scholarly journals An unusual genomic position effect on Drosophila white gene expression: pairing dependence, interactions with zeste, and molecular analysis of revertants.

Genetics ◽  
1992 ◽  
Vol 130 (1) ◽  
pp. 125-138 ◽  
Author(s):  
T Hazelrigg ◽  
S Petersen
Keyword(s):  
Gene Expression ◽  
Regulatory Element ◽  
Position Effect ◽  
Insertion Site ◽  
White Gene ◽  
Chromosome 2 ◽  
Wild Type ◽  
Gene Copies ◽  
In Trans ◽  
In Cis

Abstract The white gene in the AR4-24 P[white,rosy] insertion on chromosome 2 has a novel expression pattern, in which it is repressed in the dorsal half of the eye. X-ray mutagenesis led to the isolation of six revertants mapping to chromosome 2, which are wild type in a zeste+ background, and three extreme derivatives, in which white gene expression is repressed in ventral regions of the eye as well. By Southern blot analyses the breakpoints of five of the revertants and one of the extreme derivatives were mapped in the flanking DNA bordering each side of the AR4-24 insertion. The revertants show some dorsal repression of white in the presence of z1, and by this criterion each is only a partial revertant. The extreme derivatives act not only in cis, but also in trans to repress expression of AR4-24 and its various derivatives. We provide evidence that these trans effects are proximity-dependent effects, possibly mediated by pairing of gene copies, as they do not extend to copies of the white gene located elsewhere in the genome. We show that one extreme derivative, E1, is a small deletion spanning the insertion site at the 5' end of the white gene, and propose that the distance between a negative regulatory element in the 5' flanking DNA and the white promoter influences the degree of the repression.

scholarly journals A novel transvection phenomenon affecting the white gene of Drosophila melanogaster.

Genetics ◽  
1990 ◽  
Vol 126 (1) ◽  
pp. 167-176
Author(s):  
D Gubb ◽  
M Ashburner ◽  
J Roote ◽  
T Davis
Keyword(s):  
Drosophila Melanogaster ◽  
Homologous Chromosome ◽  
Tandem Duplication ◽  
Gamma Ray ◽  
Insertion Site ◽  
Hairpin Loop ◽  
Homologous Chromosomes ◽  
Inverted Order ◽  
In Trans ◽  
In Cis

Abstract The zeste mutation of Drosophila melanogaster suppresses the expression of white genes in the eye. This suppression is normally dependent on there being two copies of w+ located close to each other in the genome--they may either be in cis (as in a tandem duplication of w+) or in trans, i.e. on homologous chromosomes. Duplicated w+ genes carried by a giant transposing element, TE146(Z), are suppressed by z whether they are in direct (tandem) or inverted order. The tandem form of the TE is very sensitive to a rearrangement on the homologous chromosome--many rearrangements with breakpoints "opposite" the TE's insertion site prevent the interaction between the white genes on a z background. These aberrations act as dominant suppressors of zeste that are specific to the tandemly duplicated form of TE146(Z). The inverted form of the TE146(Z) presumably pairs as a hairpin loop; this is more stable than the tandem form by the criterion that its zeste phenotype is unaffected by any of the aberrations. This effect of rearrangements has been used as the basis for a screen, gamma-ray induced aberrations with at least one breakpoint opposite the TE site were recovered by their suppression of the zeste phenotype.

scholarly journals Trans-dimerization of JAM-A regulates Rap2 and is mediated by a domain that is distinct from the cis-dimerization interface

2014 ◽  
Vol 25 (10) ◽  
pp. 1574-1585 ◽  
Author(s):  
Ana C. Monteiro ◽  
Anny-Claude Luissint ◽  
Ronen Sumagin ◽  
Caroline Lai ◽  
Franziska Vielmuth ◽  
...  
Keyword(s):  
Epithelial Cell Proliferation ◽  
Wild Type ◽  
Transfected Cells ◽  
Force Microscopy ◽  
Atomic Force ◽  
Unique Site ◽  
Dimerization Interface ◽  
In Trans ◽  
In Cis ◽  
Common Cell

