2 pieces of AFE papers——initiation，Alternative Promoters（both for the first exon splice）
---恢復內容開始---
《A paired-end sequencing strategy to map the complex landscape of transcription initiation》
《Tissue-Specific and Ubiquitous Expression Patterns from Alternative Promoters of Human Genes》
第一篇：來自nature method
用的是果蠅的胚胎RNASeq數據分析了其TSS部位的initiation landscape，也就是本人所感興趣的AFE，在哺乳動物體內也發現了可以用特定motif表征的相似的啟動子部位特征。再有，他們發現了5‘帽子端的轉錄起源於編碼的外顯子，從本文章中看來，他們的發現TSS的存在並不是形成轉錄本的過程中選擇性剪切的結果，而是轉錄前的基因coding region的改造作用所產生的產物，證明了paired-end tss analysis
其中想說的是作者的開篇：
recent studies using high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by rnA polymerase ii, helping to de ne several initiation patterns in which transcription start sites (tsss) cluster in both narrow and broad genomic windows. 
key words：
TSS：Central to this process is the core promoter region of ~100 nucleotides (nt) surrounding the transcription start site (TSS) of a gene
TSS區域的作用是其間DNA motif sequence 保證了RNA轉錄酶的召集，從而啟動轉錄，
CAGE：the capped analysis of gene expres-sion (CAGE) protocol has been used to generate comprehensive
mammalian libraries of short sequence tags, （CAGE的一般作用）which have led to the identification of distinct transcription initiation patterns
TATA box：an over- representation of the canonical TATA box sequence motif in ‘single-peak’ promoters and CpG islands overlapping ‘broad range’ promoters
目前5‘端的seqing technology有CAGE protocol，deep CAGE protocol，PEAT（本篇作者團隊開發的，杜克大學藥學院）
PEAT：paired--end analysis of TSSs
PEAT的strategy圖示：RCA：rolling circle amplification（特色）
##########################
3′ reads were mostly mapped to coding regions of annotated genes, indicating the success of the paired-end library construction.
mapping之後的reads類型分布，類型不僅僅顯示了3’、5’的測序結果異同，多少也顯示了測序深度的大小。3’端數據大多映射到了編碼區域也反映了雙端建庫的成功。
Characterization of read clusters and initiation patterns：TSS clusters and initiation patterns identified in the Drosophila embryo.
a圖揭示了5‘端的TSS Tags 組成的density estimate plot，並且TSS 包含95% of the reads的cluster被密集的表示在黑線以及棕黃色area。
b圖是所有大於100bpreads的cluster的基因位置餅圖，分類的依據則是相應轉錄組的註釋位置以及所給cluster分配的模式。
c圖很直觀，d圖：TSS的窄峰、寬峰、弱峰的分布情況
Promoter motifs associated with distinct promoter types：Initiation patterns are linked to specific core promoter
In mammals, ‘single-peak’ and ‘broad-range’ promoters tend to be associated with TATA box sequence and CpG islands As the fly genome does not contain CpG islands, our identification of BP and WP promoters was intriguing
#######
Unlike mammalian WP promoters, which have been associated with CpG islands,Drosophila WP promoters were strongly associated with three motifs (motif 1, DRE and motif 7)：果蠅種屬中的weak promoter不似哺乳動物中的weak peak與CpG islands呈很高的相關性，而是與三種motifs有很高的相關性。
BP promoters, which have characteristics of both NP and WP promoters, showed a combination of the most frequent motifs found in the other promoter types。而對於broad peak的 promoter的motifs則是結合NP以及WP的motifs的結合體，擁有兩種promoters的motifs的co-features
其中：
The Inr motif and motif 1 had in common a strongly conserved ‘TCA’ trinucleotide (the minimal initiator consensus sequence，而TCA又是最小啟動子一致序列).
