Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice
DOI(url): https://doi.org/10.1016/j.cell.2019.03.008
發(fā)表日期：4 April 2019
關(guān)鍵點(diǎn)
反義 lncRNA 轉(zhuǎn)錄可以影響DNA甲基化憨奸，進(jìn)而改變?nèi)旧w結(jié)構(gòu)促進(jìn)增強(qiáng)子與啟動(dòng)子結(jié)合罗标，調(diào)控基因表達(dá)材鹦。
參考意義
Pcdhα基因有13個(gè)可以隨機(jī)啟動(dòng)的可變外顯子力奋，每個(gè)啟動(dòng)子都可以由自身的啟動(dòng)子驅(qū)動(dòng)，還有3個(gè)c型外顯子以及穩(wěn)定表達(dá)的編碼pcdh結(jié)構(gòu)域的外顯子松逊，同時(shí)盾沫，還有一個(gè)enhancer調(diào)控沸毁。
研究者發(fā)現(xiàn)，反義lncRNA的轉(zhuǎn)錄亥鬓，會(huì)造成該位點(diǎn)DNA去甲基化的發(fā)生完沪，從而使遠(yuǎn)端增強(qiáng)子靠近該外顯子的啟動(dòng)子，促進(jìn)它的表達(dá)嵌戈。如圖2所示覆积，Pcdhα基因座位均帶有抑制表達(dá)的DNA甲基化修飾，而當(dāng)反義lncRNA表達(dá)時(shí)咕别，該外顯子附近的DNA被DNA去甲基化酶TET3識(shí)別技健，去除了甲基化修飾，cohesin蛋白重塑了染色體的結(jié)構(gòu)惰拱，HS5-1增強(qiáng)子與該基因座位的啟動(dòng)子結(jié)合雌贱，啟動(dòng)相應(yīng)Pcdhα變體的表達(dá)。
相關(guān)內(nèi)容
關(guān)于反義lncRNA影響正義鏈基因表達(dá)的作用機(jī)制偿短，主要有3類
- 反義lncRNA的轉(zhuǎn)錄過(guò)程欣孤，抑制正義鏈基因的轉(zhuǎn)錄，該機(jī)制認(rèn)為反義鏈轉(zhuǎn)錄事件本身昔逗，而不是反義lncRNA降传，調(diào)控了基因的表達(dá)。
- 反義lncRNA結(jié)合DNA或組蛋白修飾酶勾怒，調(diào)控所在基因座位的表觀遺傳學(xué)婆排，從而影響正義鏈基因的表達(dá)。
- 反義lncRNA與正義鏈mRNA通過(guò)堿基互補(bǔ)配對(duì)結(jié)合笔链，影響mRNA的可變剪接等段只。
CTCF:
CTCF is an enhancer-blocking protein that inhibits the access of Igf2 to the enhancer elements located downstream from the H19 transcription start site.
Cohesin
Cohesin is a multiprotein complex that holds sister chromatids together from S phase until the start of mitosis, helping to ensure genomic integrity (Haarhuis, Elbatsh, & Rowland, 2014).
另一篇植物中相關(guān)lncRNA 鑒定方法
First, only transcripts with TAIR10 annotation [Cufflinks class codes ‘u’ (intergenic transcripts),’x’ (Exonic overlap with reference on the opposite strand),’i’ (transcripts entirely within intron) were retained. Second, transcripts of short length (length <150 nt) or low abundance (FPKMmax?<?1, FPKMmax stands for the maximum expression level of a lncRNA from all samples) were removed. Third, transcripts with protein-coding potential were removed. Protein-coding potential was determined by using two programs: (1) transcripts were subjected to a BlastX search against all plant protein sequences in the Swiss-Prot database70 with a cutoff e-value?<?10-4 and the transcripts with strong hits (alignment length ≥40 aa, percent identity ≥35% and coverage of the alignment region in either query or subject sequence ≥35%) to known proteins were considered to have protein-coding potential; For antisense transcripts, open reading frames were checked. (2) the CPC (Coding Potential Calculator) score71, a value to assess protein-coding potential of a transcript based on six biologically meaningful sequence features, was calculated for each transcript. When the CPC score is positive, we considered the transcript to have protein-coding potential. Transcripts that passed the three filtering steps were annotated as lncRNAs.
exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling
DOI(url): https://doi.org/10.1016/j.cels.2019.03.004
發(fā)表日期：April 4, 2019
關(guān)鍵點(diǎn)
一套分析 exRNA 的完整方案
參考意義
exRNA 就是細(xì)胞外RNA，也就是在細(xì)胞內(nèi)轉(zhuǎn)錄但是在細(xì)胞外發(fā)揮功能鉴扫？最近c(diǎn)ell 有一個(gè)屧拚恚刊介紹了很多exRNA的文章，我掃了一眼，感覺(jué)主要內(nèi)容是小RNA居多炕婶。所以這個(gè)分類和lncRNA類似姐赡，一個(gè)從長(zhǎng)度一個(gè)從位置來(lái)進(jìn)行區(qū)分。既然是這樣柠掂，exRNA 的處理方法應(yīng)該就和小RNA以及一般的 RNAseq 分析類似项滑。看看這個(gè)流程里面有哪些不一樣的地方陪踩。這里提供的分析方法從內(nèi)容來(lái)看主要針對(duì)小RNA杖们，但是官方說(shuō)也可以很方便的移植到其它RNA，在GitHub的代碼里也有針對(duì) longRNA 的腳本肩狂。主要流程如下圖摘完，質(zhì)控后會(huì)同時(shí)比對(duì)到多個(gè)數(shù)據(jù)庫(kù)，具體內(nèi)容可以參考 GitHub傻谁。
相關(guān)內(nèi)容
什么是 exRNA
exRNA: Extracellular RNA (also known as exRNA or exosomal RNA) describes RNA species present outside of the cells from which they were transcribed. In Homo sapiens, exRNAs have been discovered in bodily fluids such as venous blood, saliva, breast milk, urine, semen, menstrual blood, and vaginal fluid. Although their biological function is not fully understood, exRNAs have been proposed to play a role in a variety of biological processes including syntrophy, intercellular communication, and cell regulation.
exRNA 的種類
Extracellular RNA should not be viewed as a category describing a set of RNAs with a specific biological function or belonging to a particular RNA family. Similar to the term "non-coding RNA", "extracellular RNA" defines a group of several types of RNAs whose functions are diverse, yet they share a common attribute which, in the case of exRNAs, is existence in an extracellular environment. The following types of RNA have been found outside the cell:
- Messenger RNA (mRNA)
- Transfer RNA (tRNA)
- MicroRNA (miRNA)
- Small interfering RNA (siRNA)
- Long non-coding RNA (lncRNA)
研究 exRNA 的關(guān)鍵似乎應(yīng)該是如何分離得到確實(shí)是細(xì)胞外的 RNA孝治。
比如 Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. Cell. 2019 Apr 4;177(2):446-462.e16. doi: 10.1016/j.cell.2019.03.024. 這篇文章就比較了集中 exRNA Isolation Methods，通過(guò)對(duì)5種生物液體中10種exRNA分離方法的系統(tǒng)比較审磁，發(fā)現(xiàn)所得到的小RNA-seq圖譜的復(fù)雜性和重現(xiàn)性存在顯著差異谈飒。每種方法對(duì)不同的exRNA載體亞類的相對(duì)效率是通過(guò)估計(jì)細(xì)胞外囊泡(EV)-、核糖核蛋白(RNP)-和高密度脂蛋白(HDL)特異性miRNA在每個(gè)圖譜中的比例來(lái)確定的态蒂。開(kāi)發(fā)了一種基于 web 的交互式應(yīng)用(miRDaR)杭措，幫助研究人員為他們的研究選擇最佳的 exRNA 分離方法。
另外钾恢，還有一篇文章：exRNA Atlas Analysis Reveals Distinct Extracellular RNACargo Types and Their Carriers Present across Human Biofluids. Cell. 2019 Apr 4;177(2):463-477.e15. doi: 10.1016/j.cell.2019.02.018.
exRNA Atlas resource 包含來(lái)自19項(xiàng)研究的5309個(gè) exRNA-seq 和 exRNAqPCR 概要文件手素，以及一套分析和可視化工具。通過(guò)分析瘩蚪，該研究得到了一個(gè)包含六種exRNA類型(CT1泉懦、CT2、CT3A疹瘦、CT3B崩哩、CT3C、CT4)的模型言沐，每種 exRNA 類型都可以在多種生物體液(血清邓嘹、血漿、腦脊液险胰、唾液吴超、尿液)中檢測(cè)到。
A statistical normalization method and differential expression analysis for RNA-seq data between different species
DOI(url): https://doi.org/10.1186/s12859-019-2745-1
發(fā)表日期：29 March 2019
關(guān)鍵點(diǎn)
不同物種之間 RNA-seq 怎么分析確實(shí)是一個(gè)問(wèn)題鸯乃，那么 ChIP-seq 呢？
參考意義
propose a scale based normalization (SCBN) method by taking into account the available knowledge of conserved orthologous genes and by using the hypothesis testing framework.
