scholarly journals Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements

2017 ◽  
Vol 31 (6) ◽  
pp. 590-602 ◽  
Author(s):  
Jelena Erceg ◽  
Tibor Pakozdi ◽  
Raquel Marco-Ferreres ◽  
Yad Ghavi-Helm ◽  
Charles Girardot ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Response Elements ◽  
Polycomb Response Elements

scholarly journals Transcriptional read-through is not sufficient to induce an epigenetic switch in the silencing activity of Polycomb response elements

2015 ◽  
Vol 112 (48) ◽  
pp. 14930-14935 ◽  
Author(s):  
Maksim Erokhin ◽  
Pavel Elizar’ev ◽  
Aleksander Parshikov ◽  
Paul Schedl ◽  
Pavel Georgiev ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Division ◽  
Regulatory Elements ◽  
Epigenetic Switch ◽  
Response Elements ◽  
Histone Marks ◽  
Polycomb Response Elements ◽  
Dna Regulatory Elements ◽  
Universal Mechanism

In Drosophila, Polycomb (PcG) and Trithorax (TrxG) group proteins are assembled on Polycomb response elements (PREs) to maintain tissue and stage-specific patterns of gene expression. Critical to coordinating gene expression with the process of differentiation, the activity of PREs can be switched “on” and “off.” When on, the PRE imposes a silenced state on the genes in the same domain that is stably inherited through multiple rounds of cell division. When the PRE is switched off, the domain is in a state permissive for gene expression that can be stably inherited. Previous studies have suggested that a burst of transcription through a PRE sequence displaces PcG proteins and provides a universal mechanism for inducing a heritable switch in PRE activity from on to off; however, the evidence favoring this model is indirect. Here, we have directly tested the transcriptional read-through mechanism. Contrary to previous suggestions, we show that transcription through the PRE is not sufficient for inducing an epigenetic switch in PRE activity. In fact, even high levels of continuous transcription through a PRE fails to dislodge the PcG proteins, nor does it remove repressive histone marks. Our results indicate that other mechanisms involving adjacent DNA regulatory elements must be implicated in heritable switch of PRE activity.

Role of Transcriptional Read-Through in PRE Activity in Drosophila melanogaster

Acta Naturae ◽  
2016 ◽  
Vol 8 (2) ◽  
pp. 79-86 ◽  
Author(s):  
P. V. Elizar’ev ◽  
D. V. Lomaev ◽  
D. A. Chetverina ◽  
P. G. Georgiev ◽  
M. M. Erokhin
Keyword(s):  
Dna Sequences ◽  
Cell Types ◽  
Transcription Terminator ◽  
Response Elements ◽  
Polycomb Response Elements ◽  
The Individual ◽  
Multicellular Organisms ◽  
Different Cell Types ◽  
Main Factor

Maintenance of the individual patterns of gene expression in different cell types is required for the differentiation and development of multicellular organisms. Expression of many genes is controlled by Polycomb (PcG) and Trithorax (TrxG) group proteins that act through association with chromatin. PcG/TrxG are assembled on the DNA sequences termed PREs (Polycomb Response Elements), the activity of which can be modulated and switched from repression to activation. In this study, we analyzed the influence of transcriptional read-through on PRE activity switch mediated by the yeast activator GAL4. We show that a transcription terminator inserted between the promoter and PRE doesnt prevent switching of PRE activity from repression to activation. We demonstrate that, independently of PRE orientation, high levels of transcription fail to dislodge PcG/TrxG proteins from PRE in the absence of a terminator. Thus, transcription is not the main factor required for PRE activity switch.

scholarly journals Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhiwei Chen ◽  
Longhua Zhou ◽  
Panpan Jiang ◽  
Ruiju Lu ◽  
Nigel G. Halford ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Gene Family ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Related Protein ◽  
Rna Seq ◽  
Response Elements ◽  
Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

scholarly journals A Common Motif within the Negative Regulatory Regions of Multiple Factors Inhibits Their Transcriptional Synergy

2000 ◽  
Vol 20 (16) ◽  
pp. 6040-6050 ◽  
Author(s):  
Jorge A. Iñiguez-Lluhí ◽  
David Pearce
Keyword(s):  
Binding Sites ◽  
Regulatory Elements ◽  
General Mechanism ◽  
Proper Function ◽  
Protein Motif ◽  
Regulatory Regions ◽  
Response Elements ◽  
Common Motif ◽  
Single Response ◽  
Dna Regulatory Elements