Likewise, motif 6 was enriched at the same location as the TATA box and contains a minimal TAT consensus sequence that is also present in the canonical TATA motif, suggesting that motif 6 and motif 1 combination is an alternative to the classic TATA box and Inr motif pair
---恢復內容開始---
《A paired-end sequencing strategy to map the complex landscape of transcription initiation》
《Tissue-Specific and Ubiquitous Expression Patterns from Alternative Promoters of Human Genes》
第一篇：來自nature method
用的是果蠅的胚胎RNASeq數據分析了其TSS部位的initiation landscape，也就是本人所感興趣的AFE，在哺乳動物體內也發現了可以用特定motif表征的相似的啟動子部位特征。再有，他們發現了5‘帽子端的轉錄起源於編碼的外顯子，從本文章中看來，他們的發現TSS的存在並不是形成轉錄本的過程中選擇性剪切的結果，而是轉錄前的基因coding region的改造作用所產生的產物，證明了paired-end tss analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes.
其中想說的是作者的開篇：
recent studies using high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by rnA polymerase ii, helping to de ne several initiation patterns in which transcription start sites (tsss) cluster in both narrow and broad genomic windows. 遣詞造句還不錯
key words：
TSS：Central to this process is the core promoter region of ~100 nucleotides (nt) surrounding the transcription start site (TSS) of a gene
TSS區域的作用是其間DNA motif sequence 保證了RNA轉錄酶的召集，從而啟動轉錄，
CAGE：the capped analysis of gene expres-sion (CAGE) protocol has been used to generate comprehensive
mammalian libraries of short sequence tags, （CAGE的一般作用）which have led to the identification of distinct transcription initiation patterns
TATA box：an over- representation of the canonical TATA box sequence motif in ‘single-peak’ promoters and CpG islands overlapping ‘broad range’ promoters
目前5‘端的seqing technology有CAGE protocol，deep CAGE protocol，PEAT（本篇作者團隊開發的，杜克大學藥學院）
PEAT：paired--end analysis of TSSs
PEAT的strategy圖示：RCA：rolling circle amplification（特色）
##########################
3′ reads were mostly mapped to coding regions of annotated genes, indicating the success of the paired-end library construction.
mapping之後的reads類型分布，類型不僅僅顯示了3’、5’的測序結果異同，多少也顯示了測序深度的大小。3’端數據大多映射到了編碼區域也反映了雙端建庫的成功。
Characterization of read clusters and initiation patterns：TSS clusters and initiation patterns identified in the Drosophila embryo.
a圖揭示了5‘端的TSS Tags 組成的density estimate plot，並且TSS 包含95% of the reads的cluster被密集的表示在黑線以及棕黃色area。
b圖是所有大於100bpreads的cluster的基因位置餅圖，分類的依據則是相應轉錄組的註釋位置以及所給cluster分配的模式。
c圖很直觀，d圖：TSS的窄峰、寬峰、弱峰的分布情況
Promoter motifs associated with distinct promoter types：Initiation patterns are linked to specific core promoter
In mammals, ‘single-peak’ and ‘broad-range’ promoters tend to be associated with TATA box sequence and CpG islands As the fly genome does not contain CpG islands, our identification of BP and WP promoters was intriguing
#######
Unlike mammalian WP promoters, which have been associated with CpG islands,Drosophila WP promoters were strongly associated with three motifs (motif 1, DRE and motif 7)：果蠅種屬中的weak promoter不似哺乳動物中的weak peak與CpG islands呈很高的相關性，而是與三種motifs有很高的相關性。
BP promoters, which have characteristics of both NP and WP promoters, showed a combination of the most frequent motifs found in the other promoter types。而對於broad peak的 promoter的motifs則是結合NP以及WP的motifs的結合體，擁有兩種promoters的motifs的co-features
其中：
The Inr motif and motif 1 had in common a strongly conserved ‘TCA’ trinucleotide (the minimal initiator consensus sequence，而TCA又是最小啟動子一致序列).
Likewise, motif 6 was enriched at the same location as the TATA box and contains a minimal TAT consensus sequence that is also present in the canonical TATA motif, suggesting that motif 6 and motif 1 combination is an alternative to the classic TATA box and Inr motif pair
2 pieces of AFE papers——initiation，Alternative Promoters（both for the first exon splice）