scholarly journals Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Riccardo Lorrai ◽  
Francesco Gandolfi ◽  
Alessandra Boccaccini ◽  
Veronica Ruta ◽  
Marco Possenti ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Hypocotyl Elongation ◽  
Auxin Signaling ◽  
Rna Seq ◽  
Genome Wide

scholarly journals ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis

2018 ◽  
Vol 115 (19) ◽  
pp. E4503-E4511 ◽  
Author(s):  
Giorgio Perrella ◽  
Mhairi L. H. Davidson ◽  
Liz O’Donnell ◽  
Ana-Marie Nastase ◽  
Pawel Herzyk ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Zinc Finger ◽  
Transcriptional Regulators ◽  
Hypocotyl Elongation ◽  
Transcriptional Level ◽  
Hypocotyl Growth ◽  
Environmental Signals ◽  
Genome Wide ◽  
A Genome

Integration of environmental signals and interactions among photoreceptors and transcriptional regulators is key in shaping plant development. TANDEM ZINC-FINGER PLUS3 (TZP) is an integrator of light and photoperiodic signaling that promotes flowering in Arabidopsis thaliana. Here we elucidate the molecular role of TZP as a positive regulator of hypocotyl elongation. We identify an interacting partner for TZP, the transcription factor ZINC-FINGER HOMEODOMAIN 10 (ZFHD10), and characterize its function in coregulating the expression of blue-light–dependent transcriptional regulators and growth-promoting genes. By employing a genome-wide approach, we reveal that ZFHD10 and TZP coassociate with promoter targets enriched in light-regulated elements. Furthermore, using a targeted approach, we show that ZFHD10 recruits TZP to the promoters of key coregulated genes. Our findings not only unveil the mechanism of TZP action in promoting hypocotyl elongation at the transcriptional level but also assign a function to an uncharacterized member of the ZFHD transcription factor family in promoting plant growth.

scholarly journals Genome-wide RNA-seq Analysis of Differentially Expressed Transcription Factor Genes Against Bacterial Leaf Pustule in Soybean

2015 ◽  
Vol 3 (3) ◽  
pp. 197-207 ◽  
Author(s):  
Kil Hyun Kim ◽  
Yang Jae Kang ◽  
Sangrea Shim ◽  
Min-Jung Seo ◽  
Seong-Bum Baek ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Genome Wide ◽  
Transcription Factor Genes

scholarly journals A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq

PLoS ONE ◽  
2016 ◽  
Vol 11 (7) ◽  
pp. e0159011 ◽  
Author(s):  
Takaaki Kojima ◽  
Emi Kunitake ◽  
Kunio Ihara ◽  
Tetsuo Kobayashi ◽  
Hideo Nakano
Keyword(s):  
Transcription Factor ◽  
Combinatorial Analysis ◽  
Rna Seq ◽  
Genome Wide

scholarly journals An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion

2019 ◽  
Author(s):  
Kizhakke Mattada Sathyan ◽  
Brian D. McKenna ◽  
Warren D. Anderson ◽  
Fabiana M. Duarte ◽  
Leighton Core ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Protein Function ◽  
Specific Protein ◽  
Auxin Signaling ◽  
Auxin Response ◽  
Protein Levels ◽  
Genome Wide ◽  
Pb1 Domain ◽  
Inducible Protein ◽  
Endogenous Loci

Rapid perturbation of protein function permits the ability to define primary molecular responses while avoiding down-stream cumulative effects of protein dysregulation. The auxin-inducible degron (AID) system was developed as a tool to achieve rapid and inducible protein degradation in non-plant systems. However, tagging proteins at their endogenous loci results in chronic, auxin-independent degradation by the proteasome. To correct this deficiency, we expressed the Auxin Response Transcription Factor (ARF) in an improved inducible degron system. ARF is absent from previously engineered AID systems, but ARF is a critical component of native auxin signaling. In plants, ARF directly interacts with AID in the absence of auxin and we found that expression of the ARF Phox and Bem1 (PB1) domain suppresses constitutive degradation of AID-tagged proteins. Moreover, the rate of auxin-induced AID degradation is substantially faster in the ARF-AID system. To test the ARF-AID system in a quantitative and sensitive manner, we measured genome-wide changes in nascent transcription after rapidly depleting the ZNF143 transcription factor. Transciptional profiling indicates that ZNF143 activates transcription in cis and ZNF143 regulates promoter-proximal paused RNA Polymerase density. Rapidly inducible degradation systems that preserve the target protein’s native expression levels and patterns will revolutionize the study of biological systems by enabling specific and temporally defined protein dysregulation.

scholarly journals The Scleraxis Transcription Factor Directly Regulates Multiple Distinct Molecular and Cellular Processes During Early Tendon Cell Differentiation

