Ying Liu

Ying Liu

Associate Professor

Primary fields of research

Our group aims to understand the processes cells use to counteract replication stress caused by either internal factors (i.e. oncogene activation), or external factors (i.e. folate deficiency), and why some regions in the genome are particularly susceptible to those factors (e.g. common or rare fragile sites). Specifically, we focus on the following two areas to achieve our goals. We employ techniques in the fields of cellular and molecular biology, cytogenetics, biochemistry, advanced imaging, whole genome sequencing, and mass spectrometry-based proteomics.

Current research

On-going projects 

1) The characterization of helicases that play a role in resolving DNA or RNA associated secondary structures

It is well established that incomplete replication can cause a delay in chromatin condensation that leads to the ‘expression’ of common fragile sites (CFSs) [1, 2]. CFSs are hot spots for deletions and chromosome rearrangements in cancer [3]. We previously discovered that a process called mitotic DNA synthesis (MiDAS) that operates in mitosis is a strategy used by human cells to rescue the incomplete replication at those loci, particularly in cancers cells [4-7]. Our current findings demonstrate that RTEL1, a DNA helicase, can prevent the accumulation of G-quadruplex-associated R-loops at difficult-to-replicate loci including CFSs in the human genome in S phase, and can facilitate MiDAS in M phase [8]. We are now investigating how RTEL1 accomplish these important roles using in vitro or in vivo assays. 

  2) The analysis of folate deficiency induced genome instability

Folate deficiency is known to be associated with a diverse range of human disorders including fetal neural tube defects, age-associated dementia, infertility, and some type of cancers. Intriguingly, folate deficiency is known can cause the expression of group of rare fragile sites, all of which contain long stretch of CGG simple repeats.  The most well studied locus of this kind is called FRAXA that is associated with Fragile X syndrome (FXS). Using FXS cells as a model, we have demonstrated that (i) folate deprivation triggers the extensive missegregation and aneuploidy of chromosome X [9], and (ii) MiDAS at the FRAXA locus occurs via break-induced DNA replication (BIR) and this process requires the SLX1/SLX4 endonuclease complex, the RAD51 recombinase and POLD3 [10]. We are currently investigating other regions that are vulnerable to folate deficiency in the human genome, and the strategies cells employ to maintain the stability of those regions. 

References (The names of the authors from our group are in bold.):

1.  Helmrich, A., M. Ballarino, and L. Tora, Collisions between Replication and Transcription Complexes Cause Common Fragile Site Instability at the Longest Human Genes. Molecular Cell, 2011. 44(6): p. 966-977.

2.  Letessier, A., G.A. Millot, S. Koundrioukoff, A.M. Lachages, N. Vogt, R.S. Hansen, B. Malfoy, O. Brison, and M. Debatisse, Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site. Nature, 2011. 470(7332): p. 120-3.

3.  Richards, R.I., Fragile and unstable chromosomes in cancer: causes and consequences. Trends Genet, 2001. 17(6): p. 339-45.

4.  Bjerregaard, V.A., O. Ozer, I.D. Hickson, and Y. LiuThe Detection and Analysis of Chromosome Fragile Sites. Methods Mol Biol, 2018. 1672: p. 471-482.

5.  Garribba, L.W. Wu, O. Ozer, R. Bhowmick, I.D. Hickson, and Y. LiuInducing and Detecting Mitotic DNA Synthesis at Difficult-to-Replicate Loci. Mechanisms of DNA Recombination and Genome Rearrangements: Intersection between Homologous Recombination, DNA Replication and DNA Repair, 2018. 601: p. 45-58.

6.  Minocherhomji, S., S. Ying, V.A. BjerregaardS. Bursomanno, A. Aleliunaite, W. Wu, H.W. Mankouri, H. Shen, Y. Liu, and I.D. Hickson, Replication stress activates DNA repair synthesis in mitosis. Nature, 2015. 528(7581): p. 286-90.

7.  Ren, L., L. Chen, W. WuL. Garribba, H. Tian, Z. Liu, I. Vogel, C. Li, I.D. Hickson, and Y. LiuPotential biomarkers of DNA replication stress in cancer. Oncotarget, 2017. 8(23): p. 36996-37008.

8.  Wu, W., R. Bhowmick, I. Vogel, O. Ozer, F. Ghisays, R.S. Thakur, E. Sanchez de Leon, P.H. RichterL. Ren, J.H. Petrini, I.D. Hickson, and Y. LiuRTEL1 suppresses G-quadruplex-associated R-loops at difficult-to-replicate loci in the human genome. Nat Struct Mol Biol, 2020. 27(5): p. 424-437.

9.  Bjerregaard, V.A., L. Garribba, C.T. McMurray, I.D. Hickson, and Y. LiuFolate deficiency drives mitotic missegregation of the human FRAXA locus. Proc Natl Acad Sci U S A, 2018.

10.  Garribba, L., V.A. Bjerregaard, M.M. Goncalves Dinis, O. Ozer, W. Wu, D. Sakellariou, J. Pena-Diaz, I.D. Hickson, and Y. LiuFolate stress induces SLX1- and RAD51-dependent mitotic DNA synthesis at the fragile X locus in human cells. Proc Natl Acad Sci U S A, 2020. 

Teaching

Teaching

Teach Molecular Biology and Genetics in the first year course of the Human Biology master program, a Copenhagen Master of Excellence programme, which is one of the 12 elite master educations sponsored by the Danish Ministry of Science, Technology and Innovation: http://humanbiology.ku.dk/fullprogrammes/ , since 2010. Lectures (4 hours):  Introductions to Genetics, Cancer genetics, Bioinformatics Experimental course, including the bioinformatic computing course (46 hours)

Course organiser of the IARU COP3 summer school since 2011: https://healthyaging.ku.dk/education/iaru-summer-school/

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