Dr. Britta Meyer

@article{e2f9bb95771140f892f9982ee6a26d52,

title = "Complete sequencing of ape genomes",

abstract = "The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1,2,3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.",

author = "DongAhn Yoo and Arang Rhie and Prajna Hebbar and Francesca Antonacci and Logsdon, {Glennis A.} and Solar, {Steven J.} and Dmitry Antipov and Pickett, {Brandon D.} and Yana Safonova and Francesco Montinaro and Yanting Luo and Joanna Malukiewicz and Storer, {Jessica M.} and Jiadong Lin and Sequeira, {Abigail N.} and Mangan, {Riley J.} and Glenn Hickey and {Monfort Anez}, Graciela and Parithi Balachandran and Anton Bankevich and Beck, {Christine R.} and Arjun Biddanda and Matthew Borchers and Bouffard, {Gerard G.} and Emry Brannan and Brooks, {Shelise Y.} and Lucia Carbone and Laura Carrel and Chan, {Agnes P.} and Juyun Crawford and Mark Diekhans and Eric Engelbrecht and Cedric Feschotte and Giulio Formenti and Garcia, {Gage H.} and {de Gennaro}, Luciana and David Gilbert and Green, {Richard E.} and Andrea Guarracino and Ishaan Gupta and Diana Haddad and Junmin Han and Harris, {Robert S.} and Hartley, {Gabrielle A.} and Harvey, {William T.} and Michael Hiller and Kendra Hoekzema and Houck, {Marlys L.} and Hyeonsoo Jeong and Kaivan Kamali and Manolis Kellis and Bryce Kille and Chul Lee and Youngho Lee and William Lees and Lewis, {Alexandra P.} and Qiuhui Li and Mark Loftus and Loh, {Yong Hwee Eddie} and Hailey Loucks and Jian Ma and Yafei Mao and Martinez, {Juan F. I.} and Patrick Masterson and McCoy, {Rajiv C.} and Barbara McGrath and Sean McKinney and Meyer, {Britta S.} and Miga, {Karen H.} and Mohanty, {Saswat K.} and Munson, {Katherine M.} and Karol Pal and Matt Pennell and Pevzner, {Pavel A.} and David Porubsky and Tamara Potapova and Ringeling, {Francisca R.} and Rocha, {Joana L.} and Ryder, {Oliver A.} and Samuel Sacco and Swati Saha and Takayo Sasaki and Schatz, {Michael C.} and Schork, {Nicholas J.} and Cole Shanks and Linn{\'e}a Smeds and Son, {Dongmin R.} and Cynthia Steiner and Sweeten, {Alexander P.} and Tassia, {Michael G.} and Fran{\c c}oise Thibaud-Nissen and Edmundo Torres-Gonz{\'a}lez and Mihir Trivedi and Wenjie Wei and Julie Wertz and Muyu Yang and Panpan Zhang and Shilong Zhang and Yang Zhang and Zhenmiao Zhang and Zhao, {Sarah A.} and Yixin Zhu and Jarvis, {Erich D.} and Gerton, {Jennifer L.} and Iker Rivas-Gonz{\'a}lez and Benedict Paten and Szpiech, {Zachary A.} and Huber, {Christian D.} and Lenz, {Tobias L.} and Konkel, {Miriam K.} and Yi, {Soojin V.} and Stefan Canzar and Watson, {Corey T.} and Sudmant, {Peter H.} and Erin Molloy and Erik Garrison and Lowe, {Craig B.} and Mario Ventura and O{\textquoteright}Neill, {Rachel J.} and Sergey Koren and Makova, {Kateryna D.} and Phillippy, {Adam M.} and Eichler, {Evan E.}",

