基于滑动窗口的原核转录起始位点计算定位方法

转录起始位点的计算定位是基因转录调控研究的重要内容,但现有方法的识别性能较低。文章作者在已有原核启动子识别算法的基础上,提出了一种基于滑动窗口的原核转录起始位点计算定位方法,通过在合理限定的定位范围内对序列进行滑动扫描,来预测转录起始位点的位置。首先根据窗口序列的交迭组分特征和启动子其它特征分别建立二次判别分类器,用其计算对应位置的似然得分,再利用转录起始位点与翻译起始位点的间隔经验分布信息对似然得分进行修正,最后依照似然得分的分布情况由阈值定位算法确定预测位置。对大肠杆菌真实序列数据的测试结果表明,该定位算法可实现对真实转录起始位点位置的有效预测,与已有算法相比,当敏感性指标同为0.85左右时,特异性指标可从0.20提高至0.65,从而使得定位准确率提高了约20个百分点。     

DREB2s转录因子基因的表达调控机制研究进展

DREB2s是植物特有的转录因子,隶属于AP2/EREBP转录因子家族,对干旱、高盐或低温、高温等非生物胁迫应答基因的表达有重要的调控作用。不同植物来源的DREB2在基因结构上有细微差异,对非生物胁迫的响应亦有不同表现。本文阐述了DREB2s的蛋白质结构特征及其对多种非生物胁迫的应答反应,并深入分析了DREB2s转录水平和转录后加工水平的表达调控分子机制的最新研究进展,为理解DREB2s基因功能、分子调控机制及作物抗逆基因工程提供理论依据。     

籼稻232蜡质基因转录起始位点的鉴定

Ｎｏｒｔｈｅｒｎｂｌｏｔ杂交分析和蜡质基因ｃＤＮＡ的序列分析表明水稻蜡质基因的转录本可能延伸到翻译起始密码子（ＡＴＧ）上游１２ｋｂ处。据此设计了２１Ｎｔ的寡核苷酸引物,并以籼稻２３２胚乳ＲＮＡ为模板,以引物延伸法确定籼稻２３２蜡质基因的转录起始点,籼稻蜡质基因的转录起始旁邻顺序ＣＴＣＡＣＣＡ与高等植物基因的转录起始点一致顺序ＣＴＣＡＴＣＡ仅相差１个碱基。通过顺序比较,对东乡野生稻蜡质基因中的转录起始位点的位置,以及对此两稻种中ＴＡＴＡ盒的可能顺序进行了讨论。     

IRESbase:A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites

Internal ribosome entry sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA (circRNA), with no 5′ cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidence will be useful for further studies. In this study, we present IRESbase, a comprehensive database of IRESs, by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNAs. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses, respectively. As IRESbase collects only IRES of minimal length with functional evidence, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and long non-coding RNAs (lncRNAs), 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequence. IRESbase is available at http://reprod.njmu.edu.cn/cgi-bin/iresbase/index.php.