Article
Biochemistry & Molecular Biology
Anthony S. Zannas
Summary: When cells are exposed to prolonged natural stress hormone levels, profound and widespread epigenetic changes may occur, primarily at selected CpG sites and potentially spreading to nearby sites. The findings help understand how prolonged stress could impact the epigenome, with important implications for stress-related phenotypes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Athina Vidaki, Diego Montiel Gonzalez, Benjamin Planterose Jimenez, Manfred Kayser
Summary: A male-specific age predictor based on Y chromosome was constructed, accurately predicting male age without decreased accuracy with increasing age.
Article
Plant Sciences
Xuan Ma, Feng Xing, Qingxiao Jia, Qinglu Zhang, Tong Hu, Baoguo Wu, Lin Shao, Yu Zhao, Qifa Zhang, Dao-Xiu Zhou
Summary: Heterosis refers to the superior performance of hybrid lines over inbred parental lines. The study found that there are significant DNA methylation differences between parental varieties in hybrid rice, and dynamic methylation variations during development in hybrids. Additionally, most of the allelic-specific expression genes in hybrid rice are associated with DNA methylation, with a negative correlation between ASE and allelic-specific methylation.
Article
Genetics & Heredity
Mette Viuff, Anne Skakkebaek, Emma B. Johannsen, Simon Chang, Steen Bonlykke Pedersen, Katrine Meyer Lauritsen, Mette Glavind Bulow Pedersen, Christian Trolle, Jesper Just, Claus H. Gravholt
Summary: This study comprehensively analyzed the effects of the X chromosome number on the transcriptome and methylome in blood, fat, and muscle tissue of individuals with sex chromosome aneuploidies (SCAs). It was found that X chromosome number globally affected the transcriptome and methylome in a tissue-specific manner. The study also identified different gene expression and methylation patterns between 45,X and 47,XXY, and observed a significant effect of sex in fat and muscle tissue. Additionally, the study found regulatory functions of Y chromosomal genes on X chromosomal genes.
Article
Biochemistry & Molecular Biology
C. Gomez-Martin, E. Aparicio-Puerta, J. M. Medina, Guillermo Barturen, J. L. Oliver, M. Hackenberg
Summary: Genetic variation, gene expression, and DNA methylation influence each other in a complex way. The geno(5)mC database is created to study the impact of sequence variation and DNA methylation on gene expression. By analyzing SNP-CpG associations and correlations with gene expression levels, previously unknown interactions between disease-associated SNPs and their functional targets can be inferred.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Gaolian Xu, Hao Yang, Jiani Qiu, Julien Reboud, Linqing Zhen, Wei Ren, Hong Xu, Jonathan M. M. Cooper, Hongchen Gu
Summary: The authors propose a method called STEM-PCR for rapid and facile detection of specific nucleic acid modifications. This method utilizes a simple and widely accessible PCR-based workflow, and exhibits sensitivity 20 times greater than current gold-standard techniques by using a bisulfite-free process. They successfully demonstrate the clinical applicability of this method by detecting methylation of SEPTIN9 and SFRP2 genes, which are key biomarkers in tumor prognosis and diagnosis.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Paul J. J. McLaren, Immacolata Porreca, Gennaro Iaconis, Hoi Ping Mok, Subhankar Mukhopadhyay, Emre Karakoc, Sara Cristinelli, Cristina Pomilla, Istvan Bartha, Christian W. W. Thorball, Riley H. H. Tough, Paolo Angelino, Cher S. S. Kiar, Tommy Carstensen, Segun Fatumo, Tarryn Porter, Isobel Jarvis, William C. C. Skarnes, Andrew Bassett, Marianne K. K. DeGorter, Mohana Prasad Sathya Moorthy, Jeffrey F. F. Tuff, Eun-Young Kim, Miriam Walter, Lacy M. M. Simons, Arman Bashirova, Susan Buchbinder, Mary Carrington, Andrea Cossarizza, Andrea De Luca, James J. J. Goedert, David B. B. Goldstein, David W. W. Haas, Joshua T. T. Herbeck, Eric O. O. Johnson, Pontiano Kaleebu, William Kilembe, Gregory D. D. Kirk, Neeltje A. A. Kootstra, Alex H. H. Kral, Olivier Lambotte, Ma Luo, Simon Mallal, Javier Martinez-Picado, Laurence Meyer, Jose M. Miro, Pravi Moodley, Ayesha A. A. Motala, James I. I. Mullins, Kireem Nam, Niels Obel, Fraser Pirie, Francis A. A. Plummer, Guido Poli, Matthew A. A. Price, Andri Rauch, Ioannis Theodorou, Alexandra Trkola, Bruce D. D. Walker, Cheryl A. A. Winkler, Jean-Francois Zagury, Stephen B. B. Montgomery, Angela Ciuffi, Judd F. F. Hultquist, Steven M. M. Wolinsky, Gordon Dougan, Andrew M. L. Lever, Deepti Gurdasani, Harriet Groom, Manjinder S. S. Sandhu, Jacques Fellay
Summary: This study identified a previously undescribed association signal on chromosome 1 that is specific to African populations and is associated with lower set-point viral load in individuals living with HIV-1. Experimental studies showed that the gene CHD1L, which is involved in DNA repair, may play a role in limiting HIV-1 replication.
