scholarly journals Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the D. melanogaster embryo

2021 ◽  
Author(s):  
Lily Li ◽  
Rachel Waymack ◽  
Mario Elabd ◽  
Zeba Wunderlich
Keyword(s):  
Burst Size ◽  
Expression Patterns ◽  
Housekeeping Genes ◽  
The Other ◽  
Wild Type ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Core Promoters ◽  
Multiple Promoters ◽  
Transcription Process

Proper development depends on precise spatiotemporal gene expression patterns. Most genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that these multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical sharp developmental promoter, while the other resembles a broad promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter. By analyzing the dynamics of these reporters, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the specific combination of promoter and enhancer. Using locus-sized reporters, we discovered that even enhancers that show no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is both due to enhancer preference and a need for redundancy and that broad promoters with dispersed transcription start sites are common among developmental genes. Our results also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where many variables shape a genes overall expression pattern.

scholarly journals Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the D. melanogaster embryo

Genetics ◽  
2021 ◽  
Author(s):  
Lily Li ◽  
Rachel Waymack ◽  
Mario Gad ◽  
Zeba Wunderlich
Keyword(s):  
Burst Size ◽  
Expression Patterns ◽  
Housekeeping Genes ◽  
Wild Type ◽  
Transcription Start ◽  
Developmental Genes ◽  
Transcription Start Sites ◽  
Core Promoters ◽  
Multiple Promoters ◽  
Transcription Process

Abstract Proper development depends on precise spatiotemporal gene expression patterns. Most developmental genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical “sharp” developmental promoter, while the other resembles a “broad” promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter, indicating that promoters provide both redundancy and specificity. By analyzing the reporter dynamics, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the combination of promoter and enhancer. Using locus-sized reporters, we discovered that enhancers with no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is due both to enhancer preference and a need for redundancy and that “broad” promoters with dispersed transcription start sites are common among developmental genes. They also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where other variables shape a gene’s overall expression pattern.

scholarly journals Constitutive Expression of Escherichia coli tat Genes Indicates an Important Role for the Twin-Arginine Translocase during Aerobic and Anaerobic Growth

2001 ◽  
Vol 183 (5) ◽  
pp. 1801-1804 ◽  
Author(s):  
Rachael L. Jack ◽  
Frank Sargent ◽  
Ben C. Berks ◽  
Gary Sawers ◽  
Tracy Palmer
Keyword(s):  
Constitutive Expression ◽  
Protein Export ◽  
The Other ◽  
Anaerobic Growth ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Expression Studies ◽  
Twin Arginine Translocase ◽  
Aerobic And Anaerobic Growth ◽  
Aerobic And Anaerobic

ABSTRACT The transcription start sites for the tatABCD andtatE loci, encoding components of the Tat (twin-arginine translocase) protein export pathway, have been identified. Expression studies indicate that the tatABCD and tatEtranscription units are expressed constitutively. Translational fusion experiments suggest that TatA is synthesized at a much higher level than the other Tat proteins.

scholarly journals Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites

2021 ◽  
Author(s):  
Jose M. G. Vilar ◽  
Leonor Saiz
Keyword(s):  
Expression Patterns ◽  
Cell Types ◽  
Coordinate Space ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Functional Relationships ◽  
Complex Dependence ◽  
Dna Elements ◽  
Genomic Signals ◽  
Dependent Processes

The prevalent one-dimensional alignment of genomic signals to a reference landmark is a cornerstone of current methods to study transcription and its DNA-dependent processes but it is prone to mask potential relations among multiple DNA elements. We developed a systematic approach to align genomic signals to multiple locations simultaneously by expanding the dimensionality of the genomic-coordinate space. We analyzed transcription in human and uncovered a complex dependence on the relative position of neighboring transcription start sites (TSSs) that is consistently conserved among cell types. The dependence ranges from enhancement to suppression of transcription depending on the relative distances to the TSSs, their intragenic position, and the transcriptional activity of the gene. Our results reveal a conserved hierarchy of alternative TSS usage within a previously unrecognized level of genomic organization and provide a general methodology to analyze complex functional relationships among multiple types of DNA elements.

scholarly journals Apparent Role for Borrelia burgdorferi LuxS during Mammalian Infection

2015 ◽  
Vol 83 (4) ◽  
pp. 1347-1353 ◽  
Author(s):  
William K. Arnold ◽  
Christina R. Savage ◽  
Alyssa D. Antonicello ◽  
Brian Stevenson
Keyword(s):  
Borrelia Burgdorferi ◽  
Expression Patterns ◽  
The Other ◽  
Infection Cycle ◽  
Wild Type ◽  
Content Type ◽  
Significant Function ◽  
Autoinducer 2 ◽  
Associated Proteins ◽  
Mammalian Infection

