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Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

Nature - Wed, 09/14/2016 - 00:00

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

Nature 537, 7621 (2016). doi:10.1038/nature19360

Authors: John Arne Dahl, Inkyung Jung, Håvard Aanes, Gareth D. Greggains, Adeel Manaf, Mads Lerdrup, Guoqiang Li, Samantha Kuan, Bin Li, Ah Young Lee, Sebastian Preissl, Ingunn Jermstad, Mads Haugland Haugen, Rajikala Suganthan, Magnar Bjørås, Klaus Hansen, Knut Tomas Dalen, Peter Fedorcsak, Bing Ren & Arne Klungland

Maternal-to-zygotic transition (MZT) is essential for the formation of a new individual, but is still poorly understood despite recent progress in analysis of gene expression and DNA methylation in early embryogenesis. Dynamic histone modifications may have important roles in MZT, but direct measurements of chromatin states have been hindered by technical difficulties in profiling histone modifications from small quantities of cells. Recent improvements allow for 500 cell-equivalents of chromatin per reaction, but require 10,000 cells for initial steps or require a highly specialized microfluidics device that is not readily available. We developed a micro-scale chromatin immunoprecipitation and sequencing (μChIP–seq) method, which we used to profile genome-wide histone H3 lysine methylation (H3K4me3) and acetylation (H3K27ac) in mouse immature and metaphase II oocytes and in 2-cell and 8-cell embryos. Notably, we show that ~22% of the oocyte genome is associated with broad H3K4me3 domains that are anti-correlated with DNA methylation. The H3K4me3 signal becomes confined to transcriptional-start-site regions in 2-cell embryos, concomitant with the onset of major zygotic genome activation. Active removal of broad H3K4me3 domains by the lysine demethylases KDM5A and KDM5B is required for normal zygotic genome activation and is essential for early embryo development. Our results provide insight into the onset of the developmental program in mouse embryos and demonstrate a role for broad H3K4me3 domains in MZT.

Categories: Literature

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

Nature - Wed, 09/14/2016 - 00:00

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

Nature 537, 7621 (2016). doi:10.1038/nature19361

Authors: Bingjie Zhang, Hui Zheng, Bo Huang, Wenzhi Li, Yunlong Xiang, Xu Peng, Jia Ming, Xiaotong Wu, Yu Zhang, Qianhua Xu, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Wenteng He, Chong Li, Bo Chen, Yuanyuan Li, Qiujun Wang, Jing Ma, Qiangzong Yin, Kehkooi Kee, Anming Meng, Shaorong Gao, Feng Xu, Jie Na & Wei Xie

Histone modifications are fundamental epigenetic regulators that control many crucial cellular processes. However, whether these marks can be passed on from mammalian gametes to the next generation is a long-standing question that remains unanswered. Here, by developing a highly sensitive approach, STAR ChIP–seq, we provide a panoramic view of the landscape of H3K4me3, a histone hallmark for transcription initiation, from developing gametes to post-implantation embryos. We find that upon fertilization, extensive reprogramming occurs on the paternal genome, as H3K4me3 peaks are depleted in zygotes but are readily observed after major zygotic genome activation at the late two-cell stage. On the maternal genome, we unexpectedly find a non-canonical form of H3K4me3 (ncH3K4me3) in full-grown and mature oocytes, which exists as broad peaks at promoters and a large number of distal loci. Such broad H3K4me3 peaks are in contrast to the typical sharp H3K4me3 peaks restricted to CpG-rich regions of promoters. Notably, ncH3K4me3 in oocytes overlaps almost exclusively with partially methylated DNA domains. It is then inherited in pre-implantation embryos, before being erased in the late two-cell embryos, when canonical H3K4me3 starts to be established. The removal of ncH3K4me3 requires zygotic transcription but is independent of DNA replication-mediated passive dilution. Finally, downregulation of H3K4me3 in full-grown oocytes by overexpression of the H3K4me3 demethylase KDM5B is associated with defects in genome silencing. Taken together, these data unveil inheritance and highly dynamic reprogramming of the epigenome in early mammalian development.

Categories: Literature

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

Nature - Wed, 09/14/2016 - 00:00

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

Nature 537, 7621 (2016). doi:10.1038/nature19362

Authors: Xiaoyu Liu, Chenfei Wang, Wenqiang Liu, Jingyi Li, Chong Li, Xiaochen Kou, Jiayu Chen, Yanhong Zhao, Haibo Gao, Hong Wang, Yong Zhang, Yawei Gao & Shaorong Gao