Article
Chemistry, Analytical
Xin-Ying Zhong, Qian-Yu Zhou, Jia-Hui Dong, Yue Yu, Ying-Lin Zhou, Xin-Xiang Zhang
Summary: A simple and highly-selective method for 5-methylcytosine detection of specific gene sequences was developed based on binary-probe DNA hybridization. The successful design of binary probes allowed for quantification of the average methylation levels of the target, demonstrating potential for pre-diagnosis of methylation-related diseases.
Article
Cell Biology
Guyanan Li, Chenming Wang, Xin Guan, Yansen Bai, Yue Feng, Wei Wei, Hua Meng, Ming Fu, Meian He, Xiaomin Zhang, Yanjun Lu, Yong Lin, Huan Guo
Summary: This study aimed to investigate the role of sex chromosomes in the aging process and discovered age-related DNA methylation changes on the Y chromosome. The findings suggest that certain methylation levels of specific genes are associated with male aging and all-cause mortality risk.
Article
Immunology
Ravesh Singh, Veron Ramsuran, Vivek Naranbhai, Nonhlanhla Yende-Zuma, Nigel Garrett, Koleka Mlisana, Krista L. Dong, Bruce D. Walker, Salim S. Abdool Karim, Mary Carrington, Thumbi Ndungu
Summary: Elevated levels of BST-2 may be associated with viral control in HIV-infected females, and DNA methylation plays a role in regulating BST-2 levels.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Genetics & Heredity
Timothy J. Stanek, Weihuan Cao, Rohan M. Mehra, Christopher E. Ellison
Summary: In this study, the authors used DRIP-seq to assess the sex-specific variability of R-loop formation in Drosophila melanogaster adults. They found that most R-loops are located in regions of high transcriptional activity and are more common on the X chromosome compared to autosomes. They also identified a subset of sex-biased R-loops, which are associated with genes showing ovary-biased expression in females and dosage-compensated genes on the X chromosome in males.
Article
Cardiac & Cardiovascular Systems
Meng Zhao, Ting Xu, Jiahui Lei, Bingyu Ji, Qinqin Gao
Summary: This study is the first to suggest that DNA methylation may be involved in regulating tissue-specific expression and vasoconstriction function of CACNA1C in the vascular system. It also strengthens the idea that DNA methylation plays important roles in regulating vascular smooth muscle cell function and the occurrence of vascular diseases.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Plant Sciences
Yajie Xue, Chengwu Zou, Chao Zhang, Hang Yu, Baoshan Chen, Haifeng Wang
Summary: This study analyzed the genome-wide methylation patterns in different tissues of sugarcane, revealing the important role of DNA methylation in gene expression regulation. Differences in methylation levels among tissues resulted in various differentially methylated regions (DMRs), particularly those related to biological pathways associated with tissue function.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Ecology
Monique Weemstra, Gregoire T. Freschet, Alexia Stokes, Catherine Roumet
Summary: Intraspecific trait variation in roots is influenced more by species identity than elevation, with root traits showing different responses to environmental changes across species. The relationships between root traits and elevation rarely matched the hypotheses, indicating complex species-specific patterns in response to environmental gradients. Climate, soil, and vegetation properties explain intraspecific root variation better than elevation, but these relationships are highly dependent on species.
