CLOCK:BMAL1 is a pioneer-like transcription factor

Menet, Jérôme S.; Pescatore, Stefan; Rosbash, Michael

doi:10.1101/gad.228536.113

Cited by 209 publications

(213 citation statements)

References 40 publications

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“…The CLOCK protein itself was reported to show HAT activity (Doi et al 2006). BMAL1 was recently described as a pioneer transcription factor capable of opening the chromatin (Menet et al 2014). This is particularly interesting because rhythmic chromatin remodeling and time varying nucleosome occupancy were previously observed (Ripperger and Schibler 2006).…”

Section: Transcriptional Regulation Of Clock Controlled Genesmentioning

confidence: 94%

“…Also, the roles of histone variants (Menet et al 2014) and distal regulatory sequences in controlling circadian transcription are still understudied and challenging. For example, a large fraction of BMAL1 binding sites (60%) is located .10 kb away from the nearest TSS (Rey et al 2011), raising questions about whether these distal sites are enhancers.…”

Section: Systems Chronobiologymentioning

confidence: 99%

See 1 more Smart Citation

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Yeung

Naef

2016

Cold Spring Harb Perspect Biol

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Mammals have evolved an internal timing system, the circadian clock, which synchronizes physiology and behavior to the daily light and dark cycles of the Earth. The master clock, located in the suprachiasmatic nucleus (SCN) of the brain, takes fluctuating light input from the retina and synchronizes other tissues to the same internal rhythm. The molecular clocks that drive these circadian rhythms are ticking in nearly all cells in the body. Efforts in systems chronobiology are now being directed at understanding, on a comprehensive scale, how the circadian clock controls different layers of gene regulation to provide robust timing cues at the cellular and tissue level. In this review, we introduce some basic concepts underlying periodicity of gene regulation, and then highlight recent genome-wide investigations on the propagation of rhythms across multiple regulatory layers in mammals, all the way from chromatin conformation to protein accumulation.

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Section: Transcriptional Regulation Of Clock Controlled Genesmentioning

confidence: 94%

Section: Systems Chronobiologymentioning

confidence: 99%

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Yeung

Naef

2016

Cold Spring Harb Perspect Biol

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“…The mammalian circadian clock is driven by the CLOCK and BMAL1 transcription factors that rhythmically bind to nucleosomal target sites, promote incorporation of the histone variant H2A.Z, and enable the subsequent binding of other transcription factors (Menet et al 2014). Thus, the mammalian clock appears to employ pioneer factors to activate genes at specific times of the daily cycle.…”

Section: Pioneer Factors In Cell Programming During Developmentmentioning

confidence: 99%

“…Increasing DNA accessibility in native chromatin Menet et al 2014 p53 Tumor suppression by regulating cell cycle progression and apoptosis (human) Increasing DNA accessibility in native chromatin Laptenko et al 2011 Binding to chromatin that encodes high intrinsic nucleosome occupancy…”

Section: Gata1 Mitotic Bookmarking (Mouse)mentioning

confidence: 99%

Pioneer transcription factors in cell reprogramming

2014

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A subset of eukaryotic transcription factors possesses the remarkable ability to reprogram one type of cell into another. The transcription factors that reprogram cell fate are invariably those that are crucial for the initial cell programming in embryonic development. To elicit cell programming or reprogramming, transcription factors must be able to engage genes that are developmentally silenced and inappropriate for expression in the original cell. Developmentally silenced genes are typically embedded in ''closed'' chromatin that is covered by nucleosomes and not hypersensitive to nuclease probes such as DNase I. Biochemical and genomic studies have shown that transcription factors with the highest reprogramming activity often have the special ability to engage their target sites on nucleosomal DNA, thus behaving as ''pioneer factors'' to initiate events in closed chromatin. Other reprogramming factors appear dependent on pioneer factors for engaging nucleosomes and closed chromatin. However, certain genomic domains in which nucleosomes are occluded by higher-order chromatin structures, such as in heterochromatin, are resistant to pioneer factor binding. Understanding the means by which pioneer factors can engage closed chromatin and how heterochromatin can prevent such binding promises to advance our ability to reprogram cell fates at will and is the topic of this review.Cell fate control represents the most extreme form of gene regulation. Genes specific to the function of a particular type of cell may be antagonistic to the function of another type of cell, so nature has evolved diverse regulatory mechanisms to ensure stable patterns of gene activation and repression. In prokaryotes, self-sustaining regulatory networks of transcription factors bound to DNA can be sufficient to regulate gene activation and repression (Ptashne 2011). In eukaryotes, ;200-base-pair (bp) segments of the genome are wound nearly twice around an octamer of the four core histones to form nucleosomes, providing steric constraints on how transcription factors can bind DNA (Kornberg and Lorch 1999). As described below, pioneer transcription factors have the special property of being able to overcome such constraints, enabling the factors to engage closed chromatin that is not accessible by other types of transcription factors (Fig. 1). However, further higher-order packaging of nucleosomes into heterochromatin can occlude access to DNA altogether, presenting an additional barrier to cell fate conversion (Fig. 1). This review focuses on the most recent studies of pioneer factors in cell programming and reprogramming, how pioneer factors have special chromatinbinding properties, and facilitators and impediments to chromatin binding. We project that such knowledge will greatly aid future efforts to change the fates of cells at will for research, diagnostic, and therapeutic purposes.

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“…Blue arrows with (+) signs mean induction and/or activation, and red arrows with (-) signs mean repression of transcription. Unauthenticated Download Date | 5/12/18 10:16 AM modifications of chromatin, with the participation of other transcription factors such as HNF6 (hepatocyte nuclear factors) that are involved in cholesterol, fatty acid, glucose transport and metabolism in many different tissues [124].…”

Section: Endoplasmic Reticulum Stress and The Circadian Clock Of The Scnmentioning

confidence: 99%

The unfolded protein response, inflammation, oscillators, and disease: a systems biology approach

Rangel-Aldao

2015

Endoplasmic Reticulum Stress in Diseases

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Non-communicable diseases (NCDs) such as cardiovascular disease, cancers, diabetes and obesity are responsible for about two thirds of mortality worldwide, and all of these ailments share a common low-intensity systemic chronic inflammation, endoplasmic reticulum stress (ER stress), and the ensuing Unfolded Protein Response (UPR). These adaptive mechanisms are also responsible for significant metabolic changes that feedback with the central clock of the suprachiasmatic nucleus (SCN) of the hypothalamus, as well as with oscillators of peripheral tissues. In this review we attempt to use a systems biology approach to explore such interactions as a whole; to answer two fundamental questions: (1) how dependent are these adaptive responses and subsequent events leading to NCD with their state of synchrony with the SCN and peripheral oscillators? And, (2) How could modifiers of the activity of SCN for instance, food intake, exercise, and drugs, be potentially used to modulate systemic inflammation and ER stress to ameliorate or even prevent NCDs?

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CLOCK:BMAL1 is a pioneer-like transcription factor

Cited by 209 publications

References 40 publications

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Pioneer transcription factors in cell reprogramming

The unfolded protein response, inflammation, oscillators, and disease: a systems biology approach

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