2021 ◽  
Vol 9 ◽  
Author(s):  
Han Liu ◽  
Jingyue Xu ◽  
Yu Lan ◽  
Hee-Woong Lim ◽  
Rulang Jiang
Keyword(s):  
Transcription Factor ◽  
Cell Differentiation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Rna Seq ◽  
Tendon Cell ◽  
Tendon Development ◽  
Genome Wide ◽  
Direct Target ◽  
Embryonic Tendon

Proper development of tendons is crucial for the integration and function of the musculoskeletal system. Currently little is known about the molecular mechanisms controlling tendon development and tendon cell differentiation. The transcription factor Scleraxis (Scx) is expressed throughout tendon development and plays essential roles in both embryonic tendon development and adult tendon healing, but few direct target genes of Scx in tendon development have been reported and genome-wide identification of Scx direct target genes in vivo has been lacking. In this study, we have generated a ScxFlag knockin mouse strain, which produces fully functional endogenous Scx proteins containing a 2xFLAG epitope tag at the carboxy terminus. We mapped the genome-wide Scx binding sites in the developing limb tendon tissues, identifying 12,097 high quality Scx regulatory cis-elements in-around 7,520 genes. Comparative analysis with previously reported embryonic tendon cell RNA-seq data identified 490 candidate Scx direct target genes in early tendon development. Furthermore, we characterized a new Scx gene-knockout mouse line and performed whole transcriptome RNA sequencing analysis of E15.5 forelimb tendon cells from Scx–/– embryos and control littermates, identifying 68 genes whose expression in the developing tendon tissues significantly depended on Scx function. Combined analysis of the ChIP-seq and RNA-seq data yielded 32 direct target genes that required Scx for activation and an additional 17 target genes whose expression was suppressed by Scx during early tendon development. We further analyzed and validated Scx-dependent tendon-specific expression patterns of a subset of the target genes, including Fmod, Kera, Htra3, Ssc5d, Tnmd, and Zfp185, by in situ hybridization and real-time quantitative polymerase chain reaction assays. These results provide novel insights into the molecular mechanisms mediating Scx function in tendon development and homeostasis. The ChIP-seq and RNA-seq data provide a rich resource for aiding design of further studies of the mechanisms regulating tendon cell differentiation and tendon tissue regeneration. The ScxFlag mice provide a valuable new tool for unraveling the molecular mechanisms involving Scx in the protein interaction and gene-regulatory networks underlying many developmental and disease processes.

scholarly journals Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors:diffTF

2018 ◽  
Author(s):  
Ivan Berest ◽  
Christian Arnold ◽  
Armando Reyes-Palomares ◽  
Giovanni Palla ◽  
Kasper Dindler Rasmussen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Case Studies ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Lymphocytic Leukemia ◽  
Transcriptional Activators ◽  
Rna Seq ◽  
Data Set ◽  
Genome Wide

Transcription factor (TF) activity is an important read-out of cellular signalling pathways and thus to assess regulatory differences across conditions. However, current technologies lack the ability to simultaneously assess activity changes for multiple TFs and in particular to determine whether a specific TF acts globally as transcriptional repressor or activator. To this end, we introduce a widely applicable genome-wide methoddiffTFto assess differential TF activity and to classify TFs as activator or repressor (available athttps://git.embl.de/grp-zaugg/diffTF). This is done by integrating any type of genome-wide chromatin accessibility data with RNA-Seq data and in-silico predicted TF binding sites. We corroborated the classification of TFs into repressors and activators by three independent analyses based on enrichments of active/repressive chromatin states, correlation of TF activity with gene expression, and activator-and repressor-specific chromatin footprints. To show the power ofdiffTF, we present two case studies: First, we applieddiffTFin to a large ATAC-Seq/RNA-Seq dataset comparing mutated and unmutated chronic lymphocytic leukemia samples, where we identified dozens of known (40%) and potentially novel (60%) TFs that are differentially active. We were also able to classify almost half of them as either repressor and activator. Second, we applieddiffTFto a small ATAC-Seq/RNA-Seq data set comparing two cell types along the hematopoietic differentiation trajectory (multipotent progenitors – MPP – versus granulocyte-macrophage progenitors – GMP). Here we identified the known drivers of differentiation and found that the majority of the differentially active TFs are transcriptional activators. Overall,diffTFwas able to recover the known TFs in both case studies, additionally identified TFs that have been less well characterized in the given condition, and provides a classification of the TFs into transcriptional activators and repressors.

scholarly journals High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Cancer Cells ◽  
High Throughput ◽  
Regulatory Networks ◽  
Temporal Dynamics ◽  
Chromatin Accessibility ◽  
Regulatory Regions ◽  
Factor Binding ◽  
Genome Wide

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

Sign in / Sign up

Export Citation Format

Share Document