Yi Yin, Ph.D.


Work Titles
UCLA Assistant Professor, Human Genetics Member, Bioinformatics GPB Home Area Member, Genetics & Genomics GPB Home Area
Education:
Degrees:
Ph.D., Duke University, 2009 - 2015
M.S., Duke University, 2013 - 2015
B.S., Beijing Normal University, 2005 - 2009

Contact Information:

Email Address:

yeastyin@g.ucla.edu


Website:

Lab Website
Twitter

Research Interest:

Genomic DNA experiences various types of lesions that can potentially lead to double strand breaks (DSBs). Failure to resolve such insults correctly has implications in cancer. Homologous recombination (HR) is a major pathway for repairing DSBs. HR is essential 1) for life: null mutations in BRCA genes are embryonic lethal; 2) in meiosis, which is initiated by hundreds of DSBs; and 3) in tumorigenesis. The central vision of our lab is to build a fully probabilistic understanding of HR by developing high-throughput single-cell sequencing technologies. Given one’s genotype, our long term goal is to be able to predict: 1) which genome regions are fragile; 2) what (epi)genetic contexts regulate DNA breakage; 3) how mutations and expression levels of DNA repair genes affect repair processes; and 4) what consequences HR and resulting rearrangements have from a single cell to an individual. 

The majority of HR events, however, occur between identical sister chromatids and is error-free. Unlike error-prone repair, HR is difficult to track by bulk whole-genome sequencing (WGS). For example, pan-cancer mutation signature studies read “scars” in the genome and by definition miss these error-free events. Rare spontaneous HR in development is even harder to analyze and thus its cell-type variation is poorly understood. The lack of high-throughput global assay for error-free HR hinders our understanding of DNA repair. We developed sci-L3 suite of singel-cell sequencing technologies, which enables linear amplification of single-cell genomes that scales to 1M cells and generalizes to multi-omics, including WGS, targeted-sequencing and DNA/RNA co-assay. Recently, we have expanded sci-L3 to Strand-seq, which provides the first high-throughput global assay for error-free HR.

Our lab will focus on developing a full-fledged HR mapping platform to characterize genome, tissue and evolutionary variation in mitotic HR rates and machinery, and to rapidly generate and test thousands of hypotheses in the space of mutants and/or genetic variants of DNA repair genes. We also aim to develop tools for studying HR in non-model organisms in a scalable manner. We are broadly interested in the following directions: 
A. Genome-wide characterization of HR partner choice between homologs and sister chromatids; 
B. Systematically investigate cell-type variation on DNA repair pathway usage; 
C. Construct dense linkage maps in non-model organisms;
D. New DNA repair gene finding in unculturable microbes.

Detailed Biography:

Dr. Yi Yin obtained a B.S. degree in Biotechnology from Beijing Normal University (BNU) in 2009. She then trained with Dr. Tom Petes at Duke University (University Program in Genetics and Genomics, 2009-2015) for her Ph.D. and studied mechanisms of mitotic recombination in yeast. Concurrently she also earned an M.S. degree in Statistical Science at Duke. She completed her postdoctoral training in Dr. Sunney Xie's lab at Harvard University (Chemistry and Chemical Biology, 2015-2016) and in Jay Shendure's lab at the University of Washington (Genome Sciences, 2016-2020) on developing single-cell sequencing technologies. Dr. Yin started her lab in the Department of Human Genetics at UCLA in March, 2020.

Publications:

A selected list of publications:

Yin Yi, Jiang Yue, Lam Kwan-Wood Gabriel, Berletch Joel B, Disteche Christine M, Noble William S, Steemers Frank J, Camerini-Otero R Daniel, Adey Andrew C, Shendure Jay   High-Throughput Single-Cell Sequencing with Linear Amplification Molecular cell, 2019; 76(4): 676-690.e10.
Chen Wei, McKenna Aaron, Schreiber Jacob, Haeussler Maximilian, Yin Yi, Agarwal Vikram, Noble William Stafford, Shendure Jay   Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair Nucleic acids research, 2019; 47(15): 7989-8003.
Klein Hannah L, Bačinskaja Giedrė, Che Jun, Cheblal Anais, Elango Rajula, Epshtein Anastasiya, Fitzgerald Devon M, Gómez-González Belén, Khan Sharik R, Kumar Sandeep, Leland Bryan A, Marie Léa, Mei Qian, Miné-Hattab Judith, Piotrowska Alicja, Polleys Erica J, Putnam Christopher D, Radchenko Elina A, Saada Anissia Ait, Sakofsky Cynthia J, Shim Eun Yong, Stracy Mathew, Xia Jun, Yan Zhenxin, Yin Yi, Aguilera Andrés, Argueso Juan Lucas, Freudenreich Catherine H, Gasser Susan M, Gordenin Dmitry A, Haber James E, Ira Grzegorz, Jinks-Robertson Sue, King Megan C, Kolodner Richard D, Kuzminov Andrei, Lambert Sarah Ae, Lee Sang Eun, Miller Kyle M, Mirkin Sergei M, Petes Thomas D, Rosenberg Susan M, Rothstein Rodney, Symington Lorraine S, Zawadzki Pawel, Kim Nayun, Lisby Michael, Malkova Anna   Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways Microbial cell (Graz, Austria), 2019; 6(1): 1-64.
Guo Xiaoge, Chavez Alejandro, Tung Angela, Chan Yingleong, Kaas Christian, Yin Yi, Cecchi Ryan, Garnier Santiago Lopez, Kelsic Eric D, Schubert Max, DiCarlo James E, Collins James J, Church George M   High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast Nature biotechnology, 2018; 36(6): 540-546.
Yin Yi, Dominska Margaret, Yim Eunice, Petes Thomas D   High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast eLife, 2017; 6(3): 500-8.
Deng Sarah K, Yin Yi, Petes Thomas D, Symington Lorraine S   Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification Molecular cell, 2015; 60(3): 500-8.
Yin Yi, Petes Thomas D   Recombination between homologous chromosomes induced by unrepaired UV-generated DNA damage requires Mus81p and is suppressed by Mms2p PLoS genetics, 2015; 11(3): e1005026.
Yin Yi, Petes Thomas D   The role of Exo1p exonuclease in DNA end resection to generate gene conversion tracts in Saccharomyces cerevisiae Genetics, 2014; 197(4): 1097-109.
Yin Yi, Petes Thomas D   Genome-wide high-resolution mapping of UV-induced mitotic recombination events in Saccharomyces cerevisiae PLoS genetics, 2013; 9(10): e1003894.
St Charles Jordan, Hazkani-Covo Einat, Yin Yi, Andersen Sabrina L, Dietrich Fred S, Greenwell Patricia W, Malc Ewa, Mieczkowski Piotr, Petes Thomas D   High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events Genetics, 2012; 190(4): 1267-84.

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