Junctional adhesion molecule-A (JAM-A) is a tight junction–associated signaling protein that regulates epithelial cell proliferation, migration, and barrier function. JAM-A dimerization on a common cell surface (in cis) has been shown to regulate cell migration, and evidence suggests that JAM-A may form homodimers between cells (in trans). Indeed, transfection experiments revealed accumulation of JAM-A at sites between transfected cells, which was lost in cells expressing cis- or predicted trans-dimerization null mutants. Of importance, microspheres coated with JAM-A containing alanine substitutions to residues 43NNP45 (NNP-JAM-A) within the predicted trans-dimerization site did not aggregate. In contrast, beads coated with cis-null JAM-A demonstrated enhanced clustering similar to that observed with wild-type (WT) JAM-A. In addition, atomic force microscopy revealed decreased association forces in NNP-JAM-A compared with WT and cis-null JAM-A. Assessment of effects of JAM-A dimerization on cell signaling revealed that expression of trans- but not cis-null JAM-A mutants decreased Rap2 activity. Furthermore, confluent cells, which enable trans-dimerization, had enhanced Rap2 activity. Taken together, these results suggest that trans-dimerization of JAM-A occurs at a unique site and with different affinity compared with dimerization in cis. Trans-dimerization of JAM-A may thus act as a barrier-inducing molecular switch that is activated when cells become confluent.

scholarly journals Histone H3K9 methylation promotes formation of genome compartments inCaenorhabditis elegansvia chromosome compaction and perinuclear anchoring

2020 ◽  
Vol 117 (21) ◽  
pp. 11459-11470 ◽  
Author(s):  
Qian Bian ◽  
Erika C. Anderson ◽  
Qiming Yang ◽  
Barbara J. Meyer
Keyword(s):  
Gene Expression ◽  
Nuclear Periphery ◽  
Chromosome Conformation ◽  
C Elegans ◽  
Genome Wide ◽  
Central Regions ◽  
In Trans ◽  
Genomic Regions ◽  
In Cis ◽  
Gene Expression Levels

Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explore mechanisms controlling genome compartment organization inCaenorhabditis elegansand investigate roles for compartments in regulating gene expression. Distal arms ofC. eleganschromosomes, which are enriched for heterochromatic histone modifications H3K9me1/me2/me3, interact with each other bothin cisandin trans,while interacting less frequently with central regions, leading to genome compartmentalization. Arms are anchored to the nuclear periphery via the nuclear envelope protein CEC-4, which binds to H3K9me. By performing genome-wide chromosome conformation capture experiments (Hi-C), we showed that eliminating H3K9me1/me2/me3 through mutations in the methyltransferase genesmet-2andset-25significantly impaired formation of inactive Arm and active Center compartments.cec-4mutations also impaired compartmentalization, but to a lesser extent. We found that H3K9me promotes compartmentalization through two distinct mechanisms: Perinuclear anchoring of chromosome arms via CEC-4 to promote theircisassociation, and an anchoring-independent mechanism that compacts individual chromosome arms. In bothmet-2 set-25andcec-4mutants, no dramatic changes in gene expression were found for genes that switched compartments or for genes that remained in their original compartment, suggesting that compartment strength does not dictate gene-expression levels. Furthermore, H3K9me, but not perinuclear anchoring, also contributes to formation of another prominent feature of chromosome organization, megabase-scale topologically associating domains on X established by the dosage compensation condensin complex. Our results demonstrate that H3K9me plays crucial roles in regulating genome organization at multiple levels.

The role of the Shigella flexneri yihE gene in LPS synthesis and virulence

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 1079-1084 ◽  
Author(s):  
Bryn Edwards-Jones ◽  
Paul R. Langford ◽  
J. Simon Kroll ◽  
Jun Yu
Keyword(s):  
Gene Expression ◽  
Global Change ◽  
Unknown Function ◽  
Guinea Pigs ◽  
Antimicrobial Agents ◽  
Shigella Flexneri ◽  
Global Gene Expression ◽  
Wild Type ◽  
In Trans

Previously, the authors have shown that inactivation of Shigella flexneri yihE, a gene of unknown function upstream of dsbA, which encodes a periplasmic disulphide catalyst, results in a global change of gene expression. Among the severely down-regulated genes are galETKM, suggesting that the yihE mutant, Sh54, may inefficiently produce the UDP-glucose and UDP-galactose required for LPS synthesis. This paper demonstrates that LPS synthesis in Sh54 is impaired. As a result, Sh54 is unable to polymerize host cell actin, due to aberrant localization of IcsA, or to cause keratoconjunctivitis in guinea pigs. Furthermore, Sh54 is more sensitive to some antimicrobial agents, and exhibits epithelial cytotoxicity characteristic of neither wild-type nor dsbA mutants. Supplying galETK in trans restores LPS synthesis and corrects all the defects. Hence, it is clear that the Shigella yihE gene is important not only in regulating global gene expression, as shown previously, but also in virulence through LPS synthesis via regulating the expression of the galETK operon.

