Searching journal content for articles similar to Ulianov et al. 26 (1): 70.

Displaying results 1-10 of 98

For checked items

view abstracts
download to citation manager

Select this article
Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...architectural features; these include A/B compartments, topologically associating domains (TADs), and chromatin loops (Lieberman-Aiden et al. 2009; Dixon et al. 2012; Nora et al. 2012; Sexton et al. 2012; Rao et al. 2014). Improvements in 3C sequencing technologies resulted in improved sequencing depth...
OPEN ACCESS ARTICLE
Select this article
Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...(Pol II) -wide. These approaches provide a high-resolution view of transcription initiation, pausing, and elongation, enabling rapid detection of transcriptional changes following TF perturbation.Other methods survey Pol II–associated chromatin-bound RNAs, such as chromatin-associated RNA-seq (Chr...
OPEN ACCESS ARTICLE
Select this article
Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...chromatin domains, often referred to as topological associating domains (TADs), as fundamental units of three-dimensional (3D) organization (Szabo et al. 2018). Such domains are closely linked to important DNA-dependent and cellular processes, such as DNA replication (Pope et al. 2014), transcription...
Select this article
Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...modifications, and other aspects of chromatin remains mysterious.3D chromatin domains3D chromatin research often examines topologically associated domains (TADs), which manifest as triangles of high signal intensity in chromatin contact maps, indicative of interactions among loci in close linear proximity...
OPEN ACCESS ARTICLE
Select this article
Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
....zabet@qmul.ac.ukAbstractThe DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here...
OPEN ACCESS ARTICLE
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
...@cse.cuhk.edu.hk, xin.gao@kaust.edu.saAbstractChromatin loop identification plays an important role in molecular biology and 3D genomics research, as it constitutes a fundamental process in transcription and gene regulation. Such precise chromatin structures can be identified across -wide interaction matrices via Hi...
OPEN ACCESS ARTICLE
Select this article
Research: Orc4 spatiotemporally stabilizes centromeric chromatin
- Lakshmi Sreekumar,
- Kiran Kumari,
- Krishnendu Guin,
- Asif Bakshi,
- Neha Varshney,
- Bhagya C. Thimmappa,
- Leelavati Narlikar,
- Ranjith Padinhateeri,
- Rahul Siddharthan,
- and Kaustuv Sanyal
Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
...in every chromosome and are clustered throughout the cell cycle. In this study, the -wide occupancy of the replication initiation protein Orc4 reveals its abundance at all centromeres in C. albicans. Orc4 is associated with four different DNA sequence motifs, one of which coincides with tRNA genes (t...
Select this article
Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...–J) Predicted domain boundaries fall within regions of heterochromatin. Domain boundaries are associated with reduced chromatin accessibility (F), H3K4me1 (G), and sequence conservation (H) and with elevated repeat element density (I) and H3K27me3 (J).We next explored intra-chromosomal interactions in our Hi...
Select this article
Research: Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
- Zubairul Islam,
- Bharath Saravanan,
- Kaivalya Walavalkar,
- Umer Farooq,
- Anurag Kumar Singh,
- Sabarinathan Radhakrishnan,
- Jitendra Thakur,
- Awadhesh Pandit,
- Steven Henikoff,
- and Dimple Notani
Genome Res. January 2023 33: 1-17; Published in Advance January 17, 2023, doi:10.1101/gr.276643.122
...Cancer Research Center, Seattle, Washington 98109, USA ↵6 These authors contributed equally to this work. Corresponding author: dnotani@ncbs.res.inAbstractVertebrate s are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs...
OPEN ACCESS ARTICLE
Select this article
Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...species and cell types revealed that interphase chromosomes are partitioned at different scales (Rowley and Corces 2018): from topologically associating domains (TADs) (Dixon et al. 2012) at a few hundreds of kilobase pairs, to the euchromatic “A” and heterochromatic “B” compartments at megabase pair...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ulianov et al. 26 (1): 70.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: