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Article ; Online: Evolutionary Divergence of Phosphorylation to Regulate Interactive Protein Networks in Lower and Higher Species.

Pasquier, Claude / Robichon, Alain

International journal of molecular sciences

2022 Volume 23, Issue 22

Abstract: The phosphorylation of proteins affects their functions in extensively documented circumstances. However, the role of phosphorylation in many interactive networks of proteins remains very elusive due to the experimental limits of exploring the transient ... ...

Abstract	The phosphorylation of proteins affects their functions in extensively documented circumstances. However, the role of phosphorylation in many interactive networks of proteins remains very elusive due to the experimental limits of exploring the transient interaction in a large complex of assembled proteins induced by stimulation. Previous studies have suggested that phosphorylation is a recent evolutionary process that differently regulates ortholog proteins in numerous lineages of living organisms to create new functions. Despite the fact that numerous phospho-proteins have been compared between species, little is known about the organization of the full phospho-proteome, the role of phosphorylation to orchestrate large interactive networks of proteins, and the intertwined phospho-landscape in these networks. In this report, we aimed to investigate the acquired role of phosphate addition in the phenomenon of protein networking in different orders of living organisms. Our data highlighted the acquired status of phosphorylation in organizing large, connected assemblages in
MeSH term(s)	Humans ; Phosphorylation ; Saccharomyces cerevisiae/metabolism ; Biological Evolution ; Proteome/metabolism
Chemical Substances	Proteome
Language	English
Publishing date	2022-11-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232214429
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Temporal and sequential order of nonoverlapping gene networks unraveled in mated female Drosophila.

Pasquier, Claude / Robichon, Alain

Life science alliance

2021 Volume 5, Issue 2

Abstract: In this study, we reanalyzed available datasets of gene expression changes in female Drosophila head induced by mating. Mated females present metabolic phenotypic changes and display behavioral characteristics that are not observed in virgin females, ... ...

Abstract	In this study, we reanalyzed available datasets of gene expression changes in female Drosophila head induced by mating. Mated females present metabolic phenotypic changes and display behavioral characteristics that are not observed in virgin females, such as repulsion to male sexual aggressiveness, fidelity to food spots selected for oviposition, and restriction to the colonization of new niches. We characterize gene networks that play a role in female brain plasticity after mating using AMINE, a novel algorithm to find dysregulated modules of interacting genes. The uncovered networks of altered genes revealed a strong specificity for each successive period of life span after mating in the female head, with little conservation between them. This finding highlights a temporal order of recruitment of waves of interconnected genes which are apparently transiently modified: the first wave disappears before the emergence of the second wave in a reversible manner and ends with few consolidated gene expression changes at day 20. This analysis might document an extended field of a programmatic control of female phenotypic traits by male seminal fluid.
MeSH term(s)	Animals ; Drosophila/physiology ; Drosophila Proteins/genetics ; Female ; Gene Expression Regulation ; Gene Regulatory Networks ; Male ; Reproduction/genetics ; Sexual Behavior, Animal
Chemical Substances	Drosophila Proteins
Language	English
Publishing date	2021-11-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202101119
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains.

Pasquier, Claude / Robichon, Alain

Heliyon

2021 Volume 7, Issue 6, Page(s) e07284

Abstract: The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral ... ...

Abstract	The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundant viral small interference and micro RNAs (VsiRNAs and VmiRNAs) in both cell-line and whole organism based experiments, indicating a contribution of these molecules in host responses and/or viral replication. We explore the theoretical possibility that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction, although this hypothesis seems counterintuitive. The SARS-CoV-2 genome was therefore computationally searched for exact intrapairing within the viral RNA and exact hybrid pairing with the human transcriptome over a minimum of 20 bases in length. Minimal segments of 20-base lengths of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, including mitochondrial deubiquitinase USP30, the subunit of ubiquitin protein ligase complex FBXO21 and two long noncoding RNAs, were retrieved. The hypothesis that viral-originated RNAi might mediate degradation of host transcriptome messages was corroborated by published high throughput sequencing of RNA from infected tissues and cultured cells, clinical observation and phylogenetic comparative analysis, indicating a strong specificity of these SARS-CoV-2 hybrid pairing sequences for human genomes.
Language	English
Publishing date	2021-06-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e07284
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains

Pasquier, Claude / Robichon, Alain

Heliyon. 2021 June, v. 7, no. 6

2021

Abstract	The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundant viral small interference and micro RNAs (VsiRNAs and VmiRNAs) in both cell-line and whole organism based experiments, indicating a contribution of these molecules in host responses and/or viral replication. We explore the theoretical possibility that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction, although this hypothesis seems counterintuitive. The SARS-CoV-2 genome was therefore computationally searched for exact intrapairing within the viral RNA and exact hybrid pairing with the human transcriptome over a minimum of 20 bases in length. Minimal segments of 20-base lengths of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, including mitochondrial deubiquitinase USP30, the subunit of ubiquitin protein ligase complex FBXO21 and two long noncoding RNAs, were retrieved. The hypothesis that viral-originated RNAi might mediate degradation of host transcriptome messages was corroborated by published high throughput sequencing of RNA from infected tissues and cultured cells, clinical observation and phylogenetic comparative analysis, indicating a strong specificity of these SARS-CoV-2 hybrid pairing sequences for human genomes.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; humans ; interferons ; mitochondria ; phylogeny ; transcriptome ; ubiquitin-protein ligase ; virus replication
Language	English
Dates of publication	2021-06
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e07284
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains

Claude Pasquier / Alain Robichon

Heliyon, Vol 7, Iss 6, Pp e07284- (2021)

2021

Abstract	The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundant viral small interference and micro RNAs (VsiRNAs and VmiRNAs) in both cell-line and whole organism based experiments, indicating a contribution of these molecules in host responses and/or viral replication. We explore the theoretical possibility that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction, although this hypothesis seems counterintuitive. The SARS-CoV-2 genome was therefore computationally searched for exact intrapairing within the viral RNA and exact hybrid pairing with the human transcriptome over a minimum of 20 bases in length. Minimal segments of 20-base lengths of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, including mitochondrial deubiquitinase USP30, the subunit of ubiquitin protein ligase complex FBXO21 and two long noncoding RNAs, were retrieved. The hypothesis that viral-originated RNAi might mediate degradation of host transcriptome messages was corroborated by published high throughput sequencing of RNA from infected tissues and cultured cells, clinical observation and phylogenetic comparative analysis, indicating a strong specificity of these SARS-CoV-2 hybrid pairing sequences for human genomes.
Keywords	SARS-CoV-2 ; dsRNA ; Dicer ; RNA cleavage ; Host transcriptome ; Viral genome ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	572
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Computational prediction of miRNA/mRNA duplexomes at the whole human genome scale reveals functional subnetworks of interacting genes with embedded miRNA annealing motifs.

Pasquier, Claude / Robichon, Alain

Computational biology and chemistry

2020 Volume 88, Page(s) 107366

Abstract: Perfect annealing between microRNAs (miRNAs) and messenger RNAs (mRNAs) was computationally searched at a broad scale in the human genome to determine whether theoretical pairing is restrictively represented in functional subnetworks or is randomly ... ...

Abstract	Perfect annealing between microRNAs (miRNAs) and messenger RNAs (mRNAs) was computationally searched at a broad scale in the human genome to determine whether theoretical pairing is restrictively represented in functional subnetworks or is randomly distributed. Massive RNA interference (RNAi) pairing motifs in genes constitute a remarkable subnetwork that displays highly genetically and biochemically interconnected genes. These analyses show unexpected repertoires of genes defined by their congruence in comatching with miRNAs at numerous sites and by their interconnection based on protein/protein interactions or proteins regulating the activity of others. This offers insights into the putatively coregulated homeostasis of large networks of genes by RNAi, whereas other networks seem to be independent of this regulatory mode. Genes accordingly defined by theoretical RNAi pairing cluster mainly in subnetworks related to cellular, metabolic and developmental processes and their regulation. Indeed, genes harboring numerous potential sites of hybridization with miRNAs are highly enriched with GO terms depicting the abovementioned processes and are grouped in a subnetwork of genes that are significantly more highly connected than they would be according to a random distribution. The significant number of interacting genes that present numerous potential comatches with miRNAs suggests that they may be under the control of the integrative and concerted action of multiple miRNAs.
MeSH term(s)	Computational Biology ; Gene Regulatory Networks ; Genome, Human/genetics ; Humans ; MicroRNAs/genetics ; RNA, Messenger/genetics
Chemical Substances	MicroRNAs ; RNA, Messenger
Language	English
Publishing date	2020-08-22
Publishing country	England
Document type	Journal Article ; Review
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2020.107366
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A network embedding approach to identify active modules in biological interaction networks.

Pasquier, Claude / Guerlais, Vincent / Pallez, Denis / Rapetti-Mauss, Raphaël / Soriani, Olivier

Life science alliance

2023 Volume 6, Issue 9

Abstract: The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical methods of differential expression analysis, designed to ... ...