year = "2025",

month = apr,

day = "9",

doi = "10.1038/s41586-025-08816-3",

language = "English",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

@article{4658eff0a2144e4ea5077531c143cdbb,

title = "Benchmarking sample pooling for epigenomics of natural populations",

abstract = "DNA methylation (DNAm) is a mechanism for rapid acclimation to environmental conditions. In natural systems, small effect sizes relative to noise necessitates large sampling efforts to detect differences. Large numbers of individually sequenced libraries are costly. Pooling DNA prior to library preparation may be an efficient way to reduce costs and increase sample size, yet there are to date no recommendations in ecological epigenetics research. We test whether pooled and individual libraries yield comparable DNAm signals in a natural system exposed to different pollution levels by generating whole-epigenome data from two invasive molluscs (Corbicula fluminea, Dreissena polymorpha) collected from polluted and unpolluted localities (Italy). DNA of the same individuals were used for pooled and individual epigenomic libraries and sequenced with equivalent resources per individual. We found that pooling effectively captures similar genome-wide and global methylation signals as individual libraries, highlighting that pooled libraries are representative of the global population signal. However, pooled libraries yielded orders of magnitude more data than individual libraries, which was a consequence of higher coverage. We would therefore recommend aiming for a high initial coverage of individual libraries (15×) in future studies. Consequently, we detected many more differentially methylated regions (DMRs) with the pooled libraries and a significantly lower statistical power for regions from individual libraries. Computationally pooled data from the individual libraries produced fewer DMRs and the overlap with wet-lab pooled DMRs was relatively low. We discuss possible causes for discrepancies, list benefits and drawbacks of pooling, and provide recommendations for future epigenomic studies.",

author = "Daniels, {Ryan J.} and Meyer, {Britta S.} and Marco Giulio and Signorini, {Silvia G.} and Nicoletta Riccardi and Camilla Della Torre and Weber, {Alexandra A.‐T.}",

year = "2024",

month = nov,

doi = "10.1111/1755-0998.14021",

language = "English",

journal = "Molecular Ecology Resources",

issn = "1755-098X",

publisher = "Wiley-Blackwell Publishing Ltd",

@article{f18dc2f663d945dbbde23268d15fed30,

title = "Autoimmunity Against Surfactant Protein B Is Associated with Pneumonitis During Checkpoint Blockade",

abstract = "Rationale: Immune checkpoint inhibitor (ICI)–related pneumonitis is a serious autoimmune event affecting as many as 20% of patients with non–small-cell lung cancer (NSCLC), yet the factors underpinning its development in some patients and not others are poorly understood. Objectives: To investigate the role of autoantibodies and autoreactive T cells against surfactant-related proteins in the development of pneumonitis. Methods: The study cohort consisted of patients with NSCLC who provided blood samples before and during ICI treatment. Serum was used for proteomics analyses and to detect autoantibodies present during pneumonitis. T-cell stimulation assays and single-cell RNA sequencing were performed to investigate the specificity and functionality of peripheral autoreactive T cells. The findings were confirmed in a validation cohort comprising patients with NSCLC and patients with melanoma. Measurements and Main Results: Across both cohorts, patients in whom pneumonitis developed had higher pretreatment levels of immunoglobulin G autoantibodies targeting surfactant protein (SP)-B. At the onset of pneumonitis, these patients also exhibited higher frequencies of CD41 IFN-g-positive SP-B-specific T cells and expanding T-cell clonotypes recognizing this protein, accompanied by a proinflammatory serum proteomic profile. Conclusions: Our data suggest that the cooccurrence of SP-B-specific immunoglobulin G autoantibodies and CD41 T cells is associated with the development of pneumonitis during ICI therapy. Pretreatment levels of these antibodies may represent a potential biomarker for an increased risk of developing pneumonitis, and on-treatment levels may provide a diagnostic aid.",

keywords = "autoimmunity, immune checkpoint inhibitor, non–small-cell lung cancer, pneumonitis, surfactant protein B",

author = "Nina Wyss and Fiamma Berner and Vincent Walter and Jochum, {Ann Kristin} and Purde, {Mette T.} and Abdou, {Marie Therese} and Tobias Sinnberg and Kathrin Hofmeister and Pop, {Oltin T.} and Ali, {Omar Hasan} and Jens Bauer and Cheng, {Hung Wei} and Mechthild Lutge and Niklas Klumper and Stefan Diem and Zeynep Kosaloglu-Yalcin and Yizheng Zhang and Laura Sellmer and Boris Macek and Julia Karbach and David Konig and Heinz Laubli and Lars Zender and Meyer, {Britta S.} and Christoph Driessen and Schurch, {Christian M.} and Wolfram Jochum and Teresa Amaral and Lucie Heinzerling and Antonio Cozzio and Hegazy, {Ahmed N.} and Tino Schneider and Brutsche, {Martin H.} and Alessandro Sette and Lenz, {Tobias L.} and Juliane Walz and Rammensee, {Hans Georg} and Martin Fruh and Elke Jager and Burkhard Becher and Amanda Tufman and Nicolas Nu{\~n}ez and Markus Joerger and Lukas Flatz",

