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In Vitro Corticogenesis from Embryonic Stem Cells Recapitulates the In Vivo Epigenetic Control of Imprinted Gene Expression

Bouschet, Tristan ; Dubois, Emeric ; Reynès, Christelle ; [et al.]

Oxford University Press (OUP) ; 2016

In: Cerebral Cortex

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In: Cerebral Cortex, Oxford University Press (OUP)

Type of Medium: Online Resource

ISSN: 1047-3211 , 1460-2199

URL: Article

DOI: 10.1093/cercor/bhw102

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2016

detail.hit.zdb_id: 1483485-6

SSG: 12

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Table_4.xlsx

Poupet, Cyril ; Rifa, Étienne ; Theil, Sébastien ; [et al.]

Frontiers Media SA ; 2022

In: Frontiers in Microbiology Vol. 13 ( 2022-12-23)

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In: Frontiers in Microbiology, Frontiers Media SA, Vol. 13 ( 2022-12-23)

Abstract: Lactic acid bacteria, including the microorganisms formerly designated as Lactobacillus , are the major representatives of Live Biotherapeutic Microorganisms (LBM) when used for therapeutic purposes. However, in most cases, the mechanisms of action remain unknown. The antifungal potential of LBM has already been demonstrated using preclinical models (cell cultures, laboratory animals). Understanding their mechanisms of action is strategic for the development of new therapeutics for humans. Here, Caenorhabditis elegans was used as an in vivo model to analyze pro-longevity, anti-aging and anti-candidiasis effects of the LBM Lacticaseibacillus rhamnosus (formerly Lactobacillus rhamnosus ) Lcr35 ® . A high-throughput transcriptomic analysis revealed a specific response of C. elegans depending on whether it is in the presence of the LBM L. rhamnosus Lcr35 ® (structural response), the yeast Candida albicans (metabolic response) or both (structural and metabolic responses) in a preventive and a curative conditions. Studies on C. elegans mutants demonstrated that the p38 MAPK ( sek-1 , skn-1 ) and the insulin-like ( daf-2 , daf-16 ) signaling pathways were involved in the extended lifespan provided by L. rhamnosus Lcr35 ® strain whereas the JNK pathway was not involved (jnk-1) . In addition, the anti C. albicans effect of the bacterium requires the daf-16 and sek-1 genes while it is independent of daf-2 and skn-1 . Moreover, the anti-aging effect of Lcr35 ® , linked to the extension of longevity, is not due to protection against oxidative stress (H 2 O 2 ). Taken together, these results formally show the involvement of the p38 MAP kinase and insulin-like signaling pathways for the longevity extension and anti- Candida albicans properties of Lcr35 ® with, however, differences in the genes involved. Overall, these findings provide new insight for understanding the mechanisms of action of a probiotic strain with antimicrobial potential.

Type of Medium: Online Resource

ISSN: 1664-302X

URL: Article

DOI: 10.3389/fmicb.2022.1062113

DOI: 10.3389/fmicb.2022.1062113.s001

DOI: 10.3389/fmicb.2022.1062113.s002

DOI: 10.3389/fmicb.2022.1062113.s003

DOI: 10.3389/fmicb.2022.1062113.s004

DOI: 10.3389/fmicb.2022.1062113.s005

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2022

detail.hit.zdb_id: 2587354-4

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Transcriptional Profiling of Cutaneous MRGPRD Free Nerve Endings and C-LTMRs

Reynders, Ana ; Mantilleri, Annabelle ; Malapert, Pascale ; [et al.]

