文章一

Hi-C as a tool for precise detection and characterisation of chromosomal re arrangements and copy number variation in human tumours

用Hi-C技术检测人类肿瘤的拷贝数差异以及染色体重组

Louise Harewood, Kamal Kishore, Matthew D. Eldridge, Steven Wingett, Danita Pearson,Stefan Schoenfelder, V. Peter Collins and Peter Fraser

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1253-8

【导读】 染色体异位通常通过FISH检测,近年来许多人也尝试用二代测序技术在基因组范围内筛查染色体异位现象。由于基因拷贝数在异位情况下往往并没有出现变化,而且在异位断裂点序列未知的情况下,想要用二代测序完成这个任务就非常困难。本周这一工作利用Hi-C辅助二代测序完成染色体异位的检测。这是一个飞快发展的领域,就在这篇稿件进行同行评审以及修改的过程中,非常类似的工作在preprint服务器BioRxiv上发表,感兴趣的读者可以比较我们发表的这一工作和BioRxiv上另一个研究组工作的异同之处。

http://www.biorxiv.org/content/early/2017/03/28/119651

Abstract

Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples,with the potential to define chromosome breakpoints to bp resolution. Inaddition, we show copy number profiles can also be obtained from the same data,all at a significantly lower cost than standard sequencing approaches.

 

文章二

BRIE: transcriptome-wide splicing quantification in single cells

BRIE:单细胞中的剪切定量

Yuanhua Huang and Guido Sanguinetti

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1248-5

【导读】单细胞测序由于覆盖率低,能否通过普通的RNA测序的分析技术来推断单细胞间的剪切差异鲜有人知。这个工作先测试了原有的RNA测序分析软件对单细胞数据的分析,发现并不能完成这一功能。再进一步发展出BRIE这一专门针对单细胞的数据模型,缺陷是如果测序是采用的偏向于转录本末端的方法,比如STRT-seq或者CEL-seq,这个计算模型就不太管用了。所以如果是对单细胞的剪切差异感兴趣的读者们,选用BRIE的时候请注意自己的测序方法。

Abstract

Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity in transcription, but the limitations of the technology have prevented its application to dissect variability in RNA processing events such as splicing. Here, we present BRIE (Bayesian regression for isoform estimation), a Bayesian hierarchical model that resolves these problems by learning an informative prior distribution from sequence features. We show that BRIE yields reproducible estimates of exon inclusion ratios in single cells and provides an effective tool for differential isoform quantification between scRNA-seq data sets. BRIE, therefore, expands the scope of scRNA-seq experiments to probe the stochasticity of RNA processing.

 

文章三

NicE-seq: high resolution open chromatin profiling

NicE-seq:高分辨率开放染色体研究工具

V. K.Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin,Stephanie Sian, Shuang-yong Xu, Touati Benoukraf and Sriharsa Pradhan

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1247-6

【导读】六月小编出访高校的时候,用这篇方法学工作举了很多例子,解释编辑可能通过哪些方面来“折磨”作者,今天终于能够揭晓这个工作是由来自新英格兰生物实验室(NEB)的老手们完成的一个技术手段,能够弥补ATAC-seq不太适合在固定细胞上研究开放染色体的不足。从GenomeWeb上周末采访中可以看到,作者对这个方法的使用简易度和可重复性具有非常强的信心,欢迎读者们写信索取NicE-seq做需要的酶,来和大名鼎鼎的ATAC-seq作比较吧。

Abstract

Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin profiling on both native and formaldehyde-fixed cells. NicE-seqcaptures and reveals open chromatin sites (OCSs) and transcription factoro ccupancy at single nucleotide resolution, coincident with DNase hypersensitive and ATAC-seq sites at a low sequencing burden. OCSs correlate with RNA polymerase II occupancy and active chromatin marks, while displaying a contrasting pattern to CpG methylation. Decitabine-mediated hypomethylation of HCT116 displays higher numbers of OCSs.

 

文章四 (植物表观遗传学特刊)

Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants

植物通过表观遗传和染色质介导的机制产生对环境压力的记忆

Jörn Lämke and Isabel Bäurle

http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1263-6

【导读】 前几周断断续续的植物表观遗传学特刊中,我们已经看到了许多植物通过表观遗传来产生对环境变化和压力的反应。本周我们邀请来自Potsdam大学的两位作者为我们综述这种对环境压力的反应又是如何通过表观遗传机制传递到子代而形成一种表观遗传学“记忆”。

Abstract

Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations. Given their potential epigenetic nature, such modifications may provide a mechanistic basis for a stress memory,enabling plants to respond more efficiently to recurring stress or even toprepare their offspring for potential future assaults. In this review, we discuss both the involvement of chromatin in stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.

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