Review
Genetics & Heredity
Emmanuelle Lerat
Summary: Transposable elements (TEs) have a significant impact on the functioning and evolution of host genomes, leading to the evolution of regulatory epigenetic mechanisms to control their activity. Despite their negative effects, TEs play an important role in genome evolution by promoting genetic diversity and new regulatory elements. Therefore, studying the epigenetic modifications associated with TEs is important for understanding their influence on gene functioning.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Gabrielle A. Hartley, Mariam Okhovat, Rachel J. O'Neill, Lucia Carbone
Summary: The study reveals dynamic shifts in the repeat content that define gibbon centromeres, with the presence of retroelements dominating the centromeric repeat sequences across gibbon genera. Hoolock centromeres show an independent evolutionary trajectory compared to other genera, with the presence of retroelement-derived macrosatellite SST1. Additionally, transcripts originating from gibbon centromeres recapitulate the species-specific TE composition, indicating evolutionary divergence within the gibbon lineage.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Maria Isabel Navarro-Mendoza, Carlos Perez-Arques, Joseph Heitman
Summary: Chromatin modifications, specifically H3K9 methylation, play a crucial role in repressing transcription in early-diverging fungi. RNA interference (RNAi) and heterochromatin formation are independent regulatory mechanisms in Mucor, contributing to genome stability and defense.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Yi Feng, Rafik Neme, Leslie Y. Beh, Xiao Chen, Jasper Braun, Michael W. Lu, Laura F. Landweber
Summary: Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement. This study compares the genomes of different ciliate species and reveals the origin and evolution of complex genomes with discontinuous and scrambled genes. The findings support a gradual model for the origin of complex genomes through small events of DNA duplication and decay.
Article
Biochemistry & Molecular Biology
Taku Sasaki, Kyudo Ro, Erwann Caillieux, Riku Manabe, Gregoire Bohl-Viallefond, Pierre Baduel, Vincent Colot, Tetsuji Kakutani, Leandro Quadrana
Summary: Research has shown that anti-silencing systems have rapidly diversified in eudicots, determining specificity through gaining and losing specific domains and target sequence motifs. At least 10 distinct VANC-induced anti-silencing systems have been identified in Arabidopsis. Anti-silencing of non-autonomous VANDALs is crucial to prevent the demise of cognate autonomous TEs and ensure their propagation.
Article
Biotechnology & Applied Microbiology
Bin Zuo, Lotanna Micah Nneji, Yan-Bo Sun
Summary: By analyzing the whole-genome sequences of 14 frog species, this study investigated the variation and evolutionary causes of frog genome size. The results showed that the recent accumulation of transposable elements and the lack of deletion of ancient transposable elements primarily accounted for the evolution of frog genome sizes. Additionally, the abundance and density of simple repeat sequences positively correlated with genome size. However, there was no clear relationship between genome size and habitat types. This study provides important insights into the evolution of frog genome size.
Article
Biochemistry & Molecular Biology
Iskander Said, Michael P. McGurk, Andrew G. Clark, Daniel A. Barbash
Summary: Competition between transposable elements (TEs) may lead to the emergence of new variants, with hosts preferentially producing antisense piRNAs to silence these emerging variants.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Marta Coronado-Zamora, Judit Salces-Ortiz, Josefa Gonzalez
Summary: The development of long-read sequencing technologies has enabled the creation of high-quality genome assemblies for multiple species, including well-known model species like Drosophila melanogaster. However, there is currently a lack of efficient visual tools to display multiple genome assemblies simultaneously. In this study, the researchers introduce DrosOmics, a population genomics browser that allows the simultaneous visualization of 52 high-quality reference genomes of D. melanogaster, along with annotations of transposable elements and functional transcriptomics and epigenomics data for 26 genomes. DrosOmics is based on the highly scalable platform JBrowse 2 and provides important insights into the structural and functional features of natural populations of D. melanogaster.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Plant Sciences
Federico D. Ariel, Pablo A. Manavella
Summary: Transposable elements (TEs) contribute significantly to genome complexity in eukaryotes, driving genome diversity through evolution. TE mobilization can cause genome instability and affect the transcriptional activity of neighboring genes, while small RNAs and long non-coding RNAs derived from TEs play important roles in regulating gene expression through various mechanisms.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Yoon Hee Jung, Hsiao-Lin V. Wang, Samir Ali, Victor G. G. Corces, Isaac Kremsky
Summary: We performed deep genomic DNA sequencing of CD-1 mice and identified genome-wide SNPs, indels, and germline transposable elements relative to the mm10 reference genome. We constructed a CD-1-specific reference genome using the identified variants, which improved mappability and reduced experimental biases. Genetic variation between CD-1 mice can affect transcription factor binding and translation of genes.
