scholarly journals A low affinity cis-regulatory BMP response element restricts target gene activation to subsets of Drosophila neurons

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Anthony JE Berndt ◽  
Katerina M Othonos ◽  
Tianshun Lian ◽  
Stephane Flibotte ◽  
Mo Miao ◽  
...  
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Bmp Signaling ◽  
Regulatory Mechanisms ◽  
Efferent Neuron ◽  
Enhancer Activity ◽  
Binding Motifs ◽  
High Affinity ◽  
Efferent Neurons

Retrograde BMP signaling and canonical pMad/Medea-mediated transcription regulate diverse target genes across subsets of Drosophila efferent neurons, to differentiate neuropeptidergic neurons and promote motor neuron terminal maturation. How a common BMP signal regulates diverse target genes across many neuronal subsets remains largely unresolved, although available evidence implicates subset-specific transcription factor codes rather than differences in BMP signaling. Here we examine the cis-regulatory mechanisms restricting BMP-induced FMRFa neuropeptide expression to Tv4-neurons. We find that pMad/Medea bind at an atypical, low affinity motif in the FMRFa enhancer. Converting this motif to high affinity caused ectopic enhancer activity and eliminated Tv4-neuron expression. In silico searches identified additional motif instances functional in other efferent neurons, implicating broader functions for this motif in BMP-dependent enhancer activity. Thus, differential interpretation of a common BMP signal, conferred by low affinity pMad/Medea binding motifs, can contribute to the specification of BMP target genes in efferent neuron subsets.

FLT3ITD Target Enhancers Are Primed but Inaccessible in Fetal Hematopoietic Progenitors

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1228-1228
Author(s):  
Yanan Li ◽  
Riddhi M Patel ◽  
Emily Casey ◽  
Jeffrey A. Magee
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Gene Activation ◽  
Chromatin Accessibility ◽  
Luciferase Reporter ◽  
Enhancer Activity ◽  
Target Gene Expression

The FLT3 Internal Tandem Duplication (FLT3ITD) is common somatic mutation in acute myeloid leukemia (AML). We have previously shown that FLT3ITD fails to induce changes in HSC self-renewal, myelopoiesis and leukemogenesis during fetal stages of life. FLT3ITD signal transduction pathways are hyperactivated in fetal progenitors, but FLT3ITD target genes are not. This suggests that postnatal-specific transcription factors may be required to help induce FLT3ITD target gene expression. Alternatively, repressive histone modifications may impose a barrier to FLT3ITD target gene activation in fetal HPCs that is relaxed during postnatal development. To resolve these possibilities, we used ATAC-seq, as well as H3K4me1, H3K27ac and H3K27me3 ChIP-seq, to identify cis-elements that putatively control FLT3ITD target gene expression in fetal and adult hematopoietic progenitor cells (HPCs). We identified many enhancer elements (ATAC-seq peaks with H3K4me1 and H3K27ac) that exhibited increased chromatin accessibility and activity in FLT3ITD adult HPCs relative to wild type adult HPCs. These elements were enriched near FLT3ITD target genes. HOMER analysis showed enrichment for STAT5, ETS, RUNX1 and IRF binding motifs within the FLT3ITD target enhancers, but motifs for temporally dynamic transcription factors were not identified. We cloned a subset of the enhancers and confirmed that they could synergize with their promoter to activate a luciferase reporter. For representative enhancers, STAT5 binding sites were required to activate the enhancer - as anticipated - and RUNX1 repressed enhancer activity. We tested whether accessibility or priming changed between fetal and adult stages of HPC development. FLT3ITD-dependent changes in chromatin accessibility were not observed in fetal HPCs, though the enhancers were primed early in development as evidenced by the presence of H3K4me1. Repressive H3K27me3 were not present at FLT3ITD target enhancers in either or adult HPCs. The data show that FLT3ITD target enhancers are demarcated early in hematopoietic development, long before they become responsive to FLT3ITD signaling. Repressive marks do not appear to create an epigenetic barrier to enhancer activation in the fetal stage. Instead, age-specific transcription factors are likely required to pioneer enhancer elements so that they can respond to STAT5 and other FLT3ITD effectors. Disclosures No relevant conflicts of interest to declare.

