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Article ; Online: Root Development in Medicago truncatula: Lessons from Genetics to Functional Genomics.

Proust, Hélène / Hartmann, Caroline / Crespi, Martin / Lelandais-Brière, Christine

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1822, Page(s) 205–239

Abstract: This decade introduced "omics" approaches, such as genomics, transcriptomics, proteomics, and metabolomics in association with reverse and forward genetic approaches, developed earlier, to try to identify molecular pathways involved in the development or ...

Abstract	This decade introduced "omics" approaches, such as genomics, transcriptomics, proteomics, and metabolomics in association with reverse and forward genetic approaches, developed earlier, to try to identify molecular pathways involved in the development or in the response to environmental conditions as well as in animals and plants. This review summarizes studies that utilized "omics" strategies to unravel the root development in the model legume Medicago truncatula and how external factors such as soil mineral status or the presence of bacteria and fungi affect root system architecture in this species. We also compare these "omics" data to the knowledges concerning the Arabidopsis thaliana root development, nowadays considered as the model of allorhiz root systems. However, unlike legumes, this species is unable to interact with soil nitrogen-fixing rhizobia and arbuscular-mycorrhizal (AM) fungi to develop novel root-derived symbiotic structures. Differences in root organization, development, and regulatory pathways between these two model species have been highlighted.
MeSH term(s)	Environment ; Gene Expression Regulation, Plant ; Genome, Plant ; Genomics/methods ; Medicago truncatula/genetics ; Medicago truncatula/growth & development ; Medicago truncatula/metabolism ; Plant Development/genetics ; Plant Growth Regulators/metabolism ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Roots/genetics
Chemical Substances	Plant Growth Regulators ; Plant Proteins
Language	English
Publishing date	2018-07-24
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8633-0_15
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Article ; Online: Stable Inactivation of MicroRNAs in Medicago truncatula Roots.

Proust, Hélène / Bazin, Jérémie / Sorin, Céline / Hartmann, Caroline / Crespi, Martin / Lelandais-Brière, Christine

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1822, Page(s) 123–132

Abstract: MicroRNAs are key regulators in the development processes or stress responses in plants. In the last decade, several conserved or non-conserved microRNAs have been identified in Medicago truncatula. Different strategies leading to the inactivation of ... ...

Abstract	MicroRNAs are key regulators in the development processes or stress responses in plants. In the last decade, several conserved or non-conserved microRNAs have been identified in Medicago truncatula. Different strategies leading to the inactivation of microRNAs in plants have been described. Here, we propose a protocol for an effective inactivation of microRNAs using a STTM strategy in M. truncatula transgenic roots.
MeSH term(s)	Agrobacterium ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Silencing ; Medicago truncatula/genetics ; Medicago truncatula/microbiology ; MicroRNAs/genetics ; Plant Roots/genetics ; RNA Interference ; Transformation, Genetic
Chemical Substances	MicroRNAs
Language	English
Publishing date	2018-07-24
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8633-0_9
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Article: Noncoding RNAs, Emerging Regulators in Root Endosymbioses.

Lelandais-Brière, Christine / Moreau, Jérémy / Hartmann, Caroline / Crespi, Martin

Molecular plant-microbe interactions : MPMI

2016 Volume 29, Issue 3, Page(s) 170–180

Abstract: Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for ... ...

Abstract	Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for certain plants, notably major crop legumes. The signaling pathways triggered by specific lipochitooligosaccharide molecules involved in these interactions have common components that also overlap with plant root development. These pathways include receptor-like kinases, transcription factors (TFs), and various intermediate signaling effectors, including noncoding (nc)RNAs. These latter molecules have emerged as major regulators of gene expression and small ncRNAs, composed of micro (mi)RNAs and small interfering (si)RNAs, are known to control gene expression at transcriptional (chromatin) or posttranscriptional levels. In this review, we describe exciting recent data connecting variants of conserved si/miRNAs with the regulation of TFs, such as NSP2, NFY-A1, auxin-response factors, and AP2-like proteins, known to be involved in symbiosis. The link between hormonal regulations and these si- and miRNA-TF nodes is proposed in a model in which different feedback loops or regulations controlling endosymbiosis signaling are integrated. The diversity and emerging regulatory networks of young legume miRNAs are also highlighted.
MeSH term(s)	Mycorrhizae/physiology ; Nitrogen Fixation/physiology ; Plant Roots/microbiology ; RNA, Fungal/genetics ; RNA, Fungal/metabolism ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; Symbiosis
Chemical Substances	RNA, Fungal ; RNA, Untranslated
Language	English
Publishing date	2016-03
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-10-15-0240-FI
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Article ; Online: Les ARN non-codants impliqués dans la réponse des plantes aux contraintes environnementales.

