Hervé Seitz

Institut de Génétique Humaine · Genetics and Development

RNA interference (RNAi) offers an efficient way to repress genes of interest, and it is widely used in research settings. Clinical applications emerged more recently, with 5 approved siRNAs (the RNA guides of the RNAi effector complex) against human diseases. The development of siRNAs against the SARS-CoV-2 virus could therefore provide the basis o...

Assessment of the functionality of individual microRNA/target sites is a crucial issue. Genome editing techniques should theoretically permit a fine functional exploration of such interactions, allowing the mutation of microRNAs or individual binding sites in a complete in vivo setting, therefore abrogating or restoring individual interactions on d...

A prolific scientific literature attributes pro- or anti-oncogenic properties to many human microRNAs (“miRNAs”). While many of these studies are based on unpersuasive analyses, one candidate suppressor tumour miRNA, miR-34a, appeared convincing enough to be administered to human patients in a clinical trial—with disappointing outcomes. Here, we re...

Assessment of the functionality of individual microRNA/target sites is a crucial issue. Genome editing techniques should theoretically permit a fine functional exploration of such interactions, allowing the mutation of microRNAs or individual binding sites in a complete in vivo setting, therefore abrogating or restoring individual interactions on d...

RNA interference (RNAi) offers an efficient way to repress genes of interest, and it is widely used in research settings. Clinical applications emerged more recently, with 5 approved siRNAs (the RNA guides of the RNAi effector complex) against human diseases. The development of siRNAs against the SARS-CoV-2 virus could therefore provide the basis o...

While several microRNAs (miRNAs) have been proposed to act as tumor suppressors, a consensual definition of tumor suppressing miRNAs is still missing. Similarly to coding genes, we propose that tumor suppressor miRNAs must show evidence of genetic or epigenetic inactivation in cancers, and exhibit an anti-tumorigenic (e.g., anti-proliferative) acti...

The miR-34a microRNA (miRNA) is currently thought to act as a tumor suppressor: its locus is frequently deleted in human tumors and it is believed to repress cell proliferation. We re-visited the evidence of its anti-cancer activity. Our results show that miR-34a is not generally down-regulated in primary tumors relatively to normal adjacent tissue...

A key approach for improving siRNA efficacy is chemical modifications. Through an in-silico screening of modifications at the 5'-end nucleobase of the guide strand, an adenine-derived compound called 6-(3-(2-carboxyethyl)phenyl)-purine (6-mCEPh-purine) was identified to improve the RNAi activity in cultured human cells and in vivo mouse models. Nev...

SNORD115 has been proposed to promote the activity of serotonin (HTR2C) receptor via its ability to base-pair with its pre-mRNA and regulate alternative RNA splicing and/or A-to-I RNA editing. Because SNORD115 genes are deleted in most patients with the Prader-Willi syndrome (PWS), diminished HTR2C receptor activity could contribute to the impaired...

SNORD115 has been proposed to promote the activity of serotonin (HTR2C) receptor via its ability to base-pair with its pre-mRNA and regulate alternative RNA splicing and/or A-to-I RNA editing. Because SNORD115 genes are deleted in most patients with the Prader-Willi syndrome (PWS), diminished HTR2C receptor activity could contribute to the impaired...

SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, wher...

Introductory course, in French, for the CNRS summer school "InteRNAt" (held in Sète from October 6 to 10, 2019).

Exposure of cells or organisms to chemicals can trigger a series of effects at the regulatory pathway level, which involve changes of levels, interactions, and feedback loops of biomolecules of different types. A single-omics technique, e.g., transcriptomics, will detect biomolecules of one type and thus can only capture changes in a small subset o...

MicroRNAs and their Argonaute protein partners constitute the RISC complex, which can repress specific target mRNAs. The identification of microRNA targets is of central importance, and various experimental and computational methods have been developed over the last 15 years. Most experimental methods are based on the assumption that mRNAs which in...

RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more...

Small RNA coverage of the Acanthocystis turfacea Chlorella virus 1 (ATCV1) genome. x axis: genomic coordinate along the ATCV1 genome. y axis: number of reads covering each bp in the viral genome. Numbers of reads are expressed as parts per million (ppm) after normalization to the total number of Branchiostoma genome-matching reads that do not match...