Histone modifications have critical roles in regulating the expression of developmental genes during embryo development in mammals. However, genome-wide analyses of histone modifications in pre-implantation embryos have been impeded by the scarcity of the required materials. Here, by using a small-scale chromatin immunoprecipitation followed by sequencing (ChIP–seq) method, we map the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3), which are associated with gene activation and repression, respectively, in mouse pre-implantation embryos. We find that the re-establishment of H3K4me3, especially on promoter regions, occurs much more rapidly than that of H3K27me3 following fertilization, which is consistent with the major wave of zygotic genome activation at the two-cell stage. Furthermore, H3K4me3 and H3K27me3 possess distinct features of sequence preference and dynamics in pre-implantation embryos. Although H3K4me3 modifications occur consistently at transcription start sites, the breadth of the H3K4me3 domain is a highly dynamic feature. Notably, the broad H3K4me3 domain (wider than 5 kb) is associated with higher transcription activity and cell identity not only in pre-implantation development but also in the process of deriving embryonic stem cells from the inner cell mass and trophoblast stem cells from the trophectoderm. Compared to embryonic stem cells, we found that the bivalency (that is, co-occurrence of H3K4me3 and H3K27me3) in early embryos is relatively infrequent and unstable. Taken together, our results provide a genome-wide map of H3K4me3 and H3K27me3 modifications in pre-implantation embryos, facilitating further exploration of the mechanism for epigenetic regulation in early embryos.

Categories: Literature

A blue-light photoreceptor mediates the feedback regulation of photosynthesis

Nature - Wed, 09/14/2016 - 00:00

A blue-light photoreceptor mediates the feedback regulation of photosynthesis

Nature 537, 7621 (2016). doi:10.1038/nature19358

Authors: Dimitris Petroutsos, Ryutaro Tokutsu, Shinichiro Maruyama, Serena Flori, Andre Greiner, Leonardo Magneschi, Loic Cusant, Tilman Kottke, Maria Mittag, Peter Hegemann, Giovanni Finazzi & Jun Minagawa

In plants and algae, light serves both as the energy source for photosynthesis and a biological signal that triggers cellular responses via specific sensory photoreceptors. Red light is perceived by bilin-containing phytochromes and blue light by the flavin-containing cryptochromes and/or phototropins (PHOTs), the latter containing two photosensory light, oxygen, or voltage (LOV) domains. Photoperception spans several orders of light intensity, ranging from far below the threshold for photosynthesis to values beyond the capacity of photosynthetic CO2 assimilation. Excess light may cause oxidative damage and cell death, processes prevented by enhanced thermal dissipation via high-energy quenching (qE), a key photoprotective response. Here we show the existence of a molecular link between photoreception, photosynthesis, and photoprotection in the green alga Chlamydomonas reinhardtii. We show that PHOT controls qE by inducing the expression of the qE effector protein LHCSR3 (light-harvesting complex stress-related protein 3) in high light intensities. This control requires blue-light perception by LOV domains on PHOT, LHCSR3 induction through PHOT kinase, and light dissipation in photosystem II via LHCSR3. Mutants deficient in the PHOT gene display severely reduced fitness under excessive light conditions, indicating that the sensing, utilization, and dissipation of light is a concerted process that plays a vital role in microalgal acclimation to environments of variable light intensities.

Categories: Literature

Researchers should join protests over detained scientist

Nature - Wed, 09/14/2016 - 00:00

Researchers should join protests over detained scientist

Nature 537, 7620 (2016). doi:10.1038/537279b

Questions abound over the deportation and subsequent house arrest of a physicist.

Categories: Literature

Using waste water to flush out drug dealers

Nature - Wed, 09/14/2016 - 00:00

Using waste water to flush out drug dealers

Nature 537, 7620 (2016). doi:10.1038/537280a

Assessing the contents of the toilet bowl in the name of crime prevention.

Categories: Literature

Genomics: History of brewer's yeast revealed

Nature - Wed, 09/14/2016 - 00:00

Genomics: History of brewer's yeast revealed

Nature 537, 7620 (2016). doi:10.1038/537282a

People began to domesticate beer yeasts in the late sixteenth or early seventeenth century, when beer-making in Europe moved from homes to pubs and monasteries.Kevin Verstrepen at the University of Leuven and Steven Maere at the University of Ghent, both in Belgium, and their

Categories: Literature

Meteorology: Air particles boost rain extremes

Nature - Wed, 09/14/2016 - 00:00

Meteorology: Air particles boost rain extremes

Nature 537, 7620 (2016). doi:10.1038/537282b

As the climate warms, tiny particles suspended in the atmosphere may have a greater effect than greenhouse gases on increasing the frequency of extreme rain and snowfall.Greenhouse gases and atmospheric aerosols both drive extreme precipitation, which is expected to increase with climate change. To

Categories: Literature

Evolution: Why some groups have more species

Nature - Wed, 09/14/2016 - 00:00

Evolution: Why some groups have more species

Nature 537, 7620 (2016). doi:10.1038/537282c

Plants have diversified at almost twice the rate of animals, and animals and plants have accumulated new species some ten times faster than prokaryotes such as bacteria.Across the tree of life, some groups have many more species than others. To find out why, Joshua