Lelandais-Brière, Christine / Sorin, Céline / Crespi, Martin / Hartmann, Caroline

Biologie aujourd'hui

2012 Volume 206, Issue 4, Page(s) 313–322

Abstract: In recent years, in addition to mRNAs, the non-protein-coding RNAs (or ncRNAs) have emerged as a major part of the eukaryotic transcriptome. New genomic approaches allowed the discovery of many novel long and small ncRNAs that may be linked to the ... ...

Title translation	Non-coding RNAs involved in plant responses to environmental constraints.
Abstract	In recent years, in addition to mRNAs, the non-protein-coding RNAs (or ncRNAs) have emerged as a major part of the eukaryotic transcriptome. New genomic approaches allowed the discovery of many novel long and small ncRNAs that may be linked to the generation of evolutionary complexity in multicellular organisms. Many long ncRNAs are regulated by abiotic stresses although only very few long ncRNAs have been functionally analyzed. On the other hand, small RNAs act in the regulation of gene expression at transcriptional or post-transcriptional level and several among them have been linked to abiotic stress responses. Here we describe various ncRNAs associated with environmental stress responses such as to salt, cold or nutrient deprivation. The understanding of these RNA networks may reveal novel mechanisms involved in plant adaptation to changing environmental conditions.
MeSH term(s)	Environment ; Gene Expression Regulation, Plant ; MicroRNAs/genetics ; MicroRNAs/physiology ; Plant Physiological Phenomena ; Plants/genetics ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/physiology ; RNA, Plant/physiology ; RNA, Untranslated/physiology ; Stress, Physiological/genetics ; Stress, Physiological/physiology
Chemical Substances	MicroRNAs ; RNA, Long Noncoding ; RNA, Plant ; RNA, Untranslated
Language	French
Publishing date	2012
Publishing country	France
Document type	English Abstract ; Journal Article ; Review
ISSN	2105-0686
ISSN (online)	2105-0686
DOI	10.1051/jbio/2012032
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Article: Small RNA pathways and diversity in model legumes: lessons from genomics.

Bustos-Sanmamed, Pilar / Bazin, Jérémie / Hartmann, Caroline / Crespi, Martin / Lelandais-Brière, Christine

Frontiers in plant science

2013 Volume 4, Page(s) 236

Abstract: Small non-coding RNAs (smRNA) participate in the regulation of development, cell differentiation, adaptation to environmental constraints and defense responses in plants. They negatively regulate gene expression by degrading specific mRNA targets, ... ...

Abstract	Small non-coding RNAs (smRNA) participate in the regulation of development, cell differentiation, adaptation to environmental constraints and defense responses in plants. They negatively regulate gene expression by degrading specific mRNA targets, repressing their translation or modifying chromatin conformation through homologous interaction with target loci. MicroRNAs (miRNA) and short-interfering RNAs (siRNA) are generated from long double stranded RNA (dsRNA) that are cleaved into 20-24-nucleotide dsRNAs by RNase III proteins called DICERs (DCL). One strand of the duplex is then loaded onto effective complexes containing different ARGONAUTE (AGO) proteins. In this review, we explored smRNA diversity in model legumes and compiled available data from miRBAse, the miRNA database, and from 22 reports of smRNA deep sequencing or miRNA identification genome-wide in three legumes: Medicago truncatula, soybean (Glycine max) and Lotus japonicus. In addition to conserved miRNAs present in other plant species, 229, 179, and 35 novel miRNA families were identified respectively in these 3 legumes, among which several seems legume-specific. New potential functions of several miRNAs in the legume-specific nodulation process are discussed. Furthermore, a new category of siRNA, the phased siRNAs, which seems to mainly regulate disease-resistance genes, was recently discovered in legumes. Despite that the genome sequence of model legumes are not yet fully completed, further analysis was performed by database mining of gene families and protein characteristics of DCLs and AGOs in these genomes. Although most components of the smRNA pathways are conserved, identifiable homologs of key smRNA players from non-legumes, like AGO10 or DCL4, could not yet be detected in M. truncatula available genomic and expressed sequence (EST) databases. In contrast to Arabidopsis, an important gene diversification was observed in the three legume models (for DCL2, AGO4, AGO2, and AGO10) or specifically in soybean for DCL1 and DCL4. Functional significance of these variant isoforms may reflect peculiarities of smRNA biogenesis and functions in legumes.
Language	English
Publishing date	2013-07-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2013.00236
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Article ; Online: Analyzing protein distribution in plant tissues using "whole-mount" immunolocalization.

Bustos-Sanmamed, Pilar / Laffont, Carole / Frugier, Florian / Lelandais-Brière, Christine / Crespi, Martin

Methods in molecular biology (Clifton, N.J.)

2013 Volume 959, Page(s) 317–322

Abstract: Proteins are distributed in different cellular compartments. Our group studies the role of non-coding RNAs and associated RNPs in the development and stress response in legumes. Ribonucleoproteins (RNPs) are RNA-protein complexes that play different ... ...