Transcriptomics-based expression analysis of the 6 Branchiostoma RdRP genes. For each of the six RdRP genes, mRNA abundance in various developmental stages was measured by RNA-Seq, and reported as cRPKM (corrected-for-mappability reads per kb and per million mapped reads; [105]). RdRP genes where an intact active site is predicted (see Fig 1B) are...

Small RNA coverage in 15 hpf embryos for the two genes with highest antisense exon-exon junction read coverage. Exons are represented by black rectangles. Detected small RNAs mapping on these genes in the sense orientation are shown in blue, those mapping in antisense orientation are in red. For antisense reads mapping on exon-exon junctions, their...

A Branchiostoma Hen1 candidate contains the known essential amino acids for Hen1 activity. Sequences of 5 known Hen1 proteins (from Nematostella vectensis, Danio rerio, Mus musculus, Arabidopsis thaliana and Drosophila melanogaster) were aligned with the identified Branchiostoma lanceolatum Hen1 candidate (only the part of the alignment spanning am...

Exclusion of dubious proteomes still indicates many independent RdRP losses. Among the 538 analyzed proteomes, 442 contain at least 1,000 proteins of at least 1,000 amino acids (left panel) and 383 contain at least 5,000 proteins of at least 500 amino acids (right panel). Selective analysis of these species does not fundamentally change the results...

Size and quality of the Small RNA-Seq libraries. “No adapter” indicates that the 3′ adapter was not detected in the read. “Extragenomic” means that the adapter-trimmed read does not match the B. lanceolatum genome assembly. “Abundant ncRNA” means that it maps on the genome assembly, on one of the genes for known abundant non-coding RNAs (rRNAs, tRN...

Size distribution and logo analyses of various small RNA classes. For each of the following classes, small RNA populations were analyzed as in Figs 3B, 3C, 4 and 5: reads matching the B. lanceolatum genome without matching abundant non-coding RNAs (section 1); reads matching B. lanceolatum pre-miRNA hairpins (section 2); reads matching the B. lance...

Detection of conserved miRNAs. Branchiostoma lanceolatum orthologs for B. floridae or B. belcheri pre-miRNA hairpins (as described in miRBase v.22) were screened for their predicted secondary structure and the abundance of the small RNAs they generate. Only those hairpins that comply with these rules are shown in this table. First column: name of o...

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes a...

RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more...

RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more...

microRNAs and their Argonaute protein partners constitute the RISC complex, which can repress specific target mRNAs. The identification of microRNA targets is of central importance, and various experimental and computational methods have been developed over the last 15 years. Most experimental methods are based on the assumption that mRNAs which in...

Prevailing knowledge gaps in linking specific molecular changes to apical outcomes and methodological uncertainties in the generation, storage, processing, and interpretation of 'omics data limit the application of 'omics technologies in regulatory toxicology. Against this background, the European Centre for Ecotoxicology and Toxicology of Chemical...

microRNAs are currently believed to control a large diversity of physiological processes, through the collective repression of thousands of target genes. Both experimental and computational analyses indeed suggest that each microRNA regulates tens or hundreds of genes. But some observations suggest that the phenotypic consequences of many published...

Although some features underlying replication-origin activation in metazoan cells have been determined, little is known about their regulation during metazoan development. Using the nascent-strand purification method, here we identified replication origins throughout Caenorhabditis elegans embryonic development and found that the origin repertoire...

Argonaute (Ago) proteins associate with microRNAs (miRNAs) to form the core of the RNA-induced silencing complex (RISC) that mediates post-transcriptional gene silencing of target mRNAs. As key players in anti-viral defense, Ago proteins are thought to have the ability to interact with human immunodeficiency virus type 1 (HIV-1) RNA. However, the r...

According to the current view, each microRNA regulates hundreds of genes. Computational tools aim at identifying microRNA targets, usually selecting evolutionarily conserved microRNA binding sites. Here we provide evidence that such predictions are often biologically irrelevant. Focusing on miR-223-guided repression, we observed that it is often sm...

