Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation.
全面轉(zhuǎn)錄分析驗證人紅系分化中編碼與非編碼RNA的相互作用
Abstract :
摘要
Methods:
方法
Fousing on the integration of the three RNA types, the writer compared the dynamics of coding genes,miRNA, and IncRNA expression profiles in erythropoiesis after taking advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differientiation stages and muture red blood cells.
集中于整合三種不同類型的RNA數(shù)據(jù)類型氏仗，作者再利用高通量技術(shù)獲得造血干細胞，以及以后四個紅系分化階段二號成熟紅細胞的轉(zhuǎn)錄數(shù)據(jù)后帚稠，比較了紅系分化中編碼RAN, miRNA, IncRNA的動態(tài)表達數(shù)據(jù)滋早。
Results:
結(jié)果：
IncRNAs were promising cell marker candidates for erythroid differentiation.
IncRANs 有望成為紅系分化的分子標(biāo)志物。
Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation.
根據(jù)分化的動態(tài)變化性從干性的維持搁进，到分化中期昔头。到成熟期。對差異表達基因進行聚類分成四個子類莱革。
Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation,and especially associated with heme metabolism and response to oxygen species and DNA damage.
整合分析揭示非編碼RNAs潛在參與了成熟紅細胞的形成盅视，特別是和heme的代謝旦万，攜揚功能和DNA損傷有關(guān)。
These regulatory interactions were displayed in a comprehensive networks, thereby inferring correlations between RNAs and their associated funtions.
這些調(diào)控的相互作用被一個全面的調(diào)控網(wǎng)絡(luò)呈現(xiàn)赏半，有不同RNAs之間的聯(lián)系和他們聯(lián)系的功能作用淆两。
Results:
Similar expression patterns of genes, miRNAs, and IncRNAs.
在gens, miRNA, IncRNAs中相似的表達模式琼腔。
Fig1: Quantitative real-time PCR of several erythroid genes. A: Expression patterns of several erythroid genes validated using qRT-PCR B: Bar plots show the expression of patterns of eythroid genes during HSC development and in red blood cells.
定量實時PCR分析幾個紅系分化基因。
A: 用qRT-PCR驗證 幾個紅系分化中基因的表達模式光坝。
B: 這幾個紅系分化中基因的表達柱圖甥材，在HSC(造血干細胞)洲赵，分化和成熟細胞中的表達商蕴。
mRNA, miRNA, and IncRNA expression profiles.
mRNA,miRNA, IncRNA 表達圖譜
A: Bar plotes showing numbers of expressed RNAs at various FPKM/RPKM levels.Most RNAs were expressed with FPKM lower than 30.A small number of mRNAs and miRNAs were expressed at a relatively high levelat above 100 FPKM.
柱圖顯示在不同 FPKM水平的表達數(shù)據(jù)分布绪商， 大多數(shù)RNAs 表達的FPLKM低于 30辅鲸， 少量的mRNAs 和 miRNA 表達在相對高水平（FPKM大于100）
B: Scatter plot of expressed IncRNAs in different eythroid differentiation stages.The y-axis represent the FPKM value of each IncRNA(colored dots). Few IncRNAs were expressed with FPKM > 30. C-D. Heatmatps of mRNA, miRNA and IncRNA expressions, respectively.
B: 不同紅系分化時期的IncRNA 表達散點圖独悴， y軸代表 每個IncRNA的FPKM 的值。少量IncRNA 表達高于FPKM.
C-D: mRNA, miRNA, IncRNA 各自的表達熱圖决采。
K-means clustering of differentially expressed genes.
差異表達基因的K均值聚類
Genes that were highly expressed in differentitaion but signifcantly downregulated at muturation stage were classified under subtype 1.
在分化中高表達但是在成熟時期下調(diào)的基因被分為 子類1.
Genes that were higly expressed in HSC, but decreased at the following stages were classified under subtype 2.
在HSC(造血干細胞)中高表達树瞭，但是在隨后分化階段低表達的基因被分為 子類 2.
In subtype 3, gene expression gradually decreased during primary differentiation, but increased during maturation.
在子類 3 中筏勒，是風(fēng)化階段表達逐漸下調(diào)旺嬉，但是在成熟階段又高表達的基因邪媳。
The expression of genes altered more than once during differentiation were classified under subtype 4.
在分化中基因表達變化了不止一次的被分類為 子類4.
Transcription factors and hemoglobin, which were detected in distinct subtypes, are show on the right side of the figure.