Article
Biotechnology & Applied Microbiology
Nikhil Kumar Singh, Thomas Badet, Leen Abraham, Daniel Croll
Summary: This study conducted a genome-wide association study (GWAS) on a highly polymorphic mapping population of Zymoseptoria tritici, identifying a major locus associated with significant variation in reproductive success and damage caused by the pathogen on wheat. The locus contained multiple families of transposable elements (TEs) and exhibited strong genomic defense mechanisms, indicating recent sequence evolution and rapid diversification. The combination of GWAS and population-scale genome analysis demonstrated the power of investigating major effect loci in pathogens.
Article
Biology
C. P. Stelzer, J. Blommaert, A. M. Waldvogel, M. Pichler, B. Hecox-Lea, D. B. Mark Welch
Summary: This study identified large copy number variable regions (CNVs) within a geographic population that exhibited significant coverage differences among individuals and scaled with genome size. These CNVs were composed mainly of satellite DNA with high GC-content and showed inheritance and accumulation across generations. By pinpointing the genomic elements responsible for within-population genome size variation, this study opens new avenues for investigating genome size evolution in contemporary populations.
Review
Genetics & Heredity
Dareen Almojil, Yann Bourgeois, Marcin Falis, Imtiyaz Hariyani, Justin Wilcox, Stephane Boissinot
Summary: Transposable elements (TEs) are widespread in eukaryotes and have had a significant impact on genome organization and evolution, playing roles in regulating genes and providing a source for genetic novelties. This impact is now being more fully appreciated and their role in various biological processes, such as speciation and adaptation, is still being deciphered.
Article
Biochemistry & Molecular Biology
Claire Merot, Kristina S. R. Stenlokk, Clare Venney, Martin Laporte, Michel Moser, Eric Normandeau, Mariann Arnyasi, Matthew Kent, Clement Rougeux, Jullien M. Flynn, Sigbjorn Lien, Louis Bernatchez
Summary: Nascent pairs of ecologically differentiated species provide an opportunity to study the genetic architecture of speciation. By utilizing long-read sequencing, we analyzed the genomic patterns of differentiation between sympatric species pairs of lake whitefish. We found that structural variants (SVs), particularly insertions and deletions of transposable elements, play a significant role in species differentiation. The integration of different sequencing technologies allows us to incorporate SVs into speciation genomics.
Article
Biochemistry & Molecular Biology
Pol Fernandez, Ilia J. Leitch, Andrew R. Leitch, Oriane Hidalgo, Maarten J. M. Christenhusz, Lisa Pokorny, Jaume Pellicer
Summary: Giant genomes are rare in the plant kingdom, with most research focusing on angiosperms and gymnosperms. However, a study on ferns reveals differences in genome organization and dynamics. The genus Tmesipteris has two species with giant genomes, which exhibit high repeat diversity compared to small-genome taxa.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Computer Science, Interdisciplinary Applications
Toby Dylan Hocking, Guillem Rigaill, Paul Fearnhead, Guillaume Bourque
Summary: The algorithm utilizes constrained changepoint models for peak detection in genomic data sets and proposes a dynamic programming algorithm and sequential search algorithm, which have low computational cost and high speed.
JOURNAL OF STATISTICAL SOFTWARE
(2022)
Article
Multidisciplinary Sciences
Vinicius M. Fava, Mathieu Bourgey, Pubudu M. Nawarathna, Marianna Orlova, Pauline Cassart, Donald C. Vinh, Matthew Pellan Cheng, Guillaume Bourque, Erwin Schurr, David Langlais
Summary: This study used a systems biology approach to investigate severely ill COVID patients and found significant differences in monocyte epigenetic and transcriptomic attributes between those who survived and those who succumbed to the disease. Messenger RNA metabolism, RNA splicing, and interferon signaling pathways were identified as key host responses associated with non-survival. Tacrolimus, zotatifin, and nintedanib were identified as strong candidate drugs for the treatment of severely ill COVID patients at the time of hospital admission.
