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The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system

BMC GENETICS (2012)

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BMC GENETICS
卷 13, 期 -, 页码 -

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BIOMED CENTRAL LTD
DOI: 10.1186/1471-2156-13-31

关键词

piRNA; PIWI; LINE-1; Transposable element; Germline; Methylation; Epigenetics

类别

Genetics & Heredity

资金

  1. University of Iceland Research Fund
  2. Icelandic Student Innovation Fund
  3. Landspitali University Hospital Science Fund
  4. Memorial Fund of Bergbora Magnusdottir and Jakob Bjarnason

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Background: A defense system against transposon activity in the human germline based on PIWI proteins and piRNA has recently been discovered. It represses the activity of LINE-1 elements via DNA methylation by a largely unknown mechanism. Based on the dispersed distribution of clusters of piRNA genes in a strand-specific manner on all human chromosomes, we hypothesized that this system might work preferentially on local and proximal sequences. We tested this hypothesis with a methylation-associated SNP (mSNP) marker which is based on the density of C-T transitions in CpG dinucleotides as a surrogate marker for germline methylation. Results: We found significantly higher density of mSNPs flanking piRNA clusters in the human genome for flank sizes of 1-16 Mb. A dose-response relationship between number of piRNA genes and mSNP density was found for up to 16 Mb of flanking sequences. The chromosomal density of hypermethylated LINE-1 elements had a significant positive correlation with the chromosomal density of piRNA genes (r = 0.41, P = 0.05). Genome windows of 1-16 Mb containing piRNA clusters had significantly more hypermethylated LINE-1 elements than windows not containing piRNA clusters. Finally, the minimum distance to the next piRNA cluster was significantly shorter for hypermethylated LINE-1 compared to normally methylated elements (14.4 Mb vs 16.1 Mb). Conclusions: Our observations support our hypothesis that the piRNA-PIWI system preferentially methylates sequences in close proximity to the piRNA clusters and perhaps physically adjacent sequences on other chromosomes. Furthermore they suggest that this proximity effect extends up to 16 Mb. This could be due to an unknown localization signal, transcription of piRNA genes near the nuclear membrane or the presence of an unknown RNA molecule that spreads across the chromosome and targets the methylation directed by the piRNA-PIWI complex. Our data suggest a region specific molecular mechanism which can be sought experimentally.

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Article Genetics & Heredity

Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

Nick Shrine, Abril G. Izquierdo, Jing Chen, Richard Packer, Robert J. Hall, Anna L. Guyatt, Chiara Batini, Rebecca J. Thompson, Chandan Pavuluri, Vidhi Malik, Brian D. Hobbs, Matthew Moll, Wonji Kim, Ruth Tal-Singer, Per Bakke, Katherine A. Fawcett, Catherine John, Kayesha Coley, Noemi Nicole Piga, Alfred Pozarickij, Kuang Lin, Iona Y. Millwood, Zhengming Chen, Liming Li, Sara R. A. Wijnant, Lies Lahousse, Guy Brusselle, Andre G. Uitterlinden, Ani Manichaikul, Elizabeth C. Oelsner, Stephen S. Rich, R. Graham Barr, Shona M. Kerr, Veronique Vitart, Michael R. Brown, Matthias Wielscher, Medea Imboden, Ayoung Jeong, Traci M. Bartz, Sina A. Gharib, Claudia Flexeder, Stefan Karrasch, Christian Gieger, Annette Peters, Beate Stubbe, Xiaowei Hu, Victor E. Ortega, Deborah A. Meyers, Eugene R. Bleecker, Stacey B. Gabriel, Namrata Gupta, Albert Vernon Smith, Jian'an Luan, Jing-Hua Zhao, Ailin F. Hansen, Arnulf Langhammer, Cristen Willer, Laxmi Bhatta, David Porteous, Blair H. Smith, Archie Campbell, Tamar Sofer, Jiwon Lee, Martha L. Daviglus, Bing Yu, Elise Lim, Hanfei Xu, George T. O'Connor, Gaurav Thareja, Omar M. E. Albagha, Said I. Ismail, Wadha Al-Muftah, Radja Badji, Hamdi Mbarek, Dima Darwish, Tasnim Fadl, Heba Yasin, Maryem Ennaifar, Rania Abdellatif, Fatima Alkuwari, Muhammad Alvi, Yasser Al-Sarraj, Chadi Saad, Asmaa Althani, Eleni Fethnou, Fatima Qafoud, Eiman Alkhayat, Nahla Afifi, Sara Tomei, Wei Liu, Stephan Lorenz, Najeeb Syed, Hakeem Almabrazi, Fazulur Rehaman Vempalli, Ramzi Temanni, Tariq Abu Saqri, Mohammedhusen Khatib, Mehshad Hamza, Tariq Abu Zaid, Ahmed El Khouly, Tushar Pathare, Shafeeq Poolat, Rashid Al-Ali, Souhaila Al-Khodor, Mashael Alshafai, Ramin Badii, Lotfi Chouchane, Xavier Estivill, Khalid Fakhro, Younes Mokrab, Jithesh Puthen, Zohreh Tatari, Karsten Suhre, Raquel Granell, Tariq O. Faquih, Pieter S. Hiemstra, Annelies M. Slats, Benjamin H. Mullin, Jennie Hui, Alan James, John Beilby, Karina Patasova, Pirro Hysi, Jukka T. Koskela, Annah B. Wyss, Jianping Jin, Sinjini Sikdar, Mikyeong Lee, Sebastian May-Wilson, Nicola Pirastu, Katherine A. Kentistou, Peter K. Joshi, Paul R. H. J. Timmers, Alexander T. Williams, Robert C. Free, Xueyang Wang, John L. Morrison, Frank D. Gilliland, Zhanghua Chen, Carol A. Wang, Rachel E. Foong, Sarah E. Harris, Adele Taylor, Paul Redmond, James P. Cook, Anubha Mahajan, Lars Lind, Teemu Palviainen, Terho Lehtimaki, Olli T. Raitakari, Jaakko Kaprio, Taina Rantanen, Kirsi H. Pietilainen, Simon R. Cox, Craig E. Pennell, Graham L. Hall, W. James Gauderman, Chris Brightling, James F. Wilson, Tuula Vasankari, Tarja Laitinen, Veikko Salomaa, Dennis O. Mook-Kanamori, Nicholas J. Timpson, Eleftheria Zeggini, Josee Dupuis, Caroline Hayward, Ben Brumpton, Claudia Langenberg, Stefan Weiss, Georg Homuth, Carsten Oliver Schmidt, Nicole Probst-Hensch, Marjo-Riitta Jarvelin, Alanna C. Morrison, Ozren Polasek, Igor Rudan, Joo-Hyeon Lee, Ian Sayers, Emma L. Rawlins, Frank Dudbridge, Edwin K. Silverman, David P. Strachan, Robin G. Walters, Andrew P. Morris, Stephanie J. London, Michael H. Cho, Louise Wain, Ian P. Hall, Martin Tobin

