Quantitative evaluation of all hexamers as exonic splicing elements

RNA剪接 小基因 生物 外显子 选择性拼接 遗传学 剪接 外显子剪接增强剂 背景(考古学) 计算生物学 核糖核酸 外显子跳跃 增强子 基因 基因表达 古生物学
作者
Shengdong Ke,Shulian Shang,Sergey Kalachikov,Irina Morozova,Lin Yu,James J. Russo,Jingyue Ju,Lawrence A. Chasin
出处
期刊:Genome Research [Cold Spring Harbor Laboratory Press]
卷期号:21 (8): 1360-1374 被引量:200
标识
DOI:10.1101/gr.119628.110
摘要

We describe a comprehensive quantitative measure of the splicing impact of a complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts. All 4096 6-mers were substituted at five positions within two different internal exons in a 3-exon minigene, and millions of successfully spliced transcripts were sequenced after transfection of human cells. The results allowed the assignment of a relative splicing strength score to each mutant molecule. The effect of 6-mers on splicing often depended on their location; much of this context effect could be ascribed to the creation of different overlapping sequences at each site. Taking these overlaps into account, the splicing effect of each 6-mer could be quantified, and 6-mers could be designated as enhancers (ESEseqs) and silencers (ESSseqs), with an ESRseq score indicating their strength. Some 6-mers exhibited positional bias relative to the two splice sites. The distribution and conservation of these ESRseqs in and around human exons supported their classification. Predicted RNA secondary structure effects were also seen: Effective enhancers, silencers and 3' splice sites tend to be single stranded, and effective 5' splice sites tend to be double stranded. 6-mers that may form positive or negative synergy with another were also identified. Chromatin structure may also influence the splicing enhancement observed, as a good correspondence was found between splicing performance and the predicted nucleosome occupancy scores of 6-mers. This approach may prove of general use in defining nucleic acid regulatory motifs, substitute for functional SELEX in most cases, and provide insights about splicing mechanisms.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
刚刚
刚刚
打打应助傲娇的厉采纳,获得10
刚刚
穆若发布了新的文献求助10
刚刚
Dr.coco发布了新的文献求助10
1秒前
宁听白发布了新的文献求助10
1秒前
shisong发布了新的文献求助10
2秒前
2秒前
2秒前
2秒前
君无邪完成签到,获得积分10
3秒前
yydragen应助DD采纳,获得30
3秒前
3秒前
Jasper应助cxszt采纳,获得10
3秒前
芋泥泥泥发布了新的文献求助10
5秒前
田様应助qq采纳,获得10
5秒前
ser发布了新的文献求助10
5秒前
5秒前
葱油饼发布了新的文献求助10
6秒前
穆若完成签到,获得积分10
7秒前
量子星尘发布了新的文献求助10
7秒前
大个应助蒋小亮采纳,获得10
7秒前
嘟嘟嘟嘟发布了新的文献求助10
8秒前
10秒前
小马甲应助www采纳,获得10
10秒前
隐形曼青应助you采纳,获得10
10秒前
shisong完成签到,获得积分10
10秒前
阳光女孩完成签到,获得积分10
10秒前
Dr.coco完成签到,获得积分10
11秒前
马尔尼菲蓝状菌完成签到,获得积分10
13秒前
Natforever完成签到 ,获得积分10
14秒前
zsj完成签到,获得积分10
14秒前
彭于晏应助能干的吐司采纳,获得10
14秒前
14秒前
15秒前
很腻害的人完成签到,获得积分20
16秒前
Kenny发布了新的文献求助10
16秒前
深情安青应助张茜采纳,获得10
17秒前
桐桐应助xwzz采纳,获得10
18秒前
18秒前
高分求助中
A new approach to the extrapolation of accelerated life test data 1000
ACSM’s Guidelines for Exercise Testing and Prescription, 12th edition 500
Picture Books with Same-sex Parented Families: Unintentional Censorship 500
Nucleophilic substitution in azasydnone-modified dinitroanisoles 500
不知道标题是什么 500
A Preliminary Study on Correlation Between Independent Components of Facial Thermal Images and Subjective Assessment of Chronic Stress 500
Phylogenetic study of the order Polydesmida (Myriapoda: Diplopoda) 360
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 3970802
求助须知:如何正确求助?哪些是违规求助? 3515474
关于积分的说明 11178714
捐赠科研通 3250627
什么是DOI,文献DOI怎么找? 1795390
邀请新用户注册赠送积分活动 875818
科研通“疑难数据库(出版商)”最低求助积分说明 805183