Elsevier BV ; 2015

In: Cell Reports Vol. 10, No. 6 ( 2015-02), p. 1007-1019

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In: Cell Reports, Elsevier BV, Vol. 10, No. 6 ( 2015-02), p. 1007-1019

Type of Medium: Online Resource

ISSN: 2211-1247

URL: Article

DOI: 10.1016/j.celrep.2015.01.022

Language: English

Publisher: Elsevier BV

Publication Date: 2015

detail.hit.zdb_id: 2649101-1

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A Duplicated NUCLEOLIN Gene with Antagonistic Activity Is Required for Chromatin Organization of Silent 45S rDNA in Arabidopsis

Durut, Nathalie ; Abou-Ellail, Mohamed ; Pontvianne, Frédéric ; [et al.]

Oxford University Press (OUP) ; 2014

In: The Plant Cell Vol. 26, No. 3 ( 2014-03), p. 1330-1344

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In: The Plant Cell, Oxford University Press (OUP), Vol. 26, No. 3 ( 2014-03), p. 1330-1344

Type of Medium: Online Resource

ISSN: 1040-4651 , 1532-298X

URL: Article

DOI: 10.1105/tpc.114.123893

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2014

detail.hit.zdb_id: 623171-8

detail.hit.zdb_id: 2004373-9

SSG: 12

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Cell Type-Specific mRNA Dysregulation in Hippocampal CA1 Pyramidal Neurons of the Fragile X Syndrome Mouse Model

Ceolin, Laura ; Bouquier, Nathalie ; Vitre-Boubaker, Jihane ; [et al.]

Frontiers Media SA ; 2017

In: Frontiers in Molecular Neuroscience Vol. 10 ( 2017-10-20)

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In: Frontiers in Molecular Neuroscience, Frontiers Media SA, Vol. 10 ( 2017-10-20)

Type of Medium: Online Resource

ISSN: 1662-5099

URL: Article

DOI: 10.3389/fnmol.2017.00340

Language: Unknown

Publisher: Frontiers Media SA

Publication Date: 2017

detail.hit.zdb_id: 2452967-9

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Functional and molecular heterogeneity of D2R neurons along dorsal ventral axis in the striatum

Puighermanal, Emma ; Castell, Laia ; Esteve-Codina, Anna ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Nature Communications Vol. 11, No. 1 ( 2020-04-23)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2020-04-23)

Abstract: Action control is a key brain function determining the survival of animals in their environment. In mammals, neurons expressing dopamine D2 receptors (D2R) in the dorsal striatum (DS) and the nucleus accumbens (Acb) jointly but differentially contribute to the fine regulation of movement. However, their region-specific molecular features are presently unknown. By combining RNAseq of striatal D2R neurons and histological analyses, we identified hundreds of novel region-specific molecular markers, which may serve as tools to target selective subpopulations. As a proof of concept, we characterized the molecular identity of a subcircuit defined by WFS1 neurons and evaluated multiple behavioral tasks after its temporally-controlled deletion of D2R. Consequently, conditional D2R knockout mice displayed a significant reduction in digging behavior and an exacerbated hyperlocomotor response to amphetamine. Thus, targeted molecular analyses reveal an unforeseen heterogeneity in D2R-expressing striatal neuronal populations, underlying specific D2R’s functional features in the control of specific motor behaviors.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/s41467-020-15716-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2553671-0

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ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses

Reynès, Christelle ; Kister, Guilhem ; Rohmer, Marine ; [et al.]

Oxford University Press (OUP) ; 2020

In: Bioinformatics Vol. 36, No. 2 ( 2020-01-15), p. 504-513

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In: Bioinformatics, Oxford University Press (OUP), Vol. 36, No. 2 ( 2020-01-15), p. 504-513