Abstract	Proteins are distributed in different cellular compartments. Our group studies the role of non-coding RNAs and associated RNPs in the development and stress response in legumes. Ribonucleoproteins (RNPs) are RNA-protein complexes that play different roles in many cellular processes. Long and small non-coding RNAs determine the specificity of action of several RNPs as the RNA Induced Silencing Complex (RISC), or affect mRNA translation, splicing and stability by interacting with other RNPs such as P-bodies, spliceosome or polysomes. Together with small and long RNAs (Chapter 20), the precise localization of the associated RNPs or the translational products regulated by small RNAs (ie target proteins regulated by miRNAs, or translationally-regulated products) by immunocytochemistry could bring novel insights into these regulatory processes. The protocol described is currently used for detection of RNP associated proteins in nodules and roots of Medicago truncatula but could be extended to any other protein. The critical points, as the choice of the antibody and the fixation and permeabilization steps, that allow preservation of tissue and cell integrity and increase the accessibility to epitopes, will be discussed.
MeSH term(s)	Medicago truncatula/metabolism ; Plant Proteins/metabolism ; RNA, Untranslated/metabolism ; Ribonucleoproteins/metabolism ; Ribonucleoproteins, Small Nuclear/metabolism ; Spliceosomes/metabolism
Chemical Substances	Plant Proteins ; RNA, Untranslated ; Ribonucleoproteins ; Ribonucleoproteins, Small Nuclear
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-221-6_21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Analyzing small and long RNAs in plant development using non-radioactive in situ hybridization.

Bustos-Sanmamed, Pilar / Laffont, Carole / Frugier, Florian / Lelandais-Brière, Christine / Crespi, Martin

Methods in molecular biology (Clifton, N.J.)

2013 Volume 959, Page(s) 303–316

Abstract: In the past decade, hundreds of non-coding RNAs (small and long RNAs) have been identified as crucial elements in developmental processes and stress response in plants. Among small RNAs, the microRNAs or miRNAs control levels of specific mRNA by ... ...

Abstract	In the past decade, hundreds of non-coding RNAs (small and long RNAs) have been identified as crucial elements in developmental processes and stress response in plants. Among small RNAs, the microRNAs or miRNAs control levels of specific mRNA by inhibiting translation or reducing the stability of their mRNA targets through integration into different ribonucleoproteins (RNP). Spatio-temporal expression of small and long RNAs, using reporter genes or in situ hybridization, is essential to understand their functions. We are interested in understanding the role of various non-coding RNAs (including miRNAs) in the regulation of root and nodule development in legumes, which are agriculturally important crops. Here, we present the protocol we are currently using for detection of small and long RNA in model legume plants and tissues, like nodules and roots. The probe selection, as well as the fixation and permeabilization steps allowing to preserve tissues and cell integrity and to increase accessibility to RNA targets, will be specifically discussed.
MeSH term(s)	Gene Expression Regulation, Plant ; In Situ Hybridization/methods ; MicroRNAs/genetics ; RNA, Messenger/genetics ; RNA, Plant/genetics
Chemical Substances	MicroRNAs ; RNA, Messenger ; RNA, Plant
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-221-6_20
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Article ; Online: Complexity of miRNA-dependent regulation in root symbiosis.

Bazin, Jérémie / Bustos-Sanmamed, Pilar / Hartmann, Caroline / Lelandais-Brière, Christine / Crespi, Martin

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2012 Volume 367, Issue 1595, Page(s) 1570–1579

Abstract: The development of root systems may be strongly affected by the symbiotic interactions that plants establish with soil organisms. Legumes are able to develop symbiotic relationships with both rhizobial bacteria and arbuscular mycorrhizal fungi leading to ...

