文章一(植物表观遗传学特刊)

The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility

拟南芥BAF60通过调节DNA的可及度来介导发芽生长

Teddy Jégu,Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, MagaliePerez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, StéphanieLegras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux,Martin Crespi, Magdy M. Mahfouz,  Heribert Hirt, Cécile Raynaud and Moussa Benhamed

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1246-7

【导读】植物对光的敏感性帮助它们适应四季变化，适应昼夜更替。表观遗传调控往往是植物面对昼夜、四季更替时用来调节发育的利器。这一工作研究的是SWI/SNF的一个组成成分BAF60如何在光节律中调节染色质的开放性，从而调节相关基因的表达。这一工作之所以入得编辑“法眼”是因为其工作的完整性，并且在全基因组水平上研究发芽发育并不多见。

Abstract

Background:Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored.

Results:In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes. BAF60 binds nucleosome-free regions of multiple Gbox-containing genes, opposing in cis the promoting effect ofthe photomorphogenic and thermomorphogenic regulator Phytochrome InteractingFactor 4 (PIF4) on hypocotyl elongation. Furthermore,BAF60 expression level is regulated in response to light and daily rhythms.

Conclusions:These results unveil a short path between a chromatin remodeler and a signaling component to fine-tune plant morphogenesis in response to environmental conditions.

 

文章二

MicroRNAs control mRNA fate by compartmentalization based on 3′ UTR length in male germ cells

小鼠雄性生殖细胞中的microRNA研究

Ying Zhang, ChongTang, Tian Yu, Ruirui Zhang, Huili Zheng and Wei Yan

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1243-x

【导读】非编码RNA在生殖系统中的作用一直是个热点问题，同时也是个难点问题。不同于近期热议的piRNA 在生精过程中的作用，这篇工作主要着眼的是miRNA 如何在小鼠生精过程中调节信使RNA的空间定位；并发现3’非转录末端的长度在这个调控过程中有着很重要的作用。这类工作并不容易提出板上钉钉的结论，经过审稿人的建议，编辑斟酌再三，请作者把摘要结论里的“reveal”修改成了“suggest”，也许读者们能从这篇工作中体会出科学语言使用上细微但十分重要的区别。

 

Abstract

Background: Post-transcriptional regulation of gene expression can be achieved through the control of mRNA stability, cytoplasmic compartmentalization, 3′ UTR length and translational efficacy. Spermiogenesis,a process through which haploid male germ cells differentiate into spermatozoa,represents an ideal model for studying post-transcriptional regulation in vivo because it involves a large number of transcripts that are physically sequestered in ribonucleoprotein particles (RNPs) and thus subjected to delayed translation. To explore how small RNAs regulate mRNA fate, we conducted RNA-Seq analyses to determine not only the levels of both mRNAs and small noncoding RNAs, but also their cytoplasmic compartmentalization during spermiogenesis.

Result: Among all small noncoding RNAs studied, miRNAs displayed the most dynamic changes in both abundance and subcytoplasmic localization. mRNAswith shorter 3′ UTRs became increasingly enriched in RNPs from pachytenespermatocytes to round spermatids, and the enrichment of shorter 3′ UTR mRNAsin RNPs coincided with newly synthesized miRNAs that target these mRNAs atsites closer to the stop codon. In contrast, the translocation of longer 3′ UTRmRNAs from RNPs to polysomes correlated with the production of new miRNAs thattarget these mRNAs at sites distal to the stop codon.

Conclusions: miRNAs appear to control cytoplasmic compartmentalization of mRNAs based on 3′ UTR length. Our data suggest that transcripts with longer 3′ UTRs tend to contain distal miRNA binding sites and are thus targeted to polysomes for translation followed by degradation. Incontrast, those with shorter 3′ UTRs only possess proximal miRNA binding sites,which, therefore, are targeted into RNPs for enrichment and delayed translation.