scholarly journals The BMP signaling gradient is interpreted through concentration thresholds in dorsal–ventral axial patterning

PLoS Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. e3001059
Author(s):  
Hannah Greenfeld ◽  
Jerome Lin ◽  
Mary C. Mullins
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Spatial Relationship ◽  
Bmp Signaling ◽  
Target Gene Expression ◽  
Gradient Slope ◽  
Distinct Cell

Bone Morphogenetic Protein (BMP) patterns the dorsal–ventral (DV) embryonic axis in all vertebrates, but it is unknown how cells along the DV axis interpret and translate the gradient of BMP signaling into differential gene activation that will give rise to distinct cell fates. To determine the mechanism of BMP morphogen interpretation in the zebrafish gastrula, we identified 57 genes that are directly activated by BMP signaling. By using Seurat analysis of single-cell RNA sequencing (scRNA-seq) data, we found that these genes are expressed in at least 3 distinct DV domains of the embryo. We distinguished between 3 models of BMP signal interpretation in which cells activate distinct gene expression through interpretation of thresholds of (1) the BMP signaling gradient slope; (2) the BMP signal duration; or (3) the level of BMP signal activation. We tested these 3 models using quantitative measurements of phosphorylated Smad5 (pSmad5) and by examining the spatial relationship between BMP signaling and activation of different target genes at single-cell resolution across the embryo. We found that BMP signaling gradient slope or BMP exposure duration did not account for the differential target gene expression domains. Instead, we show that cells respond to 3 distinct levels of BMP signaling activity to activate and position target gene expression. Together, we demonstrate that distinct pSmad5 threshold levels activate spatially distinct target genes to pattern the DV axis.

scholarly journals Differential Target Gene Activation by the Staphylococcus aureus Two-Component System saeRS

2009 ◽  
Vol 192 (3) ◽  
pp. 613-623 ◽  
Author(s):  
Markus Mainiero ◽  
Christiane Goerke ◽  
Tobias Geiger ◽  
Christoph Gonser ◽  
Silvia Herbert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Gene Expression Pattern ◽  
Class Ii ◽  
Class I ◽  
Single Amino Acid ◽  
Single Amino Acid Change

ABSTRACT The saePQRS system of Staphylococcus aureus controls the expression of major virulence factors and encodes a histidine kinase (SaeS), a response regulator (SaeR), a membrane protein (SaeQ), and a lipoprotein (SaeP). The widely used strain Newman is characterized by a single amino acid change in the sensory domain of SaeS (Pro18 in strain Newman [SaeSP], compared with Leu18 in other strains [SaeSL]). SaeSP determines activation of the class I sae target genes (coa, fnbA, eap, sib, efb, fib, sae), which are highly expressed in strain Newman. In contrast, class II target genes (hla, hlb, cap) are not sensitive to the SaeS polymorphism. The SaeSL allele (saeSL ) is dominant over the SaeSP allele, as shown by single-copy integration of saePQRSL in strain Newman, which results in severe repression of class I target genes. The differential effect on target gene expression is explained by different requirements for SaeR phosphorylation. From an analysis of saeS deletion strains and strains with mutated SaeR phosphorylation sites, we concluded that a high level of SaeR phosphorylation is required for activation of class I target genes. However, a low level of SaeR phosphorylation, which can occur independent of SaeS, is sufficient to activate class II target genes. Using inducible saeRS constructs, we showed that the expression of both types of target genes is independent of the saeRS dosage and that the typical growth phase-dependent gene expression pattern is not driven by SaeRS.

scholarly journals MED14 Tethers Mediator to the N-Terminal Domain of Peroxisome Proliferator-Activated Receptor γ and Is Required for Full Transcriptional Activity and Adipogenesis

