Identification of novel genes in human genome

人类基因组中新基因的鉴定

• 批准号: 6906514
• 负责人: SAN MING WANG
• 金额: $ 50.42万
• 依托单位: NORTHSHORE UNIVERSITY HEALTHSYSTEM
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-19 至 2007-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6906514
• 关键词: CD34 molecule; RNA; clinical research; complementary DNA; functional /structural genomics; gene expression; genes; genetic mapping; genetic techniques; genome; high throughput technology; human genetic material tag; pseudogenes; sequence tagged sites; serial analysis of gene expression; stem cells

DESCRIPTION (provided by applicant): A comprehensive understanding of the complexity of gene expression during development and differentiation requires the identification of all of the mRNA transcripts. The SAGE (serial analysis of gene expression) technique is one of the most comprehensive methods presently available to achieve this goal. Because it does not require the prior knowledge of the expressed transcripts present in a sample, SAGE can identify novel transcripts. We have identified a large number of novel SAGE tags from hematopoietic cells. Our analysis of the nature of the novel SAGE tags indicates that most of the novel SAGE tags are derived from novel transcripts, and many of these novel transcripts may represent novel genes not identified in the human genome. In his proposal, we have set three specific aims to isolate full-length novel cDNAs starting from novel SAGE tags: Specific Aim 1. Convert 10,000 novel SAGE tags identified in human CD34+ stem/progenitor cells into 3' cDNAs; Specific Aim 2. Convert about 6,000 novel 3' cDNAs generated from Specific Aim 1 into 8,000 to 10,000 full-length cDNAs including alternatively spliced variants; and Specific Aim 3. Annotate full-length novel cDNAs generated by Specific Aim 2 to the human genome sequence. We have developed a high-throughput system to achieve these aims. In this system, a SAGE tag of 14 bases is extended to the 3' end of the cDNA averaging 140 bases that can be mapped to the human genomic sequences. For the mapped sequences that show novelty, we will use the putative first exon predicted by the computational program First EF to design a sense primer. Together with the antisense primer designed based on the 3' cDNA, we will amplify the full-length cDNA represented by the novel SAGE tag and integrate the information into the human genome. Our analysis should reveal a significant number of novel genes, novel alternatively spliced transcripts originating from novel genes or known genes, non-coding RNAs, and transcripts from pseudogenes. The success of our proposal should make a significant contribution for the annotation of human genome. It should also provide information for studying normal and abnormal hematopoiesis. The information should also be useful for the improvement of genome annotation algorithms. Our approach should also be applicable for studies on other tissues of both human and non-human origins.

描述（由申请人提供）：全面了解发育和分化过程中基因表达的复杂性需要鉴定所有mRNA转录本。SAGE（基因表达系列分析）技术是目前实现这一目标的最全面的方法之一。因为它不需要事先知道样品中存在的表达转录本，SAGE可以识别新的转录本。我们已经从造血细胞中鉴定出大量新的SAGE标签。我们对新型SAGE标签性质的分析表明，大多数新型SAGE标签来源于新型转录本，并且这些新型转录本中的许多可能代表人类基因组中未鉴定的新型基因。在他的提议中，我们设定了三个具体目标，从新的SAGE标签开始分离全长新cDNA：具体目标1。将在人CD 34+干/祖细胞中鉴定的10，000个新SAGE标签转化为3'cDNA;特异性目的2。将特异性目标1产生的约6，000个新的3'cDNA转化为8，000至10，000个全长cDNA，包括可变剪接变体;和特异性目标3。将特异性目的2产生的全长新cDNA注释到人类基因组序列中。我们开发了一个高通量系统来实现这些目标。在该系统中，将14个碱基的SAGE标签延伸至cDNA的3’末端，平均140个碱基，其可被定位至人基因组序列。对于显示新奇的映射序列，我们将使用计算程序First EF预测的推定的第一外显子来设计有义引物。与基于3' cDNA设计的反义引物一起，我们将扩增由新型SAGE标签代表的全长cDNA，并将信息整合到人类基因组中。我们的分析应该揭示了大量的新基因，新的选择性剪接转录本来自新基因或已知基因，非编码RNA，和转录本假基因。该方案的成功将为人类基因组注释做出重要贡献。它还应该为研究正常和异常造血提供信息。这些信息也应该是有用的基因组注释算法的改进。我们的方法也应该适用于人类和非人类起源的其他组织的研究。

项目成果

SAGE detects microRNA precursors.

• DOI: 10.1186/1471-2164-7-285
• 发表时间: 2006-11-07
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Ge X;Wu Q;Wang SM
• 通讯作者: Wang SM

Long-short-long games in mRNA identification: the length matters.

mRNA 识别中的长-短-长博弈：长度很重要。

• DOI: 10.2174/138920108785915166
• 发表时间: 2008
• 期刊: Current pharmaceutical biotechnology
• 影响因子: 2.8
• 作者: Wang,SanMing

SAGE is far more sensitive than EST for detecting low-abundance transcripts.

• DOI: 10.1186/1471-2164-5-1
• 发表时间: 2004-01-05
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Sun M;Zhou G;Lee S;Chen J;Shi RZ;Wang SM
• 通讯作者: Wang SM

Poly A- transcripts expressed in HeLa cells.

在HeLa细胞中表达的聚A-转录本。

• DOI: 10.1371/journal.pone.0002803
• 发表时间: 2008-07-30
• 期刊: PLOS ONE
• 影响因子: 3.7
• 作者: Wu, Qingfa;Kim, Yeong C.;Lu, Jian;Xuan, Zhenyu;Chen, Jun;Zheng, Yonglan;Zhou, Tom;Zhang, Michael Q.;Wu, Chung-I;Wang, San Ming
• 通讯作者: Wang, San Ming

Consistent deregulation of gene expression between human and murine MLL rearrangement leukemias.

• DOI: 10.1158/0008-5472.can-08-3381
• 发表时间: 2009-02-01
• 期刊: Cancer research
• 影响因子: 11.2
• 作者: Li Z;Luo RT;Mi S;Sun M;Chen P;Bao J;Neilly MB;Jayathilaka N;Johnson DS;Wang L;Lavau C;Zhang Y;Tseng C;Zhang X;Wang J;Yu J;Yang H;Wang SM;Rowley JD;Chen J;Thirman MJ
• 通讯作者: Thirman MJ