 

文章三

Translational contributions to tissue specificity in rhythmic and constitutive gene expression

RNA翻译对昼夜节律组织特异性的贡献

VioletaCastelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich and David Gatfield

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1222-2

【导读】 你也许是从异国旅行的晚上睡不着，早上起不来体会到身体的昼夜节律（或者反过来：还没到晚饭点就不省人事，半夜时分又精神百倍），你身上的细胞却是从忠实的遵循昼夜节律的分子信号日复一日地工作着。过去的研究工作中，我们已经了解RNA转录的昼夜节律，蛋白质丰度的昼夜节律；但是从RNA到蛋白质，从肝脏到肾脏，如何从翻译水平遵从昼夜更替的规律，尚少有人问津。这一工作是一篇RNA翻译效率在肝、肾两个脏器的组织特异性资源类文献，希望能为从事生物钟研究的各位同学老师们提供有用的资源。

Abstract

Background: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporalgene expression in kidney and contrasted our findings with liver data availablefrom the same mice.

Results: Rhythmic translation of constantly abundant messenger RNAs (mRNAs) affects largelynon-overlapping transcript sets with distinct phase clustering in the two organs. Moreover, tissue differences in translation efficiency modulate the timing and amount of protein biosynthesis from rhythmic mRNAs, consistent with organ specificity in clock output gene repertoires and rhythmicity parameters.Our comprehensive datasets provided insights into translational control beyondtemporal regulation. Between tissues, many transcripts show differences intranslation efficiency, which are, however, of markedly smaller scale than mRNA abundance differences. Tissue-specific changes in translation efficiency are associated with specific transcript features and, intriguingly, globally counteracted and compensated transcript abundance variations, leading to higher similarity at the level of protein biosynthesis between both tissues.

Conclusions: We show that tissue specificity in rhythmic gene expression extends to the translatome and contributes to define the identities, the phases and theexpression levels of rhythmic protein biosynthesis. Moreover, translational compensation of transcript abundance divergence leads to overall higher similarity at the level of protein production across organs. The unique resources provided through our study will serve to address fundamental questions of post-transcriptional control and differential gene expression in vivo.

  

文章四 (植物表观遗传学特刊)

Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives

玉米的稳定着丝粒与卫星着丝粒的序列差异

Jonathan I. Gent,Na Wang and R. Kelly Dawe

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1249-4

【导读】 前不久重新组装的玉米B73基因组再次提醒我们这个基因组的复杂性。玉米基因组的复杂并不仅体现在遍布基因组的重复序列，还体现在着丝粒序列的复杂性。通过比较农作物玉米和野生玉米的着丝粒序列，这一工作发现复杂的着丝粒并不是由于玉米培育过程中密集近交产生的。构成2Mb玉米着丝粒的序列具有复杂的多样性，为真核生物着丝粒序列研究提供一个新的模式生物。

Abstract

Background: Paradoxically,centromeres are known both for their characteristic repeat sequences (satelliteDNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large(~2 Mb) centromeres are not dominated by satellite DNA. These centromeres,which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3).

Results: We found frequent complex centromeres in maize and its wild relatives Z. mays parviglumis, Z. mays mexicana, and particularly Z. mays huehuetenangensis. Analysis of individual plants reveals minor variation inthe positions of complex centromeres among siblings. However, such positionalshifts are stochastic and not heritable, consistent with prior findings thatcentromere positioning is stable at the population level. Centromeres are alsostable in multiple F1 hybrid contexts. Analysis of repeats in Z. mays andother species (Zea diploperennis, Zea luxurians, and Tripsacumdactyloides) reveals tenfold differences in abundance of the majorsatellite CentC, but similar high levels of sequence polymorphismin individual CentC copies. Deviation from the CentC consensushas little or no effect on binding of cenH3.

Conclusions: These data indicate that complex centromeres are neither a peculiarity of cultivation nor inbreeding in Z. mays. While extensive arrays of CentC maybe the norm for other Zea and Tripsacum species,these data also reveal that a wide diversity of DNA sequences and multiple types of genetic elements in and near centromeres support centromere function and constrain centromere positions.

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