Showing papers by "Huaming Chen published in 2016"
TL;DR: Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules in the 1001 Genomes collection of Arabidopsis thaliana.
534 citations
TL;DR: It is proposed that dynamic, multi-TF binding could be a criterion for prioritizing the characterization of TF binding events, cis-regulatory elements, and functionally unknown genes in both plants and other species.
Abstract: To respond to environmental changes, such as drought, plants must regulate numerous cellular processes. Working in the model plant Arabidopsis , Song et al. profiled the binding of 21 transcription factors to chromatin and mapped the complex gene regulatory networks involved in the response to the plant hormone abscisic acid. The work provides a framework for understanding and modulating plant responses to stress.
Science , this issue p. [598][1]
[1]: http://www.sciencemag.org/content/354/6312/aag1550.full
353 citations
TL;DR: The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor–protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.
Abstract: Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein-protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literature-curated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor-protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.
67 citations
TL;DR: In this paper, the y-axis label in Fig. 3f of this Letter should read ‘mCAC/CAC]/[mCAG/CA/CAG]’ rather than ‘[mCA/CA]/ [mCA[CAC][CAG][CA]], and Fig. 4c in the description of Fig.
Abstract: Nature 523, 212–216 (2015); doi:10.1038/nature14465 The y-axis label in Fig. 3f of this Letter should read ‘[mCAC/CAC]/[mCAG/CAG]’ rather than ‘[mCAC/CAC]/[mCAC/CAG]’. In addition, in the description of Fig. 4c in the main text, ‘tissue’ and ‘individual’ were swapped; it should read, “Of the ASM events that varied, 4.
12 citations