Abstract: Allelic imbalance (AI), i.e. the unequal expression of the alleles of the same gene in a single cell, affects a subset of genes in diploid organisms. One prominent example of AI is parental genomic imprinting, which results in parent-of-origin-dependent, mono-allelic expression of a limited number of genes in metatherian and eutherian mammals and in angiosperms. Currently available methods for identifying AI rely on data modeling and come with the associated limitations. Results We have designed ISoLDE (Integrative Statistics of alleLe Dependent Expression), a novel nonparametric statistical method that takes into account both AI and the characteristics of RNA-seq data to infer allelic expression bias when at least two biological replicates are available for reciprocal crosses. ISoLDE learns the distribution of a specific test statistic from the data and calls genes ‘allelically imbalanced’, ‘bi-allelically expressed’ or ‘undetermined’. Depending on the number of replicates, predefined thresholds or permutations are used to make calls. We benchmarked ISoLDE against published methods, and showed that ISoLDE compared favorably with respect to sensitivity, specificity and robustness to the number of replicates. Using ISoLDE on different RNA-seq datasets generated from hybrid mouse tissues, we did not discover novel imprinted genes (IGs), confirming the most conservative estimations of IG number. Availability and implementation ISoLDE has been implemented as a Bioconductor package available at http://bioconductor.org/packages/ISoLDE/. Supplementary information Supplementary data are available at Bioinformatics online.

Type of Medium: Online Resource

ISSN: 1367-4803 , 1367-4811

URL: Article

DOI: 10.1093/bioinformatics/btz564

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2020

detail.hit.zdb_id: 1468345-3

SSG: 12

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Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

Stadelmayer, Bernd ; Micas, Gaël ; Gamot, Adrien ; [et al.]

Springer Science and Business Media LLC ; 2014

In: Nature Communications Vol. 5, No. 1 ( 2014-11-20)

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In: Nature Communications, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2014-11-20)

Abstract: RNA polymerase II (RNAPII) pausing/termination shortly after initiation is a hallmark of gene regulation. Here, we show that negative elongation factor (NELF) interacts with Integrator complex subunits (INTScom), RNAPII and Spt5. The interaction between NELF and INTScom subunits is RNA and DNA independent. Using both human immunodeficiency virus type 1 promoter and genome-wide analyses, we demonstrate that Integrator subunits specifically control NELF-mediated RNAPII pause/release at coding genes. The strength of RNAPII pausing is determined by the nature of the NELF-associated INTScom subunits. Interestingly, in addition to controlling RNAPII pause-release INTS11 catalytic subunit of the INTScom is required for RNAPII processivity. Finally, INTScom target genes are enriched in human immunodeficiency virus type 1 transactivation response element/NELF binding element and in a 3' box sequence required for small nuclear RNA biogenesis. Revealing these unexpected functions of INTScom in regulating RNAPII pause-release and completion of mRNA synthesis of NELF-target genes will contribute to our understanding of the gene expression cycle.

Type of Medium: Online Resource

ISSN: 2041-1723

URL: Article

DOI: 10.1038/ncomms6531

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2014

detail.hit.zdb_id: 2553671-0

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Narbonne-Reveau, Karine ; Lanet, Elodie ; Dillard, Caroline ; [et al.]

eLife Sciences Publications, Ltd ; 2016

In: eLife Vol. 5 ( 2016-06-14)

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In: eLife, eLife Sciences Publications, Ltd, Vol. 5 ( 2016-06-14)

