Inference and Differential Analysis of Extended Core Networks: a way to study Anti-Sense Regulation

A key issue in bioinformatics is to decipher cell regulation mechanisms. By comparing networks observed in two different situations, differential network analysis enables to highlight differences that reveal specific cellular responses. The aim of our work is to study the role of natural anti-sense transcription on cellular regulation mechanisms. Our proposal is to build and compare networks obtained from two different sets of actors: the “usual” sense actors on one hand and the sense and anti-sense actors on the other hand. Our study only considers themost significant interactions, called an Extended Core Network; therefore our differential analysis identifies important interactions that are on the influence of anti-sense transcription. Our inference method of an Extended Core Network is inspired by C3NET, but whereas C3NET only computes one interaction per gene, we propose to consider the most significant interactions for each gene. We define the differential network analysis of two extended core networks inferred with and without anti-sense actors. This relies on change motifs that describe which gene-gene interactions of the extended core network are modified when we integrate anti-sense actors in the data. As our method ocuses on the most significant interactions, these motifs highlight the impact of anti-sense transcription. The networks motifs obtained by our workflow are then compared with assessed biological knowledge. The study reported in this paper is realized on transcriptional data from apple fruit in a context of fruit ripening; the change motifs revealed by our analysis are matched on a protein-protein interaction network and give a small set of interesting actors thatdeserve further biological investigation

Differential Network Analysis of Anti-sense Regulation

A challenging task in systems biology is to decipher cell regulation mechanisms. By comparing networks observed in two different situations, the differential network analysis approach enables to highlight interaction differences that reveal specific cellular responses. The aim of our work is to study the role of natural anti-sense transcription on cellular regulation mechanisms. Our proposal is to build and compare networks obtained from two different sets of actors: the “usual” sense actors on one hand and the sense and anti-sense actors on the other hand. Our study only considers the most significant interactions, called an Extended Core Network; therefore our differential analysis identifies important interactions that are impacted by anti-sense transcription. This paper first introduces our inference method of an Extended Core Network; this method is inspired by C3NET, but whereas C3NET only computes one interaction per gene, we propose to consider the most significant interactions for each gene. Secondly, we define the differential network analysis of two extended core networks inferred with and without anti-sense actors. On a local view, this analysis relies on change motifs that describe which genes have their most important interactions modified when the anti-sense transcripts are considered; they are called AS-impacted genes. Then from a more global view, we consider how the relationships between these AS-impacted genes are rewired in the network with anti-sense actors. Our analysis is performed by computing Steiner trees that represent minimal subnetworks connecting the AS-impacted genes. We show that the visualisation of these results help the biologists to identify interesting parts of the networks

Differential Functional Analysis and Change Motifs in Gene Networks to Explore the Role of Anti-sense Transcription

Several transcriptomic studies have shown the widespread existence of anti-sense transcription in cell. Anti-sense RNAs may be important actors in transcriptional control, especially in stress response processes. The aim of our work is to study gene networks, with the particularity to integrate in the process anti-sense transcripts. In this paper, we first present a method that highlights the importance of taking into account anti-sense data into functional enrichment analysis. Secondly, we propose the differential analysis of gene networks built with and without anti-sense actors in order to discover interesting change motifs that involve the anti-sense transcripts. For more reliability, our network comparison only studies the conservative causal part of a network, inferred by the C3NET method. Our work is realized on transcriptomic data from apple fruit

Live imaging of DORNRÖSCHEN and DORNRÖSCHEN-LIKE promoter activity reveals dynamic changes in cell identity at the microcallus surface of Arabidopsis embryonic suspensions

Key message Transgenic DRN::erGFP and DRNL::erGFP reporters access the window from explanting Arabidopsis embryos to callus formation and provide evidence for the acquisition of shoot meristem cell fates at the microcalli surface. Abstract The DORNRÖSCHEN (DRN) and DORNRÖSCHEN-LIKE (DRNL) genes encode AP2-type transcription factors, which are activated shortly after fertilisation in the zygotic Arabidopsis embryo. We have monitored established transgenic DRN::erGFP and DRNL::erGFP reporter lines using live imaging, for expression in embryonic suspension cultures and our data show that transgenic fluorophore markers are suitable to resolve dynamic changes of cellular identity at the surface of microcalli and enable fluorescence-activated cell sorting. Although DRN::erGFP and DRNL::erGFP are both activated in surface cells, their promoter activity marks different cell identities based on real-time PCR experiments and whole transcriptome microarray data. These transcriptome analyses provide no evidence for the maintenance of embryogenic identity under callus-inducing high-auxin tissue culture conditions but are compatible with the acquisition of shoot meristem cell fates at the surface of suspension calli

The MIK2/SCOOP Signaling System Contributes to Arabidopsis Resistance Against Herbivory by Modulating Jasmonate and Indole Glucosinolate Biosynthesis.