ABSTRACT DNA regulatory elements frequently harbor multiple recognition sites for several transcriptional activators. The response mounted from such compound response elements is often more pronounced than the simple sum of effects observed at single binding sites. The determinants of such transcriptional synergy and its control, however, are poorly understood. Through a genetic approach, we have uncovered a novel protein motif that limits the transcriptional synergy of multiple DNA-binding regulators. Disruption of these conserved synergy control motifs (SC motifs) selectively increases activity at compound, but not single, response elements. Although isolated SC motifs do not regulate transcription when tethered to DNA, their transfer to an activator lacking them is sufficient to impose limits on synergy. Mechanistic analysis of the two SC motifs found in the glucocorticoid receptor N-terminal region reveals that they function irrespective of the arrangement of the receptor binding sites or their distance from the transcription start site. Proper function, however, requires the receptor's ligand-binding domain and an engaged dimer interface. Notably, the motifs are not functional in yeast and do not alter the effect of p160 coactivators, suggesting that they require other nonconserved components to operate. Many activators across multiple classes harbor seemingly unrelated negative regulatory regions. The presence of SC motifs within them, however, suggests a common function and identifies SC motifs as critical elements of a general mechanism to modulate higher-order interactions among transcriptional regulators.

Induction of labial expression in the Drosophila endoderm: response elements for dpp signalling and for autoregulation

Development ◽  
1992 ◽  
Vol 116 (2) ◽  
pp. 447-456 ◽  
Author(s):  
G. Tremml ◽  
M. Bienz
Keyword(s):  
Reporter Gene ◽  
Regulatory Elements ◽  
The Other ◽  
Homeotic Gene ◽  
Signal Molecule ◽  
Response Elements ◽  
Extracellular Signal ◽  
Dependent Activity ◽  
Flanking Sequences ◽  
Drosophila Embryos

Extracellular signal proteins induce the homeotic gene labial (lab) to high levels of localised expression in the endoderm of Drosophila embryos. We aimed to identify cis-regulatory elements within the lab gene that respond to this induction by analysing the activity of stably integrated reporter gene constructs. Dissection of lab 5′ flanking sequences reveals two types of response elements. One of these mediates lab dependent activity, providing evidence that lab induction in the endoderm is autoregulatory. The other element, to a large extent independent of lab function, responds to decapentaplegic (dpp), a signal molecule related to mammalian TGF-beta. Our evidence suggests that lab induction in the endoderm reflects coordinate action of two distinct factors one of which may be lab protein itself, and another whose localised activity or expression in the midgut depends on the dpp signal.

Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex

2007 ◽  
Vol 9 (10) ◽  
pp. 1167-1174 ◽  
Author(s):  
Chiara Lanzuolo ◽  
Virginie Roure ◽  
Job Dekker ◽  
Frédéric Bantignies ◽  
Valerio Orlando
Keyword(s):  
Higher Order ◽  
Bithorax Complex ◽  
Response Elements ◽  
Polycomb Response Elements ◽  
Order Structures

scholarly journals The quest for mammalian Polycomb response elements: are we there yet?

Chromosoma ◽  
2015 ◽  
Vol 125 (3) ◽  
pp. 471-496 ◽  
Author(s):  
Moritz Bauer ◽  
Johanna Trupke ◽  
Leonie Ringrose
Keyword(s):  
Response Elements ◽  
Polycomb Response Elements

scholarly journals The MCP silencer of theDrosophila Abd-Bgene requires both Pleiohomeotic and GAGA factor for the maintenance of repression

Development ◽  
2001 ◽  
Vol 128 (11) ◽  
pp. 2163-2173 ◽  
Author(s):  
Ana Busturia ◽  
Alan Lloyd ◽  
Fernando Bejarano ◽  
Michael Zavortink ◽  
Hua Xin ◽  
...  
Keyword(s):  
Reporter Gene ◽  
Binding Sites ◽  
Mutational Analysis ◽  
Regulatory Elements ◽  
Homeotic Gene ◽  
Gaga Factor ◽  
Polycomb Response Elements ◽  
Silencer Element

Silencing of homeotic gene expression requires the function of cis-regulatory elements known as Polycomb Response Elements (PREs). The MCP silencer element of the Drosophila homeotic gene Abdominal-B has been shown to behave as a PRE and to be required for silencing throughout development. Using deletion analysis and reporter gene assays, we defined a 138 bp sequence within the MCP silencer that is sufficient for silencing of a reporter gene in the imaginal discs. Within the MCP138 fragment, there are four binding sites for the Pleiohomeotic protein (PHO) and two binding sites for the GAGA factor (GAF), encoded by the Trithorax-like gene. PHO and the GAF proteins bind to these sites in vitro. Mutational analysis of PHO and GAF binding sequences indicate that these sites are necessary for silencing in vivo. Moreover, silencing by MCP138 depends on the function of the Trithorax-like gene, and on the function of the PcG genes, including pleiohomeotic. Deletion and mutational analyses show that, individually, either PHO or GAF binding sites retain only weak silencing activity. However, when both PHO and GAF binding sites are present, they achieve strong silencing. We present a model in which robust silencing is achieved by sequential and facilitated binding of PHO and GAF.

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