The . European Centre for the Ecotoxicology and Toxicology of Chemicals (ECETOC) organised a workshop to discuss the state-of-the-art research on noncoding RNAs (ncRNAs) as biomarkers in regulatory toxicology and as analytical and therapeutic agents. There was agreement that ncRNA expression profiling data requires careful evaluation to determine t...

Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia with a strong genetic component. Molecular pathways involving the homeodomain transcription factor Shox2 control the development and function of the cardiac conduction system in mouse and zebrafish. Here we report the analysis of human SHOX2 as a potential susceptibility gene for ear...

During the pachytene stage of meiosis in male mammals, the X and Y chromosomes are transcriptionally silenced by Meiotic Sex Chromosome Inactivation (MSCI). MSCI is conserved in therian mammals and is essential for normal male fertility. Transcriptomics approaches have demonstrated that in mice, most or all protein-coding genes on the X chromosome...

There is currently convincing evidence that microRNAs have evolved independently in at least six different eukaryotic lineages: animals, land plants, chlorophyte green algae, demosponges, slime molds and brown algae. MicroRNAs from different lineages are not homologous but some structural features are strongly conserved across the eukaryotic tree a...

In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA "seed") to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary tar...

Small regulatory RNAs (microRNAs, siRNAs, and piRNAs) exhibit several unique features that clearly distinguish them from other known gene regulators. Their genomic organization, mode of action, and proposed biological functions raise specific questions. In this review, we focus on the quantitative aspect of small regulatory RNA biology. The origina...

Drosophila melanogaster has two Dicer proteins with specialized functions. Dicer-1 liberates miRNA-miRNA* duplexes from precursor miRNAs (pre-miRNAs), whereas Dicer-2 processes long double-stranded RNAs into small interfering RNA duplexes. It was recently demonstrated that Dicer-2 is rendered highly specific for long double-stranded RNA substrates...

Figure S5. Identity of miRNA nucleotide 1 affects duplex asymmetry. (A) Changing the 5′-uridine (5′-U) of miR-14 to 5′-adenosine (5′-A) decreased miRNA loading. (B) Changing the 5′-U of miR-184 into 5′-cytidine (5′-C) decreased miRNA loading; mutating it to ribothymidine increased miRNA loading. Changing the 5′-nt of miR-2a (C) or miR-184 (D) into...

Figure S7. The sequence of the miRNA* 3′ overhang is not responsible for miRNA-specific preferences for nt 1. The modest effect of the identity of the miRNA* 3′-most nucleotide does not correlate with the base-pairing ability of miRNA nt 1 to the miRNA* 3′ terminus.

Figure S8. Structure and sequence features covarying with the identity of miRNA nt 1 in C. elegans and mouse. See Figure 4A legend for details. (A) Covariation in Mus musculus miRNA/miRNA* duplexes. (B) Covariation in C. elegans miRNA/miRNA* duplexes.

Figure S9. Pre-miRNA nucleotides flanking miRNA nt 1 are depleted of U. U frequency was measured in pre-miRNA covered by at least 100 reads in the pooled deep-sequencing libraries. The 5′-most nucleotide of mature miRNA is enriched in U (position 0 on the x-axis), while its flanking nucleotides are depleted. The horizontal line indicates the mean U...

Figure S3. Faithful in vitro reconstitution of miRNA loading. (A and B) miR-2a, let-7, miR-2c and miR-184 are correctly loaded into Ago1 in fly embryo lysate, and a let-7/anti-let-7 small interfering RNA is correctly loaded into Ago2. Left: lysate prepared from embryos from dcr-2L811fsX- and ago2414-mutant mothers; Ago1-depleted and HA-depleted, wi...

Figure S6. Duplex-specific order of preference on the identity of the first nucleotide. (A) Regardless of the identity of the facing (p19*) nucleotide, miR-2a is better loaded if it starts with a U than if it starts with an A than if it starts with a C (U > A > C). (B) miR-14 is better loaded if it starts with a U or a C than if it starts with an A...

Figure S1. Caenorhabditis elegans miRNA tend to start with a uridine. Gray, nucleotide frequency at position 1; white, nucleotide frequency at random positions in the miRNA or miRNA* sequence (means ± standard deviation (SD)).

