scholarly journals Association of Ddx5/p68 protein with the upstream erythroid enhancer element (EHS1) of the Klf1 gene

2019 ◽  
Author(s):  
Xiaoyong Chen ◽  
Felix Lohmann ◽  
James J Bieker
Keyword(s):  
Transcription Factor ◽  
Expression Pattern ◽  
Transcriptional Activation ◽  
Affinity Purification ◽  
Hypersensitive Site ◽  
Enhancer Element ◽  
Restricted Expression Pattern ◽  
Dnase Hypersensitive Site ◽  
Essential Transcription Factor ◽  
Klf1 Gene

AbstractEKLF/KLF1 is an essential transcription factor that plays a global role in erythroid transcriptional activation. It’s own regulation is of interest, as it displays a highly restricted expression pattern, limited to erythroid cells and its progenitors. Here we use biochemical affinity purification to identify the Ddx5/p68 protein as a potential activator of KLF1 by virtue of its interaction with the erythroid-specific DNAse hypersensitive site (EHS1) upstream enhancer element. We postulate that its range of interactions with other proteins known to interact with this element render it part of the enhanseosome complex critical for optimal expression of KLF1.

scholarly journals Global analysis of the RpaB regulon based on the positional distribution of HLR1 sequences and comparative differential RNA-Seq data

2018 ◽  
Author(s):  
Matthias Riediger ◽  
Taro Kadowaki ◽  
Ryuta Nagayama ◽  
Jens Georg ◽  
Yukako Hihara ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Target Genes ◽  
Global Analysis ◽  
Affinity Purification ◽  
Electron Flow ◽  
Positional Distribution ◽  
State Transitions ◽  
Northern Hybridization

ABSTRACTThe transcription factor RpaB regulates the expression of genes encoding photosynthesis-associated proteins during light acclimation. The binding site of RpaB is the HLR1 motif, a pair of imperfect octameric direct repeats, separated by two random nucleotides. Here, we used high-resolution mapping data of transcriptional start sites (TSSs) in the modelSynechocystissp. PCC 6803 in conjunction with the positional distribution of HLR1 sites for the global prediction of the RpaB regulon. The results demonstrate that RpaB regulates the expression of more than 150 promoters, driving the transcription of protein-coding and non-coding genes and antisense transcripts under low light and upon the shift to high light when DNA binding activity is lost. Transcriptional activation by RpaB is achieved when the HLR1 motif is located 66 to 45 nt upstream, repression occurs when it is close to or overlapping the TSS. Selected examples were validated by multiple experimental approaches, including chromatin affinity purification, reporter gene, northern hybridization and electrophoretic mobility shift assays. We found that RpaB controlsssr2016/pgr5, which is involved in cyclic electron flow and state transitions; six out of nine ferredoxins; three of four FtsH proteases;gcvP/slr0293, encoding a crucial photorespiratory protein; andnirAandisiAfor which we suggest cross-regulation with the transcription factors NtcA or FurA, respectively. In addition to photosynthetic gene functions, RpaB contributes to the control of genes affiliated with nitrogen assimilation, cofactor biosyntheses, the CRISPR system and the circadian clock, making it one of the most versatile regulators in cyanobacteria.Significance StatementRpaB is a transcription factor in cyanobacteria and in the chloroplasts of several lineages of eukaryotic algae. Like other important transcription factors, the gene encoding RpaB cannot be deleted, making the study of deletion mutants impossible. Based on a bioinformatic approach, we increased the number of known genes controlled by RpaB by a factor of 5. Depending on the distance to the TSS, RpaB mediates transcriptional activation or repression. The high number and functional diversity among its target genes and co-regulation with other transcriptional regulators characterize RpaB as a regulatory hub.

scholarly journals Transcription Factor Action Orchestrates the Complex Expression Pattern of CRABS CLAW in Arabidopsis

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1663
Author(s):  
Thomas Gross ◽  
Annette Becker
Keyword(s):  
Transcription Factor ◽  
Expression Pattern ◽  
Transcriptional Activation ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Transcript Abundance ◽  
Dna Interaction ◽  
Complex Expression

