Germano Cecere

• Ph.D.
• Group Leader at Institut Pasteur

Transcription introduces torsional stress in the DNA fiber causing it to transition from a relaxed to a supercoiled state that can propagate across several kilobases and modulate the binding and activity of DNA-associated proteins. As a result, transcription at one locus has the potential to impact nearby transcription events. In this study, we ask...

Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 (H3K9me3) and recruitment of its epigenetic reader, heterochromatin protein 1a (HP1a), are hall...

The SET-2 /SET1 histone H3K4 methyltransferase and RNAi pathway components are required to maintain fertility across generations in C. elegans . SET-2 preserves the germline transcriptional program transgenerationally, and RNAi pathways rely on small RNAs to establish and maintain transgenerational gene silencing. We investigated whether the functi...

In this review article, I summarize the intervention I made during the "Hommage à François Gros" held at the Institut Pasteur in Paris on the 25th of April, 2023. I discuss how the discovery of the existence of an RNA intermediate between genetic information and protein translation has changed our perspective on the role of RNA in gene regulation i...

Heritable traits are predominantly encoded within genomic DNA, but it is now appreciated that epigenetic information is also inherited through DNA methylation, histone modifications, and small RNAs. Several examples of transgenerational epigenetic inheritance of traits have been documented in plants and animals. These include even the inheritance o...

SARS-CoV-2 infection results in impaired interferon response in patients with severe COVID-19. However, how SARS-CoV-2 interferes with host immune responses is incompletely understood. Here, we sequence small RNAs from SARS-CoV-2-infected human cells and identify a microRNA (miRNA) derived from a recently evolved region of the viral genome. We show...

During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila , the pioneer factor Zelda is known to be essential for the progression of development; still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of g...

Global Run-On sequencing (GRO-seq) is one of the most sensitive techniques to detect nascent transcription from RNA polymerase (Pol) at a genome-wide level. The protocol incorporates labeled ribonucleotides into nascent RNAs from Pol I, II, and III. We have adapted the GRO-seq protocol to the nematode Caenorhabditis elegans to measure transcription...

Eukaryotic genomes harbor invading transposable elements that are silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatog...

SARS-CoV-2 infection results in impaired interferon response in severe COVID-19 patients. However, how SARS-CoV-2 interferes with host immune response is incompletely understood. Here, we sequenced small RNAs from SARS-CoV-2-infected human cells and identified a micro RNA (miRNA) encoded in a recently evolved region of the viral genome. We show tha...

In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved i...

Infection with the unicellular eukaryotic pathogen Plasmodium falciparum

Inheritance and clearance of maternal mRNAs are two of the most critical events required for animal early embryonic development. However, the mechanisms regulating this process are still largely unknown. Here, we show that together with maternal mRNAs, C. elegans embryos inherit a complementary pool of small non-coding RNAs that facilitate the clea...

In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved i...

In the Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remains unknown. Here, we show that CSR-1 slicer activity is primarily involved i...

Argonaute proteins and their interacting small RNAs play a key role in regulating complementary mRNA targets during animal development. Here, we investigate a novel and essential function of the catalytically active Argonaute protein CSR-1 in maternal mRNA degradation during early embryogenesis in Caenorhabditis elegans. We show that CSR-1 interact...

PIWI-interacting RNAs (piRNAs) promote fertility in many animals. However, whether this is due to their conserved role in repressing repetitive elements (REs) remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets but, rather, is medi...

The RNA chromatin immunoprecipitation assay (RNA-ChIP) allows detection and quantification of RNA-protein interactions using in vivo cross-linking with formaldehyde followed by immunoprecipitation of the RNA-protein complexes. Here we describe the RNA-ChIP protocol that we have adapted for Caenorhabditis elegans (C. elegans) to detect interaction b...

Argonaute proteins and their small RNA cofactors short interfering RNAs are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) that are antisense to germline transcripts. However, its role in gene expression regula...