轉(zhuǎn)錄和分化因子，在不同的子類中被檢測到迅涮，顯示在圖右邊徽龟。
Expressions of genes in signaling pathways were activated/inhibited during erythroid differentiation.
紅系分化中，信號通路中基因表達被激活/抑制
A: Green nodes indicate genes that were decreased during maturation, whereas red nodes indicated genes that were increased.
綠色點表示基因下調(diào)在成熟中传透，紅色代表增加朱盐。
Most of the genes in P53 pathway were inhibited. As TP53 was inhibited, the part of this pathway was supposed to be inative.
P53信號通路中大多數(shù)基因表達被抑制菠隆，隨著TP53被抑制狂秘，此通路是被激活了者春。
B: Expression profiles of activated/inhibited genes in the p53 signaling pythways: 5 genes were upregulated during maturation, but 19 genes were observed downregulated during that peroid.
在p53信號通路中激活/抑制基因表達模式清女，在成熟期，5個基因被上調(diào)忠售，19個基因被下調(diào)迄沫。
C: Expression profiles of chemokines in HSC. All know chemokines, except CCL13 and CCL18, were expressed in HSC and decreased during differentiation.
在HSC中趨化因子的表達模式。 所有已知的趨化因子泰佳，除了CCL13和CCL18 , 其它都在HSC表達并在分化過程中表達下調(diào)尘吗。
Correlation heatmap between miRNA and their target genes in subtype 3.
子類3中,miRNA 和靶基因的作用熱圖
Fifty miRNAs and 256 genes are shown in the left side of the figure. Subtypes 3 comprised 29 genes involved in 'metablism of heme' and reactive to oxygen species", among which 21 genes were possibly regulated by hsa-miR-532-3p, as highligted by the red box.
50個 miRNAs 和256 個基因 被顯示在圖右邊睬捶， 子類3中包含的29個基因涉及heme的代謝和攜氧激活，其中21個基因可能被hsa-miR-532-3p 調(diào)控臀晃，被紅色方框標(biāo)出介劫。
Green color boxes represent significant negative correlation between miRNAs and target genes with Pearson correlation coeficient of <= -0.9 , p value <= 0.01(P values are not shown)
綠色方框代表miRNA和靶基因顯著的負相關(guān)座韵，Pearson 相關(guān)系數(shù)小于等于-0.9.P 值未顯示。
Analysis of IncRNAs during erythroid differentiation.
紅系分化中IncRNAs 的分析
A: Significant Pearson correlation coefiicient between 60 IncRNAs and coding genes with functions associated with "hemopoiesis and leucocyte activation" and "DNA repair".
顯著的Pearson 相關(guān)性在60 IncRNAs 和 編碼基因之間宦棺，這些編碼基因和hemopoiesis以及 leucocyte 激活 以及 DNA 修復(fù)相關(guān)渺氧。
Postive correlations are colored red, whereas negative correlations are colored blue.正相關(guān)被標(biāo)為紅色蹬屹，負相關(guān)被標(biāo)為藍色白华。
B: Expression patterns of RP11-326C3.2 and its downstream gene ATHL1 were validated using qPCR in the K562 cell line.
RP11-326C3.2和它的下游基因ATHL1被表達模式 被qPCP在K562細胞系中被驗證贩耐。
C:Integrative Genomics Viewer expressed reads for RP11-326C3.2 and its downstream coding gene ATHL1 on chromosome 5.
整合 基因組視圖 顯示 RP11-326C3.2 和其下游編碼基因 ATHL1在染色體5上的位置潮太。
A comprehensive network illutrates the interations of coding genes, miRNAs, IncRNAs that participate in controlling red blood cell maturation.
全面的調(diào)控網(wǎng)絡(luò)說明編碼基因，miRNA, IncRN間的相互作用更鲁，起都參與了紅細胞成熟的調(diào)控奇钞。
Coding genes are marked with square nodes, whereas miRNAs and IncRNA are marked with "V" and round nodes,respectively.
編碼基因用方向節(jié)點來標(biāo)記景埃，miRNA 用 V,IncRNA 用圓。
RANs that were upregulated during eythroid cell development are colored red, and downregulated RANs are colored green. RNAs downregulated during maturation, but not significant, were colored light green.
RNAs 在紅系分化中上調(diào)的被標(biāo)為紅色拒啰，下調(diào)的被標(biāo)為綠色完慧，RNA,在成熟時下調(diào)，但是不明顯的被標(biāo)為淺綠色蛤织。
