Publications associées à High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites

Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

Denis Duboule, Marion Leleu, Pierre Raymond Fabre

Background: Global analyses of gene expression during development reveal specific transcription patterns associated with the emergence of various cell types, tissues, and organs. These heterogeneous patterns are instrumental to ensure the proper formation ...

BMC2018

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Giovanna Ambrosini, Philipp Bucher, Romain Fernand Pietro Groux

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-r ...

2018

Essential Nucleoid Associated Protein mIHF (Rv1388) Controls Virulence and Housekeeping Genes in Mycobacterium tuberculosis

Stewart Cole, Nina Theres Odermatt, Claudia Sala, Andrej Benjak

Tight control of gene expression is crucial for Mycobacterium tuberculosis to adapt to the changing environments encountered when infecting or exiting human cells. While three nucleoid associated proteins (NAPs) EspR, HupB and Lsr2 have been investigated, ...

NATURE PUBLISHING GROUP2018

What shapes eukaryotic transcriptional bursting?

Felix Naef, Damien Lionel Nicolas, Nicholas Edward Phillips

Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous p ...

Royal Society of Chemistry2017

Profiling of Single-Cell Transcriptomes

Bart Deplancke, Vincent Roland Julien Gardeux, Antonio Carlos Alves Meireles Filho, Wanze Chen

Complex biological systems are composed of multiple cell types whose transcriptional activity can vary due to differences in cell state, environmental stimulation or intrinsic programs. Conventional bulk analysis methods capture the average transcriptional ...

2017

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers

Johan Auwerx, Bart Deplancke, Murielle Bochud, Hao Li, Vincenzo Sorrentino, Maria Litovchenko, Roel Paulus Josephus Bevers, Sina Rüeger, Andrea Komljenovic

The enormous variation in human lifespan is in part due to a myriad of sequence variants, only a few of which have been revealed to date. Since many life-shortening events are related to diseases, we developed a Mendelian randomization-based method combini ...

Nature Publishing Group2017

Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

Giovanni Dietler, Aleksandre Japaridze, Sylvain Renevey

Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring pro ...

American Society for Biochemistry & Molecular Biology (ASBMB)2017

The evolution of gene expression and binding specificity of the largest transcription factor family in primates

Didier Trono, Jeffrey David Jensen, Adamantia Kapopoulou, Lisha Mathew

The KRAB-containing zinc finger (KRAB-ZF) proteins represent the largest family of transcription factors (TFs) in humans, yet for the great majority, their function and specific genomic target remain unknown. However, it has been shown that a large fractio ...

Wiley-Blackwell2016

A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression

Didier Trono, Gabriela Ecco, Helen Mary Rowe

Deposition of epigenetic marks is an important layer of the transcriptional control of retrotransposons, especially during early embryogenesis. Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are one of the largest families of transcription ...

2016

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High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites

Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Essential Nucleoid Associated Protein mIHF (Rv1388) Controls Virulence and Housekeeping Genes in Mycobacterium tuberculosis

What shapes eukaryotic transcriptional bursting?

Profiling of Single-Cell Transcriptomes

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers

Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

The evolution of gene expression and binding specificity of the largest transcription factor family in primates

Unraveling the KRAB/KAP1 control of transposable elements in pluripotent and somatic cells

A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression

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Chattez avec Graph Search

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

What shapes eukaryotic transcriptional bursting?

Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers

Unraveling the KRAB/KAP1 control of transposable elements in pluripotent and somatic cells

Essential Nucleoid Associated Protein mIHF (Rv1388) Controls Virulence and Housekeeping Genes in Mycobacterium tuberculosis

The evolution of gene expression and binding specificity of the largest transcription factor family in primates

Profiling of Single-Cell Transcriptomes

A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression