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Method: Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
- Minjie Zhang,
- Irena T. Hwang,
- Kongpan Li,
- Jianhui Bai,
- Jian-Fu Chen,
- Tsachy Weissman,
- James Y. Zou,
- and Zhipeng Lu
Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
...These authors contributed equally to this work. Corresponding author: zhipengl@usc.eduAbstractThe recent development and application of methods based on the general principle of “crosslinking and proximity ligation” (crosslink-ligation) are revolutionizing RNA structure studies in living cells. However...
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Research: Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
- Arttu Jolma,
- Jilin Zhang,
- Estefania Mondragón,
- Ekaterina Morgunova,
- Teemu Kivioja,
- Kaitlin U. Laverty,
- Yimeng Yin,
- Fangjie Zhu,
- Gleb Bourenkov,
- Quaid Morris,
- Timothy R. Hughes,
- Louis James Maher III,
- and Jussi Taipale
Genome Res. July 2020 30: 962-973; Published in Advance July 23, 2020, doi:10.1101/gr.258848.119
...(Loughlin et al. 2009). However, such direct repeats were also bound by RBPs having only a single RBD (12 of 27), suggesting that some RBPs could form homodimers or interact to form a homodimer when bound to RNA (Supplemental Table S2). The gap between the direct repeats was generally short, with a median...
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Research: Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome
- Ville Paakinaho,
- Thomas A. Johnson,
- Diego M. Presman,
- and Gordon L. Hager
Genome Res. August 2019 29: 1223-1234; Published in Advance July 23, 2019, doi:10.1101/gr.244814.118
...@fbmc.fcen.uba.arAbstractMost transcription factors, including nuclear receptors, are widely modeled as binding regulatory elements as monomers, homodimers, or heterodimers. Recent findings in live cells show that the glucocorticoid receptor NR3C1 (also known as GR) forms tetramers on enhancers, owing to an allosteric alteration induced...
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Research: Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo
- Hee-Woong Lim,
- N. Henriette Uhlenhaut,
- Alexander Rauch,
- Juliane Weiner,
- Sabine Hübner,
- Norbert Hübner,
- Kyoung-Jae Won,
- Mitchell A. Lazar,
- Jan Tuckermann,
- and David J. Steger
Genome Res. June 2015 25: 836-844; Published in Advance May 8, 2015, doi:10.1101/gr.188581.114
...-site-facilitated tethering. We performed ChIP-seq for RNA polymerase II (RNAPII), which is recruited to active enhancers on a global scale (Szutorisz et al. 2005; Koch et al. 2008; Kim et al. 2010), to explore a potential transcriptional function for the prednisolone-regulated sites. A direct correlation was found between...
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Research: Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers
- Tao Deng,
- Z. Iris Zhu,
- Shaofei Zhang,
- Yuri Postnikov,
- Di Huang,
- Marion Horsch,
- Takashi Furusawa,
- Johannes Beckers,
- Jan Rozman,
- Martin Klingenspor,
- Oana Amarie,
- Jochen Graw,
- Birgit Rathkolb,
- Eckhard Wolf,
- Thure Adler,
- Dirk H. Busch,
- Valérie Gailus-Durner,
- Helmut Fuchs,
- Martin Hrabě de Angelis,
- Arjan van der Velde,
- Lino Tessarollo,
- Ivan Ovcherenko,
- David Landsman,
- and Michael Bustin
Genome Res. September 2015 25: 1295-1308; Published in Advance July 8, 2015, doi:10.1101/gr.192229.115
...organization in NPs and with previous FRAP analyses of living cells, which demonstrated competition among HMGN variants for chromatin binding sites (Catez et al. 2002). Taken together, the results suggest that loss of an HMGN variant is compensated by increased chromatin binding of the remaining variant...
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Method: SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
- Liyang Zhang,
- Gabriella D. Martini,
- H. Tomas Rube,
- Judith F. Kribelbauer,
- Chaitanya Rastogi,
- Vincent D. FitzPatrick,
- Jon C. Houtman,
- Harmen J. Bussemaker,
- and Miles A. Pufall
Genome Res. January 2018 28: 111-121; Published in Advance December 1, 2017, doi:10.1101/gr.222844.117
...site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA-binding preferences of AR and GR homodimers differ significantly, both within and outside the 15-bp core binding site. The relative preference between the two factors can...
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LETTER: Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
- Byung-Kwan Cho,
- Eric M. Knight,
- Christian L. Barrett,
- and Bernhard Ø. Palsson
Genome Res. June 2008 18: 900-910; Published in Advance March 13, 2008, doi:10.1101/gr.070276.107
...it difficult to discern between noise and the true signals. The general concept of binding patterns of global transcription factors is that their target sites are located at promoter regions. Through interacting with RNA polymerase and/or other proteins, and/or hindering the binding of RNA polymerase...
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Methods: Development of a microscopic platform for real-time monitoring of biomolecular interactions
- Yasuhiro Sasuga,
- Tomomi Tani,
- Masahito Hayashi,
- Hisashi Yamakawa,
- Osamu Ohara,
- and Yoshie Harada
Genome Res. January 2006 16: 132-139; Published in Advance December 12, 2005, doi:10.1101/gr.4235806
...et al. 2005 ), and other microfluidic systems ( Thorsen et al. 2002 ; Hong et al. 2004 ). More importantly, recent progress in bioimaging ( Sako et al. 2000 ; Itoh et al. 2002 ; Murakoshi et al. 2004 ; Michalet et al. 2005 ), allowing the study of the dynamic behavior of various proteins in living...
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ARTICLE: Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network
- Daniel E. Zak,
- Gregory E. Gonye,
- James S. Schwaber,
- and Francis J. Doyle III
Genome Res. November 2003 13: 2396-2405; doi:10.1101/gr.1198103
...structural knowledge, prior knowledge of kinetic parameters, particularly mRNA degradation rate constants, was necessary for the network to be identifiable. Also, with the exception of cases where the noise due to stochastic gene expression was high, complex perturbations were more favorable for identifying...
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METHODS: Novel Fluorescence Labeling and High-Throughput Assay Technologies for In Vitro Analysis of Protein Interactions
- Nobuhide Doi,
- Hideaki Takashima,
- Masataka Kinjo,
- Kyoko Sakata,
- Yuko Kawahashi,
- Yuko Oishi,
- Rieko Oyama,
- Etsuko Miyamoto-Sato,
- Tatsuya Sawasaki,
- Yaeta Endo,
- and Hiroshi Yanagawa
Genome Res. March 1, 2002 12: 487-492; Published in Advance February 15, 2002, doi:10.1101/gr.218802
...crucial and laborious steps in such fluorescence assay systems is obtaining the protein samples labeled with fluorescent dyes. Most frequently, the proteins have been expressed in living cells, purified to homogeneity, and then fluorescently labeled by chemical modification of the amino, sulfhydryl...

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