Genomic analysis of RNA binding protein target specificity

RNA结合蛋白靶标特异性的基因组分析

• 批准号: 8007539
• 负责人: Jeremy Robert Sanford
• 金额: $ 11.01万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-01-22 至 2011-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8007539
• 关键词: Address; Affect; Alternative Splicing; Arginine; Binding; Binding Sites; Biochemical; Biochemistry; Bioinformatics; Biological; Biological Assay; Biological Process; Biometry; Cell Proliferation; Cells; Code; Complex; Computational Biology; DNA Sequence; Data; Elements; Employee Strikes; Exons; Family; Functional RNA; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genomics; Goals; Human; Human Genome; In Situ; In Vitro; Indiana; Interdisciplinary Study; Introns; Life; Location; Medical center; Methodology; Methods; Molecular Biology; Molecular Weight; Physiological; Post-Transcriptional RNA Processing; Post-Transcriptional Regulation; Protein Binding; Protein Family; Proteins; RNA; RNA Splicing; RNA-Binding Proteins; RNA-Protein Interaction; Reaction; Regulation; Regulatory Element; Research Infrastructure; Reverse Transcriptase Polymerase Chain Reaction; Serine; Signal Transduction; Specificity; Transcript; Universities; Validation; cis acting element; genome wide association study; genome-wide; genome-wide analysis; human disease; in vivo; mRNA Precursor; novel; protein complex; protein expression

DESCRIPTION (provided by applicant): The complexity of human transcriptome is far greater than previously anticipated. Transcript diversity can be expanded through post-transcriptional RNA processing reactions as well as extensive inter-genic transcription. The genomic organization of cisacting RNA elements regulating expression of protein coding genes and non-coding inter-genic transcripts is poorly defined. This deficiency not only hampers our understanding of how the information stored within the human genome is utilized, but also weakens the connections between post-transcriptional control of gene expression and biological processes such as cell proliferation, differentiation and even human disease. The goal of this proposal is to illuminate post-transcriptional networks coordinated by RNA binding proteins. To achieve this goal we will identify cis-acting RNA elements recognized by a complete family of phylogenetically conserved, essential RNA binding proteins on a genome-wide scale. Our application focuses on the Serine and Arginine-rich family of pre-mRNA splicing factors (SR proteins). Biochemical methods will be employed to purify SR protein-RNA complexes under conditions that preserve the physiological context of RNA-protein interactions in the intact cell. Copurifying RNA molecules will be directly identified by two independent high throughput methods, pyrosequencing and hybridization to tiled genomic microarrays. Our R01 application will address the following specific aims: (1) Comprehensively identify cis-acting RNA elements recognized by the SR protein family. (2) Determine the genomic landscape of cis-acting RNA elements recognized by SR proteins. (3) Functionally validate SR protein cis-acting RNA elements.

描述（由申请人提供）：人类转录组的复杂性远远高于之前的预期。转录后多样性可以通过转录后 RNA 加工反应以及广泛的基因间转录来扩展。调节蛋白质编码基因和非编码基因间转录物表达的顺式作用RNA元件的基因组组织尚不清楚。这种缺陷不仅阻碍了我们对如何利用人类基因组中存储的信息的理解，而且削弱了基因表达的转录后控制与细胞增殖、分化甚至人类疾病等生物过程之间的联系。该提案的目标是阐明由 RNA 结合蛋白协调的转录后网络。为了实现这一目标，我们将在全基因组范围内鉴定出由系统发育保守的必需 RNA 结合蛋白完整家族识别的顺式作用 RNA 元件。我们的应用重点关注富含丝氨酸和精氨酸的前 mRNA 剪接因子（SR 蛋白）家族。将采用生化方法在保留完整细胞中 RNA-蛋白质相互作用的生理背景的条件下纯化 SR 蛋白质-RNA 复合物。共纯化 RNA 分子将通过两种独立的高通量方法直接鉴定，即焦磷酸测序和平铺基因组微阵列杂交。我们的R01应用将解决以下具体目标：（1）全面鉴定SR蛋白家族识别的顺式作用RNA元件。 (2)确定SR蛋白识别的顺式作用RNA元件的基因组图谱。 (3) 功能验证SR蛋白顺式作用RNA元件。

项目成果

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.

• DOI: 10.1101/gr.213595.116
• 发表时间: 2017-05
• 期刊: Genome research
• 影响因子: 7
• 作者: Rice ES;Kohno S;John JS;Pham S;Howard J;Lareau LF;O'Connell BL;Hickey G;Armstrong J;Deran A;Fiddes I;Platt RN 2nd;Gresham C;McCarthy F;Kern C;Haan D;Phan T;Schmidt C;Sanford JR;Ray DA;Paten B;Guillette LJ Jr;Green RE
• 通讯作者: Green RE

Frac-seq reveals isoform-specific recruitment to polyribosomes.

• DOI: 10.1101/gr.148585.112
• 发表时间: 2013-10
• 期刊: Genome research
• 影响因子: 7
• 作者: Sterne-Weiler T;Martinez-Nunez RT;Howard JM;Cvitovik I;Katzman S;Tariq MA;Pourmand N;Sanford JR
• 通讯作者: Sanford JR

Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing.

• DOI: 10.1186/1471-2164-10-s1-s4
• 发表时间: 2009-07-07
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Wang X;Wang K;Radovich M;Wang Y;Wang G;Feng W;Sanford JR;Liu Y
• 通讯作者: Liu Y

Splicing factor TRA2B is required for neural progenitor survival.

• DOI: 10.1002/cne.23405
• 发表时间: 2014-02-01
• 期刊: JOURNAL OF COMPARATIVE NEUROLOGY
• 影响因子: 2.5
• 作者: Roberts, Jacqueline M.;Ennajdaoui, Hanane;Edmondson, Carina;Wirth, Brunhilde;Sanford, Jeremy R.;Chen, Bin
• 通讯作者: Chen, Bin

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

• DOI: 10.1186/gb-2012-13-1-415
• 发表时间: 2012-01-31
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: St John JA;Braun EL;Isberg SR;Miles LG;Chong AY;Gongora J;Dalzell P;Moran C;Bed'hom B;Abzhanov A;Burgess SC;Cooksey AM;Castoe TA;Crawford NG;Densmore LD;Drew JC;Edwards SV;Faircloth BC;Fujita MK;Greenwold MJ;Hoffmann FG;Howard JM;Iguchi T;Janes DE;Khan SY;Kohno S;de Koning AJ;Lance SL;McCarthy FM;McCormack JE;Merchant ME;Peterson DG;Pollock DD;Pourmand N;Raney BJ;Roessler KA;Sanford JR;Sawyer RH;Schmidt CJ;Triplett EW;Tuberville TD;Venegas-Anaya M;Howard JT;Jarvis ED;Guillette LJ Jr;Glenn TC;Green RE;Ray DA
• 通讯作者: Ray DA