2010 ◽  
Vol 30 (9) ◽  
pp. 2155-2169 ◽  
Author(s):  
Lars Grøntved ◽  
Maria S. Madsen ◽  
Michael Boergesen ◽  
Robert G. Roeder ◽  
Susanne Mandrup
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activity ◽  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Proximal Promoter ◽  
Peroxisome Proliferator ◽  
Independent Manner ◽  
Peroxisome Proliferator Activated Receptor ◽  
Terminal Domain

ABSTRACT The Mediator subunit MED1/TRAP220/DRIP205/PBP interacts directly with many nuclear receptors and was long thought to be responsible for tethering Mediator to peroxisome proliferator-activated receptor (PPAR)-responsive promoters. However, it was demonstrated recently that PPARγ can recruit Mediator by MED1-independent mechanisms. Here, we show that target gene activation by ectopically expressed PPARγ and PPARα is independent of MED1. Consistent with this finding, recruitment of PPARγ, MED6, MED8, TATA box-binding protein (TBP), and RNA polymerase II (RNAPII) to the enhancer and proximal promoter of the PPARγ target gene Fabp4 is also independent of MED1. Using a small interfering RNA (siRNA)-based approach, we identify MED14 as a novel critical Mediator component for PPARγ-dependent transactivation, and we demonstrate that MED14 interacts directly with the N terminus of PPARγ in a ligand-independent manner. Interestingly, MED14 knockdown does not affect the recruitment of PPARγ, MED6, and MED8 to the Fabp4 enhancer but does reduce their occupancy of the Fabp4 proximal promoter. In agreement with the necessity of MED14 for PPARγ transcriptional activity, we show that knockdown of MED14 impairs adipogenesis of 3T3-L1 cells. Thus, MED14 constitutes a novel anchoring point between Mediator and the N-terminal domain of PPARγ that is necessary for functional PPARγ-mediated recruitment of Mediator and transactivation of PPARγ subtype-specific target genes.

scholarly journals Wnt target enhancer regulation by a CDX/TCF transcription factor collective and a novel DNA motif

2021 ◽  
Author(s):  
Aravinda-Bharathi Ramakrishnan ◽  
Lisheng Chen ◽  
Peter Burby ◽  
Ken M. Cadigan
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Mechanisms Of Action ◽  
Wnt Signalling ◽  
Complex Nature ◽  
Enhancer Activity ◽  
Dna Motif ◽  
Responsive Element ◽  
Cis And Trans ◽  
Enhancer Regulation

AbstractTranscriptional regulation by Wnt signalling is primarily thought to be accomplished by a complex of β-catenin and TCF family transcription factors (TFs). Although numerous studies have suggested that additional TFs play roles in regulating Wnt target genes, their mechanisms of action have not been investigated in detail. We characterised a Wnt-responsive element (WRE) downstream of the Wnt target gene Axin2 and found that TCFs and Caudal-related homeodomain (CDX) proteins were required for its activation. Using a new separation-of-function TCF mutant, we found that WRE activity requires the formation of a TCF/CDX complex. Our systematic mutagenesis of this enhancer identified other sequences essential for activation by Wnt signalling, including several copies of a novel CAG DNA motif. Computational and experimental evidence indicates that the TCF/CDX/CAG mode of regulation is prevalent in multiple WREs. Put together, our results demonstrate the complex nature of cis- and trans- interactions required for signal-dependent enhancer activity.

The role of brinker in mediating the graded response to Dpp in early Drosophila embryos

Development ◽  
1999 ◽  
Vol 126 (15) ◽  
pp. 3323-3334 ◽  
Author(s):  
A. Jazwinska ◽  
C. Rushlow ◽  
S. Roth
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Gene Activation ◽  
Ectopic Expression ◽  
Intermediate Level ◽  
Graded Response ◽  
High Level ◽  
Drosophila Embryos ◽  
Novel Protein