Abstract: Some aggressive brain tumors that affect children start to form before the child is even born. These tumors often develop much more rapidly than tumors found in adults, and require fewer genetic mutations to become dangerous and invasive. However, it is not known why this happens. Fruit flies are often used as animal models for cancer studies. As the fly brain develops, cells called neural stem cells divide several times, each time producing one stem cell and another cell known as the intermediate progenitor. The intermediate progenitor can itself divide one more time before maturing to become a neuron. Different types of neurons form in different stages of brain development. This is due to the sequential production of proteins called transcription factors in neural stem cells. Each transcription factor is inherited by a different set of intermediate progenitors and alters the activity of certain genes to determine the type of neuron the cells become. Some genetic mutations can prevent intermediate progenitors from maturing and cause them to revert to a stem-cell-like state, which allows them to rapidly divide and form tumors. Here, Narbonne-Reveau, Lanet, Dillard et al. use fruit flies to investigate why tumors that form early on in development progress so rapidly. The experiments uncover a ‘molecular clock’ in the neural stem cells that marks out a window of time in which they generate intermediate progenitors that are prone to becoming cancerous. This clock is represented by the sequential production of transcription factors that, in addition to determining neuronal identity, also turn off various growth-promoting genes in cells as brain development proceeds. These genes sustain normal cell division, but are silenced later on to prevent cells from dividing too many times. If the maturation of intermediate progenitors is disrupted early on in brain development while the growth-promoting genes are still active, the molecular clock fails to switch off the growth-promoting genes. As a result, these cells acquire an unlimited ability to divide, which drives tumor growth. However, later in development when the growth-promoting genes have already been switched off, disrupting the maturation of intermediate progenitors does not lead to these cells becoming cancerous. Therefore, Narbonne-Reveau, Lanet, Dillard et al.’s findings explain why intermediate progenitors that mature early on in brain development are more prone to becoming cancerous than those that mature later, and why they need fewer mutations to become invasive. Most of the genes involved in this process are also found in humans. Therefore, the same mechanism might govern how aggressive childhood brain tumors are, which is a question for future studies to address.

Type of Medium: Online Resource

ISSN: 2050-084X

URL: Article

DOI: 10.7554/eLife.13463

DOI: 10.7554/eLife.13463.001

DOI: 10.7554/eLife.13463.002

DOI: 10.7554/eLife.13463.003

DOI: 10.7554/eLife.13463.004

DOI: 10.7554/eLife.13463.005

DOI: 10.7554/eLife.13463.006

DOI: 10.7554/eLife.13463.007

DOI: 10.7554/eLife.13463.008

DOI: 10.7554/eLife.13463.009

DOI: 10.7554/eLife.13463.010

DOI: 10.7554/eLife.13463.011

DOI: 10.7554/eLife.13463.012

DOI: 10.7554/eLife.13463.013

DOI: 10.7554/eLife.13463.014

DOI: 10.7554/eLife.13463.015

DOI: 10.7554/eLife.13463.016

DOI: 10.7554/eLife.13463.017

DOI: 10.7554/eLife.13463.018

DOI: 10.7554/eLife.13463.019

DOI: 10.7554/eLife.13463.020

DOI: 10.7554/eLife.13463.021

DOI: 10.7554/eLife.13463.022

DOI: 10.7554/eLife.13463.023

DOI: 10.7554/eLife.13463.024

DOI: 10.7554/eLife.13463.025

DOI: 10.7554/eLife.13463.026

DOI: 10.7554/eLife.13463.027

DOI: 10.7554/eLife.13463.028

DOI: 10.7554/eLife.13463.029

DOI: 10.7554/eLife.13463.030

DOI: 10.7554/eLife.13463.031

DOI: 10.7554/eLife.13463.032

DOI: 10.7554/eLife.13463.033

DOI: 10.7554/eLife.13463.034

DOI: 10.7554/eLife.13463.035

DOI: 10.7554/eLife.13463.036

DOI: 10.7554/eLife.13463.039

DOI: 10.7554/eLife.13463.040

Language: English

Publisher: eLife Sciences Publications, Ltd

Publication Date: 2016

detail.hit.zdb_id: 2687154-3

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Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness

Bogeas, Alexandra ; Morvan-Dubois, Ghislaine ; El-Habr, Elias A. ; [et al.]

Springer Science and Business Media LLC ; 2018

In: Acta Neuropathologica Vol. 135, No. 2 ( 2018-2), p. 267-283

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In: Acta Neuropathologica, Springer Science and Business Media LLC, Vol. 135, No. 2 ( 2018-2), p. 267-283

Type of Medium: Online Resource

ISSN: 0001-6322 , 1432-0533

URL: Article

DOI: 10.1007/s00401-017-1783-x

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 1458410-4

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