Searching journal content for articles similar to Lian et al. 18 (8): 1224.

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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
...have significant functional implications as elongation rate affects the timing of cotranscriptional processing events such as RNA splicing, polyadenylation, and 3′ end formation. Additionally, these changes may influence chromatin modifications that depend on RNAPII progression speed.A major advantage...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
..., the bulk of which is the result of the opening of the DNA double-strand associated with engaged RNA polymerase molecules. We use KAS-ATAC to answer several questions regarding the relationship between active transcription/ssDNA formation and fine-scale chromatin architecture.We show that the genomic...
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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
..., important for loop extrusion, is RNA dependent, and RNA binding of CTCF is required for TAD chromatin organization (Hansen et al. 2019; Saldaña-Meyer et al. 2019), but how CTCF:RNA interactions maintain TADs is not clear.In some instances, TAD boundaries are found near sites of enhancers (Nandy Mazumdar et...
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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
.... This demonstrates the potential for ONT direct RNA sequencing to identify problematic sites in LVs, to inform the design of optimized vectors, and to verify that introduced modifications reduce truncated lentiviral RNA.Artificial polyadenylation reveals additional sites of truncationWe then explored the use...
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Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
- Juncheng Lin,
- Fu-Yu Hung,
- Congting Ye,
- Liwei Hong,
- Yuan-Hsin Shih,
- Keqiang Wu,
- and Qingshun Q. Li
Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
..., suggesting the regulatory role of chromatin status in orchestrating mRNA polyadenylation (Huang et al. 2013; Lee and Chen 2013). Overall, the compactness of chromatin is determined by histone modifications such as methylation and acetylation. Within these modifications, histone acetylation is known...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...: wyzhang@nwpu.edu.cn, tautz@evolbio.mpg.deAbstractThe ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full...
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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
....feigin@roswellpark.orgAbstractAlternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3′-UTR length, resulting in changes in mRNA stability and localization. APA is frequently disrupted in cancer and promotes tumorigenesis through altered expression of oncogenes and tumor suppressors. Pan-cancer analyses have revealed common APA...
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Research: Accumulation of RNA on chromatin disrupts heterochromatic silencing
- Cornelia Brönner,
- Luca Salvi,
- Manuel Zocco,
- Ilaria Ugolini,
- and Mario Halic
Genome Res. July 2017 27: 1174-1183; Published in Advance April 12, 2017, doi:10.1101/gr.216986.116
.... Scale bars on the right denote read numbers per million reads normalized to the TAS region (Chr 2: 4534 kb–4538 kb) where H3K9me2 is not lost in the mutant. RNA on chromatin disrupts heterochromatin Genome Research 1175 www..org subtelomeric, centromeric, and mat locus in caf1Δdcr1Δ and caf1Δago1Δ cells...
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Research: Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation
- Jonathan Neve,
- Kaspar Burger,
- Wencheng Li,
- Mainul Hoque,
- Radhika Patel,
- Bin Tian,
- Monika Gullerova,
- and Andre Furger
Genome Res. January 2016 26: 24-35; Published in Advance November 6, 2015, doi:10.1101/gr.193995.115
...Hoque K Burger Gullerova Tian, B Furger Andre Monika Gullerova Wencheng Burger, K 10.1101/gr.193995.115 1549-5469 genome;gr.193995.115 1088-9051 Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation Neve et al. APA and subcellular fractionation...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...have been shown to govern RNA polymerase II (RNAP II) recruitment followed by TF and cofactor binding, leading to cell- and tissue-specific expression through the initiation of mRNA transcription. In the mouse liver, for example, 24-h periodic occupancy by chromatin remodeling enzymes permits RNAP II...
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