Article
Oncology
Bryn Golesworthy, Yifan Wang, Amanda Tanti, Alain Pacis, Joan Miguel Romero, Adeline Cuggia, Celine Domecq, Guillaume Bourdel, Robert E. Denroche, Gun Ho Jang, Robert C. Grant, Ayelet Borgida, Barbara T. Grunwald, Anna Dodd, Julie M. Wilson, Guillaume Bourque, Grainne M. O'Kane, Sandra E. Fischer, Chelsea Maedler Kron, Pierre-Olivier Fiset, Atilla Omeroglu, William D. Foulkes, Steven Gallinger, Marie-Christine Guiot, Zu-Hua Gao, George Zogopoulos
Summary: This study investigated the immune contexture of HR-d PDAC using multiplex immunohistochemistry. The results showed higher infiltration of intra-tumoral CD8+ T-cells and increased FOXP3+ Tregs in HR-d PDAC compared to HR/MMR-intact PDAC. Additionally, PD-L1 positivity was observed in a subset of HR-d PDAC cases. These findings suggest that HR-d PDAC may be responsive to immune checkpoint inhibitor treatment strategies.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zeenat Farooq, Fedho Kusuma, Phillip Burke, Catherine R. Dufour, Duckgue Lee, Negar Tabatabaei, Phoenix Toboz, Ernest Radovani, Jack F. Greenblatt, Jalees Rehman, Jacob Class, Arkady Khoutorsky, Bruno D. Fonseca, Justin M. Richner, Eloi Mercier, Guillaume Bourque, Vincent Giguere, Arvind R. Subramaniam, Jaeseok Han, Soroush Tahmasebi
Summary: In this study, the researchers identify the involvement of the nutrient sensing kinase GCN2 in regulating LARP1-mediated inhibition of TOP mRNA translation. They demonstrate that GCN2 controls LARP1 activity through two mechanisms: ATF4-dependent transcriptional induction of LARP1 mRNA and GCN1-mediated recruitment of LARP1 to stalled ribosomes. These findings provide new insights into the regulation of TOP mRNA translation and shed light on the role of GCN2 in this process.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Genetics & Heredity
Guillaume Butler-Laporte, Gundula Povysil, Jack A. Kosmicki, Elizabeth T. Cirulli, Theodore Drivas, Simone Furini, Chadi Saad, Axel Schmidt, Pawel Olszewski, Urszula Korotko, Mathieu Quinodoz, Elifnaz Celik, Kousik Kundu, Klaudia Walter, Junghyun Jung, Amy D. Stockwell, Laura G. Sloofman, Daniel M. Jordan, Ryan C. Thompson, Diane Del Valle, Nicole Simons, Esther Cheng, Robert Sebra, Eric E. Schadt, Seunghee Kim-Schulze, Sacha Gnjatic, Miriam Merad, Joseph D. Buxbaum, Noam D. Beckmann, Alexander W. Charney, Bartlomiej Przychodzen, Timothy Chang, Tess D. Pottinger, Ning Shang, Fabian Brand, Francesca Fava, Francesca Mari, Karolina Chwialkowska, Magdalena Niemira, Szymon Pula, J. Kenneth Baillie, Alex Stuckey, Antonio Salas, Xabier Bello, Jacobo Pardo-Seco, Alberto Gomez-Carballa, Irene Rivero-Calle, Federico Martinon-Torres, Andrea Ganna, Konrad J. Karczewski, Kumar Veerapen, Mathieu Bourgey, Guillaume Bourque, Robert Jm Eveleigh, Vincenzo Forgetta, David Morrison, David Langlais, Mark Lathrop, Vincent Mooser, Tomoko Nakanishi, Robert Frithiof, Michael Hultstrom, Miklos Lipcsey, Yanara Marincevic-Zuniga, Jessica Nordlund, Kelly M. Schiabor Barrett, William Lee, Alexandre Bolze, Simon White, Stephen Riffle, Francisco Tanudjaja, Efren Sandoval, Iva Neveux, Shaun Dabe, Nicolas Casadei, Susanne Motameny, Manal Alaamery, Salam Massadeh, Nora Aljawini, Mansour S. Almutairi, Yaseen M. Arabi, Saleh A. Alqahtani, Fawz S. Al Harthi, Amal Almutairi, Fatima Alqubaishi, Sarah Alotaibi, Albandari Binowayn, Ebtehal A. Alsolm, Hadeel El Bardisy, Mohammad Fawzy, Fang Cai, Nicole Soranzo, Adam Butterworth, Daniel H. Geschwind, Stephanie Arteaga, Alexis Stephens, Manish J. Butte, Paul C. Boutros, Takafumi N. Yamaguchi, Shu Tao, Stefan Eng, Timothy Sanders, Paul J. Tung, Michael E. Broudy, Yu Pan, Alfredo Gonzalez, Nikhil Chavan, Ruth Johnson, Bogdan Pasaniuc, Brian Yaspan, Sandra Smieszek, Carlo Rivolta, Stephanie Bibert, Pierre-Yves Bochud, Maciej Dabrowski, Pawel Zawadzki, Mateusz Sypniewski, Elzbieta Kaja, Pajaree Chariyavilaskul, Voraphoj Nilaratanakul, Nattiya