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KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

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Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2

Pierre Magistretti, Jean-René Cardinaux

CREB-binding protein (CBP) and p300 are transcriptional coactivators involved in numerous biological processes that affect cell growth, transformation, differentiation, and development. In this study, we provide evidence of the involvement of homeodomain-i ...

Elsevier2015

A fast and exact algorithm for the exemplar breakpoint distance

Bernard Moret, Mingfu Shao

A fundamental problem in comparative genomics is to compute the distance between two genomes. For two genomes without duplicate genes, we can easily compute a variety of distance measures in linear time, but the problem is NP-hard under most models when ge ...

Springer2015

Principles of ChIP-seq Data Analysis Illustrated with Examples

Giovanna Ambrosini, Philipp Bucher, René Dreos

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single C ...

Copicentro Granada S L2014

Computational studies in epigenomics using histone modification data

Nishanth Ulhas Nair

Epigenetic factors like histone modifications are known to play an important role in gene regulation and cell differentiation. Recently, thanks to advances in technologies like ChIP-Seq which is a high-throughput, high resolution, and low cost technology ...

EPFL2014

GuavaH: a compendium of host genomic data in HIV biology and disease

Jacques Fellay, Amalio Telenti, Istvan Bartha

Background: There is an ever-increasing volume of data on host genes that are modulated during HIV infection, influence disease susceptibility or carry genetic variants that impact HIV infection. We created GuavaH (Genomic Utility for Association and Viral ...

BioMed Central2014

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

Felix Naef, Cédric Gobet, Kyle Gustafson, Mathieu Quinodoz

Background: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles th ...

BioMed Central2014

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis

Stewart Cole, Jacques Rougemont, Claudia Sala, Andrej Benjak, Swapna Uplekar

The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead ...

Public Library of Science2014

Considerations when investigating IncRNA function in vivo

Denis Duboule

Although a small number of the vast array of animal long non-coding RNAs (IncRNAs) have known effects on cellular processes examined in vitro, the extent of their contributions to normal cell processes throughout development, differentiation and disease fo ...

Elife Sciences Publications Ltd2014

Corrinoid auxotrophy in the obligate organohalide-respiring Dehalobacter restrictus strain PER-K23

Christof Holliger, Julien Maillard, Yue Lu, Aamani Rupakula Boyanapalli, Hauke Smidt

Background Corrinoids are an essential cofactor of reductive dehalogenases, the key enzymes of organohalide respiration (OHR). Dehalobacter restrictus is an obligate OHR bacterium (OHRB) able to conserve energy with tetrachloroethene, but is unable to de n ...

2014

Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations

Andrew Charles Oates, Daniele Soroldoni

We study the effects of multiple binding sites in the promoter of a genetic oscillator. We evaluate the regulatory function of a promoter with multiple binding sites in the absence of cooperative binding, and consider different hypotheses for how the numbe ...

2014

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Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations

Andrew Charles Oates, Daniele Soroldoni

2014

A fast and exact algorithm for the exemplar breakpoint distance

Bernard Moret, Mingfu Shao

Springer2015

Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2

Pierre Magistretti, Jean-René Cardinaux

Elsevier2015