Angiosperm flowers are the most complex organs that plants generate, and in their center, the gynoecium forms, assuring sexual reproduction. Gynoecium development requires tight regulation of developmental regulators across time and tissues. How simple on and off regulation of gene expression is achieved in plants was described previously, but molecular mechanisms generating complex expression patterns remain unclear. We use the gynoecium developmental regulator CRABS CLAW (CRC) to study factors contributing to its sophisticated expression pattern. We combine in silico promoter analyses, global TF-DNA interaction screens, and mutant analyses. We find that miRNA action, DNA methylation, and chromatin remodeling do not contribute substantially to CRC regulation. However, 119 TFs, including SEP3, ETT, CAL, FUL, NGA2, and JAG bind to the CRC promoter in yeast. These TFs finetune transcript abundance as homodimers by transcriptional activation. Interestingly, temporal–spatial aspects of expression regulation may be under the control of redundantly acting genes and require higher order complex formation at TF binding sites. Our work shows that endogenous regulation of complex expression pattern requires orchestrated transcription factor action on several conserved promotor sites covering almost 4 kb in length. Our results highlight the utility of comprehensive regulators screens directly linking transcriptional regulators with their targets.

scholarly journals Positive and Negative Regulation of the Cardiovascular Transcription Factor KLF5 by p300 and the Oncogenic Regulator SET through Interaction and Acetylation on the DNA-Binding Domain

2003 ◽  
Vol 23 (23) ◽  
pp. 8528-8541 ◽  
Author(s):  
Saku Miyamoto ◽  
Toru Suzuki ◽  
Shinsuke Muto ◽  
Kenichi Aizawa ◽  
Akatsuki Kimura ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Affinity Purification ◽  
Gene Activation ◽  
Negative Regulation ◽  
Binding Domain ◽  
Negative Regulator ◽  
The Other ◽  
Dna Binding Domain

ABSTRACT Here we show a novel pathway of transcriptional regulation of a DNA-binding transcription factor by coupled interaction and modification (e.g., acetylation) through the DNA-binding domain (DBD). The oncogenic regulator SET was isolated by affinity purification of factors interacting with the DBD of the cardiovascular transcription factor KLF5. SET negatively regulated KLF5 DNA binding, transactivation, and cell-proliferative activities. Down-regulation of the negative regulator SET was seen in response to KLF5-mediated gene activation. The coactivator/acetylase p300, on the other hand, interacted with and acetylated KLF5 DBD, and activated its transcription. Interestingly, SET inhibited KLF5 acetylation, and a nonacetylated mutant of KLF5 showed reduced transcriptional activation and cell growth complementary to the actions of SET. These findings suggest a new pathway for regulation of a DNA-binding transcription factor on the DBD through interaction and coupled acetylation by two opposing regulatory factors of a coactivator/acetylase and a negative cofactor harboring activity to inhibit acetylation.

scholarly journals The DEK Oncoprotein Is a Critical Component of the EKLF/KLF1 Enhancer in Erythroid Cells

2015 ◽  
Vol 35 (21) ◽  
pp. 3726-3738 ◽  
Author(s):  
Felix Lohmann ◽  
Mohan Dangeti ◽  
Shefali Soni ◽  
Xiaoyong Chen ◽  
Antanas Planutis ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Affinity Purification ◽  
Critical Factor ◽  
Signaling Cascades ◽  
Chromatin Domain ◽  
Open Chromatin ◽  
Enhancer Element ◽  
Core Set ◽  
Local Enrichment ◽  
Positive Effect

Understanding how transcriptional regulators are themselves controlled is important in attaining a complete picture of the intracellular effects that follow signaling cascades during early development and cell-restricted differentiation. We have addressed this issue by focusing on the regulation of EKLF/KLF1, a zinc finger transcription factor that plays a necessary role in the global regulation of erythroid gene expression. Using biochemical affinity purification, we have identified the DEK oncoprotein as a critical factor that interacts with an essential upstream enhancer element of the EKLF promoter and exerts a positive effect on EKLF levels. This element also binds a core set of erythroid transcription factors, suggesting that DEK is part of a tissue-restricted enhanceosome that contains BMP4-dependent and -independent components. Together with local enrichment of properly coded histones and an open chromatin domain, optimal transcriptional activation of the EKLF locus can be established.