scholarly journals THE GENETIC SYSTEM CONTROLLING RECOMBINATION IN THE SILKWORM

Genetics ◽  
1981 ◽  
Vol 99 (2) ◽  
pp. 231-245
Author(s):  
Hiroyasu Ebinuma ◽  
Narumi Yoshitake
Keyword(s):  
Chromosomal Aberrations ◽  
Recombination Frequency ◽  
Genetic System ◽  
Chromosome 2 ◽  
Chromosome 5 ◽  
Recombination Rates ◽  
Heterozygous Condition ◽  
In Trans ◽  
The Mean ◽  
In Cis

ABSTRACT The nature of recombination modifiers was investigated in Bombyx mori lines selected for high (H) and low (L) recombination rates between the pS and Y loci in chromosome 2. Since the mean recombination rates for the H × L and L × H F1 crosses were approximately intermediate between those of high and low lines, the cytoplasmic maternal effect and difference in the activity of recombination modifiers between marked and unmarked second chromosomes were not detected. The H × (L × H), H × (H × L), L × (L × H) and L × (H × L) backcrosses indicated the presence of additive and dominance effects of marked and unmarked second chromosomes and the remaining chromosomes.——Recombination rates between the pS and Y loci in chromosome 2 and half-nonrecombination rates between the pe and re loci in chromosome 5 of high and low lines indicated that these recombination modifiers caused changes in the recombination frequency between pS and Y in chromosome 2, but not between pe and re in chromosome 5.——There were no differences in viability between individuals having the second chromosomes of the recombinant types [pS +, pY (H); pS +, + Y (L)] and those of the nonrecombinant types [pS Y, p + (H); pS Y, + + (L)] in both high and low lines. Mean recombination rates measured in cis [pS Y/p + (H); pS Y/+ + (L)] and trans [pS +/p Y (H); pS +/+ Y (L)] males were the same in the high but not in the low line. No segregation of a single recombination modifier was indicated by the distribution of recombination rates measured in trans males [pS +/p Y (H); pS +/+ Y (L)] of high and low lines. Accordingly, the recombination modifiers distributed on chromosome 2 in the heterozygous condition were not gross chromosomal aberrations, but polygenic factors in the low line.

Being in a loop: how long non-coding RNAs organise genome architecture

2019 ◽  
Vol 63 (1) ◽  
pp. 177-186 ◽  
Author(s):  
Giuseppina Pisignano ◽  
Ioanna Pavlaki ◽  
Adele Murrell
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Potential Role ◽  
Conclusive Evidence ◽  
Genome Architecture ◽  
Chromatin Interactions ◽  
In Trans ◽  
Non Coding Rnas ◽  
Expression Evidence ◽  
In Cis

Abstract Chromatin architecture has a significant impact on gene expression. Evidence in the last two decades support RNA as an important component of chromatin structure [Genes Dev. (2005) 19, 1635–1655; PLoS ONE (2007) 2, e1182; Nat. Genet. (2002) 30, 329–334]. Long non-coding RNAs (lncRNAs) are able to control chromatin structure through nucleosome positioning, interaction with chromatin re-modellers and chromosome looping. These functions are carried out in cis at the site of lncRNAs transcription or in trans at distant loci. While the evidence for a role in lncRNAs in regulating gene expression through chromatin interactions is increasing, there is still very little conclusive evidence for a potential role in looping organisation. Here, we review models for the involvement of lncRNAs in genome architecture and the experimental evidence to support them.

scholarly journals Transcription attenuation-derived small RNA rnTrpL regulates tryptophan biosynthesis gene expression in trans

2019 ◽  
Vol 47 (12) ◽  
pp. 6396-6410 ◽  
Author(s):  
Hendrik Melior ◽  
Siqi Li ◽  
Ramakanth Madhugiri ◽  
Maximilian Stötzel ◽  
Saina Azarderakhsh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Posttranscriptional Regulation ◽  
Sinorhizobium Meliloti ◽  
Regulation Mechanism ◽  
Base Pairs ◽  
Bacterial Gene ◽  
Bacterial Gene Expression ◽  
In Trans ◽  
Transcription Attenuation ◽  
In Cis