Summary: Through a large-scale multi-ancestry genome-wide association meta-analysis, 1020 independent association signals implicating 559 genes related to COPD were identified. These genes were enriched in 29 pathways. Variants showed heterogeneity across ancestries, age and smoking groups, and the genetic risk score was strongly associated with COPD across ancestry groups. New potential causal variants, genes, proteins and pathways were highlighted, including those targeted by existing drugs. These findings contribute to a better understanding of lung function and COPD mechanisms and have implications for functional genomics experiments and future COPD therapies.

NATURE GENETICS (2023)

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Article Clinical Neurology

Association of Mitochondrial DNA Copy Number With Brain MRI Markers and Cognitive Function A Meta-analysis of Community-Based Cohorts

Yuankai Zhang, Xue Liu, Kerri L. Wiggins, Nuzulul L. Kurniansyah, Xiuqing Guo, Amanda L. Rodrigue, Wei Zhao, Lisa R. Yanek, Scott M. Ratliff, Achilleas Pitsillides, Juan Sebastian Aguirre Patino, Tamar Sofer, Dan E. Arking, Thomas R. Austin, Alexa S. Beiser, John Blangero, Eric E. Boerwinkle, Jan Bressler, Joanne E. Curran, Lifang Hou, Timothy J. Hughes, Sharon L. R. Kardia, Lenore J. Launer, Daniel Levy, Thomas H. Mosley, Ilya M. Nasrallah, Stephen S. Rich, Jerome Rotter, Sudha Seshadri, Wassim Tarraf, Kevin A. Gonzalez, Vasan Ramachandran, Kristine Yaffe, Paul A. Nyquist, Bruce M. Psaty, Charles C. DeCarli, Jennifer M. Smith, David C. Glahn, Hector M. Gonzalez, Joshua R. Bis, Myriam L. Fornage, Susan Heckbert, Annette L. Fitzpatrick, Chunyu Liu, Claudia L. Satizabal

Summary: This study found that higher mitochondrial DNA copy number (CN) in blood is associated with better cognitive function in both current and future settings, but is not causally related to cognition. This suggests that circulating mtDNA CN could serve as a biomarker of cognitive function in the community.

NEUROLOGY (2023)

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Correction Multidisciplinary Sciences

Clonal haematopoiesis and risk of chronic liver disease (vol 616, pg 747, 2023)

Waihay J. Wong, Connor Emdin, Alexander G. Bick, Seyedeh M. Zekavat, Abhishek Niroula, James Pirruccello, Laura Dichtel, Gabriel Griffin, Md Mesbah E. Uddin, Christopher Gibson, Veronica T. Kovalcik, Amy Lin, Marie McConkey, Amelie Vromman, Rob Sellar, Peter Kim, Mridul Agrawal, Joshua Weinstock, Michelle Long, Bing Yu, Rajarshi Banerjee, Rowan Nicholls, Andrea Dennis, Matt Kelly, Po-Ru Loh, Steve McCarroll, Eric Boerwinkle, Ramachandran Vasan, Siddhartha Jaiswal, Andrew Johnson, Raymond Chung, Kathleen Corey, Daniel Levy, Christie Ballantyne, Benjamin Ebert, Pradeep Natarajan

NATURE (2023)

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Review Biochemical Research Methods

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

Saori Sakaue, Saisriram Gurajala, Michelle Curtis, Yang Luo, Wanson Choi, Kazuyoshi Ishigaki, Joyce B. Kang, Laurie Rumker, Aaron J. Deutsch, Sebastian Schoenherr, Lukas Forer, Jonathon LeFaive, Christian Fuchsberger, Buhm Han, Tobias L. Lenz, Paul I. W. de Bakker, Yukinori Okada, Albert V. Smith, Soumya Raychaudhuri

Summary: The HLA locus is associated with more complex diseases than any other locus in the human genome, and it explains more heritability in many diseases than all other known loci combined. In silico HLA imputation methods allow for rapid and accurate estimation of HLA alleles in genotyped individuals. This tutorial provides guidance on performing HLA imputation, association testing, and fine mapping, and aims to contribute to understanding the role of HLA in human diseases.

NATURE PROTOCOLS (2023)

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