Brinker (Brk), a novel protein with features of a transcriptional repressor, regulates the graded response to Decapentaplegic (Dpp) in appendage primordia of Drosophila. Here, we show that in the embryo brk also has differential effects on Dpp target genes, depending on the level of Dpp activity required for their activation. Low-level target genes, like dpp itself, tolloid and early zerknullt, show strong ectopic expression in ventrolateral regions of brk mutant embryos; intermediate-level target genes like pannier show weak ectopic expression, while high-level target genes like u-shaped and rhomboid are not affected. Ectopic target gene activation in the absence of brk is independent of Dpp, Tkv and Medea, indicating that Dpp signaling normally antagonizes brk's repression of these target genes. brk is expressed like short gastrulation (sog) in ventrolateral regions of the embryo abutting the dpp domain. Here, both brk and sog antagonize the antineurogenic activity of Dpp so that only in brk sog double mutants is the neuroectoderm completely deleted.

scholarly journals In Vivo Mitochondrial p53 Translocation Triggers a Rapid First Wave of Cell Death in Response to DNA Damage That Can Precede p53 Target Gene Activation

2004 ◽  
Vol 24 (15) ◽  
pp. 6728-6741 ◽  
Author(s):  
Susan Erster ◽  
Motohiro Mihara ◽  
Roger H. Kim ◽  
Oleksi Petrenko ◽  
Ute M. Moll
Keyword(s):  
Target Gene ◽  
Caspase 3 ◽  
Target Genes ◽  
Cultured Cells ◽  
Gene Activation ◽  
Lag Phase ◽  
Cell Fractionation ◽  
Γ Irradiation ◽  
P53 Target Gene

ABSTRACT p53 promotes apoptosis in response to death stimuli by transactivation of target genes and by transcription-independent mechanisms. We recently showed that wild-type p53 rapidly translocates to mitochondria in response to multiple death stimuli in cultured cells. Mitochondrial p53 physically interacts with antiapoptotic Bcl proteins, induces Bak oligomerization, permeabilizes mitochondrial membranes, and rapidly induces cytochrome c release. Here we characterize the mitochondrial p53 response in vivo. Mice were subjected to γ irradiation or intravenous etoposide administration, followed by cell fractionation and immunofluorescence studies of various organs. Mitochondrial p53 accumulation occurred in radiosensitive organs like thymus, spleen, testis, and brain but not in liver and kidney. Of note, mitochondrial p53 translocation was rapid (detectable at 30 min in thymus and spleen) and triggered an early wave of marked caspase 3 activation and apoptosis. This caspase 3-mediated apoptosis was entirely p53 dependent, as shown by p53 null mice, and preceded p53 target gene activation. The transcriptional p53 program had a longer lag phase than the rapid mitochondrial p53 program. In thymus, the earliest apoptotic target gene products PUMA, Noxa, and Bax appeared at 2, 4, and 8 h, respectively, while Bid, Killer/DR5, and p53DinP1 remained uninduced even after 20 h. Target gene induction then led to further increase in active caspase 3. Similar biphasic kinetics was seen in cultured human cells. Our results suggest that in sensitive organs mitochondrial p53 accumulation in vivo occurs soon after a death stimulus, triggering a rapid first wave of apoptosis that is transcription independent and may precede a second slower wave that is transcription dependent.

scholarly journals The Drosophila Genesdisconnectedanddisco-relatedAre Redundant With Respect to Larval Head Development and Accumulation of mRNAs From Deformed Target Genes

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 225-236
Author(s):  
James W Mahaffey ◽  
Charles M Griswold ◽  
Quynh-Mai Cao
Keyword(s):  
Transcription Factors ◽  
Zinc Finger ◽  
Target Gene ◽  
Target Genes ◽  
Hox Genes ◽  
Current Model ◽  
Gene Activation ◽  
Body Region ◽  
Protein Accumulation ◽  
Body Pattern

