Searching journal content for articles similar to Papatsenko et al. 12 (3): 470.

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Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
- James L. Shepherdson,
- Ryan Z. Friedman,
- Yiqiao Zheng,
- Chi Sun,
- Inez Y. Oh,
- David M. Granas,
- Barak A. Cohen,
- Shiming Chen,
- and Michael A. White
Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
...corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, and p.E168d2 has distinct effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are derepressed in the presence of p.E168d2. Chromatin environments of CRX...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
..., demonstrating an unprecedented putative cis-regulatory role of Helitrons in Drosophila. Differential expression analysis between species with different preferred hosts reveals divergence in gene expression in heads and larvae. Although TEs’ presence does not affect overall gene expression, we observe 6...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...translocates to the nucleus to occupy estrogen receptor binding sites (ERBS), which are characterized by a palindromic consensus motif (AGGTCAnnnTGACCT) (Klinge 2001). These ERBS are predominantly located at enhancers in distal intergenic and intronic regions, where their accessibility depends critically...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...analysis on iPSC-CMs under various states of maturation. We identified novel regulatory regions that function in CMs. We developed a more comprehensive model by which MYH6 and MYH7 are regulated, adding to previous work related to the C3 enhancer (Gacita et al. 2021). We found evidence of dynamic...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...and ISWI1 on nucleosomes.ICOP paralogs might contribute to the directionality of the remodeling complex, as shown for Drosophila Acf1, a protein that regulates ISWI-containing complex CHRAC directionality (Eberharter et al. 2001). In contrast to ISWI1, ICOP KDs caused a preference both for partial internal...
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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
...enriched along the gene bodies in CySC-like cells (Fig. 3G; Supplemental Table S4). This differential enrichment indicates a cell-type-specific regulatory mechanism for which H3K27me3 plays a more prominent role in CySC-like cells than in GSC-like cells.Previous functional studies in Drosophila testes...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...Global 3′ UTR shortening, exhibiting cell type–specific patterns, has been reported in some model organisms, such as mice and Drosophila (Shulman and Elkon 2019; Lee et al. 2022). However, in pigs, the dynamics of these patterns, particularly at single-cell resolution, remain largely unexplored. Given...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...-class HD family possesses a unique feature in that members of this class confer cooperative dimerization on specific dimeric DNA sequences. The “cooperative” interaction here is when the first HD–DNA half-site binding greatly enhances the binding of a second molecule to the other half-site (Fig. 1A...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...in evolution. WGDs can increase TE activity directly through cellular stress or indirectly by relaxing selection against TE insertions in functionally redundant, duplicated regions. Because TEs can function as, or evolve into, TE-derived cis-regulatory elements (TE-CREs), bursts of TE activity following WGD...
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Research: Enhancers display constrained sequence flexibility and context-specific modulation of motif function
- Franziska Reiter,
- Bernardo P. de Almeida,
- and Alexander Stark
Genome Res. March 2023 33: 346-358; Published in Advance March 20, 2023, doi:10.1101/gr.277246.122
...).Random variant libraries of Drosophila enhancers and UMI-STARR-seqTwo strong S2 developmental enhancers with different TF motif compositions were selected to test a diversity of random 8-nt variants in different positions: ced-6 (Chr 2R: 5,326,628–5,326,876) and ZnT63C (Chr 3L: 3...

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