Figure S2. Mouse miRNA tend to start with a uridine. Gray, nucleotide frequency at position 1; white, nucleotide frequency at random positions in the miRNA or miRNA* sequence (means ± SD).

Figure S4. The Ago2 loading machinery has a moderate effect on miR-184 loading preferences, while it strongly affects miR-184* loading preferences. Left: miR-184 and miR-184* capture assay in dcr-2L811fsX-null mutant embryo lysate. Right: miR-184 and miR-184* capture assay in wild-type lysate.

MicroRNA (miRNA) are diverse in sequence and have a single known sequence bias: they tend to start with uridine (U). Our analyses of fly, worm and mouse miRNA sequence data reveal that the 5'-U is recognized after miRNA production. Only one of the two strands can be assembled into Argonaute protein from a single miRNA/miRNA* molecule: in fly embryo...

MicroRNAs (miRNAs) are post-transcriptional regulators that have been uncovered over the last seventeen years. They recognize specific targets by base-pairing to a target mRNA (the actual regulation of targets is mediated by miRNA-associated proteins). Elucidating the biological function of miRNAs requires the identification of their targets and se...

MicroRNAs are believed to control many physiological processes in animals. Now, two studies show that some of their presumptive functions are actually fulfilled by another class of RNAs - siRNAs.

In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character-as is found in small interfering RNAs (siRNAs)-directs duplexes into Ago2, whereas central mismatches, like those found in miR...

Piwi-interacting RNAs (piRNAs) silence transposons and maintain genome integrity during germline development. In Drosophila, transposon-rich heterochromatic clusters encode piRNAs either on both genomic strands (dual-strand clusters) or predominantly one genomic strand (uni-strand clusters). Primary piRNAs derived from these clusters are proposed t...

MicroRNAs (miRNAs) regulate expression of their target mRNAs through the RNA-induced silencing complex (RISC), which contains an Argonaute (Ago) family protein as a core component. In Drosophila melanogaster, miRNAs are generally sorted into Ago1-containing RISC (Ago1-RISC). We established a native gel system that can biochemically dissect the Ago1...

Animal microRNAs (miRNAs) guide proteins to repress the translation of target mRNAs via imperfect base pairing between the miRNA and the target. Computational analyses suggest that each miRNA regulates tens or hundreds of targets [1, 2], yet genetic studies usually show that the repression of a few targets plays a physiological role [3-5]. The exte...

Piwi-interacting RNAs (piRNAs) silence transposons in animal germ cells. piRNAs are thought to derive from long transcripts spanning transposon-rich genomic loci and to direct an autoamplification loop in which an antisense piRNA, bound to Aubergine or Piwi protein, triggers production of a sense piRNA bound to the PIWI protein Argonaute3 (Ago3). I...

Small interfering RNAs (siRNAs) direct RNA interference (RNAi) in eukaryotes. In flies, somatic cells produce siRNAs from exogenous double-stranded RNA (dsRNA) as a defense against viral infection. We identified endogenous siRNAs (endo-siRNAs), 21 nucleotides in length, that correspond to transposons and heterochromatic sequences in the somatic cel...

MicroRNAs (miRNAs) are short regulatory RNAs that direct repression of their mRNA targets. The miRNA "seed"-nucleotides 2-7-establishes target specificity by mediating target binding. Accurate processing of the miRNA 5' end is thought to be under strong selective pressure because a shift by just one nucleotide in the 5' end of a miRNA alters its se...

Reports. Submitted on March 5, 2008 Accepted on March 31, 2008. .

Genomic imprinting is an epigenetic mechanism controlling parental-origin-specific gene expression. Perturbing the parental origin of the distal portion of mouse chromosome 12 causes alterations in the dosage of imprinted genes resulting in embryonic lethality and developmental abnormalities of both embryo and placenta. A 1 Mb imprinted domain iden...

In the Drosophila germline, repeat-associated small interfering RNAs (rasiRNAs) ensure genomic stability by silencing endogenous selfish genetic elements such as retrotransposons and repetitive sequences. Whereas small interfering RNAs (siRNAs) derive from both the sense and antisense strands of their double-stranded RNA precursors, rasiRNAs arise...