The Lyme disease spirochete,Borrelia burgdorferi, controls protein expression patterns during its tick-mammal infection cycle. Earlier studies demonstrated thatB. burgdorferisynthesizes 4,5-dihydroxy-2,3-pentanedione (autoinducer-2 [AI-2]) and responds to AI-2 by measurably changing production of several infection-associated proteins.luxSmutants, which are unable to produce AI-2, exhibit altered production of several proteins.B. burgdorfericannot utilize the other product of LuxS, homocysteine, indicating that phenotypes ofluxSmutants are not due to the absence of that molecule. Although a previous study found that aluxSmutant was capable of infecting mice, a critical caveat to those results is that bacterial loads were not quantified. To more precisely determine whether LuxS serves a role in mammalian infection, mice were simultaneously inoculated with congenic wild-type andluxSstrains, and bacterial numbers were assessed using quantitative PCR. The wild-type bacteria substantially outcompeted the mutants, suggesting that LuxS performs a significant function during mammalian infection. These data also provide further evidence that nonquantitative infection studies do not necessarily provide conclusive results and that regulatory factors may not make all-or-none, black-or-white contributions to infectivity.

Nucleosome Positioning in the Upstream of TSS from Different Expression Pattern Gene during Drosophila embryogenesis

2014 ◽  
Vol 934 ◽  
pp. 182-187
Author(s):  
Qiu Fu Shan ◽  
Ji Hua Feng ◽  
Ying Lu ◽  
Zen Hui Shan ◽  
Pan Feng Chen
Keyword(s):  
Expression Pattern ◽  
Expression Patterns ◽  
Nucleosome Positioning ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Drosophila Embryogenesis ◽  
Restricted Expression Pattern ◽  
The Difference ◽  
Yeast Genes

Some significant differences about nucleosome positioning of different expression patterns gene have been found while researching the nucleosome positioning of Drosophila embryogenesis. The difference from the previous study was the restricted expression pattern gene incorporating H2A.Z into the-1 nucleosome in the upstream of Transcription Start Sites (TSS). Interestingly, compared with the nucleosome positioning of yeast genes, this nucleosome arrangement at gene of restricted expression pattern is similar with the characteristic found in yeast.

scholarly journals A Human FSHB Promoter SNP Associated With Low FSH Levels in Men Impairs LHX3 Binding and Basal FSHB Transcription

Endocrinology ◽  
2013 ◽  
Vol 154 (9) ◽  
pp. 3016-3021 ◽  
Author(s):  
Courtney A. Benson ◽  
Troy L. Kurz ◽  
Varykina G. Thackray
Keyword(s):  
Untranslated Region ◽  
The Other ◽  
Hormone Response ◽  
Potential Mechanism ◽  
Wild Type ◽  
Nucleotide Polymorphism ◽  
Transcription Start ◽  
Single Nucleotide ◽  
Hormone Response Element ◽  
Inactivating Mutations

FSH production is important for human gametogenesis. In addition to inactivating mutations in the FSHB gene, which result in infertility in both sexes, a G/T single-nucleotide polymorphism (SNP) at −211 relative to the transcription start site of the 5′ untranslated region of FSHB has been reported to be associated with reduced serum FSH levels in men. In this study, we sought to identify the potential mechanism by which the −211 SNP reduces FSH levels. Although the SNP resides in a putative hormone response element, we showed that, unlike the murine gene, human FSHB was not induced by androgens or progestins in gonadotropes. On the other hand, we found that the LHX3 homeodomain transcription factor bound to an 11-bp element in the human FSHB promoter that includes the −211 nucleotide. Furthermore, we also demonstrated that LHX3 bound with greater affinity to the wild-type human FSHB promoter compared with the −211 G/T mutation and that LHX3 binding was more effectively competed with excess wild-type oligonucleotide than with the SNP. Finally, we showed that FSHB transcription was decreased in gonadotrope cells with the −211 G/T mutation compared with the wild-type FSHB promoter. Altogether, our results suggest that decreased serum FSH levels in men with the SNP likely result from reduced LHX3 binding and induction of FSHB transcription.

scholarly journals Tissue-specific usage of transposable element-derived promoters in mouse development

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Benpeng Miao ◽  
Shuhua Fu ◽  
Cheng Lyu ◽  
Paul Gontarz ◽  
Ting Wang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Early Embryo ◽  
Mouse Tissue ◽  
Open Chromatin ◽  
Mouse Development ◽  
Transcription Start ◽  
Specific Expression ◽  
Tissue Specific ◽  
Transcription Start Sites ◽  
Tissue Specific Expression

