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Research: Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote
- Yalan Sheng,
- Yuanyuan Wang,
- Wentao Yang,
- Xue Qing Wang,
- Jiuwei Lu,
- Bo Pan,
- Bei Nan,
- Yongqiang Liu,
- Fei Ye,
- Chun Li,
- Jikui Song,
- Yali Dou,
- Shan Gao,
- and Yifan Liu
Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
...corresponding to DNA molecules with full-6mApT congregation within an LD (Fig. 5H) and across adjacent LDs (Fig. 5I), respectively. (H) Full-6mApT congregation within an LD. (I) Full-6mApT congregation across adjacent LDs.We also analyzed human chromatin in vitro methylated by AMT1 complex or M.EcoGII (Fig. 6D...
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Research: Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
- Răzvan V. Chereji,
- Peter R. Eriksson,
- Josefina Ocampo,
- Hemant K. Prajapati,
- and David J. Clark
Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119
...in chromatin. Small DNA fragments excised from accessible DNA sequences (typically regulatory elements) are isolated and sequenced. However, the rest of the is excluded from the analysis because it is still present as very long DNA molecules. Consequently, the signal and relative amounts of each accessible...
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Research: MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites
- Yi Xiang See,
- Kaijing Chen,
- and Melissa J. Fullwood
Genome Res. April 2022 32: 629-642; Published in Advance February 3, 2022, doi:10.1101/gr.276313.121
...buffer overnight at 37°C, and DNA was precipitated using ethanol. The 4C libraries were multiplexed and single-end 1 × 150-bp sequencing was performed on the Illumina MiSeq.RNA-seq experimental procedureTotal RNA was extracted from U2OS cells with or without MYC induction in duplicate, using the RNeasy...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...L. The polymerase was then inactivated for 3 min at 65°C. MDA-amplified DNA clean-up was performed with 1:1.3 (v/v) ratio AMPure XP beads (Beckman Coulter A63881) immediately before the de-branching step. To screen nuclei for those with the most even -wide amplification, multiplexed PCR primers were designed...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
...cohort among PDAC patients. Finally, we identify and validate the casein kinase CSNK1A1 (also known as CK1alpha or CK1a) as an APA-regulated therapeutic target in PDAC. Knockdown or pharmacological inhibition of CSNK1A1 attenuates PDAC cell proliferation and clonogenic growth. Our single-cancer analysis...
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