FUNCTIONAL ECOLOGY
(2021)
Article
Multidisciplinary Sciences
Ariel Gershman, Michael E. G. Sauria, Xavi Guitart, Mitchell R. Vollger, Paul W. Hook, Savannah J. Hoyt, Miten Jain, Alaina Shumate, Roham Razaghi, Sergey Koren, Nicolas Altemose, Gina Caldas, Glennis A. Logsdon, Arang Rhie, Evan E. Eichler, Michael C. Schatz, Rachel J. O'Neill, Adam M. Phillippy, Karen H. Miga, Winston Timp
Summary: This study presents a high-resolution epigenetic analysis of the telomere-to-telomere human reference genome, revealing important insights into gene activity, clinical regulation, and providing a framework for investigating elusive regions of the genome.
Article
Biochemistry & Molecular Biology
Lars A. Forsberg, Chiara Rasi, Gyula Pekar, Hanna Davies, Arkadiusz Piotrowski, Devin Absher, Hamid Reza Razzaghian, Aleksandra Ambicka, Krzysztof Halaszka, Marcin Przewoznik, Anna Kruczak, Geeta Mandava, Saichand Pasupulati, Julia Hacker, K. Reddy Prakash, Ravi Chandra Dasari, Joey Lau, Nelly Penagos-Tafurt, Helena M. Olofsson, Gunilla Hallberg, Piotr Skotnicki, Jerzy Mitus, Jaroslaw Skokowski, Michal Jankowski, Ewa Srutek, Wojciech Zegarski, Eva Tiensuu Janson, Janusz Rys, Tibor Tot, Jan P. Dumanski
Article
Cell Biology
Gyula Pekar, Hanna Davies, Agnes P. Lukacs, Lars Forsberg, Dan Hellberg, Jan Dumanski, Tibor Tot
Article
Genetics & Heredity
Anna Ronowicz, Anna Janaszak-Jasiecka, Jaroslaw Skokowski, Piotr Madanecki, Rafal Bartoszewski, Magdalena Balut, Barbara Seroczynska, Kinga Kochan, Adam Bogdan, Malgorzata Butkus, Rafal Peksa, Magdalena Ratajska, Alina Kuzniacka, Bartosz Wasag, Magdalena Gucwa, Maciej Krzyzanowski, Janusz Jaskiewicz, Zbigniew Jankowski, Lars Forsberg, J. Renata Ochocka, Janusz Limon, Michael R. Crowley, Patrick G. Buckley, Ludwine Messiaen, Jan P. Dumanski, Arkadiusz Piotrowski
Letter
Oncology
J. Score, A. Chase, L. A. Forsberg, L. Feng, K. Waghorn, A. V. Jones, C. Rasi, D. C. Linch, J. P. Dumanski, R. E. Gale, N. C. P. Cross
Article
Oncology
A. Chase, W. Leung, W. Tapper, A. V. Jones, L. Knoops, C. Rasi, L. A. Forsberg, P. Guglielmelli, K. Zoi, V. Hall, L. Chiecchio, L. Eder-Azanza, C. Bryant, L. Lannfelt, L. Docherty, H. E. White, J. Score, D. J. G. Mackay, A. M. Vannucchi, J. P. Dumanski, N. C. P. Cross
Article
Genetics & Heredity
Jan P. Dumanski, Jean-Charles Lambert, Chiara Rasi, Vilmantas Giedraitis, Hanna Davies, Benjamin Grenier-Boley, Cecilia M. Lindgren, Dominique Campion, Carole Dufouil, Florence Pasquier, Philippe Amouyel, Lars Lannfelt, Martin Ingelsson, Lena Kilander, Lars Lind, Lars A. Forsberg
AMERICAN JOURNAL OF HUMAN GENETICS
(2016)
Review
Genetics & Heredity
Lars A. Forsberg, David Gisselsson, Jan P. Dumanski
NATURE REVIEWS GENETICS
(2017)
Article
Oncology
Jan P. Dumanski, Chiara Rasi, Peyman Bjorklund, Hanna Davies, Abir S. Ali, Malin Gronberg, Staffan Welin, Halfdan Sorbye, Henning Gronbaek, Janet L. Cunningham, Lars A. Forsberg, Lars Lind, Erik Ingelsson, Peter Stalberg, Per Hellman, Eva Tiensuu Janson
