Searching journal content for articles similar to Maksimenko et al. 25 (1): 89.

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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; 3Life Sciences Institute and The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310058, China The development of 3C-based techniques for analyzing three-dimensional chromatin structure dynamics has driven significant...
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Research: Genomic context sensitivity of insulator function
- André M. Ribeiro-dos-Santos,
- Megan S. Hogan,
- Raven D. Luther,
- Ran Brosh,
- and Matthew T. Maurano
Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
...is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites -wide function as insulator elements, depending on cellular and genomic context. To dissect the influence...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...of microRNA dynamics at the single-cell level.microRNAs (miRNAs) are ∼22 nucleotide (nt) small noncoding RNAs that guide Argonaute effector proteins to target mRNAs in a sequence-specific manner, leading to their translational inhibition and increased degradation through deadenylation and decapping (Bartel...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...could use CTCF-mediated chromatin organization to regulate target genes. To investigate this, we performed CUT&RUN in HEK293T cells to map CTCF -wide binding under Wnt-OFF (i.e., chemical inhibition of PORCN by LGK-974 [LGK]) or Wnt-ON (i.e., inhibition of GSK3 by the small molecule CHIR99021 [CHIR...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...to be a highly effective and reproducible method for capturing the binding of protein complexes or TFs (e.g., NF-kB and STAT3) and identifying genomic targets for protein–DNA binding with high signal-to-noise ratios (SNRs) (Nowak et al. 2005; Tian et al. 2012).Moreover, effective chromatin solubilization is also...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
..., complicating bulk-tissue analyses. Here, using 71 patient-derived PAAD organoids, we show that TE activities may potentially promote tumorigenesis and provide a source of novel immunotherapeutic targets. We identify 16 new TE-derived transcripts fused with 15 known oncogenes, exhibiting potential oncogenic...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...these JS divergence values to a gamma distribution, and interactions representing the strongest chromatin changes within mutant–gene pairs were highlighted (Fig. 1C). To validate our measure, we assessed the JS divergence values of mutants at known target genes and found that the values were highly...
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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
...this, we optimized a low-input cell-type-specific chromatin profiling method using updtumor testes, which employs micrococcal nuclease (MNase) digestion of targeted chromatin (Fig. 3A). In this method, we coexpressed the Upd ligand and histone H3-GFP fusion protein in either GSC-like cells (nanos > upd...
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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
...] digestion). Protein occupancy—Immunoprecipitation is used to identify loci occupied by a protein of interest. A typical implementation is ChIP-seq, as well as recent methods which use a modified protein A (pA). These include Cleavage Under Targets and Release Using Nuclease (CUT&RUN), which uses p...
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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
..., Houston, Texas 77030, USA; 6Department of Computer Science and Engineering, University of Michigan, Ann Arbor, Michigan 48103, USA ↵7 These authors contributed equally to this work. Corresponding authors: Xiaotian.Zhang@uth.tmc.edu, drjieliu@umich.eduAbstractChromatin stripes are architectural chromatin...
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