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Autor:
Lu Li, Pamela Chamales, Jared R. Stees, Mingyi Xie, Paul C. Wassel, Marissa Brackett, David T. Y. Yu, Jörg Bungert, Ekaterina Gavrilova, Aishwarya Gurumurthy, Daniel Stribling, Jinyang Chen, Alexander M. Ishov
Publikováno v:
Nucleic Acids Research
Super-enhancers (SEs) mediate high transcription levels of target genes. Previous studies have shown that SEs recruit transcription complexes and generate enhancer RNAs (eRNAs). We characterized transcription at the human and murine β-globin locus c
Autor:
Dmitri D. Pervouchine, Marina A. Kalinina, Timofei Ivanov, Svetlana Kalmykova, Dmitry A. Skvortsov, Olga A. Dontsova
Publikováno v:
Nucleic Acids Research
The mammalian Ate1 gene encodes an arginyl transferase enzyme with tumor suppressor function that depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. We report that the molecular mechanism underlying MXE splici
Autor:
Formosa, Tim, Winston, Fred
Publikováno v:
Nucleic Acids Research
FACT (FAcilitates Chromatin Transcription) has long been considered to be a transcription elongation factor whose ability to destabilize nucleosomes promotes RNAPII progression on chromatin templates. However, this is just one function of this histon
Publikováno v:
Nucleic Acids Research
Fission yeast phosphate homeostasis genes are repressed in phosphate-rich medium by transcription of upstream lncRNAs that interferes with activation of the flanking mRNA promoters. lncRNA control of PHO gene expression is influenced by the Thr4 phos
Autor:
Xiuzhu Dong, Lingyan Li, Zhihua Li, Fangqing Zhao, Xiaowei Zheng, Jie Li, Lei Qi, Lei Yue, Bing Zhang
Publikováno v:
Nucleic Acids Research
Transcription termination defines accurate transcript 3′-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological si
Publikováno v:
Nucleic Acids Research
The ChIP-exo assay precisely delineates protein-DNA crosslinking patterns by combining chromatin immunoprecipitation with 5′ to 3′ exonuclease digestion. Within a regulatory complex, the physical distance of a regulatory protein to DNA affects cr
Publikováno v:
Nucleic Acids Research
To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately ide
Autor:
Livia Caizzi, Patrick Cramer, Takayuki Nojima, Shona Murphy, Justyna Zaborowska, Michael Tellier, Daniel Blears, Björn Schwalb, Eusra Mohammad, Ivan Ferrer-Vicens, Taras Velychko
Publikováno v:
Nucleic Acids Research
Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-se
Publikováno v:
Nucleic Acids Research
Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic
Autor:
Charles C. Query, Jia Pu, Zhan Ding, Wei Shao, Yu Xian Shen, Yong-Zhen Xu, Zeng Zhang Zheng, Ji Jia Shen, Yu Jie Fan
Publikováno v:
Nucleic Acids Research
Transcription and pre-mRNA splicing are coupled to promote gene expression and regulation. However, mechanisms by which transcription and splicing influence each other are still under investigation. The ATPase Prp5p is required for pre-spliceosome as