Abstract	The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical methods of differential expression analysis, designed to assess individual gene variations, have trouble highlighting modules of small varying genes whose interaction is essential to characterize phenotypic changes. To identify these highly informative gene modules, several methods have been proposed in recent years, but they have many limitations that make them of little use to biologists. Here, we propose an efficient method for identifying these active modules that operates on a data embedding combining gene expressions and interaction data. Applications carried out on real datasets show that our method can identify new groups of genes of high interest corresponding to functions not revealed by traditional approaches. Software is available at https://github.com/claudepasquier/amine.
MeSH term(s)	Computational Biology/methods ; Software ; Gene Regulatory Networks/genetics ; Gene Expression Profiling/methods ; Signal Transduction/genetics
Language	English
Publishing date	2023-06-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202201550
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: SARS-CoV-2 might manipulate against its host the immunity RNAi/Dicer/Ago system Does mitochondria collapse upon COVID-19 infection?

Claude Pasquier / Alain Robichon

Abstract: AbstractThe role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive, which prompt authors to think that interferon (IFN) synthesis is essential, relegating the dsRNAs as accessory function. We investigate SARS-CoV-2 genome responsible ... ...

Abstract	AbstractThe role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive, which prompt authors to think that interferon (IFN) synthesis is essential, relegating the dsRNAs as accessory function. We investigate SARS-CoV-2 genome responsible of the new deadly COVID-19 pandemic for the theoretical possibilities to engage intra pairing within the viral RNA and also hybrid pairing with human transcriptome. Segmental pieces of RNAs that originate from SARS-CoV-2 were computationally searched as a potential source of one strand, the complementary strand being from the host transcriptome. We therefore considered perfect complementarity of host RNA with any piece of SARS-CoV-2 RNA as a collection of theoretical siRNAs potentially Dicer substrates. Few human genes seems targeted by SARS-CoV-2 RNA, among them mitochondrial deubiquitinase USP30 and a subunit of ubiquitin protein ligase complex FBXO21 could explain premature death of infected cell by the collapse of mitochondria.
Keywords	covid19
Publisher	biorxiv
Document type	Article ; Online
DOI	10.1101/2020.04.08.031856
Database	COVID19

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Article ; Online: L’essentiel du symposium UCAncer 2021 sur les approches multidisciplinaires de la recherche sur le cancer.

Braud, Véronique / Cazals, Frédéric / Duca, Maria / Mus-Veteau, Isabelle / Pasquier, Claude / Soriani, Olivier

Bulletin du cancer

2022 Volume 109, Issue 4, Page(s) 505–509

Title translation	Highlights of the UCAncer 2021 symposium on multidisciplinary approaches to cancer research.
MeSH term(s)	Humans ; Neoplasms/therapy ; Research
Language	French
Publishing date	2022-03-08
Publishing country	France
Document type	Clinical Conference
ZDB-ID	213270-9
ISSN	1769-6917 ; 0007-4551
ISSN (online)	1769-6917
ISSN	0007-4551
DOI	10.1016/j.bulcan.2022.02.002
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Article ; Online: Transcriptome-wide-scale-predicted dsRNAs potentially involved in RNA homoeostasis are remarkably excluded from genes with no/very low expression in all developmental stages.

Pasquier, Claude / Agnel, Sandra / Robichon, Alain

RNA biology

2020 Volume 17, Issue 4, Page(s) 554–570

Abstract: RNA interference (RNAi) refers to a conserved posttranscriptional mechanism for the degradation of RNA by short dsRNAs. A genome-wide analysis of mRNAs that are complementary to RNAs of variable length that are transcribed from the full transcriptome and ...

Abstract	RNA interference (RNAi) refers to a conserved posttranscriptional mechanism for the degradation of RNA by short dsRNAs. A genome-wide analysis of mRNAs that are complementary to RNAs of variable length that are transcribed from the full transcriptome and susceptible to being loaded onto
MeSH term(s)	Animals ; Argonaute Proteins/metabolism ; Computational Biology/methods ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/growth & development ; Exons ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Introns ; RNA Helicases/metabolism ; RNA, Double-Stranded/metabolism ; RNA, Long Noncoding/genetics ; RNA, Messenger/genetics ; Ribonuclease III/metabolism ; Whole Exome Sequencing
Chemical Substances	AGO2 protein, Drosophila ; Argonaute Proteins ; Drosophila Proteins ; RNA, Double-Stranded ; RNA, Long Noncoding ; RNA, Messenger ; DCR-2 protein, Drosophila (EC 2.7.7.-) ; Ribonuclease III (EC 3.1.26.3) ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2020-02-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.1080/15476286.2020.1717154
Database	MEDical Literature Analysis and Retrieval System OnLINE

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