Menne TF et al. (2007) Nat Genet "The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast."

Wong CC, Ancliff PJ, Warren AJ, Goyenechea B, Boone C, Brost RL, Sanchez-Puig N, Tonkin LM, Menne TF, Costanzo M

[Nat Genet, 2007]

The autosomal recessive disorder Shwachman-Diamond syndrome, characterized by bone marrow failure and leukemia predisposition, is caused by deficiency of the highly conserved Shwachman-Bodian-Diamond syndrome (SBDS) protein. Here, we identify the function of the yeast SBDS ortholog Sdo1, showing that it is critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. Using genome-wide synthetic genetic array mapping, we identified multiple TIF6 gain-of-function alleles that suppressed the pre-60S nuclear export defects and cytoplasmic mislocalization of Tif6 observed in sdo1Delta cells. Sdo1 appears to function within a pathway containing elongation factor-like 1, and together they control translational activation of ribosomes. Thus, our data link defective late 60S ribosomal subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition.

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.

Reinke, V et al. (2017) International Worm Meeting "Model organism Encyclopedia of Regulatory Networks (modERN)."

Xu, J, Celniker, SE, Weiszmann, R, White, KP, Gewirtzman, L, Ma, L, Vafeados, D, Gerstein, M, Samanta, S, Fisher, WW, Yan, KK, Reinke, V, Patton, J, Victorsen, A, Hammonds, AS, Higdon, A, Han, M, Waterston, RH, Kudron, M

[International Worm Meeting, 2017]

The goal of the modERN consortium is to create comprehensive maps of transcription factor (TF) binding sites in C. elegans and D. melanogaster. We have developed an effective high throughput pipeline to create strains of flies and worms with GFP-tagged TFs, which we use to perform ChIP-seq experiments. We are targeting 691 sequence-specific TF genes in the worm and 708 TF genes in the fly. The modERN project has generated 420 worm strains and 330 fly strains to date. A subset of worm strains had tagged TFs that localized to the cytoplasm (54), were poorly expressed (23), or did not pass quality control measures for ChIP (37). Thus, including data generated previously for the modENCODE project, we have completed ~900 ChIP-seq experiments for 235 factors (219 TFs and 16 other regulatory proteins) in the worm and 287 TFs in the fly. We processed all data sets with a uniform peak-calling pipeline for worm and fly. The resultant inferred binding sites can be useful to predict gene expression, particularly using combinations of TF binding profiles. In the worm, for example, combinatorial TF binding patterns can suggest expression in muscle, intestine, hypodermis, pharynx and neurons. For a limited number of transcription factors, we are conducting RNA-seq of strains with knock down of specific transcription factors by deletion or RNAi to identify potential target genes of the given TF and to validate targets identified by the ChIP-seq experiments. To date, we have collected RNA-seq data from 30 worm TF knockdown lines and 12 TF fly knock down lines. RNA-seq data and ChIP-seq data are deposited to the ENCODE DCC for access by the research community through the ENCODE DCC (https://www.encodeproject.org), as well as through the UCSC genome browser. A dedicated track hub for the worm data at UCSC is available as well. TF tagged lines are available through the Caenorhabditis Genetics Center and Bloomington Drosophila Stock Center. Here, we will summarize progress, present future plans, and demonstrate how to access and use the data.

Zhiping Weng et al. (2005) International Worm Meeting "A C. elegans transcription regulatory network of the digestive tract."

Lynn Doucette-Stam, Zhiping Weng, Natalia Martinez, Wanyuan Ao, Ahmed Elewa, Christian Grove, Dirk McMurray, Bart Deplancke, Reynaldo Sequerra

[International Worm Meeting, 2005]

The control of gene expression is highly combinatorial: most transcription factors (TFs) regulate the expression of multiple genes, and most genes are themselves regulated by multiple TFs. Interactions between TFs and their target genes can be visualized in transcription regulatory networks. Such networks allow insights into higher order regulation of gene expression, for example by the identification and characterization of network <sym08>hubs<sym09> and network motifs. Here, we present a transcription regulatory network of the C. elegans digestive tract. To identify TF-target gene interactions in a high-throughput manner, we developed a Gateway-compatible yeast one-hybrid (Y1H) system. This Y1H system can be used to identify TFs that can bind to a gene promoter. Our Y1H system is compatible with ORFeome (for TF-encoding ORFs) and Promoterome (for target gene promoters) resources, and allows the identification of TF-target gene interactions from a <sym08>gene centered<sym09> perspective. Thus, this system provides information that is distinct from, but complementary to data obtained from <sym08>TF centered<sym09> chromatin-immunoprecipitation-based methods. We used our Y1H system to identify TF-promoter interactions for 180 genes involved in development of the worm digestive tract. We identified >300 TF-DNA interactions and visualized these into a transcription regulatory network. The resulting network is highly connected and contains several TF and promoter <sym08>hubs<sym09> (e.g. TFs that bind to many genes and vice versa). We characterized several TF hubs in more detail. For instance, we inspected the collection of DNA fragments they can interact with to predict consensus TF binding sites. We also identified several other network motifs, including feed forward loops, regulator chains and single- and multi-input motifs. We have begun to experimentally test several hypotheses derived from this network. Taken together, the Y1H system provides a powerful tool for the high-throughput mapping of transcription regulatory networks in metazoan systems.

Reece-Hoyes, John S. et al. (2009) International Worm Meeting "High-throughput transcription regulatory network mapping by yeast one-hybrid assays with high-density transcription factor arrays."

Reece-Hoyes, John S., Barrasa, M. Inmaculada, Walhout, A.J. Marian, Carraher, Ashley, Kent, Amanda, Hill, David E., Dricot, Amelie, Brown, Katie

[International Worm Meeting, 2009]

An organism''s development and response to the environment is governed by transcription regulatory networks that control the differential regulation of the genome. This process is largely driven by the activation or repression of transcription induced by the specific binding of a regulatory transcription factor (TF) within each locus, often within gene promoters. We aim to characterize the transcription regulatory networks of the model nematode Caenorhabditis elegans. The worm genome contains about 20,000 genes, of which 941 encode TFs. In contrast to other groups, we use gene-centred (''gene-to-protein''), rather than TF-centered (''protein-to-gene'') methods for the identification of promoter-TF interactions. We will use high-throughput yeast one-hybrid assays with our resource of 795 TF and 31 putative TF clones to screen the ~6000 cloned promoters of the Promoterome. We will describe improvements that utilize a Singer HDA RoToR robot that enables the interrogation of all TFs multiple times with only three plates. The data gained from this study will primarily elucidate the networks that underlie the process of gene regulation, but additionally can be used to identify individual DNA motifs bound by the TFs studied.