Initiation of plant immune signaling requires recognition of conserved molecular patterns from microbes and herbivores by plasma membrane-localized pattern recognition receptors. Additionally, plants produce and secrete numerous small peptide hormones, termed phytocytokines, which act as secondary danger signals to modulate immunity. In Arabidopsis, the Brassicae-specific SERINE RICH ENDOGENOUS PEPTIDE (SCOOP) family consists of 14 members that are perceived by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR LIKE KINASE 2 (MIK2). Recognition of SCOOP peptides elicits generic early signaling responses but knowledge on how and if SCOOPs modulate specific downstream immune defenses is limited. We report here that depletion of MIK2 or the single PROSCOOP12 precursor results in decreased Arabidopsis resistance against the generalist herbivore Spodoptera littoralis but not the specialist Pieris brassicae. Increased performance of S. littoralis on mik2-1 and proscoop12 is accompanied by a diminished accumulation of jasmonic acid, jasmonate-isoleucine and indolic glucosinolates. Additionally, we show transcriptional activation of the PROSCOOP gene family in response to insect herbivory. Our data therefore indicate that perception of endogenous SCOOP peptides by MIK2 modulates the jasmonate pathway and thereby contributes to enhanced defense against a generalist herbivore

Kinetic transcriptomic approach revealed metabolic pathways and genotoxic-related changes implied in the Arabidopsis response to ionising radiations

Plants exposed to ionising radiation (IR) have to face direct and indirect (oxidative stress) deleterious effects whose intensity depends on the dose applied and led to differential genome regulation. Transcriptomic analyses were conducted with CATMA microarray technology on Arabidopsis thaliana plantlets, 2 and 26 h after exposure to the IR doses 10 Gy and 40 Gy. 10 Gy treatment seemed to enhance antioxidative compound biosynthetic pathways whereas the 40 Gy dose up-regulated ROS-scavenging enzyme genes. Transcriptomic data also highlighted a differential regulation of chloroplast constituent genes depending on the IR dose, 10 Gy stimulating and 40 Gy down-regulating. This probable 40 Gy decrease of photosynthesis could help for the limitation of ROS production and may be coupled with programmed cell death (PCD)/senescence phenomena. Comparisons with previous transcriptomic studies on plants exposed to a 100 Gy dose revealed 60 dose-dependent up-regulated genes, including notably cell cycle checkpoints to allow DNA repairing phenomena. Furthermore, the alteration of some cellular structure related gene expression corroborated a probable mitotic arrest after 40 Gy. Finally, numerous heat-shock protein and chaperonin genes, known to protect proteins against stress-dependent dysfunction, were up-regulated after IR exposure

Characterization of the Early Events Leading to Totipotency in an Arabidopsis Protoplast Liquid Culture by Temporal Transcript Profiling

The molecular mechanisms underlying plant cell totipotency are largely unknown. Here, we present a protocol for the efficient regeneration of plants from Arabidopsis thaliana protoplasts. The specific liquid medium used in our study leads to a high rate of reentry into the cell cycle of most cell types, providing a powerful system to study dedifferentiation/regeneration processes in independent somatic cells. To identify the early events in the establishment of totipotency, we monitored the genome-wide transcript profiles of plantlets and protoplast-derived cells (PdCs) during the first week of culture. Plant cells rapidly dedifferentiated. Then, we observed the reinitiation and reorientation of protein synthesis, accompanied by the reinitiation of cell division and de novo cell wall synthesis. Marked changes in the expression of chromatin-associated genes, especially of those in the histone variant family, were observed during protoplast culture. Surprisingly, the epigenetic status of PdCs and well-established cell cultures differed, with PdCs exhibiting rare reactivated transposons and epigenetic changes. The differentially expressed genes identified in this study are interesting candidates for investigating the molecular mechanisms underlying plant cell plasticity and totipotency. One of these genes, the plant-specific transcription factor ABERRANT LATERAL ROOT FORMATION4, is required for the initiation of protoplast division