Abstract Background Transposable elements (TEs) are a significant component of eukaryotic genomes and play essential roles in genome evolution. Mounting evidence indicates that TEs are highly transcribed in early embryo development and contribute to distinct biological functions and tissue morphology. Results We examine the epigenetic dynamics of mouse TEs during the development of five tissues: intestine, liver, lung, stomach, and kidney. We found that TEs are associated with over 20% of open chromatin regions during development. Close to half of these accessible TEs are only activated in a single tissue and a specific developmental stage. Most accessible TEs are rodent-specific. Across these five tissues, 453 accessible TEs are found to create the transcription start sites of downstream genes in mouse, including 117 protein-coding genes and 144 lincRNA genes, 93.7% of which are mouse-specific. Species-specific TE-derived transcription start sites are found to drive the expression of tissue-specific genes and change their tissue-specific expression patterns during evolution. Conclusion Our results suggest that TE insertions increase the regulatory potential of the genome, and some TEs have been domesticated to become a crucial component of gene and regulate tissue-specific expression during mouse tissue development.

scholarly journals Diversification of CpG-Island Promoters Revealed by Comparative Analysis Between Human and Rhesus Monkey Genomes

2020 ◽  
Vol 31 (7-8) ◽  
pp. 240-251
Author(s):  
Saki Aoto ◽  
Mayu Fushimi ◽  
Kei Yura ◽  
Kohji Okamura
Keyword(s):  
Rhesus Monkey ◽  
Cpg Island ◽  
Cpg Islands ◽  
Housekeeping Genes ◽  
Transcription Start ◽  
Cpg Dinucleotides ◽  
Transcription Start Sites ◽  
Cpg Sites ◽  
Mammalian Genomes ◽  
Ncbi Refseq

Abstract While CpG dinucleotides are significantly reduced compared to other dinucleotides in mammalian genomes, they can congregate and form CpG islands, which localize around the 5ʹ regions of genes, where they function as promoters. CpG-island promoters are generally unmethylated and are often found in housekeeping genes. However, their nucleotide sequences and existence per se are not conserved between humans and mice, which may be due to evolutionary gain and loss of the regulatory regions. In this study, human and rhesus monkey genomes, with moderately conserved sequences, were compared at base resolution. Using transcription start site data, we first validated our methods’ ability to identify orthologous promoters and indicated a limitation using the 5ʹ end of curated gene models, such as NCBI RefSeq, as their transcription start sites. We found that, in addition to deamination mutations, insertions and deletions of bases, repeats, and long fragments contributed to the mutations of CpG dinucleotides. We also observed that the G + C contents tended to change in CpG-poor environments, while CpG content was altered in G + C-rich environments. While loss of CpG islands can be caused by gradual decreases in CpG sites, gain of these islands appear to require two distinct nucleotide altering steps. Taken together, our findings provide novel insights into the process of acquisition and diversification of CpG-island promoters in vertebrates.

scholarly journals Aberrant Splicing and Altered Spatial Expression Patterns in fruitless Mutants of Drosophila melanogaster

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 725-745 ◽  
Author(s):  
Stephen F Goodwin ◽  
Barbara J Taylor ◽  
Adriana Villella ◽  
Margit Foss ◽  
Lisa C Ryner ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Sexual Behaviors ◽  
Expression Patterns ◽  
P Element ◽  
Wild Type ◽  
Alternative Processing ◽  
Multiple Promoters ◽  
Processing Pathways ◽  
Mutant Phenotypes

Abstract The fruitless (fru) gene functions in Drosophila males to establish the potential for male sexual behaviors. fru encodes a complex set of sex-specific and sex-nonspecific mRNAs through the use of multiple promoters and alternative pre-mRNA processing. The male-specific transcripts produced from the distal (P1) fru promoter are believed to be responsible for its role in specifying sexual behavior and are only expressed in a small fraction of central nervous system (CNS) cells. To understand the molecular etiology of fruitless mutant phenotypes, we compared wild-type and mutant transcription patterns. These experiments revealed that the fru2, fru3, fru4, and frusat mutations, which are due to P-element inserts, alter the pattern of sex-specific and sex-nonspecific fru RNAs. These changes arise in part from the P-element insertions containing splice acceptor sites that create alternative processing pathways. In situ hybridization revealed no alterations in the locations of cells expressing the P1-fru-promoter-derived transcripts in fru2, fru3, fru4, and frusat pharate adults. For the fru1 mutant (which is due to an inversion breakpoint near the P1 promoter), Northern analyses revealed no significant changes in fru transcript patterns. However, in situ hybridization revealed anomalies in the level and distribution of P1-derived transcripts: in fru1 males, fewer P1-expressing neurons are found in regions of the dorsal lateral protocerebrum and abdominal ganglion compared to wild-type males. In other regions of the CNS, expression of these transcripts appears normal in fru1 males. The loss of fruitless expression in these regions likely accounts for the striking courtship abnormalities exhibited by fru1 males. Thus, we suggest that the mutant phenotypes in fru2, fru3, fru4, and frusat animals are due to a failure to appropriately splice P1 transcripts, whereas the mutant phenotype of fru1 animals is due to the reduction or absence of P1 transcripts within specific regions of the CNS.

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