scholarly journals Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Pil Joong Chung ◽  
Harin Jung ◽  
Yang Do Choi ◽  
Ju-Kon Kim
Keyword(s):  
Transcription Factors ◽  
Drought Tolerance ◽  
Target Genes ◽  
Nac Domain ◽  
Genome Wide ◽  
Direct Target

scholarly journals Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PIF proteins

2020 ◽  
Vol 117 (6) ◽  
pp. 3261-3269 ◽  
Author(s):  
Yu Zhang ◽  
Anne Pfeiffer ◽  
James M. Tepperman ◽  
Jutta Dalton-Roesler ◽  
Pablo Leivar ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Target Genes ◽  
Direct Action ◽  
Published Data ◽  
Shade Avoidance ◽  
Response Regulators ◽  
Genome Wide ◽  
Promoter Occupancy ◽  
Factor Abundance ◽  
Direct Target

Light-environment signals, sensed by plant phytochrome photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown “trans factors” modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of colocalization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator to regulate the expression of PIF-DTGs through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF-signaling hub.

scholarly journals Ets-dependent Regulation of Target Gene Expression during Megakaryopoiesis

2004 ◽  
Vol 279 (50) ◽  
pp. 52183-52190 ◽  
Author(s):  
Pascale Jackers ◽  
Gabor Szalai ◽  
Omar Moussa ◽  
Dennis K. Watson
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase Ii ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Hematopoietic Stem ◽  
Exogenous Expression ◽  
Direct Target ◽  
Transcriptional Complex

Megakaryopoiesis is the process by which hematopoietic stem cells in the bone marrow differentiate into mature megakaryocytes. The expression of megakaryocytic genes during megakaryopoiesis is controlled by specific transcription factors. Fli-1 and GATA-1 transcription factors are required for development of megakaryocytes and promoter analysis has definedin vitrofunctional binding sites for these factors in several megakaryocytic genes, includingGPIIb,GPIX, andC-MPL. Herein, we utilize chromatin immunoprecipitation to examine the presence of Ets-1, Fli-1, and GATA-1 on these promotersin vivo. Fli-1 and Ets-1 occupy the promoters ofGPIIb,GPIX, andC-MPLgenes in both Meg-01 and CMK11-5 cells. WhereasGPIIbis expressed in both Meg-01 and CMK11-5 cells,GPIXandC-MPLare only expressed in the more differentiated CMK11–5 cells. Thus,in vivooccupancy by an Ets factor is not sufficient to promote transcription of some megakaryocytic genes. GATA-1 and Fli-1 are both expressed in CMK11-5 cells and co-occupy theGPIXandC-MPLpromoters. Transcription of all three megakaryocytic genes is correlated with the presence of acetylated histone H3 and phosphorylated RNA polymerase II on their promoters. We also show that exogenous expression of GATA-1 in Meg-01 cells leads to the expression of endogenous c-mpl and gpIX mRNA. WhereasGPIIb,GPIX, andC-MPLare direct target genes for Fli-1, both Fli-1 and GATA-1 are required for formation of an active transcriptional complex on theC-MPLandGPIXpromotersin vivo. In contrast,GPIIbexpression appears to be independent of GATA-1 in Meg-01 cells.

scholarly journals EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Fctors of a gene group

2020 ◽  
Author(s):  
Sangrea Shim ◽  
Pil Joon Seo
Keyword(s):  
Transcription Factors ◽  
Open Source ◽  
Chromatin Immunoprecipitation ◽  
Target Genes ◽  
Affinity Purification ◽  
Enrichment Analysis ◽  
Analysis Tool ◽  
Gene Group ◽  
Genome Wide ◽  
One Step

SummaryEAT-UpTF (Enrichment Analysis Tool for Upstream Transcription Factors of a gene group) is an open-source Python script that analyzes the enrichment of upstream transcription factors (TFs) in a group of genes-of-interest (GOIs). EAT-UpTF utilizes genome-wide lists of TF-target genes generated by DNA affinity purification followed by sequencing (DAP-seq) or chromatin immunoprecipitation followed by sequencing (ChIP-seq). Unlike previous methods based on the two-step prediction of cis-motifs and DNA-element-binding TFs, our EAT-UpTF analysis enabled a one-step identification of enriched upstream TFs in a set of GOIs using lists of empirically determined TF-target [email protected] or [email protected]://github.com/sangreashim/EAT-UpTF

scholarly journals Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques

2019 ◽  
Author(s):  
Jelena Petrovic ◽  
Yeqiao Zhou ◽  
Maria Fasolino ◽  
Naomi Goldman ◽  
Gregory W. Schwartz ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Long Range ◽  
Spatial Organization ◽  
Target Genes ◽  
Large Fraction ◽  
B Cell Lymphoma ◽  
3 Dimensional ◽  
Regulatory Interactions ◽  
Genome Wide ◽  
Target Promoters

AbstractChromatin loops enable transcription factor-bound distal enhancers to interact with their target promoters to regulate transcriptional programs. Although developmental transcription factors, such as active forms of Notch, can directly stimulate transcription by activating enhancers, the effect of their oncogenic subversion on the 3-dimensional (3D) organization of the cancer genome is largely undetermined. By mapping chromatin looping genome-wide in Notch-dependent triple-negative breast cancer and B-cell lymphoma, we show that far beyond the well-characterized role of Notch as an activator of distal enhancers, Notch regulates its direct target genes through establishing new long-range regulatory interactions. Moreover, a large fraction of Notch-promoted regulatory loops forms highly interacting enhancer and promoter spatial clusters, termed “3D cliques”. Loss-and gain-of-function experiments show that Notch preferentially targets hyperconnected 3D cliques that regulate the expression of crucial proto-oncogenes. Our observations suggest that oncogenic hijacking of developmental transcription factors can dysregulate transcription through widespread effects on the spatial organization of cancer genomes.