Considering the different gene lengths and unmapped genes between different species, we formulate the problem from the perspective of hypothesis testing and search for the optimal scaling factor that minimizes the deviation between the empirical and nominal type I errors.
用小鼠來(lái)研究人的疾病非常常見(jiàn)，在一些文章中也有人會(huì)用同源基因進(jìn)行比較缨睡。對(duì)于不同物種的數(shù)據(jù)來(lái)說(shuō)鸟悴，除了基因數(shù)量基因長(zhǎng)度的不同，也有測(cè)序深度的問(wèn)題奖年。讓兩個(gè)物種之間的數(shù)據(jù)可比细诸，數(shù)據(jù)的標(biāo)準(zhǔn)化方法非常重要。在之前的一些研究中陋守，有人使用RPKM值來(lái)進(jìn)行比較找到一千個(gè)保守基因震贵，然后評(píng)估每個(gè)基因在不同物種中的中位數(shù)水平，然后通過(guò)讓中位值保持一致來(lái)得到一個(gè)校正因子（median method）水评。這篇文章作者利用直系同源基因通過(guò)對(duì)已有方法的改進(jìn)來(lái)進(jìn)行不同物種之間數(shù)據(jù)的矯正猩系。
相關(guān)內(nèi)容
ChIP-seq 類的數(shù)據(jù)有哪些方法呢？
雅卡爾指數(shù)（英語(yǔ)：Jaccard index）中燥，又稱為并交比（Intersection over Union）寇甸、雅卡爾相似系數(shù)（Jaccard similarity coefficient），是用于比較樣本集的相似性與多樣性的統(tǒng)計(jì)量疗涉。雅卡爾系數(shù)能夠量度有限樣本集合的相似度拿霉，其定義為兩個(gè)集合交集大小與并集大小之間的比例。在bedtools 中有這個(gè)工具可以 對(duì) jaccard 進(jìn)行計(jì)算咱扣。
還有**余弦相似度 cosine similarity score **绽淘，比如這篇文章 A Cosine Similarity-Based Method to Infer Variability of Chromatin Accessibility at the Single-Cell Level
另外，dpca 可以用于分析轉(zhuǎn)錄因子結(jié)合位點(diǎn)處和啟動(dòng)子的不同染色質(zhì)模式闹伪，以及等位基因特異性蛋白-DNA之間的相互作用沪铭。
DNA methylation analysis in plants: review of computational tools and future perspectives
DOI(url): https://doi.org/10.1093/bib/bbz039
發(fā)表日期：09 April 2019
關(guān)鍵點(diǎn)
難得的植物DNA甲基化分析綜述文章
參考意義
在這篇綜述中，作者概述了分析DNA甲基化數(shù)據(jù)（特別是亞硫酸氫鹽測(cè)序數(shù)據(jù)）最常用的生物信息學(xué)工具祭往，也分析了這些工具的性能并且比較了計(jì)算擬南芥以及小麥甲基數(shù)據(jù)的計(jì)算時(shí)間和一致性伦意。同時(shí)舉例說(shuō)明了作物中DNA甲基化數(shù)據(jù)分析的應(yīng)用。但從軟件上看硼补，BSMap 用是最短驮肉，尤其是當(dāng)線程數(shù)上去之后，但是內(nèi)存則是Bismark 最省已骇。
關(guān)于內(nèi)存的使用情況离钝，不要被下圖迷惑。小麥那里只是展示了處理1條染色體的需要的內(nèi)存用量褪储。要知道卵渴，小麥可是有21條染色體，16G的基因組鲤竹。
相關(guān)內(nèi)容
另外一篇文章浪读，Strategies for analyzing bisulfite sequencing data 。