note = "Publisher Copyright: Copyright {\textcopyright} 2024 by the American Thoracic Society.",

year = "2024",

month = oct,

day = "1",

doi = "10.1164/rccm.202311-2136OC",

language = "English",

volume = "210",

pages = "919--930",

journal = "American journal of respiratory and critical care medicine",

issn = "1073-449X",

publisher = "American Thoracic Society",

number = "7",

@article{e53640a51eaf4e4fab549cf65f727b4e,

title = "Epigenetic diversity of genes with copy number variations among natural populations of the three‐spined stickleback",

abstract = "Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection. In this scenario, newly duplicate genes may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them to persist in populations as copy number variations (CNVs). In animals and plants, younger gene duplicates tend to have higher levels of DNA methylation and lower levels of gene expression, suggesting epigenetic regulation could promote the retention of gene duplications via expression repression or silencing. Here, we test the hypothesis that DNA methylation variation coincides with young duplicate genes that are segregating as CNVs in six populations of the three-spined stickleback that span a salinity gradient from 4 to 30 PSU. Using reduced-representation bisulfite sequencing, we found DNA methylation and CNV differentiation outliers rarely overlapped. Whereas lineage-specific genes and young duplicates were found to be highly methylated, just two gene CNVs showed a significant association between promoter methylation level and copy number, suggesting that DNA methylation might not interact with CNVs in our dataset. If most new duplications are regulated for dosage by epigenetic mechanisms, our results do not support a strong contribution from DNA methylation soon after duplication. Instead, our results are consistent with a preference to duplicate genes that are already highly methylated.",

author = "Chain, {Fr{\'e}d{\'e}ric J. J.} and Meyer, {Britta S.} and Heckwolf, {Melanie J.} and S{\"o}ren Franzenburg and Christophe Eizaguirre and Reusch, {Thorsten B. H.}",

year = "2024",

month = jul,

doi = "10.1111/eva.13753",

language = "English",

volume = "17",

journal = "Evolutionary Applications",

issn = "1752-4571",

publisher = "Wiley-Blackwell",

number = "7",

@article{df6960f4a9d44bceac538218e749909d,

title = "Disruption of a Plasmodium falciparum patatin-like phospholipase delays male gametocyte exflagellation",

abstract = "An essential process in transmission of the malaria parasite to the Anopheles vector is the conversion of mature gametocytes into gametes within the mosquito gut, where they egress from the red blood cell (RBC). During egress, male gametocytes undergo exflagellation, leading to the formation of eight haploid motile microgametes, while female gametes retain their spherical shape. Gametocyte egress depends on sequential disruption of the parasitophorous vacuole membrane and the host cell membrane. In other life cycle stages of the malaria parasite, phospholipases have been implicated in membrane disruption processes during egress, however their importance for gametocyte egress is relatively unknown. Here, we performed comprehensive functional analyses of six putative phospholipases for their role during development and egress of Plasmodium falciparum gametocytes. We localize two of them, the prodrug activation and resistance esterase (PF3D7_0709700) and the lysophospholipase 1 (PF3D7_1476700), to the parasite plasma membrane. Subsequently, we show that disruption of most of the studied phospholipase genes does neither affect gametocyte development nor egress. The exception is the putative patatin-like phospholipase 3 (PF3D7_0924000), whose gene deletion leads to a delay in male gametocyte exflagellation, indicating an important, albeit not essential, role of this enzyme in male gametogenesis.",

keywords = "egress, exflagellation, gametocyte, malaria, phospholipase",

author = "Emma Pietsch and Korbinian Niederm{\"u}ller and Mia Andrews and Meyer, {Britta S.} and Lenz, {Tobias L.} and Wilson, {Danny W.} and Gilberger, {Tim Wolf} and Burda, {Paul Christian}",

note = "Publisher Copyright: {\textcopyright} 2023 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.",

year = "2024",

month = mar,

doi = "10.1111/mmi.15211",

language = "English",

volume = "121",

pages = "529--542",

journal = "Molecular Microbiology",

issn = "0950-382X",

publisher = "John Wiley and Sons Inc.",

number = "3",

@article{69b071a36e4c4a74a5d922b20626d57f,

title = "Sex-specific changes in autosomal methylation rate in ageing common terns",

