ChIP-Seq

Applied sciences
Génie biologique
Biotechnologie
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Publications associées (30)

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ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries

Bernard Moret, Philipp Bucher, Nishanth Ulhas Nair

The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit diff ...

Public Library of Science2012

Genomics and transcriptomics of the Mycobacterium tuberculosis complex

Swapna Uplekar

The goal of eliminating tuberculosis (TB) by 2050 depends on the development of improved TB diagnostics, drugs and vaccines. Advances in these areas require a deep understanding of the disease and its causative agent, Mycobacterium tuberculosis (M. tb). My ...

EPFL2012

Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein

Stewart Cole, Florence Pojer, Jacques Rougemont, Claudia Sala, Ruben Hartkoorn, Swapna Uplekar, Benjamin Blasco, Jeffrey Chen

The principal virulence determinant of Mycobacterium tuberculosis (Mtb), the ESX-1 protein secretion system, is positively controlled at the transcriptional level by EspR. Depletion of EspR reportedly affects a small number of genes, both positively or neg ...

Public Library of Science2012

RNA Profiling and Chromatin Immunoprecipitation-Sequencing Reveal that PTF1a Stabilizes Pancreas Progenitor Identity via the Control of MNX1/HLXB9 and a Network of Other Transcription Factors

Emilie Gesina, Philipp Bucher, Anne Grapin-Botton, Nancy Thompson

Pancreas development is initiated by the specification and expansion of a small group of endodermal cells. Several transcription factors are crucial for progenitor maintenance and expansion, but their interactions and the downstream targets mediating their ...

American Society for Microbiology2012

KRAB/KAP1 Regulation of Embryonic Stem Cell Pluripotent Self-renewal

Andrea Corsinotti

KRAB-ZFPs constitute the largest family of transcription factors (TFs) encoded by the mouse genome and are known to interact with the co-repressor KAP1. KRAB/KAP1-mediated regulation is essential for several development- and ESC- specific functions, in par ...

EPFL2012

Computational analysis of protein-DNA interactions from ChIP-seq data

Felix Naef, Jacques Rougemont

Chromatin immunoprecipitation experiments followed by ultra-high-throughput sequencing (ChIP-seq) is becoming the method of choice to identify transcription factor binding sites in prokaryotes and eukaryotes in vivo. Here, we review the computational steps ...

2011

On the Relationship Between Protein-DNA Interactions and Circadian Gene Expression in Mouse Liver

Guillaume Rey

Virtually every cell in our body tracks daily time using an endogenous mechanism called the circadian clock, which has a period of about 24 hours. This timing system offers a selective advantage by enabling organisms to anticipate periodic changes in envir ...

EPFL2011

MER41 repeat sequences contain inducible STAT1 binding sites

Philipp Bucher

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we ...

Public Library of Science2010

VE-statin/egfl7 expression in endothelial cells is regulated by a distal enhancer and a proximal promoter under the direct control of Erg and GATA-2

Friedrich Beermann

Angiogenesis is the process by which new blood vessels arise from existing ones by the budding out of endothelial cell capillaries from the luminal side of blood vessels. Blood vessel formation is essential for organ development during embryogenesis and is ...

Public Library of Science2010

Protein-binding microarray technology and ChIP-sequencing for the identification of novel targets of the human tumor suppressor AP2[alpha]

Jan Kerschgens

The mis-regulation of gene transcription in the living cell can be the cause of complex human diseases like cancer. One challenge of the post-genomic era of biomedical research is the development of in vitro techniques for the rapid and cost-effective anal ...

EPFL2009

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