Kruppa TF et al. Trans R Soc Trop Med Hyg "Similar blackfly attraction by onchocerciasis patients and individuals putatively immune to Onchocerca volvulus."

Burchard GD, Kruppa TF

[Trans R Soc Trop Med Hyg]

In areas endemic for onchocerciasis, a small number of individuals show no detectable infection with Onchocerca volvulus despite an apparently similar exposure to the transmitting blackflies. Such individuals have been termed putatively immune. Since several studies have indicated marked host differences in attractiveness for blood-seeking insects, putative immunity in O. volvulus infection may result, at least in part, from low vector attractiveness of the respective individuals. In an area hyperendemic for onchocerciasis (Guinea), where Simulium yahense is the predominant vector, we organized fly catches by putatively immune individuals and individuals with moderate-to-high worm counts. No differences were found between the 2 groups with respect to (i) the attraction of blackflies, (ii) the attraction of blackflies infected with O. volvulus, or (iii) the numbers of O. volvulus larvae carried by the attracted blackflies.

Brattig NW et al. (1995) Parasitol Res "Cell-adhesion molecules expressed by activated eosinophils in Onchocerca volvulus infection."

Abakar AZ, Kruppa TF, Brattig NW, Geisinger F

[Parasitol Res, 1995]

Cell-adhesion receptors mediate the interaction between host effector cells and cellular or multicellular targets, including opsonized parasites. Our recent finding of a deposition of plasma proteins, including fibronectin, on the surface of infective larvae of the helminthic parasite Onchocerca volvulus led us to investigate the possible expression of cell-adhesion molecules (CAM), particularly fibronectin receptors, on eosinophilic granulocytes from persons infected with O. volvulus. Immunofluorescence analyses showed that freshly isolated eosinophils strongly expressed the beta 2-integrin CR3 and exhibited to a lower degree CR4 and the integrin-associated carbohydrate determinant Le(x), as well as antigen p24 (CD9). Eosinophils exposed to the eosinophil-active cytokines recombinant human interleukin 3 (rhIL-3) and granulocyte/macrophage colony-stimulating factor (rhGM-CSF) in addition to CR3, CR4, and CD9 expressed the beta 1-integrins VLA-4 and to a lesser extent VL-5 (both fibronectin receptors) as well as the intercellular adhesion molecule ICAM-1. Low-level expression of these adhesins was also observed on eosinophils cultured in the presence of these interleukins on confluent fibroblasts. The presence of VLA-4 as well as VLA-5 on activated eosinophils was confirmed by demonstration of the formation of immune rosettes using antibody-coated microspheres and by their attachment to fibronectin-coated surfaces. These results indicate the possibility of an involvement of previously unidentified antibody- and complement-independent mechanisms in cellular interactions with the parasite O. volvulus.

Burchard GD et al. Trans R Soc Trop Med Hyg "Delayed-type hypersensitivity reactions to Onchocerca volvulus antigens in exposed and non-exposed African individuals."

Horstmann RD, Brattig NW, Burchard GD, Kruppa TF

[Trans R Soc Trop Med Hyg]

Although considered of critical importance, the mode of helper T-lymphocyte function in Onchocerca volvulus infection is still unclear including the role of the Th1/Th2 dichotomy. We studied the delayed-type hypersensitivity (DTH) reaction, which is the classical Th1 response, to O. volvulus antigens in Africans exposed and not exposed to the infection. DTH reactions were found in a small percentage of patients with generalized onchocerciasis, but in a high percentage of patients with localized onchocerciasis, in putatively immune subjects, and also in non-exposed individuals, which may be due to cross-reactivity with other nematodes. These findings support the notions of (i) prenatal influence of maternal O. volvulus infection preventing development of Th1 responses and/or (ii) suppression of Th1 responses by the infection itself.

Kutin K et al. (2004) Med Vet Entomol "Efficiency of Simulium sanctipauli as a vector of Onchocerca volvulus in the forest zone of Ghana."

Kutin K, Kruppa TF, Brenya R, Garms R

[Med Vet Entomol, 2004]

The role of Simulium sanctipauli Vajime & Dunbar (Diptera: Simuliidae) as a vector of Onchocerca volvulus (Leuckart) (Spirurida: Onchocercidae) in the forest zone of central Ghana was studied in the Upper Denkyira district, where onchocerciasis is hyperendemic. Simulium sanctipauli was found to be a highly efficient vector, with a mean of 377 infective (L3) larvae in the heads of 1000 parous and 122 in the heads of 1000 biting flies. The overall infection rate of 44% of the parous flies with L1, L2 and L3 stages of O. volvulus (identity confirmed by polymerase chain reaction) demonstrates marked anthropophily. Female flies dispersed over a wide area and can transmit onchocerciasis up to at least 10 km away from their breeding sites. Annual community-directed treatments with ivermectin did not have a noticeable effect on the infection rates and parasitic loads of fly populations, which were as high 2 months after as 3 months before the distribution of ivermectin. This failure can be attributed to poor coverage, with treatment taken by only 24.4% of the population of the six study villages.

Garrigues, Jacob et al. (2021) International Worm Meeting "C. elegans transposable elements harbor diverse transcription factor DNA-binding motifs"

Pasquinelli, Amy, Garrigues, Jacob

[International Worm Meeting, 2021]

Transposable elements (TEs) are powerful agents of evolution that can rewire transcriptional programs by mobilizing and distributing transcription factor (TF) DNA-binding motifs throughout genomes. To investigate the extent that TEs provide TF-binding motifs in C. elegans, we determined the genomic positions of DNA-binding motifs for over 200 different TFs (1). Surprisingly, we found that almost all of the examined TFs have binding motifs that reside within TEs, and all types of TEs have at least one instance of a TF motif, demonstrating that TEs provide previously unappreciated numbers of TF-binding motifs to the C. elegans genome. After determining the occurrence of TF motifs in TEs relative to the rest of the genome, we identified numerous TF-binding motifs that are highly enriched within TEs compared to what would be expected by chance. Consistent with potential functional roles for these TE-enriched TF-binding sequences, we found that significantly more TEs with TF motifs display evidence for selection compared to those lacking motifs through the use of publicly available genome variation data (2). We also compared the locations of TE-residing TF motifs to published ATAC-seq (3) and ChIP-seq (4) data, which identify regions of open chromatin associated with TF DNA binding and regions bound by TFs of interest, respectively. Strikingly, we found that all of the TF motif types that occur in TEs have instances of residing within accessible chromatin, and the overwhelming majority of TF-binding motifs located within TEs associate with their cognate TFs, suggesting extensive binding of TFs to sequences within TEs. Additionally, TEs with accessible or TF-bound motifs reside in the putative promoter regions of ~14% of all protein-coding genes, providing widespread possibilities for influencing gene expression. Taken together, our work shows that TE-provided TF-binding sites are ubiquitous in C. elegans and have broad potential to rewire gene expression. 1. Weirauch et al. (2014) Cell 158:1431-1443. 2. Cook et al. (2016) Nucleic Acids Research 45:D650-D657. 3. Daugherty et al. (2017) Genome Research 27:2096-2107. 4. Kudron et al. (2018) Genetics 208:937-949.

Lloret-Fernandez, Carla et al. (2017) International Worm Meeting "Conserved transcriptional regulatory rules define the serotonergic-neuron identity."

Maicas, Miren, Chirivella, Laura, Flames, Nuria, Lloret-Fernandez, Carla, Jimeno, Angela, Weinberg , Peter, Artacho, Alejandro, Mora, Carlos

[International Worm Meeting, 2017]

Cell differentiation is controlled by individual transcription factors (TFs) that together activate a selection of enhancers in specific cell types. How these combinations of TFs identify and activate their target sequences remains unknown. Here, we identify the cis-regulatory transcriptional code that controls the differentiation of serotonergic (5HT) HSN neurons in C. elegans. Loss of function mutant and cis-regulatory analyses reveal that direct activation of the HSN transcriptome is orchestrated by a collective of six TFs. This TF code is composed by AST-1 (ETS TF family), UNC-86 (POU TF family), SEM-4 (SPALT TF family), HLH-3 (bHLH TF family), EGL-46 (INSM TF family) and EGL-18 (GATA TF family). Bioinformatically identified binding site clusters for these six TFs are enriched in known HSN expressed genes compared to a random set of genes. Through in vivo reporter analysis, we demonstrate that the clustering of TF collective binding sites constitutes a regulatory signature that is sufficient for de novo identification of HSN neuron functional enhancers. This regulatory signature contains certain syntactic constrains that further improve the prediction of enhancer expression in the cell. Mouse orthologs of most members of this TF collective are known regulators of mammalian 5HT differentiation programs and can functionally substitute for their worm counterparts. Finally, Principal Coordinates Analysis suggests that, among C. elegans neurons, the HSN transcriptome most closely resembles that of mouse 5HT neurons, which reveals deep homology. Our results?identify rules governing the transcriptional regulatory code of a critically important neuronal type in two species separated by over 700 million years.

Ivimey-Cook ER et al. (2021) Proc Biol Sci "Transgenerational fitness effects of lifespan extension by dietary restriction in Caenorhabditis elegans."