scholarly journals The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster

2022 ◽  
Author(s):  
Noriyoshi Akiyama ◽  
Shoma Sato ◽  
Kentaro M Tanaka ◽  
Takaomi Sakai ◽  
Aya Takahashi
Keyword(s):  
Expression Pattern ◽  
Transcriptional Activation ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Enhancer Element ◽  
Pigment Synthesis ◽  
Endogenous Expression ◽  
Spatiotemporal Regulation ◽  
Dark Pigmentation ◽  
In The Wild

Abstract The spatiotemporal regulation of gene expression is essential to ensure robust phenotypic outcomes. Pigmentation patterns in Drosophila are determined by pigments biosynthesized in the developing epidermis and the cis-regulatory elements (CREs) of the genes involved in this process are well-characterized. Here we report that the known primary epidermal enhancer (priEE) is dispensable for the transcriptional activation of ebony (involved in light-colored pigment synthesis) in the developing epidermis of D. melanogaster. The evidence was obtained by introducing an approximately 1 kbp deletion at the priEE by genome editing. The effect of the priEE deletion on pigmentation and on the endogenous expression pattern of a mCherry-fused ebony allele was examined in the abdomen. The expression levels of the mCherry-fused ebony in the priEE-deleted strains were slightly higher than that of the control strain, indicating that the sequences outside the priEE have an ability to drive an expression of this gene in the epidermis. Interestingly, the priEE deletion resulted in a derepression of this gene in the dorsal midline of the abdominal tergites, where dark pigmentation is present in the wild-type individuals. This indicated that the priEE fragment contains a silencer. Furthermore, the endogenous expression pattern of ebony in the two additional strains with partially deleted priEE revealed that the silencer resides within a 351-bp fragment in the 5' portion of the priEE. These results demonstrated that deletion assays combined with reporter assays are highly effective in detecting the presence of positively and negatively regulating sequences within and outside the focal CREs.

Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression

2005 ◽  
Vol 83 (4) ◽  
pp. 535-547 ◽  
Author(s):  
Gareth N Corry ◽  
D Alan Underhill
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Current Knowledge ◽  
Nuclear Architecture ◽  
Subnuclear Localization ◽  
Modular Structures

To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

scholarly journals Transcriptional Activation in Yeast Cells Lacking Transcription Factor IIA

Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1573-1581 ◽  
Author(s):  
Susanna Chou ◽  
Sukalyan Chatterjee ◽  
Mark Lee ◽  
Kevin Struhl
Keyword(s):  
Transcription Factor ◽  
Transcriptional Activation ◽  
Large Subunit ◽  
Yeast Cells ◽  
Specific Cell ◽  
Wild Type ◽  
Activation Domains ◽  
Cycle Arrest ◽  
General Transcription Factor

Abstract The general transcription factor IIA (TFIIA) forms a complex with TFIID at the TATA promoter element, and it inhibits the function of several negative regulators of the TATA-binding protein (TBP) subunit of TFIID. Biochemical experiments suggest that TFIIA is important in the response to transcriptional activators because activation domains can interact with TFIIA, increase recruitment of TFIID and TFIIA to the promoter, and promote isomerization of the TFIID-TFIIA-TATA complex. Here, we describe a double-shut-off approach to deplete yeast cells of Toa1, the large subunit of TFIIA, to <1% of the wild-type level. Interestingly, such TFIIA-depleted cells are essentially unaffected for activation by heat shock factor, Ace1, and Gal4-VP16. However, depletion of TFIIA causes a general two- to threefold decrease of transcription from most yeast promoters and a specific cell-cycle arrest at the G2-M boundary. These results indicate that transcriptional activation in vivo can occur in the absence of TFIIA.

Sign in / Sign up

Export Citation Format

Share Document