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Laurent M Sachs

Publications and source records attributed to Laurent M Sachs.

9 recordsLinked to original sources
PubMed2026

VIJB: a companion of the JBROWSE genome browser for the visually impaired people.

MOTIVATION: The availability of touch-sensitive and haptic devices has been a keystone development for the inclusion of visually impaired people (VIPs) in modern, highly digitized work environments. Braille displays have proven efficient and versatile enough to parse large and complex text files, making bioinformatics and text-heavy programming accessible to VIPs. However, the complex graphical objects -combining numerous datasets- typically generated during data integration remain challenging, even with the aid of descriptive AI. This is particularly true in functional genomics. Here, we present VIJB, a simple application that displays the multilayered output of the JBROWSE genome browser on a Braille reader, enabling VIPs to fully participate in data integration in functional genomics. AVAILABILITY AND IMPLEMENTATION: VIJB is programmed in Python and relies on the scientific library NumPy, the braillegraph and pyBigWig libraries, and the TABIX software. The architecture is summarized in Supplementary Material 1, available as supplementary data at Bioinformatics online. VIJB is available for download at the GitHub repository https://GitHub.com/NiBuMNHN/VIJB and is licenced under the GPL 3.0.

Persons with Visual Disabilities↗
PubMed2006

Unliganded thyroid hormone receptor is essential for Xenopus laevis eye development.

Thyroid hormone receptors generally activate transcription of target genes in the presence of thyroid hormone (T(3)) and repress their transcription in its absence. Here, we investigated the role of unliganded thyroid hormone receptor (TR) during vertebrate development using an amphibian model. Previous studies led to the hypothesis that before production of endogenous T(3), the presence of unliganded receptor is essential for premetamorphic tadpole growth. To test this hypothesis, we generated a Xenopus laevis TR beta mutant construct ineffective for gene repression owing to impaired corepressor NCoR recruitment. Overexpression by germinal transgenesis of the mutant receptor leads to lethality during early development with numerous defects in cranio-facial and eye development. These effects correlate with TR expression profiles at these early stages. Molecular analysis of transgenic mutants reveals perturbed expression of genes involved in eye development. Finally, treatment with iopanoic acid or NH-3, modulators of thyroid hormone action, leads to abnormal eye development. In conclusion, the data reveal a role of unliganded TR in eye development.

Animals↗
PubMed2006

The co-chaperone XAP2 is required for activation of hypothalamic thyrotropin-releasing hormone transcription in vivo.

Transcriptional control of hypothalamic thyrotropin-releasing hormone (TRH) integrates central regulation of the hypothalamo-hypophyseal-thyroid axis and hence thyroid hormone (triiodothyronine (T(3))) homeostasis. The two beta thyroid hormone receptors, TRbeta1 and TRbeta2, contribute to T(3) feedback on TRH, with TRbeta1 having a more important role in the activation of TRH transcription. How TRbeta1 fulfils its role in activating TRH gene transcription is unknown. By using a yeast two-hybrid screening of a mouse hypothalamic complementary DNA library, we identified a novel partner for TRbeta1, hepatitis virus B X-associated protein 2 (XAP2), a protein first identified as a co-chaperone protein. TR-XAP2 interactions were TR isoform specific, being observed only with TRbeta1, and were enhanced by T(3) both in yeast and mammalian cells. Furthermore, small inhibitory RNA-mediated knockdown of XAP2 in vitro affected the stability of TRbeta1. In vivo, siXAP2 abrogated specifically TRbeta1-mediated (but not TRbeta2) activation of hypothalamic TRH transcription. This study provides the first in vivo demonstration of a regulatory, physiological role for XAP2.

Animals↗
PubMed2004

Implication of bax in Xenopus laevis tail regression at metamorphosis.

Apoptosis is fundamental to normal vertebrate development. A dramatic example of postembryonic development involving apoptosis is tail regression during amphibian metamorphosis. Earlier studies led us to propose a functional role for the pro-apoptotic protein Bax in tadpole tail regression. However, its physiological relevance has never been analyzed. We have now cloned a cDNA encoding Xenopus laevis bax (xlbax) and used in vivo gene transfer in tail muscle to analyze the effects of xlbax overexpression. Furthermore, by using an antisense strategy in a similar experimental paradigm, xlbax antisense mRNA was shown to block the apoptotic effects of xlbax and protect against apoptosis in metamorphosing tadpoles. Our results suggest that xlbax is a regulator of muscle fiber death in the regressing tail during metamorphosis.

Amino Acid Sequence↗
PubMed2004

Corepressor requirement and thyroid hormone receptor function during Xenopus development.