Maklakov AA, Chapman T, Carlsson H, Immler S, Ivimey-Cook ER, Sales K

[Proc Biol Sci, 2021]

Dietary restriction (DR) increases lifespan in a broad variety of organisms and improves health in humans. However, long-term transgenerational consequences of dietary interventions are poorly understood. Here, we investigated the effect of DR by temporary fasting (TF) on mortality risk, age-specific reproduction and fitness across three generations of descendants in <i>Caenorhabditis elegans</i>. We show that while TF robustly reduces mortality risk and improves late-life reproduction of the individuals subject to TF (P₀), it has a wide range of both positive and negative effects on their descendants (F₁-F₃). Remarkably, great-grandparental exposure to TF in early life reduces fitness and increases mortality risk of F₃ descendants to such an extent that TF no longer promotes a lifespan extension. These findings reveal that transgenerational trade-offs accompany the instant benefits of DR, underscoring the need to consider fitness of future generations in pursuit of healthy ageing.

Martinez NJ et al. (2008) Genes Dev "A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity."

Ow MC, Walhout AJ, Sequerra R, Doucette-Stamm L, Ambros VR, Roth FP, Barrasa MI, Hammell M, Martinez NJ

[Genes Dev, 2008]

MicroRNAs (miRNAs) and transcription factors (TFs) are primary metazoan gene regulators. Whereas much attention has focused on finding the targets of both miRNAs and TFs, the transcriptional networks that regulate miRNA expression remain largely unexplored. Here, we present the first genome-scale Caenorhabditis elegans miRNA regulatory network that contains experimentally mapped transcriptional TF --&gt; miRNA interactions, as well as computationally predicted post-transcriptional miRNA --&gt; TF interactions. We find that this integrated miRNA network contains 23 miRNA &lt;--&gt; TF composite feedback loops in which a TF that controls a miRNA is itself regulated by that same miRNA. By rigorous network randomizations, we show that such loops occur more frequently than expected by chance and, hence, constitute a genuine network motif. Interestingly, miRNAs and TFs in such loops are heavily regulated and regulate many targets. This "high flux capacity" suggests that loops provide a mechanism of high information flow for the coordinate and adaptable control of miRNA and TF target regulons.

Reece-Hoyes, John S. et al. (2011) International Worm Meeting "A Core C. elegans Transcription Factor Regulatory Network."

Walhout, Albertha J.M., Shrestha, Shaleen, Kent, Amanda, Hill, David, Diallo, Alos, Reece-Hoyes, John S., Dricot, Amelie, Zhuang, Jiali, Weng, Zhiping, Myers, Chad

[International Worm Meeting, 2011]

Differential gene expression is controlled by a complex regulatory network of interactions between proteins, DNA, and microRNAs. Transcription factors (TFs) are primary modulators within this network, largely by binding to specific sites within a promoter and activating or repressing nearby genes. Some of these downstream genes encode TFs that subsequently also regulate a combination TFs and non-TFs. By focusing on TFs and their TF targets, the central core of the greater gene regulatory network will be revealed. Yeast one-hybrid (Y1H) assays provide a gene-centered approach for detecting interactions between genomic loci such as promoters and TF proteins. We comprehensively screened interactions between 650 TF-encoding gene promoters and 834 TF proteins using our novel enhanced Y1H (eY1H) pipeline that yields a quantitative readout of protein-DNA interactions. We will present this novel pipeline as well as insights we obtained from the core TF network that consists of more than 4500 interactions.

Fuxman Bass JI et al. (2014) Nucleic Acids Res "Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters."

Beittel N, Tamburino AM, Fuxman Bass JI, Mori A, Walhout AJ, Weirauch MT, Reece-Hoyes JS

[Nucleic Acids Res, 2014]

Gene expression is controlled through the binding of transcription factors (TFs) to regulatory genomic regions. First introns are longer than other introns in multiple eukaryotic species and are under selective constraint. Here we explore the importance of first introns in TF binding in the nematode Caenorhabditis elegans by combining computational predictions and experimentally derived TF-DNA interaction data. We found that first introns of C. elegans genes, particularly those for families enriched in long first introns, are more conserved in length, have more conserved predicted TF interactions and are bound by more TFs than other introns. We detected a significant positive correlation between first intron size and the number of TF interactions obtained from chromatin immunoprecipitation assays or determined by yeast one-hybrid assays. TFs that bind first introns are largely different from those binding promoters, suggesting that the different interactions are complementary rather than redundant. By combining first intron and promoter interactions, we found that genes that share a large fraction of TF interactions are more likely to be co-expressed than when only TF interactions with promoters are considered. Altogether, our data suggest that C. elegans gene regulation may be additive through the combined effects of multiple regulatory regions.