Hirankarn, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Katsushi Tokunaga, Masaya Sugiyama, Yosuke Kawai, Takanori Hasegawa, Tatsuhiko Naito, Ho Namkoong, Ryuya Edahiro, Akinori Kimura, Seishi Ogawa, Takanori Kanai, Koichi Fukunaga, Yukinori Okada, Seiya Imoto, Satoru Miyano, Serghei Mangul, Malak S. Abedalthagafi, Hugo Zeberg, Joseph J. Grzymski, Nicole L. Washington, Stephan Ossowski, Kerstin U. Ludwig, Eva C. Schulte, Olaf Riess, Marcin Moniuszko, Miroslaw Kwasniewski, Hamdi Mbarek, Said I. Ismail, Anurag Verma, David B. Goldstein, Krzysztof Kiryluk, Alessandra Renieri, Manuel A. R. Ferreira, J. Brent Richards
Summary: Host genetics play a crucial role in COVID-19 outcomes, and studying rare variants can provide additional insights. A study combining whole-exome and whole-genome sequencing from 21 cohorts across 12 countries found that carrying a rare deleterious variant in the TLR7 gene on chromosome X is associated with a 5.3-fold increase in severe disease. This association is consistent across genders, further supporting TLR7 as a genetic determinant of severe COVID-19.
Article
Biochemistry & Molecular Biology
Enkhjin Batdorj, Najla AlOgayil, Qinwei Kim-Wee Zhuang, Jose Hector Galvez, Klara Bauermeister, Kei Nagata, Tohru Kimura, Monika A. Ward, Teruko Taketo, Guillaume Bourque, Anna K. Naumova
Summary: Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. In this study, we identified Y chromosome dependent differentially methylated regions (yDMRs) in mice and found that most of the yDMRs were located in transposable elements (TEs) and had lower methylation in XY mice compared to XX or XO mice. Further analyses showed that genetic variation in the Y chromosome influenced methylation levels of autosomal regions.
Article
Cell Biology
Sabrina Daniela da Silva, Gregoire B. Morand, Luciana Diesel, Jefferson Muniz de Lima, Krikor Bijian, Senthilkumar Kailasam, Francois Lefebvre, Guillaume Bourque, Michael Hier, Moulay A. Alaoui-Jamali
Summary: In this study, a high-throughput RNA sequencing technology was used to investigate a group of papillary thyroid carcinomas (PTCs) with an unusually aggressive phenotype. It was found that metastatic PTCs with mutated BRAF (V600E) expressed an up-regulation of RSPO4 and genes involved in focal adhesion and cell-extracellular matrix signaling. Further validation confirmed the upregulation of these target genes in metastatic PTC cases. Preclinical studies supported the association between RSPO4 overexpression and BRAF V600E mutation, indicating the potential for co-targeting B-Raf, RSPO, and focal adhesion proteins as a pharmacological approach for aggressive BRAF V600E PTC.
Article
Biochemistry & Molecular Biology
Adda-Lee Graham-Paquin, Deepak Saini, Jacinthe Sirois, Ishtiaque Hossain, Megan S. Katz, Qinwei Kim-Wee Zhuang, Sin Young Kwon, Yojiro Yamanaka, Guillaume Bourque, Maxime Bouchard, William A. Pastor
Summary: Zmym2(-/-) mice exhibit embryonic lethality and fail to undergo proper DNA methylation, resulting in upregulation of germline genes and abnormal expression of transposon-gene fusion transcripts. It suggests that ZMYM2 plays a crucial role in early embryonic development and DNA methylation patterning.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Sean Upchurch, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared Nedzel, Keenan Graham, Meenakshi S. Kagda, Pedro Assis, Benjamin Hitz, Emilio Righi, Roderic Guigo, Barbara J. Wold
Summary: Large-scale sharing of genomic quantification data requires standardized access interfaces. In this project, RNAget, an API for secure access to genomic quantification data in matrix form, was developed. RNAget allows for slicing matrices to extract desired subsets of data and can be applied to various expression matrix-format data, including RNA sequencing and microarrays. It can also be extended to other sequence-based genomics quantification matrices such as ATAC-seq and ChIP-seq.
