News

LINE fishing... with the new bioinformatics tool CLIFinder

LINE fishing... with the new bioinformatics tool CLIFinder

Repeated elements represent 45% of the human genome. However, due to their large number and their high sequence homology, the contribution of those elements to the human genome transcriptome remains difficult to study. Particularly, implication of recent LINE-1 (L1) elements to the transcriptional expression profile of cells and tissues is probably under-evaluated. Indeed, those L1 elements possess, in addition to their sense promoter, an antisense promoter (ASP) which allow the transcription of their adjacent sequences (which may include genes) in the form of LINE-1 chimeric transcripts (LCTs). Such LCTs have been already described in literature bur the question remains of the pangenomic extent of this transcriptional activity.

In a study conducted by Catherine Barrière (Pinson, Pogorelcnik et al., 2017), Philippe Arnaud’s team has developed and validated CLIFinder (Chimeric Line Finder), a new software dedicated to the identification of LCTs from stranded paired-end RNA-seq data. Thus, CLIFinder take advantage of the strong potential of next generation sequencing to unravel the complete transcriptome composition and allow the “fishing”, among all the transcriptome’s sequences, of numerous LCTs comprising a L1 sequence and a unique sequence of the genome. The CLIFinder tool is today available for the scientific community to realize extensive analyses in normal and pathological tissues. Indeed, many LCTs have been identified specifically in tumors and are supposed to play a functional role in tumorigenesis.

This software has been published in Bioinformatics (Pinson, Pogorelcnik et al., 2017)

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Les Mardis du GRed - Novembre 2017

Les Mardis du GRed - Novembre 2017

12H45 – 13H45
Faculté de médecine
Amphi Limagne (CRBC RdC)

7 Novembre      :     Julio BUÑAY NOBOA, GReD, INSERM U1103, CNRS 6293, UCA

MiRNome Deregulation by The Exposure to Endocrine-Disrupting Chemicals : A New Mechanism in Infertility

14 Novembre    :     Pas de séminaire

21 Novembre    :     Claudine MEDIGUE, CNRS UMR8030 & CEA/DSV/IG/Genoscope, LABGeM, Evry
Contact : chantal.vaury@uca.fr

MicroScope: an integrated platform for annotation, comparative analysis and curation of microbial genomes

28 Novembre    :     Cedric PEIRS, INSERM U1107, Neuro-Dol, Trigeminal Pain and Migraine, Faculté de Chirurgie Dentaire

The Neuronal Circuit that Turns Touch into Pain

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Prostate Cancer; LXRs strike back !

Prostate Cancer; LXRs strike back !

During his life, one in five men will be diagnosed for prostate cancer. Current therapeutics are based on androgen deprivation therapy to treat advanced cancer development. Unfortunately, although this strategy gives good results, efficiency remains transient. The NuReP team work's shows for the first time that receptors present in prostatic tissue, LXR for Liver X Receptors, are able to constrain the metastatic progression of prostate cancer. Like all receptors, these can be activated by natural or pharmacological molecules; therefore these results open up important prospects in the development of future treatments to fight the metastatic evolution of prostate cancer.

This work is published in Nature Communication (Alioui et al., 2017)

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GReD meets Johan Swinnen during its 2400 km run for cancer patients

GReD meets Johan Swinnen during its 2400 km run for cancer patients

From the 21st of Auguts our colleague Johan Swinnen undertook  a journey of a lifetime: running from Leuven to Santiago de Compostela with a backpack filled with hundreds of letters from cancer patients and from people who care about them.

He will run about two marathons each day, on average, to reach hus destinattion for end of september.

Near Perigueux, Jean-Marc Lobaccaro and Silvère Baron met him;  A few kilometers of race to his side to support his run, the rain having invited on the course!

We wish a good race to Johan towards Santiago de Compostela with the GReD support's.

