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

Hybrid proteins for the screening of transcription regulators of reductive dehalogenase gene clusters

Christof Holliger, Julien Maillard, Mathilde Stéphanie Willemin

In the past decade, research on the transcription regulation of reductive dehalogenase (rdh) gene clusters (for a recent review, see [1]) revealed a new set of CRP/FNR-type transcription regulators, called RdhK [2,3]. Several members of this family have be ...

2017

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KRAB-containing poly-zinc finger proteins (KZFPs) constitute the largest family of transcription factors encoded by mammalian genomes, and growing evidence indicates that they fulfill functions critical to both embryonic development and maintenance of adul ...

Public Library of Science2017

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Didier Trono, Bart Deplancke, Giovanna Ambrosini, Philipp Bucher, Riccardo Dainese, Daniel Alpern, Michaël Imbeault, Romain Fernand Pietro Groux, Alina Isakova, Pernille Yde Rainer

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017

KRAB zinc finger proteins

Didier Trono, Michaël Imbeault, Gabriela Ecco

Kruppel-associated box domain zinc finger proteins (KRAB-ZFPs) are the largest family of transcriptional regulators in higher vertebrates. Characterized by an N-terminal KRAB domain and a C-terminal array of DNA-binding zinc fingers, they participate, toge ...

2017

A KRABsody for Embryo-Placental Development

Didier Trono

Many of the hundreds of KRAB zinc finger proteins encoded by human and mouse are involved in taming the transcriptional regulatory potential of transposable elements. Reporting recently in Science, Yang et al. (2017) reveal that one murine family member, Z ...

2017

Phase specific transcriptional regulation of circadian clock and metabolism in mouse liver

Jonathan Aryeh Sobel

The molecular clock has been conserved from cyanobacteria to mammals and is believed to align behavioral and biochemical processes with the diurnal cycle. This cellular mechanism has been an advantage to increase the fitness of organisms through the abilit ...

EPFL2016

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

Gabriela Ecco

Transposable elements (TEs) are DNA sequences able to change position in the genome, and represent more than 40% of mammalian genetic material. TEs can have positive or detrimental effects on the host, being both important motors of evolution and genomic t ...

EPFL2016

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

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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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Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key ...

Elsevier2016