The role of RNA interference (RNAi) in post-transcriptional regulation of complementary targets is well known. However, less is known about transcriptional silencing mechanisms mediated by RNAi. Such mechanisms have been characterized in yeast and plants, which suggests that similar RNA silencing mechanisms might operate in animals. A growing amoun...

The inhibition of transcriptional elongation plays an important role in gene regulation in metazoans, including C. elegans. Here, we combine genomic and biochemical approaches to dissect a role of ZFP-1, the C. elegans AF10 homolog, in transcriptional control. We show that ZFP-1 and its interacting partner DOT-1.1 have a global role in negatively m...

Plant homeodomain (PHD)-type zinc fingers play an important role in recognizing chromatin modifications and recruiting regulatory proteins to specific genes. A specific module containing a conventional PHD finger followed by an extended PHD finger exists in the mammalian AF10 protein, among a few others. AF10 has mostly been studied in the context...

C. elegans 21U-RNAs are equivalent to the piRNAs discovered in other metazoans and have important roles in gametogenesis and transposon control. The biogenesis and molecular function of 21U-RNAs and piRNAs are poorly understood. Here, we demonstrate that transcription of each 21U-RNA is regulated separately through a conserved upstream DNA motif. W...

Dataset table allowing identification of overlaps between the following datasets: microarray data listing genes misregulated in rde-4(ne299) and zfp-1(ok554) from [19], microarray data of Class 1 and Class 2 genes acting downstream of daf-16 from [23], rde-4-dependent siRNA target genes identified by [38], and ZFP-1 target genes where the ZFP-1 pea...

Increase in pdk-1 expression correlates with susceptibility to oxidative stress. (A, B) Survival of L4 larva (n = 90) from indicated strains after 20 hour incubation period in 100mM paraquat; ** indicates significance of P<0.01 and * - P<0.05 compared to wild type. (C) RT-qPCR detecting an increase in pdk-1 expression in SP940, results of three bio...

RT-qPCR confirming enhanced expression of zfp-1 mRNA in ZFP-1::FLAG and ZFP-1::GFP transgenic strains. (TIF)

ZFP-1 levels do not change in rde-4(ne299). Western blot analysis with anti-ZFP-1 C-terminal antibody; actin levels and Ponceau S staining of the membrane are shown as loading controls. (TIF)

An example of a gene with promoter siRNAs matching repetitive elements and expressed higher in rde-4(ne299) according to [19]. A screen shot from the UCSC browser and PolII ChIP results showing enhanced occupancy in rde-4(ne299). (TIF)

Examples of genes with promoter siRNAs matching repetitive elements and expressed higher in rde-4(ne299) according to [19]. Screen shots from the UCSC browser. (TIF)

Sequencing results for RNA sequences produced from the pdk-1 promoter and shown in Figure 7D. (DOC)

Insulin signaling has a profound effect on longevity and the oxidative stress resistance of animals. Inhibition of insulin signaling results in the activation of DAF-16/FOXO and SKN-1/Nrf transcription factors and increased animal fitness. By studying the biological functions of the endogenous RNA interference factor RDE-4 and conserved PHD zinc fi...

RNA silencing occurs in a broad range of organisms. Although its ancestral function is probably related to the genome defense mechanism against repetitive selfish elements, it has been found that RNA silencing regulates different cellular processes such as gene expression and chromosomal segregation. In Neurospora crassa, a RNA silencing mechanism,...

Northern blotting to detect siRNAs from NTS rDNA locus. Northern blotting analysis on total RNA extracted from WT and quelling defective strains using a riboprobe covering approximately about 800 bp of NTS rDNA region. No signal was detected.

Post-transcriptional gene silencing (PTGS) pathways play a role in genome defence and have been extensively studied, yet how repetitive elements in the genome are identified is still unclear. It has been suggested that they may produce aberrant transcripts (aRNA) that are converted by an RNA-dependent RNA polymerase (RdRP) into double-stranded RNA...