Categories: Literature

Microbiology: Nanoparticles kill resistant bacteria

Nature - Wed, 09/14/2016 - 00:00

Microbiology: Nanoparticles kill resistant bacteria

Nature 537, 7620 (2016). doi:10.1038/537282d

A synthetic polymer clears infections in mice caused by a multiple-drug-resistant bacterium.Gram-negative bacteria are particularly hard to kill once they become drug resistant. To target them, Eric Reynolds, Greg Qiao and their colleagues at the University of Melbourne in Australia designed star-shaped antimicrobial nanoparticles

Categories: Literature

Electronics: Protection for transistors

Nature - Wed, 09/14/2016 - 00:00

Electronics: Protection for transistors

Nature 537, 7620 (2016). doi:10.1038/537283a

The performance of transistors made of black phosphorus can be maintained with the addition of tellurium.Layers of black phosphorus just a few molecules thick show great promise in advanced electronic devices. But exposure to oxygen and moisture causes damaging corrosion and bubbles to form

Categories: Literature

Astronomy: Galaxy collisions make waves fast

Nature - Wed, 09/14/2016 - 00:00

Astronomy: Galaxy collisions make waves fast

Nature 537, 7620 (2016). doi:10.1038/537283b

When galaxies with supermassive black holes at their centres collide, they could produce a burst of gravitational waves within just 10 million years.Gravitational waves were first detected earlier this year, sparking great interest in finding more. Some scientists have predicted that wave production happens

Categories: Literature

Infection: Feed a virus, starve a bacterium

Nature - Wed, 09/14/2016 - 00:00

Infection: Feed a virus, starve a bacterium

Nature 537, 7620 (2016). doi:10.1038/537283c

Feeding mice helps them to fight viral infection, whereas starvation is a better strategy against bacterial infection — lending support to the proverb 'feed a cold, starve a fever'.Ruslan Medzhitov and his colleagues at Yale University School of Medicine in New Haven, Connecticut, studied

Categories: Literature

Engineering: Fabric harvests two energy forms

Nature - Wed, 09/14/2016 - 00:00

Engineering: Fabric harvests two energy forms

Nature 537, 7620 (2016). doi:10.1038/537283d

A lightweight fabric can harvest both solar and mechanical energy to power electronic devices.Zhong Lin Wang at the Georgia Institute of Technology in Atlanta, Xing Fan at Chongqing University in China and their co-workers wove a fabric (pictured) using wool fibres and

Categories: Literature

Conservation: Hawaiian bird-life collapse

Nature - Wed, 09/14/2016 - 00:00

Conservation: Hawaiian bird-life collapse

Nature 537, 7620 (2016). doi:10.1038/537283e

Populations of native birds on the Hawaiian island of Kauai have declined drastically in the face of climate change.Eben Paxton, of the US Geological Survey's Pacific Island Ecosystems Research Center in Hawaii, and his colleagues analysed data on seven native species of forest

Categories: Literature

Cancer biology: Location matters in cancer growth

Nature - Wed, 09/14/2016 - 00:00

Cancer biology: Location matters in cancer growth

Nature 537, 7620 (2016). doi:10.1038/537283f

A tumour's genetic mutations often dictate which metabolic pathways it uses for rapid growth, but the tissue it develops from can also be an important factor.Matthew Vander Heiden at the Massachusetts Institute of Technology in Cambridge and his colleagues studied tumours that bore mutations

Categories: Literature

Google’s speech machine, Lasker awards and Obama’s parasite

Nature - Wed, 09/14/2016 - 00:00

Google’s speech machine, Lasker awards and Obama’s parasite

Nature 537, 7620 (2016). http://www.nature.com/doifinder/10.1038/537284a

The week in science: 9–15 September 2016

Categories: Literature

Mystery deportation of particle physicist leads to swell of protest

Nature - Wed, 09/14/2016 - 00:00

Mystery deportation of particle physicist leads to swell of protest

Nature 537, 7620 (2016). http://www.nature.com/doifinder/10.1038/537287a

Author: Declan Butler

Adlène Hicheur’s ejection from Brazil to France remains unexplained.

Categories: Literature

Medical Nobel prize committee deals with surgical scandal

Nature - Wed, 09/14/2016 - 00:00

Medical Nobel prize committee deals with surgical scandal

Nature 537, 7620 (2016). http://www.nature.com/doifinder/10.1038/537289a

Author: Alison Abbott

Panel rocked by investigations into surgeon — but its credibility stays intact.

Categories: Literature

Technology: Selfies in space

Nature - Wed, 09/14/2016 - 00:00

Technology: Selfies in space

Nature 537, 7620 (2016). doi:10.1038/537304a

Author: Alexandra Witze

Alexandra Witze examines a book on the techheads behind commercial high-altitude travel.

Categories: Literature

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