Searching journal content for articles similar to Hari Sundar G et al. 33 (5): 715.

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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...melanogaster (Gilmour and Lis 1986; Rougvie and Lis 1988; Muse et al. 2007; Nechaev et al. 2010), and are also shown to be widespread in mammals (Kwak et al. 2013; Williams et al. 2015), most metazoans, and some plants are but absent in yeast and Arabidopsis thaliana (Chivu et al. 2023). Bacteria do exhibit...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...Corresponding authors: kitao.z7deb13@gmail.com, so@tokai.ac.jpAbstractTransposons, occasionally domesticated as novel host protein-coding genes, are responsible for the lineage-specific functions in vertebrates. LINE-1 (L1) is one of the most active transposons in the vertebrate s. Despite its abundance, few...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...correlation between RNAPII elongation rates and nascent RNA levels, suggesting that elongation speed can affect transcriptional activity. This agrees with previous observations both in human cell lines (Danko et al. 2013; Jonkers et al. 2014) and in plants (Leng et al. 2020). The application of multiple time...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...that LADs unique to our MEFs have slightly lower levels of lamin B1 association than shared LADs and may be slightly more variable across the cell population (Supplemental Fig. S1D).LAD borders show enrichment of multiple histone modificationsTo determine the structure of chromatin across LADs, we used CUT...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...with metabolically labeled transcriptomic data (Cucinotta et al. 2021), provides strong evidence for active transcription of 3% of protein-coding genes (class I), thus showing that Q cells are not transcriptionally inert. The sensitivity of 4tU-labeled transcript detection and RNAPII ChIP might cause...
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Research: High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
...identified, clustered upstream of TGFBI. Transcription was observed to overlap enhancer-associated chromatin marks. As was observed for FOS, comparison of expression dynamics revealed that lncRNA expression mirrored the activation of the adjacent protein-coding gene (Fig. 5E).As a third example, we examined...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...methylation is catalyzed by histone methyltransferases (HMTs), which typically contain a conserved SET domain that mediates lysine methylation. Evolutionary studies in plants and animals reveal considerable SET domain protein functional diversity, specializing in development and stress responses (Zhang and Ma...
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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
...to analyze the transcriptome, histone modification patterns, and replication timing of germline stem cell (GSC)–like and somatic cyst stem cell (CySC)–like cells. Single-cell RNA sequencing validates previous findings on GSC–CySC intercellular communication and reveals a high expression of chromatin...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...is required to maintain pluripotency by regulating the PSN enhancer network via the recruitment of RNA polymerase II.Acetylation of lysine residues in histone tails is an essential post-translational modification (PTM), dynamically regulated by the opposing actions of histone acetyltransferases (HATs...
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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
...comparison across tools, we observe the same EP-associated histone-tail modifications, showing cleaner peaks at 5 kb than at 10 kb (Supplemental Fig. 4C), whereas in our other experiments, Quagga is sensitive to a sequencing depth of as low as 125 million read pairs (Supplemental Fig. 3B).Quagga is effective...
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