Searching journal content for articles similar to Chu et al. 22 (10): 1889.

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RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
- Joshua L. Wetzel,
- Kaiqian Zhang,
- and Mona Singh
Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
...In a new window Figure 2. Probabilistic DNA recognition code for homeodomains derived from automatically inferred structural mappings has excellent de novo predictive performance. We compare agreement between predicted PWM columns and corresponding experimental PWM columns for 763 homeodomain proteins...
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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
...Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA ↵5 These authors contributed equally to this work. Corresponding authors: chenshiming@wustl.edu, mawhite@wustl.eduAbstractDozens of variants in the gene for the homeodomain transcription factor (TF) cone...
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Research: Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures
- Jiseon Lim,
- Wonjoo Kim,
- Jun Kim,
- and Junho Lee
Genome Res. November 2023 33: 1947-1957; Published in Advance November 2, 2023, doi:10.1101/gr.278124.123
...be reconstructed by studying ALT activity traces left in subtelomeric sequences.The present study explored TRM evolution in Nematoda using public whole- sequencing (WGS) data obtained from 100 nematode species and our high-quality assemblies. We evaluated the subtelomeric regions of TTAGGC-telomere isolates...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...-throughput approach for characterizing TF-TF competition in vitro and exploring its role in TF binding and gene regulation in vivo. The bHLH domain is an essential DNA-binding domain that is highly conserved across eukaryotes (Jones 2004). Genes encoding this domain arose in early eukaryotes and then duplicated...
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Research: A widespread role of the motif environment in transcription factor binding across diverse protein families
- Iris Dror,
- Tamar Golan,
- Carmit Levy,
- Remo Rohs,
- and Yael Mandel-Gutfreund
Genome Res. September 2015 25: 1268-1280; Published in Advance July 9, 2015, doi:10.1101/gr.184671.114
...regions around the binding motifs. Moreover, we show that the preferred nucleotide content has an overall high similarity to the core motif and exhibits unique DNA structural features. These results emphasize the intrinsic role of the sequence environment in protein–DNA recognition. We propose...
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Research: Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations
- Daniel M. Ibrahim,
- Peter Hansen,
- Christian Rödelsperger,
- Asita C. Stiege,
- Sandra C. Doelken,
- Denise Horn,
- Marten Jäger,
- Catrin Janetzki,
- Peter Krawitz,
- Gundula Leschik,
- Florian Wagner,
- Till Scheuer,
- Mareen Schmidt-von Kegler,
- Petra Seemann,
- Bernd Timmermann,
- Peter N. Robinson,
- Stefan Mundlos,
- and Jochen Hecht
Genome Res. December 2013 23: 2091-2102; Published in Advance August 30, 2013, doi:10.1101/gr.157610.113
...motif also starts with a guanine, which is then followed by a thymine residue (Fig. 1B). Intriguingly, the AT-rich core remained largely unchanged in both motifs. Therefore, we infer that both Q317 mutations alter only the 59 region of the DNA recognition sequence of HOXD13, while the 39 part remains...
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Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
- Bradford H. Casey,
- Rahul K. Kollipara,
- Karine Pozo,
- and Jane E. Johnson
Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
...for an adenine residue at this position. To explore whether the observed binding specificity was due to the presence of these additional flanking nucleotides, we compared their distribution at binding sites identified for each bHLH factor (Fig. 3C). Sites bound by ASCL1 or ASCL2 demonstrate greater association...
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Method: Anchor: trans-cell type prediction of transcription factor binding sites
- Hongyang Li,
- Daniel Quang,
- and Yuanfang Guan
Genome Res. February 2019 29: 281-292; Published in Advance December 19, 2018, doi:10.1101/gr.237156.118
...features used in our model are informative for future method development and regulatory mechanism exploration.ResultsOverview of the experimental design for cross-cell type TF binding predictionsIn this paper, we use data sets provided by the ENCODE-DREAM challenge, which consists of 84 ChIP-seq experiment...
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Research: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- Metewo Selase Enuameh,
- Yuna Asriyan,
- Adam Richards,
- Ryan G. Christensen,
- Victoria L. Hall,
- Majid Kazemian,
- Cong Zhu,
- Hannah Pham,
- Qiong Cheng,
- Charles Blatti,
- Jessie A. Brasefield,
- Matthew D. Basciotta,
- Jianhong Ou,
- Joseph C. McNulty,
- Lihua J. Zhu,
- Susan E. Celniker,
- Saurabh Sinha,
- Gary D. Stormo,
- Michael H. Brodsky,
- and Scot A. Wolfe
Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112
.... 2006; Urnov et al. 2010). The utilization of a broad range of DNA recognition preferences by naturally occurring ZFPs is in sharp contrast to homeodomains, the second most-common family of DNA-binding domains in metazoan s, which appear to utilize only a small fraction of their true recognition...
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Research: High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation
- E. Josephine Clowney,
- Angeliki Magklara,
- Bradley M. Colquitt,
- Nidhi Pathak,
- Robert P. Lane,
- and Stavros Lomvardas
Genome Res. August 2011 21: 1249-1259; Published in Advance June 24, 2011, doi:10.1101/gr.120162.110
...binding sites in 200 OR promoters identified two classes of motifs—homeodomain and O/E (Olf1/Early B-cell factor)–like sites (Michaloski et al. 2006). Genetic experiments showed that, directly or not, OR expression requires two homeodomain proteins, LHX2 and EMX2. Loss of LHX2 prevents the maturation...

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