Excellence in Research Project: Functional Characterization of the X-antigen Gene Family

卓越研究项目：X 抗原基因家族的功能表征

• 批准号: 1955975
• 负责人: Saumya Ramanathan
• 金额: $ 49.3万
• 依托单位: Fisk University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1955975&HistoricalAwards=false
• 关键词: Excellence; Research; Project; Functional; Characterization

Sequencing of the human X chromosome has revealed the existence of many genes that have a unique expression pattern; they are usually expressed in the testis and aberrantly expressed in proliferative tissue, such as cancer. This project proposes to study one family of these genes, the X-antigen gene family (XAGE) whose functions are completely uncharacterized. The overarching goal of this project is to discover the biochemical function of XAGE proteins and to determine the molecular processes that drive their expression. Consistent with Fisk University’s mission to provide students with every tool they need to emerge as future scholars and leaders, this research program will provide Fisk undergraduates with the hands-on opportunity to obtain interdisciplinary scientific knowledge as well as the technical and problem-solving skills that they need to successfully transition to post-undergraduate education and a career in the sciences. In addition to providing faculty mentored research in the investigatos's own laboratory, some of these research concepts and their applications will be introduced in a course-associated laboratory. This project focuses on identifying the underlying mechanisms that cause certain genes on the X chromosome to be expressed only in certain cells at certain times, an area of research that due to its wide scope, is particularly appealing to undergraduate students interested in biological science. X-antigen genes are located on the X-chromosome and considered to be cancer-testis antigens due to their expression in testis and aberrant expression in proliferative cells. These genes have recently evolved, and their biochemical function and mechanisms regulating either expression is entirely unknown. Using a combination of biochemical and genetic approaches such as tandem affinity IP-Mass Spectrometry and RNA-Sequencing the investogator will determine the biochemical functions of XAGE proteins and those signaling pathways that are perturbed upon aberrant expression. To determine the transcriptional networks and epigenetic mechanisms that lead to this unique expression pattern of XAGE genes, the investigator will perform bioinformatics analysis of methylome sequencing data and promoter elements and then using wet-lab experiments determine the transcription factors that bind to XAGE gene promoters to drive expression. The research will also discover which cis-acting elements, such as enhancers, regulate XAGE expression using Pro-Seq to compare chromatin accessibility in cells expressing XAGE genes versus those that do not. The proposed research will determine whether XAGEs have evolved to provide cells a proliferative or survival advantage and if so, what mechanisms drive their expression.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

人类X染色体的测序揭示了许多具有独特表达模式的基因的存在;它们通常在睾丸中表达，并在增殖组织（如癌症）中异常表达。该项目提出研究这些基因中的一个家族，X抗原基因家族（XAGE），其功能完全未知。该项目的首要目标是发现XAGE蛋白的生化功能，并确定驱动其表达的分子过程。与菲斯克大学的使命一致，为学生提供他们需要成为未来学者和领导者的每一种工具，这项研究计划将为菲斯克本科生提供动手的机会，以获得跨学科的科学知识以及他们需要成功过渡到本科后教育和科学事业的技术和解决问题的技能。除了提供教师指导的研究，在该大学自己的实验室，其中一些研究概念及其应用将在课程相关的实验室介绍。该项目的重点是确定导致X染色体上的某些基因在某些时间仅在某些细胞中表达的潜在机制，这是一个研究领域，由于其范围广泛，特别吸引对生物科学感兴趣的本科生。X抗原基因位于X染色体上，由于其在睾丸中表达和在增殖细胞中异常表达而被认为是癌症-睾丸抗原。这些基因是最近才进化出来的，它们的生化功能和调控表达的机制还完全未知。使用生物化学和遗传方法的组合，例如串联亲和IP-质谱和RNA测序，研究人员将确定XAGE蛋白的生化功能以及异常表达时受到干扰的信号通路。为了确定导致XAGE基因这种独特表达模式的转录网络和表观遗传机制，研究人员将对甲基化组测序数据和启动子元件进行生物信息学分析，然后使用湿实验室实验确定与XAGE基因启动子结合以驱动表达的转录因子。该研究还将发现哪些顺式作用元件，如增强子，使用Pro-Seq调节XAGE表达，以比较表达XAGE基因的细胞与不表达XAGE基因的细胞中的染色质可及性。这项研究将确定XAGEs是否已经进化到为细胞提供增殖或生存优势，如果是的话，是什么机制驱动它们的表达。这个奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

Systematic Transmission Electron Microscopy-Based Identification and 3D Reconstruction of Cellular Degradation Machinery

• DOI: 10.1101/2021.09.26.461841
• 发表时间: 2021-09
• 期刊: bioRxiv
• 作者: Kit Neikirk;Z. Vue;Prasanna Katti;Benjamin Rodriguez;Salem A. Omer;J. Shao;T. Christensen;E. Garza Lopez;A. Marshall;Caroline B. Palavicino-Maggio;Jessica M. Ponce;Ahmad F Alghanem;Lar L. Vang;Taylor Barongan;H. Beasley;Taylor A Rodman;Dominique C. Stephens;M. Mungai;M. Correia;V. Exil;S. Damo;Sandra A. Murray;Amber Crabtree;B. Glancy;R. Pereira;E. Abel;Antentor O. Hinton

A Comprehensive Approach to Sample Preparation for Electron Microscopy and the Assessment of Mitochondrial Morphology in Tissue and Cultured Cells

• DOI: 10.1002/adbi.202200202
• 发表时间: 2023-05-04
• 期刊: ADVANCED BIOLOGY
• 影响因子: 3.7
• 作者: Hinton Jr, Antentor;Katti, Prasanna;Abel, E. Dale
• 通讯作者: Abel, E. Dale