ENDOCRINE-RELATED CANCER
(2017)
Editorial Material
Cardiac & Cardiovascular Systems
Jan P. Dumanski, Johan Sundstrom, Lars A. Forsberg
CIRCULATION-CARDIOVASCULAR GENETICS
(2017)
Review
Genetics & Heredity
Lars Anders Forsberg, Devin Absher, Jan Piotr Dumanski
JOURNAL OF MEDICAL GENETICS
(2013)
Article
Genetics & Heredity
Lars A. Forsberg, Chiara Rasi, Niklas Malmqvist, Hanna Davies, Saichand Pasupulati, Geeta Pakalapati, Johanna Sandgren, Teresita Diaz de Stahl, Ammar Zaghlool, Vilmantas Giedraitis, Lars Lannfelt, Joannah Score, Nicholas C. P. Cross, Devin Absher, Eva Tiensuu Janson, Cecilia M. Lindgren, Andrew P. Morris, Erik Ingelsson, Lars Lind, Jan P. Dumanski
Article
Multidisciplinary Sciences
Jan P. Dumanski, Chiara Rasi, Mikael Lonn, Hanna Davies, Martin Ingelsson, Vilmantas Giedraitis, Lars Lannfelt, Patrik K. E. Magnusson, Cecilia M. Lindgren, Andrew P. Morris, David Cesarini, Magnus Johannesson, Eva Tiensuu Janson, Lars Lind, Nancy L. Pedersen, Erik Ingelsson, Lars A. Forsberg
Article
Biochemistry & Molecular Biology
Jan P. Dumanski, Jonatan Halvardson, Hanna Davies, Edyta Rychlicka-Buniowska, Jonas Mattisson, Behrooz Torabi Moghadam, Noemi Nagy, Kazimierz Weglarczyk, Karolina Bukowska-Strakova, Marcus Danielsson, Pawel Olszewski, Arkadiusz Piotrowski, Erin Oerton, Aleksandra Ambicka, Marcin Przewoznik, Lukasz Belch, Tomasz Grodzicki, Piotr L. Chlosta, Stefan Imreh, Vilmantas Giedraitis, Lena Kilander, Jessica Nordlund, Adam Ameur, Ulf Gyllensten, Asa Johansson, Alicja Jozkowicz, Maciej Siedlar, Alicja Klich-Raczka, Janusz Jaszczynski, Stefan Enroth, Jaroslaw Baran, Martin Ingelsson, John R. B. Perry, Janusz Rys, Lars A. Forsberg
Summary: Epidemiological investigations have shown that mosaic loss of chromosome Y (LOY) in leukocytes is associated with increased mortality and morbidity in men. Studies on sorted and single cells revealed significant variations in the presence of LOY across cell types and individuals, suggesting potential pleiotropic effects on gene expression and immune function.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Letter
Oncology
Viktor Ljungstrom, Jonas Mattisson, Jonatan Halvardson, Tatjana Pandzic, Hanna Davies, Edyta Rychlicka-Buniowska, Marcus Danielsson, Paul Lacaze, Lucia Cavelier, Jan P. Dumanski, Panagiotis Baliakas, Lars A. Forsberg
Article
Clinical Neurology
Malin Dorvall, Annie Pedersen, Jan P. Dumanski, Martin Soderholm, Arne G. Lindgren, Tara M. Stanne, Christina Jern
Summary: This study found an association between mosaic loss of chromosome Y (LOY) in male patients and poor outcome after ischemic stroke, which remained significant in patients not receiving recanalization therapy. Further studies on LOY and other somatic genetic alterations in larger stroke cohorts are needed.