Article
Cell Biology
Cristian Groza, Xun Chen, Alain Pacis, Marie-Michelle Simon, Albena Pramatarova, Katherine A. Aracena, Tomi Pastinen, Luis B. Barreiro, Guillaume Bourque
Summary: This study demonstrates that genome graphs can reveal regulatory regions that would have been overlooked by other approaches, providing important insights into the impact of genetic variants on processes such as immunity.
Meeting Abstract
Oncology
Michael Schwartz, Rohan Dandage, Lynn Karam, Alain Pacis, Hellen Kuasne, Anne-Marie Fortier, Sidong Huang, Guillaume Bourque, Traver Hart, Elena Kuzmin, Morag Park
Meeting Abstract
Oncology
Elena Kuzmin, Jean Monlong, Mathieu Bourgey, Jarry Barber, Tom Lesluyes, Toby Baker, Genevieve Morin, Dongmei Zou, Michael Schwartz, Yang Yang, Alain Pacis, Constanza Martinez, Hellen Kuasne, Anne-Marie Fortier, Rui Li, Claudia Kleinman, Sidong Huang, Peter van Loo, Quaid Morris, Jiannis Ragoussis, Guillaume Bourque, Morag Park
Meeting Abstract
Oncology
Kate I. Glennon, Naveen S. Vasudev, Ghislaine Scelo, Michelle Wilson, Louis Letourneau, Robert Eveleigh, Nazanin Nourbehesht, Madeleine Arseneault, Antoine Paccard, Lars Egevad, Juris Viksna, Edgars Celms, Sharon M. Jackson, Behnoush Abedi-Ardekani, Anne Y. Warren, Peter J. Selby, Sebastian Trainor, Michael Kimuli, Naeem Soomro, Adebanji Adeyoju, Poulam Patel, Magdalena B. Wozniak, Ivana Holcatova, Antonin Brisuda, Vladimir Janout, Estelle Chanudet, David Zaridze, Anush Moukeria, Oxana Shangina, Lenka Foretova, Marie Navratilova, Dana Mates, Viorel Jinga, Ljiljana Bogdanovic, Bozidar Kovacevic, Anne Cambon-Thomsen, Guillaume Bourque, Alvis Brazma, Jorg Tost, Paul Brennan, Mark Lathrop, Yasser Riazalhosseini, Rosamonde E. Banks
Meeting Abstract
Oncology
Michael Johnston, John Jy Lee, Bo Hu, Ana Nikolic, Audrey Baguette, Seungil Paik, Haifen Chen, Sachin Kumar, Carol Chen, Selin Jessa, Polina Balin, Vernon Fong, Melissa Zwaig, Kulandaimanuvel MichealRaj, Xun Chen, Yanlin Zhang, Srinidhi Varadharajan, Pierre Billon, Nikoleta Juretic, Craig Daniels, Caterina Giannini, Eric Thompson, Peter Hauser, Seung-Ki Kim, Kyu-Chang Wang, Ji Yeoun Lee, Wieslawa Grajkowska, Sameer Agnihotri, Stephen C. Mack, Benjamin Ellezam, Alex Weil, Guillaume Bourque, Jennifer Chan, Mathieu Lupien, Jiannis Ragoussis, Claudia Kleinman, Jacek Majewski, Nada Jabado, Michael Taylor, Mathieu Blanchette, Marco Gallo
Article
Biotechnology & Applied Microbiology
Charles E. Breeze, Eric Haugen, Alex Reynolds, Andrew Teschendorff, Jenny van Dongen, Qing Lan, Nathaniel Rothman, Guillaume Bourque, Ian Dunham, Stephan Beck, John Stamatoyannopoulos, Nora Franceschini, Sonja Berndt
Summary: This study developed the FORGE2 tool to investigate the functional mechanisms underlying GWAS associations by using information on cell type-specific regulatory elements. The study found that FORGE2 can identify disease risk associations specific to certain tissues and cell types and provide a greater understanding of underlying regulatory mechanisms. Additionally, the enrichment of tissue-specific repressive chromatin states and histone marks may play a role in the disease etiology mediated by GWAS.