scholarly journals Genome-wide reduction in chromatin accessibility and unique transcription factor footprints in endothelial cells and fibroblasts in scleroderma skin

2020 ◽  
Author(s):  
Pei-Suen Tsou ◽  
Pamela J. Palisoc ◽  
Mustafa Ali ◽  
Dinesh Khanna ◽  
Amr H Sawalha
Keyword(s):  
Endothelial Cells ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Target Genes ◽  
Critical Role ◽  
Vascular Complications ◽  
Chromatin Accessibility ◽  
Unknown Etiology ◽  
Healthy Controls ◽  
Genome Wide

AbstractSystemic sclerosis (SSc) is a rare autoimmune disease of unknown etiology characterized by widespread fibrosis and vascular complications. We utilized an assay for genome-wide chromatin accessibility to examine the chromatin landscape and transcription factor footprints in both endothelial cells (ECs) and fibroblasts isolated from healthy controls and patients with diffuse cutaneous (dc) SSc. In both cell types, chromatin accessibility was significantly reduced in SSc patients compared to healthy controls. Genes annotated from differentially accessible chromatin regions were enriched in pathways and gene ontologies involved in the nervous system. In addition, our data revealed that chromatin binding of transcription factors SNAI2, ETV2, and ELF1 was significantly increased in dcSSc ECs, while recruitment of RUNX1 and RUNX2 was enriched in dcSSc fibroblasts. Significant elevation of SNAI2 and ETV2 levels in dcSSc ECs, and RUNX2 levels in dcSSc fibroblasts were confirmed. Further analysis of publicly available ETV2-target genes suggests that ETV2 may play a critical role in EC dysfunction in dcSSc. Our data, for the first time, uncovered the chromatin blueprint of dcSSc ECs and fibroblasts, and suggested that neural-related characteristics of SSc ECs and fibroblasts could be a culprit for dysregulated angiogenesis and enhanced fibrosis. Targeting these pathways and the key transcription factors identified might present novel therapeutic approaches for this disease.

scholarly journals Genome-Wide Identification of Direct Target Genes Implicates Estrogen-Related Receptor α as a Determinant of Breast Cancer Heterogeneity

2009 ◽  
Vol 69 (15) ◽  
pp. 6149-6157 ◽  
Author(s):  
Geneviève Deblois ◽  
Jacqueline A. Hall ◽  
Marie-Claude Perry ◽  
Josée Laganière ◽  
Majid Ghahremani ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Target Genes ◽  
Cancer Heterogeneity ◽  
Genome Wide ◽  
Direct Target ◽  
Estrogen Related Receptor

Hox transcription factors: an overview of multi-step regulators of gene expression

2018 ◽  
Vol 62 (11-12) ◽  
pp. 723-732 ◽  
Author(s):  
Julie Carnesecchi ◽  
Pedro B. Pinto ◽  
Ingrid Lohmann
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Cell Fates ◽  
Hox Proteins ◽  
Regulatory Modules ◽  
Genome Wide ◽  
Transcription Complexes ◽  
Regulatory Functions

Hox transcription factors (TFs) function as key determinants in the specification of cell fates during development. They do so by triggering entire morphogenetic cascades through the activation of specific target genes. In contrast to their fundamental role in development, the molecular mechanisms employed by Hox TFs are still poorly understood. In recent years, a new picture has emerged regarding the function of Hox proteins in gene regulation. Initial studies have primarily focused on understanding how Hox TFs recognize and bind specific enhancers to activate defined Hox targets. However, genome-wide studies on the interactions and dynamics of Hox proteins have revealed a more elaborate function of the Hox factors. It is now known that Hox proteins are involved in several steps of gene expression with potential regulatory functions in the modification of the chromatin landscape and its accessibility, recognition and activation of specific cis-regulatory modules, assembly and activation of promoter transcription complexes and mRNA processing. In the coming years, the characterization of the molecular activity of Hox TFs in these mechanisms will greatly contribute to our general understanding of Hox activity.

scholarly journals Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

eLife ◽  
2012 ◽  
Vol 1 ◽  
Author(s):  
Jerome S Menet ◽  
Joseph Rodriguez ◽  
Katharine C Abruzzi ◽  
Michael Rosbash
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Mouse Liver ◽  
Target Genes ◽  
Feedback Loops ◽  
Substantial Fraction ◽  
Binding Profile ◽  
Regulatory Issues ◽  
Genome Wide ◽  
Post Transcriptional Regulation

A substantial fraction of the metazoan transcriptome undergoes circadian oscillations in many cells and tissues. Based on the transcription feedback loops important for circadian timekeeping, it is commonly assumed that this mRNA cycling reflects widespread transcriptional regulation. To address this issue, we directly measured the circadian dynamics of mouse liver transcription using Nascent-Seq (genome-wide sequencing of nascent RNA). Although many genes are rhythmically transcribed, many rhythmic mRNAs manifest poor transcriptional rhythms, indicating a prominent contribution of post-transcriptional regulation to circadian mRNA expression. This analysis of rhythmic transcription also showed that the rhythmic DNA binding profile of the transcription factors CLOCK and BMAL1 does not determine the transcriptional phase of most target genes. This likely reflects gene-specific collaborations of CLK:BMAL1 with other transcription factors. These insights from Nascent-Seq indicate that it should have broad applicability to many other gene expression regulatory issues.

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