Mapping genome-wide transcription-factor binding sites using DAP-seq.
Anna Bartlett,Ronan C. O'Malley,Ronan C. O'Malley,Shao-shan Carol Huang,Mary Galli,Mary Galli,Joseph R. Nery,Andrea Gallavotti,Joseph R. Ecker +8 more
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TLDR
DAP-seq is developed, a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library, enabling low-cost, high-throughput generation of cistrome and epicistrome maps for any organism.Abstract:
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX). The resulting DNA library is incubated with an affinity-tagged in vitro-expressed TF, and TF-DNA complexes are purified using magnetic separation of the affinity tag. Bound genomic DNA is eluted from the TF and sequenced using next-generation sequencing. Sequence reads are mapped to a reference genome, identifying genome-wide binding locations for each TF assayed, from which sequence motifs can then be derived. A researcher with molecular biology experience should be able to follow this protocol, processing up to 400 samples per week.read more
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Integrative Genomics Viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Journal ArticleDOI
AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis.
TL;DR: This review summarizes recent studies on AP2/ERF transcription factors in hormonal and abiotic stress responses with an emphasis on selected family members in Arabidopsis, providing context and important clues about the roles of diverse AP1/ERFs in controlling hormone and stress responses.
Journal ArticleDOI
Widespread long-range cis-regulatory elements in the maize genome.
William A. Ricci,Zefu Lu,Lexiang Ji,Alexandre P. Marand,Christina L. Ethridge,Nathalie G. Murphy,Jaclyn M. Noshay,Mary Galli,María Katherine Mejía-Guerra,Maria Colomé-Tatché,Frank Johannes,M. Jordan Rowley,Victor G. Corces,Jixian Zhai,Michael J. Scanlon,Edward S. Buckler,Andrea Gallavotti,Nathan M. Springer,Robert J. Schmitz,Robert J. Schmitz,Xiaoyu Zhang +20 more
TL;DR: Functional support is provided for the widespread existence of CREs that act over large genomic distances to control gene expression in the maize genome.
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DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
TL;DR: Jiang et al. as mentioned in this paper developed a novel pre-trained bidirectional encoder represen-tation, named DNABERT, to capture global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts.
Posted ContentDOI
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
TL;DR: A novel pre-trained bidirectional encoder representation that forms global and transferrable understanding of genomic DNA sequences based on up and downstream nucleotide contexts, named DNABERT, and can be readily applied to other organisms with exceptional performance.
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Integrative genomics viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TL;DR: In this article, the authors present an approach for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.
Journal ArticleDOI
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