 You can follow the event, send in letters and messages  and support Johan via the dedicated  website: 

http://www.post-voor-compostela.be/en/johans-journey/2400-km-run

More info at:

http://www.flanderstoday.eu/living/cancer-researcher-runs-2400km-compostela-tribute-son

 

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Chaperoning histones and controlling genome function

Chaperoning histones and controlling genome function

Histone proteins are critical components of chromatin and the incorporation of different histone variants modulates nucleosome stability. Deposition of histones at the right time and the correct place in the genome is tightly controlled by specific histone chaperone complexes. In its last study  , the team of Aline Probst and Christophe Tatout characterized the Arabidopsis ATRX (Alpha Thalassemia-mental Retardation X-linked) homologue. Using reverse genetic approaches along with genome wide analyses Duc et al show that loss of ATRX modulates the cellular balance between canonical H3.1 and its variant H3.3 and leads to reduced H3.3 deposition at set of genes with elevated H3.3 occupancy and high gene expression. This study further elucidates the network of histone chaperones in plants and reveals a specific role for ATRX in histone H3.3 deposition.

 

This work is published in The Plant Cell (Duc et al., 2017).

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FXRα  a new actor  of germinal stem cells fate.

FXRα a new actor of germinal stem cells fate.

The FXRα nuclear receptor (Farnesoid-X-Receptor alpha) is a key factor controlling the male sex hormone synthesis within the testis. However, its roles in male germ cell homeostasis have not yet been studied. Using a phenotyping approach of Fxra deficient mice, the team of David Volle has characterized unexpected roles of FXRa with germ cell lineage. There, FXRa is involved in the establishment and the maintenance of undifferentiated germ cell pool and in turn, influences male fertility during aging.

This study is  published  in  Stem Cell Reports (Martinot et al., 2017)

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INDEPTH : The GReD, in collaboration with LIMOS laboratory, holds the first  COST-Action coordinated by Clermont Auvergne University (UCA)

INDEPTH : The GReD, in collaboration with LIMOS laboratory, holds the first COST-Action coordinated by Clermont Auvergne University (UCA)

GReD and LIMOS laboratories are happy to inform you that their COST-action project entitled «Impact of Nuclear Domains on Gene Expression and Plant Traits »  (INDEPTH) has been awarded.  This pan-european project, coordinated by Pr Christophe Tatout (GReD)  in collaboration with Pr Rémy Malgouyres (LIMOS), involves for the next 4 years more than 50 laboratories over 19 countries. INDEPTH will decipher how nuclear architecture, chromatin organization and gene expression are connected and modified in response to internal and external cues in plants. To address this challenge, the INDEPTH Action gathers a network  bringing state-of-the-art technologies and fostering multidisciplinary approaches at research, training, education and industrial levels in high- and super-resolution microscopy, 3D image analysis and software development, chromatin domain mapping, genomics, bioinformatics and plant phenotyping. INDEPTH is the first cost-ation coordinated by UCA.

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Les Doctorants du GReD à l’honneur lors des JED 2017.

Les Doctorants du GReD à l’honneur lors des JED 2017.

Houda TABBAL, doctorante dans l’équipe « Pathophysiologie moléculaire des tissus surrénaux et endocriniens » et Alexandre CHAMPROUX, doctorant dans l’équipe « Mécanismes de l'infertilité mâle post-testiculaire », ont tous deux été primés lors des Journées de l’école Doctorale 2017.

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GReD internal meeting 2017

The GReD internal meeting 2017 will be held thursday the 9th and friday the 10th of february  at "amplhi de Physique" on Cézeaux Campus.

Please,click  here to download the program.

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Conference: "The unique mechanisms for the nuclear dynamics in Arabidopsis" Dr. Tamura - Kyoto University, Japan

"The unique mechanisms for the nuclear dynamics in Arabidopsis"

By Dr. Kentaro Tamura, from Kyoto University, Japan

Friday the 3rd of February. 2:30pm

Meeting room, Vegetal Biology Building- Campus des Cézeaux

Contact: Christophe TATOUT  (christophe.tatout@uca.fr)

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In a few words...

GReD

The GReD is a Research Center at Clermont-Ferrand, capital of the Auvergne region of central France. Created in 2008, the GReD is supported by the University of Auvergne, the University Blaise Pascal, the CNRS (UMR6293) and the INSERM (U1103). The center is composed of 10 research groups (totalling 130 people in April 2014) and is situated on the neighbouring campuses ...

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