Abstract	The development of root systems may be strongly affected by the symbiotic interactions that plants establish with soil organisms. Legumes are able to develop symbiotic relationships with both rhizobial bacteria and arbuscular mycorrhizal fungi leading to the formation of nitrogen-fixing nodules and mycorrhizal arbuscules, respectively. Both of these symbiotic interactions involve complex cellular reprogramming and profound morphological and physiological changes in specific root cells. In addition, the repression of pathogenic defence responses seems to be required for successful symbiotic interactions. Apart from typical regulatory genes, such as transcription factors, microRNAs (miRNAs) are emerging as riboregulators that control gene networks in eukaryotic cells through interactions with specific target mRNAs. In recent years, the availability of deep-sequencing technologies and the development of in silico approaches have allowed for the identification of large sets of miRNAs and their targets in legumes. A number of conserved and legume-specific miRNAs were found to be associated with symbiotic interactions as shown by their expression patterns or actions on symbiosis-related targets. In this review, we combine data from recent literature and genomic and deep-sequencing data on miRNAs controlling nodule development or restricting defence reactions to address the diversity and specificity of miRNA-dependent regulation in legume root symbiosis. Phylogenetic analysis of miRNA isoforms and their potential targets suggests a role for miRNAs in the repression of plant defence during symbiosis and revealed the evolution of miRNA-dependent regulation in legumes to allow for the modification of root cell specification, such as the formation of mycorrhized roots and nitrogen-fixing nodules.
MeSH term(s)	Conserved Sequence ; Fabaceae/genetics ; Fabaceae/growth & development ; Fabaceae/metabolism ; Fabaceae/microbiology ; Gene Expression Regulation, Plant ; Genes, Fungal ; Genes, Plant ; MicroRNAs/classification ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Mycorrhizae/genetics ; Mycorrhizae/growth & development ; Phylogeny ; Plant Immunity ; Root Nodules, Plant/genetics ; Root Nodules, Plant/growth & development ; Root Nodules, Plant/metabolism ; Root Nodules, Plant/microbiology ; Soil Microbiology ; Symbiosis ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	MicroRNAs ; Transcription Factors
Language	English
Publishing date	2012-04-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2011.0228
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Article: MicroRNAs as regulators of root development and architecture

Khan, Ghazanfar A / Declerck, Marie / Sorin, Céline / Hartmann, Caroline / Crespi, Martin / Lelandais-Brière, Christine

Plant molecular biology. 2011 Sept., v. 77, no. 1-2

2011

Abstract: MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. In plants, roots play essential roles in their anchorage to the soil as well as in nutrient and water uptake. In this review, we present recent ... ...

Abstract	MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. In plants, roots play essential roles in their anchorage to the soil as well as in nutrient and water uptake. In this review, we present recent advances made in the identification of miRNAs involved in embryonic root development, radial patterning, vascular tissue differentiation and formation of lateral organs (i.e., lateral and adventitious roots and symbiotic nitrogen-fixing nodules in legumes). Certain mi/siRNAs target members of the Auxin Response Factors family involved in auxin homeostasis and signalling and participate in complex regulatory loops at several crucial stages of root development. Other miRNAs target and restrict the action of various transcription factors that control root-related processes in several species. Finally, because abiotic stresses, which include nutrient or water deficiencies, generally modulate root growth and branching, we summarise the action of certain miRNAs in response to these stresses that may be involved in the adaptation of the root system architecture to the soil environment.
Keywords	abiotic stress ; adventitious roots ; auxins ; edaphic factors ; growth and development ; homeostasis ; legumes ; microRNA ; root growth ; root systems ; small interfering RNA ; stress response ; transcription (genetics) ; transcription factors ; vascular tissues ; water uptake
Language	English
Dates of publication	2011-09
Size	p. 47-58.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	778032-1
ISSN	1573-5028 ; 0167-4412
ISSN (online)	1573-5028
ISSN	0167-4412
DOI	10.1007/s11103-011-9793-x
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Article ; Online: MicroRNAs as regulators of root development and architecture.

Khan, Ghazanfar A / Declerck, Marie / Sorin, Céline / Hartmann, Caroline / Crespi, Martin / Lelandais-Brière, Christine

Plant molecular biology

2011 Volume 77, Issue 1-2, Page(s) 47–58

Abstract	MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. In plants, roots play essential roles in their anchorage to the soil as well as in nutrient and water uptake. In this review, we present recent advances made in the identification of miRNAs involved in embryonic root development, radial patterning, vascular tissue differentiation and formation of lateral organs (i.e., lateral and adventitious roots and symbiotic nitrogen-fixing nodules in legumes). Certain mi/siRNAs target members of the Auxin Response Factors family involved in auxin homeostasis and signalling and participate in complex regulatory loops at several crucial stages of root development. Other miRNAs target and restrict the action of various transcription factors that control root-related processes in several species. Finally, because abiotic stresses, which include nutrient or water deficiencies, generally modulate root growth and branching, we summarise the action of certain miRNAs in response to these stresses that may be involved in the adaptation of the root system architecture to the soil environment.
MeSH term(s)	Cell Differentiation ; Homeostasis ; Indoleacetic Acids/metabolism ; MicroRNAs/physiology ; Nitrogen Fixation ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Proteins/physiology ; Plant Root Nodulation/genetics ; Plant Roots/genetics ; Plant Roots/growth & development ; RNA, Plant/physiology ; Seedlings/genetics ; Seedlings/growth & development ; Signal Transduction
Chemical Substances	Indoleacetic Acids ; MicroRNAs ; Plant Proteins ; RNA, Plant
Language	English
Publishing date	2011-05-24
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	778032-1
ISSN	1573-5028 ; 0167-4412
ISSN (online)	1573-5028
ISSN	0167-4412
DOI	10.1007/s11103-011-9793-x
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