abstract = "Senescence, an age-related decline in survival and/or reproductive performance, occurs in species across the tree of life. Molecular mechanisms underlying this within-individual phenomenon are still largely unknown, but DNA methylation changes with age are among the candidates. Using a longitudinal approach, we investigated age-specific changes in autosomal methylation of common terns, relatively long-lived migratory seabirds known to show senescence. We collected blood at 1-, 3- and/or 4-year intervals, extracted DNA from the erythrocytes and estimated autosomal DNA methylation by mapping Reduced Representative Bisulfite Sequencing reads to a de novo assembled reference genome. We found autosomal methylation levels to decrease with age within females, but not males, and no evidence for selective (dis)appearance of birds of either sex in relation to their methylation level. Moreover, although we found positions in the genome to consistently vary in their methylation levels, individuals did not show such strong consistent variance. These results pave the way for studies at the level of genome features or specific positions, which should elucidate the functional consequences of the patterns observed, and how they translate to the ageing phenotype.",

keywords = "aging, avian senescence, epigenetics, ontogeny, RRBS, Sterna hirundo",

author = "Meyer, {Britta S.} and Maria Moiron and Calvinna Caswara and William Chow and Olivier Fedrigo and Giulio Formenti and Bettina Haase and Kerstin Howe and Jacquelyn Mountcastle and Marcela Uliano-Silva and Jonathan Wood and Jarvis, {Erich D.} and Miriam Liedvogel and Sandra Bouwhuis",

note = "Publisher Copyright: Copyright {\textcopyright} 2023 Meyer, Moiron, Caswara, Chow, Fedrigo, Formenti, Haase, Howe, Mountcastle, Uliano-Silva, Wood, Jarvis, Liedvogel and Bouwhuis.",

year = "2023",

month = jan,

day = "30",

doi = "10.3389/fevo.2023.982443",

language = "English",

volume = "11",

journal = "Frontiers in Ecology and Evolution",

issn = "2296-701X",

publisher = "Frontiers Media S. A.",

@article{ba1c975e164742709df71e26b266a059,

title = "The history and organization of the Workshop on Population and Speciation Genomics",

abstract = "With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of workshops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of {\v C}esk{\'y} Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, explain the routine for workshop organization that we have optimized over the years, and describe the most important lessons that we have learned from it. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses.",

author = "Barth, {Julia M I} and Handley, {Scott A} and Daniel Kintzl and Guy Leonard and Milan Malinsky and Michael Matschiner and Meyer, {Britta S} and Walter Salzburger and Jan Stefka and Emiliano Trucchi",

note = "{\textcopyright} The Author(s) 2023.",

year = "2023",

doi = "10.1186/s12052-023-00182-w",

language = "English",

volume = "16",

pages = "2",

journal = "Evolution: Education and Outreach",

issn = "1936-6434",

publisher = "BioMed Central",

number = "1",

@article{f880e5ce2f634f09a3860023584757e7,

title = "The time is ripe for functional genomics: Can epigenetic changes mediate reproductive timing?",

author = "Melanie Heckwolf and Meyer, {Britta S.}",

year = "2021",

month = aug,

doi = "10.1111/mec.16063",

language = "English",

journal = "Molecular Ecology",

issn = "0962-1083",

publisher = "Wiley-Blackwell",

@article{2097fb1946734ac9ab6e06ff23ca8808,

title = "Molekulare Grundlagen des Vogelzugs",

abstract = "Migration is a complex behavior of which a significant proportion is genetic. Which genes and epigenetic changes underpin migratory behavior remains largely unknown, but a revolution of sequencing technology, analytical approaches, and functional genomic tools promises rapid advances. We summarize our current understanding of the (epi)genetic architecture of seasonal traits and outline our vision of how technical developments and integrative approaches could be employed to identify and functionally validate candidate genes and regulatory elements in migratory species.",

author = "Corinna Langebrake and Meyer, {Britta S.} and Miriam Liedvogel",

year = "2021",

month = feb,

doi = "10.1007/s12268-021-1511-y",

language = "Deutsch",

journal = "Biospektrum",

issn = "0947-0867",

publisher = "Springer Spektrum",