Circulating DNA reveals a specific and higher fragmentation of the Y chromosome

An Y, Zhao X, Zhang Z et al (2023) DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation. Nat Commun 14:287. https://doi.org/10.1038/s41467-023-35959-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bianchi NO (2009) Y chromosome structural and functional changes in human malignant diseases. Mutation Res/rev Mutation Res 682:21–27. https://doi.org/10.1016/j.mrrev.2009.02.001

Article  CAS  Google Scholar 

Chan KCA, Zhang J, Hui ABY et al (2004) Size distributions of maternal and fetal DNA in maternal plasma. Clin Chem 50:88–92. https://doi.org/10.1373/clinchem.2003.024893

Article  CAS  PubMed  Google Scholar 

Chandrananda D, Thorne NP, Bahlo M (2015) High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA. BMC Med Genomics 8:29. https://doi.org/10.1186/s12920-015-0107-z

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duijf PHG, Schultz N, Benezra R (2013) Cancer cells preferentially lose small chromosomes. Int J Cancer 132:2316–2326. https://doi.org/10.1002/ijc.27924

Article  CAS  PubMed  Google Scholar 

Forsberg LA (2017) Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men. Hum Genet 136:657–663. https://doi.org/10.1007/s00439-017-1799-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guizard S, Piégu B, Bigot Y (2016) DensityMap: a genome viewer for illustrating the densities of features. BMC Bioinform 17:204. https://doi.org/10.1186/s12859-016-1055-0

Article  CAS  Google Scholar 

Han DSC, Ni M, Chan RWY et al (2020) The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3, and DFFB. Am J Hum Genet 106:202–214. https://doi.org/10.1016/j.ajhg.2020.01.008

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hauer MH, Seeber A, Singh V et al (2017) Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates. Nat Struct Mol Biol 24:99–107. https://doi.org/10.1038/nsmb.3347

Article  CAS  PubMed  Google Scholar 

Hunter S, Gramlich T, Abbott K, Varma V (1993) Y chromosome loss in esophageal carcinoma: an in situ hybridization study. Genes Chromosom Cancer 8:172–177. https://doi.org/10.1002/gcc.2870080306

Article  CAS  PubMed  Google Scholar 

Jacobs PA, Brunton M, Court Brown WM et al (1963) Change of human chromosome count distribution with age: evidence for a sex differences. Nature 197:1080–1081. https://doi.org/10.1038/1971080a0

Article  CAS  PubMed  Google Scholar 

Jahr S, Hentze H, Englisch S et al (2001) DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res 61:1659–1665

CAS  PubMed  Google Scholar 

Koyama R, Arai T, Kijima M et al (2016) DNase γ, DNase I and caspase-activated DNase cooperate to degrade dead cells. Genes Cells 21:1150–1163. https://doi.org/10.1111/gtc.12433

Article  CAS  PubMed  Google Scholar 

Kumar D, Upadhya D, Uppangala S et al (2013) Nuclear DNA fragmentation negatively affects zona binding competence of Y bearing mouse spermatozoa. J Assist Reprod Genet 30:1611–1615. https://doi.org/10.1007/s10815-013-0123-x

Article  PubMed  PubMed Central  Google Scholar 

Li G, Wang C, Guan X, et al (2022) Age-related DNA methylation on Y chromosome and their associations with total mortality among Chinese males. Aging Cell 21:e13563. https://doi.org/10.1111/acel.13563

Lo YM, Corbetta N, Chamberlain PF et al (1997) Presence of fetal DNA in maternal plasma and serum. Lancet 350:485–487. https://doi.org/10.1016/S0140-6736(97)02174-0

Article  CAS  PubMed  Google Scholar 

Lui YYN, Chik K-W, Chiu RWK et al (2002) Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. Clin Chem 48:421–427

Article  CAS  PubMed  Google Scholar 

Meddeb R, Pisareva E, Thierry AR (2019) Guidelines for the preanalytical conditions for analyzing circulating cell-free DNA. Clin Chem 65:623–633. https://doi.org/10.1373/clinchem.2018.298323

Article  CAS  PubMed  Google Scholar 

Moss J, Magenheim J, Neiman D et al (2018) Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun. https://doi.org/10.1038/s41467-018-07466-6

Article  PubMed  PubMed Central  Google Scholar 

Mouliere F, Robert B, Arnau Peyrotte E et al (2011) High fragmentation characterizes tumour-derived circulating DNA. PLoS ONE 6:e23418. https://doi.org/10.1371/journal.pone.0023418

Article  CAS  PubMed  PubMed Central  Google Scholar 

Park S-J, Jeong S-Y, Kim HJ (2006) Y chromosome loss and other genomic alterations in hepatocellular carcinoma cell lines analyzed by CGH and CGH array. Cancer Genet Cytogenet 166:56–64. https://doi.org/10.1016/j.cancergencyto.2005.08.022

Article  CAS  PubMed  Google Scholar 

Pisareva E, Mihalovičová L, Pastor B et al (2022) Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA. Genome Medicine 14:135. https://doi.org/10.1186/s13073-022-01125-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Reinhold K, Engqvist L (2013) The variability is in the sex chromosomes. Evolution 67:3662–3668. https://doi.org/10.1111/evo.12224

Article  PubMed  Google Scholar 

Sanchez C, Snyder MW, Tanos R et al (2018) New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis. NPJ Genom Med 3:31. https://doi.org/10.1038/s41525-018-0069-0

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sanchez C, Roch B, Mazard T et al (2021) Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics. JCI Insight 6:144561. https://doi.org/10.1172/jci.insight.144561

Article  PubMed  Google Scholar 

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ et al (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423:825–837. https://doi.org/10.1038/nature01722

Article  CAS  PubMed  Google Scholar 

Snyder MW, Kircher M, Hill AJ et al (2016) Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164:57–68. https://doi.org/10.1016/j.cell.2015.11.050

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun K, Jiang P, Chan KCA et al (2015) Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci USA 112:E5503-5512. https://doi.org/10.1073/pnas.1508736112

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thierry AR (2023) Circulating DNA fragmentomics and cancer screening. Cell Genomics 3:100242. https://doi.org/10.1016/j.xgen.2022.100242

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thierry AR, El Messaoudi S, Gahan PB et al (2016) Origins, structures, and functions of circulating DNA in oncology. Cancer Metastasis Rev 35:347–376. https://doi.org/10.1007/s10555-016-9629-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xue Y, Zhao G, Qiao L et al (2020) Sequencing shorter cfDNA fragments decreases the false negative rate of non-invasive prenatal testing. Front Genet 11:280. https://doi.org/10.3389/fgene.2020.00280

Article  PubMed  PubMed Central  Google Scholar 

Yates AD, Achuthan P, Akanni W et al (2020) Ensembl 2020. Nucleic Acids Res 48:D682–D688. https://doi.org/10.1093/nar/gkz966

Article  CAS  PubMed  Google Scholar 

You Y-A, Kwon W-S, Saidur Rahman M et al (2017) Sex chromosome-dependent differential viability of human spermatozoa during prolonged incubation. Hum Reprod 32:1183–1191. https://doi.org/10.1093/humrep/dex080

Article  CAS  PubMed  Google Scholar 

Zheng YWL, Chan KCA, Sun H et al (2012) Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model. Clin Chem 58:549–558. https://doi.org/10.1373/clinchem.2011.169318

Article  CAS  PubMed  Google Scholar 

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