Abstract Ribosome-mediated transcription attenuation is a basic posttranscriptional regulation mechanism in bacteria. Liberated attenuator RNAs arising in this process are generally considered nonfunctional. In Sinorhizobium meliloti, the tryptophan (Trp) biosynthesis genes are organized into three operons, trpE(G), ppiD-trpDC-moaC-moeA, and trpFBA-accD-folC, of which only the first one, trpE(G), contains a short ORF (trpL) in the 5′-UTR and is regulated by transcription attenuation. Under conditions of Trp sufficiency, transcription is terminated between trpL and trpE(G), and a small attenuator RNA, rnTrpL, is produced. Here, we show that rnTrpL base-pairs with trpD and destabilizes the polycistronic trpDC mRNA, indicating rnTrpL-mediated downregulation of the trpDC operon in trans. Although all three trp operons are regulated in response to Trp availability, only in the two operons trpE(G) and trpDC the Trp-mediated regulation is controlled by rnTrpL. Together, our data show that the trp attenuator coordinates trpE(G) and trpDC expression posttranscriptionally by two fundamentally different mechanisms: ribosome-mediated transcription attenuation in cis and base-pairing in trans. Also, we present evidence that rnTrpL-mediated regulation of trpDC genes expression in trans is conserved in Agrobacterium and Bradyrhizobium, suggesting that the small attenuator RNAs may have additional conserved functions in the control of bacterial gene expression.

scholarly journals Genomic impact of stress-induced transposable element mobility in Arabidopsis

2021 ◽  
Vol 49 (18) ◽  
pp. 10431-10447
Author(s):  
David Roquis ◽  
Marta Robertson ◽  
Liang Yu ◽  
Michael Thieme ◽  
Magdalena Julkowska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Insertion Site ◽  
Plant Evolution ◽  
Site Preference ◽  
Wild Type ◽  
Element Mobility ◽  
Regulatory Pathways ◽  
Gene Regulatory ◽  
Gene Knockouts

Abstract Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.

scholarly journals Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Scott Berry ◽  
Matthew Hartley ◽  
Tjelvar S G Olsson ◽  
Caroline Dean ◽  
Martin Howard
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Epigenetic Inheritance ◽  
Long Term Memory ◽  
Individual Gene ◽  
Polycomb Repressive Complex 2 ◽  
In Trans ◽  
Epigenetic Repression ◽  
In Cis ◽  
Polycomb Target Gene

Inheritance of gene expression states is fundamental for cells to ‘remember’ past events, such as environmental or developmental cues. The conserved Polycomb Repressive Complex 2 (PRC2) maintains epigenetic repression of many genes in animals and plants and modifies chromatin at its targets. Histones modified by PRC2 can be inherited through cell division. However, it remains unclear whether this inheritance can direct long-term memory of individual gene expression states (cis memory) or instead if local chromatin states are dictated by the concentrations of diffusible factors (trans memory). By monitoring the expression of two copies of the Arabidopsis Polycomb target gene FLOWERING LOCUS C (FLC) in the same plants, we show that one copy can be repressed while the other is active. Furthermore, this ‘mixed’ expression state is inherited through many cell divisions as plants develop. These data demonstrate that epigenetic memory of FLC expression is stored not in trans but in cis.

Differential Gene Silencing by trans-heterochromatin in Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 257-269
Author(s):  
Amy K Csink ◽  
Alexander Bounoutas ◽  
Michelle L Griffith ◽  
Joy F Sabl ◽  
Brian T Sage
Keyword(s):  
Interphase Nucleus ◽  
Insertion Site ◽  
Wild Type Allele ◽  
Wild Type ◽  
Chromosomal Distance ◽  
Highly Sensitive ◽  
In Trans ◽  
Differential Gene ◽  
Range Of Influence ◽  
Large Insertion

Abstract The brownDominant (bwD) allele contains a large insertion of heterochromatin leading to the trans-inactivation of the wild-type allele in bwD/bw+ heterozygous flies. This silencing is correlated with the localization of bw+ to a region of the interphase nucleus containing centric heterochromatin. We have used a series of transgene constructs inserted in the vicinity of the bw locus to demarcate both the extent of bwD influence along the chromosome and the relative sensitivities of various genes. Examples of regulatory regions that are highly sensitive, moderately sensitive, and insensitive were found. Additionally, by using the same transgene at increasing distances from the bwD insertion site in trans we were able to determine the range of influence of the heterochromatic neighborhood in terms of chromosomal distance. When the transgene was farther away from bw, there was, indeed, a tendency for it to be less trans-inactivated. However, insertion site also influenced silencing: a gene 86 kb away was trans-inactivated, while the same transgene 45 kb away was not. Thus location, distance, and gene-specific differences all influence susceptibility to trans-silencing near a heterochromatic neighborhood. These results have important implications for the ability of nuclear positioning to influence the expression of large blocks of a chromosome.

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