AbstractHOM-C/hox genes specify body pattern by encoding regionally expressed transcription factors that activate the appropriate target genes necessary for differentiation of each body region. The current model of target gene activation suggests that interactions with cofactors influence DNA-binding ability and target gene activation by the HOM-C/hox proteins. Currently, little is known about the specifics of this process because few target genes and fewer cofactors have been identified. We undertook a deficiency screen in Drosophila melanogaster in an attempt to identify loci potentially encoding cofactors for the protein encoded by the HOM-C gene Deformed (Dfd). We identified a region of the X chromosome that, when absent, leads to loss of specific larval mouthpart structures producing a phenotype similar to that observed in Dfd mutants. The phenotype is correlated with reduced accumulation of mRNAs from Dfd target genes, though there appears to be no effect on Dfd protein accumulation. We show that these defects are due to the loss of two functionally redundant, neighboring genes encoding zinc finger transcription factors, disconnected and a gene we call disco-related. We discuss the role of these genes during differentiation of the gnathal segments and, in light of other recent findings, propose that regionally expressed zinc finger proteins may play a central role with the HOM-C proteins in establishing body pattern.

scholarly journals Pygo2 Associates with MLL2 Histone Methyltransferase and GCN5 Histone Acetyltransferase Complexes To Augment Wnt Target Gene Expression and Breast Cancer Stem-Like Cell Expansion

2010 ◽  
Vol 30 (24) ◽  
pp. 5621-5635 ◽  
Author(s):  
Jiakun Chen ◽  
Qicong Luo ◽  
Yuanyang Yuan ◽  
Xiaoli Huang ◽  
Wangyu Cai ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Transcriptional Activation ◽  
Cell Expansion ◽  
Breast Cancer Cells ◽  
Target Gene ◽  
Target Genes ◽  
Histone Acetyltransferase ◽  
Gene Activation ◽  
Histone Methyltransferase ◽  
T Cell Factor

ABSTRACT Resent studies have identified Pygopus as a core component of the β-catenin/T-cell factor (TCF)/lymphoid-enhancing factor 1 (LEF) transcriptional activation complex required for the expression of canonical Wg/Wnt target genes in Drosophila. However, the biochemical involvement of mammalian Pygopus proteins in β-catenin/TCF/LEF gene activation remains controversial. In this study, we perform a series of molecular/biochemical experiments to demonstrate that Pygo2 associates with histone-modifying enzymatic complexes, specifically the MLL2 histone methyltransferase (HMT) and STAGA histone acetyltransferase (HAT) complexes, to facilitate their interaction with β-catenin and to augment Wnt1-induced, TCF/LEF-dependent transcriptional activation in breast cancer cells. We identify a critical domain in Pygo2 encompassing the first 47 amino acids that mediates its HMT/HAT interaction. We further demonstrate the importance of this domain in Pygo2's ability to transcriptionally activate both artificial and endogenous Wnt target genes and to expand breast cancer stem-like cells in culture. This work now links mechanistically Pygo2's role in histone modification to its enhancement of the Wnt-dependent transcriptional program and cancer stem-like cell expansion.

scholarly journals GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

2019 ◽  
Author(s):  
Rachel K. Lex ◽  
Zhicheng Ji ◽  
Kristin N. Falkenstein ◽  
Weiqiang Zhou ◽  
Joanna L. Henry ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Hedgehog Signaling ◽  
Target Gene ◽  
Target Genes ◽  
Enhancer Activity ◽  
Tissue Specific ◽  
Major Mechanism ◽  
Gli Proteins ◽  
Polycomb Repression ◽  
Repression Complex

ABSTRACTTranscriptional repression needs to be rapidly reversible during embryonic development. This extends to the Hedgehog pathway, which primarily serves to counter GLI repression by processing GLI proteins into transcriptional activators. In investigating the mechanisms underlying GLI repression, we find that a subset of these regions, termed HH-responsive enhancers, specifically loses acetylation in the absence of HH signaling. These regions are highly enriched around HH target genes and primarily drive HH-specific limb activity. They also retain H3K27ac enrichment in limb buds devoid of GLI activator and repressor, indicating that their activity is primarily regulated by GLI repression. The Polycomb repression complex is not active at most of these regions, suggesting it is not a major mechanism of GLI repression. We propose a model for tissue-specific enhancer activity in which an HDAC-associated GLI repression complex regulates target gene expression by altering the acetylation status at enhancers.

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