The biologic role of hormonal activation of nuclear receptors is well established. Only recently, however, has the biologic significance of repression begun to be appreciated. Amphibian metamorphosis is marked by dramatic thyroid hormone induced changes, including de novo morphogenesis, tissue remodeling, and organ resorption through programmed cell death. These changes involve cascades of gene regulation initiated by 3,5,3'-triiodothyronine (T(3)). T(3) functions by regulating gene expression through thyroid hormone receptor (TR). TRs are DNA-binding transcription factors that belong to the steroid hormone receptor superfamily. In the absence of a ligand, TRs can repress gene expression by recruiting corepressor complexes, whereas liganded TRs recruit coactivator complexes for gene activation. Corepressor and coactivator complexes induce chromatin remodeling to mediate TR regulation of transcription. The mechanisms of TR action permit a dual function for TRs during development. In premetamorphic tadpoles, when TRs are expressed and T(3) levels are barely detectable, unliganded TRs repress transcription through corepressor recruitment. This TR-mediated repression of target genes is critical for proper larval development, allowing tadpole growth and acquisition of metamorphic competence. In contrast, during metamorphosis, endogenous T(3) causes TRs to activate gene expression, leading to tadpole transformation. Several results also support a role for corepressors during metamorphosis. Corepressor targeted functions, however, are still speculative but may again involve TRs. The requirement of active gene repression at different stages during amphibian development establishes an important biologic role for corepressors.

Animals↗
PubMed2003

Metamorphic T3-response genes have specific co-regulator requirements.

Thyroid hormone receptors (TRs) have several regulatory functions in vertebrates. In the absence of thyroid hormone (T3; tri-iodothyronine), apo-TRs associate with co-repressors to repress transcription, whereas in the presence of T3, holo-TRs engage transcriptional coactivators. Although many studies have addressed the molecular mechanisms of T3 action, it is not known how specific physiological responses arise. We used T3-dependent amphibian metamorphosis to analyse how TRs interact with particular co-regulators to differentially regulate gene expression during development. Using chromatin immuno-precipitation to study tissue from pre-metamorphic tadpoles, we found that TRs are physically associated with T3-responsive promoters, whether or not T3 is present. Addition of T3 results in histone H4 acetylation specifically on T3-response genes. Most importantly, we show that individual T3-response genes have distinct co-regulator requirements, the T3-dependent co-repressor-to-coactivator switch being gene-specific for both co-regulator categories.

Acetylation↗
PubMed2003

A role for cofactor-cofactor and cofactor-histone interactions in targeting p300, SWI/SNF and Mediator for transcription.

Transcriptional activation from chromatin by nuclear receptors (NRs) requires multiple cofactors including CBP/p300, SWI/SNF and Mediator. How NRs recruit these multiple cofactors is not clear. Here we show that activation by androgen receptor and thyroid hormone receptor is associated with the promoter targeting of SRC family members, p300, SWI/SNF and the Mediator complex. We show that recruitment of SWI/SNF leads to chromatin remodeling with altered DNA topology, and that both SWI/SNF and p300 histone acetylase activity are required for hormone-dependent activation. Importantly, we show that both the SWI/SNF and Mediator complexes can be targeted to chromatin by p300, which itself is recruited through interaction with SRC coactivators. Furthermore, histone acetylation by CBP/p300 facilitates the recruitment of SWI/SNF and Mediator. Thus, our data indicate that multiple cofactors required for activation are not all recruited through their direct interactions with NRs and underscore a role of cofactor-cofactor interaction and histone modification in coordinating the recruitment of multiple cofactors.

Acetylation↗
PubMed2002

Nuclear receptor corepressor recruitment by unliganded thyroid hormone receptor in gene repression during Xenopus laevis development.

Thyroid hormone receptors (TR) act as activators of transcription in the presence of the thyroid hormone (T(3)) and as repressors in its absence. While many in vitro approaches have been used to study the molecular mechanisms of TR action, their physiological relevance has not been addressed. Here we investigate how TR regulates gene expression during vertebrate postembryonic development by using T(3)-dependent amphibian metamorphosis as a model. Earlier studies suggest that TR acts as a repressor during premetamorphosis when T(3) is absent. We hypothesize that corepressor complexes containing the nuclear receptor corepressor (N-CoR) are key factors in this TR-dependent gene repression, which is important for premetamorphic tadpole growth. To test this hypothesis, we isolated Xenopus laevis N-CoR (xN-CoR) and showed that it was present in pre- and metamorphic tadpoles. Using a chromatin immunoprecipitation assay, we demonstrated that xN-CoR was recruited to the promoters of T(3) response genes during premetamorphosis and released upon T(3) treatment, accompanied by a local increase in histone acetylation. Furthermore, overexpression of a dominant-negative N-CoR in tadpole tail muscle led to increased transcription from a T(3)-dependent promoter. Our data indicate that N-CoR is recruited by unliganded TR to repress target gene expression during premetamorphic animal growth, an important process that prepares the tadpole for metamorphosis.

Amino Acid Sequence↗