XX individuals, one X is randomly silenced in each cell during development, with methylation maintaining gene repression on the inactive X (Xi). This random...
OPEN ACCESS ARTICLE
Select this article
Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
OPEN ACCESS ARTICLE
Select this article
Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...were irrespective of the repeat motif, GTTTTTT, because even random sequences (NNNNNNN) reduced the splicing efficiency, whereas those containing TNA recovered it (Supplemental Fig. S6B). Thus, in the regulatory machinery that SpliceAI learned, the NARS2 GTTTTTT repeat regulates splicing through...
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
...abundances of accessible ssDNA and accessible DNA). (C) KAS-seq, ATAC-seq, and KAS-ATAC mitochondrial profiles in human GM12878 cells. (D) Fragment length distribution in biotin-ATAC-seq and KAS-ATAC libraries (GM12878 cells). (E) Genome-wide TSS metaprofiles for biotin-ATAC-seq and KAS-ATAC libraries (GM...
Select this article
Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
- Monica R. Sanchez,
- Celia Payen,
- Frances Cheong,
- Blake T. Hovde,
- Sarah Bissonnette,
- Adam P. Arkin,
- Jeffrey M. Skerker,
- Rachel B. Brem,
- Amy A. Caudy,
- and Maitreya J. Dunham
Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
...-based mutagenesis methods used to create random insertional mutant collections, eliminating requirements for a priori knowledge about defined coding regions and providing information about partial loss-of-function or gain-of-function mutations. Random insertional profiling has been widely applied across various...
Select this article
Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...to perform loop calling, with their recommended hyperparameter configurations. Those loop predictions were subsequently thresholded and evaluated. For Peakachu, following its official instructions, an individual random forest model was trained per chromosome using the remainder of the , followed by loop...
OPEN ACCESS ARTICLE
Select this article
Method: A systematic genome-wide account of binding sites for the model transcription factor Gcn4
- Christopher T. Coey and
- David J. Clark
Genome Res. February 2022 32: 367-377; Published in Advance December 16, 2021, doi:10.1101/gr.276080.121
...is apparent in our findings. However, because the 6xHis tag was inserted in the C terminus, where the DNA-binding and leucine zipper dimerization domains also reside, the degraded forms of Gcn4-6xHis-FLAG should not interfere with its ability to bind the AP-1 consensus sequence (TGACTCA). Indeed, as shown...
Select this article
Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...number of genomic mutations in just a few cell cycles. In contrast, despite clear deaminase activity and DNA damage, APOBEC3B upregulation does not generate a significant increase in mutations in the gastric epithelium. APOBEC3B-associated mutagenesis remains minimal even in the context of TP53...
OPEN ACCESS ARTICLE
Select this article
Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...and demographic conditions than their counterparts on the continent, resulting in divergent evolutionary forces affecting their s. Random genetic drift and selection both may leave their imprints on island populations, although the relative impact depends strongly on the specific conditions. Here we address...
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
...variation of an STR might regulate local DNA methylation can be proposed. A logical mechanism implies the alteration of CpG density in a given locus by the insertion of CpG-containing repeats. This is the proposed mechanism for some repeat expansion disorders such as fragile X syndrome [MIM: 300624], where...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Castaño et al. 13 (5): 905.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: