Article
Multidisciplinary Sciences
Seyoun Byun, Kajsa E. Affolter, Angela K. Snow, Karen Curtin, Austin R. Cannon, Lisa A. Cannon-Albright, Ramya Thota, Deborah W. Neklason
Summary: This study identified significant methylation differences in NETs of the small intestine, with genes from the GPCR pathways being overrepresented in the differentially methylated genes. The results suggest that multiple GPCRs and their ligands are regulated through methylation and correlated with patient survival, providing opportunities for better treatment strategies for NETs based on molecular features.
SCIENTIFIC REPORTS
(2021)
Review
Biology
Anja M. Westram, Rui Faria, Kerstin Johannesson, Roger Butlin, Nick Barton
Summary: Local adaptation and parallel evolution are major topics in evolutionary genomics. Genetic structures that reduce recombination, such as chromosomal inversions, play an important role in local adaptation. However, the contribution of inversions to parallel evolution is still not well understood.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Oren Milman, Idan Yelin, Roy Kishony
Summary: Programmed chromosomal inversions allow bacteria to generate genotypic and functional heterogeneity, and a predictive model of gene-altering inversions reveals key attributes of their genomic sequence, including size asymmetry and orientation bias. This study identified over 11,000 gene-altering loci covering known and novel targeted gene families, confirming the prevalence and importance of programmed inversions in maintaining intra-population genetic heterogeneity across the bacterial domain.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Christopher M. M. Hollenbeck, David S. S. Portnoy, Daniel Garcia de la Serrana, Thorolf Magnesen, Iveta Matejusova, Ian A. A. Johnston
Summary: The study reveals the association between chromosome structure variation and local adaptation in king scallops, suggesting a potential mechanism where recombination-suppressing chromosomal inversions play a significant role in local adaptation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Jiyeon Kweon, Hye-Yeon Hwang, Haesun Ryu, An-Hee Jang, Daesik Kim, Yongsub Kim
Summary: Researchers developed a method using prime editor 2 nuclease (PE2 nuclease) and paired pegRNA to achieve programmable chromosomal translocations and inversions. They successfully introduced DNA recombination and precise chromosomal translocations in human cells. This method can be used to create cancer-associated translocations and inversions as well as for disease modeling or gene therapy.
Article
Genetics & Heredity
Jiangbo Qu, Shuo Li, Dongyi Yu
Summary: Chromosomal structural variations (SVs) are a major cause of human genetic diseases. Current routine diagnostics have limitations in detecting certain types of SVs. Optical genome mapping (OGM) is a novel technology that shows better performance in detecting chromosomal SVs compared to current routine diagnostics. Therefore, OGM should be utilized in clinical examinations to improve the efficiency and accuracy of genetic disease diagnosis.
Article
Biochemistry & Molecular Biology
Maria Akopyan, Anna Tigano, Arne Jacobs, Aryn P. Wilder, Hannes Baumann, Nina O. Therkildsen
Summary: The study compares the recombination landscape and genome collinearity between two populations of Atlantic silverside. It finds higher recombination rates in females than males and restricted recombination to only the terminal ends of male chromosomes. Additionally, massive chromosomal inversions suppress recombination and coincide with highly differentiated genomic regions between locally adapted populations. Furthermore, the study identifies significantly higher recombination rates on chromosomes in the northern population.
Editorial Material
Biochemistry & Molecular Biology
Marius Roesti, Kimberly J. Gilbert, Kieran Samuk
Summary: Chromosomal inversions can promote local adaptation and population divergence by linking multiple adaptive alleles into nonrecombining genomic blocks. However, reduced recombination within inversions when ecological conditions change may limit their ability to adapt to novel ecological conditions, contributing to the maintenance of polymorphism within species.
Article
Biology
Geoffrey C. Waldbieser, Shikai Liu, Zihao Yuan, Caitlin E. Older, Dongya Gao, Chenyu Shi, Brian G. Bosworth, Ning Li, Lisui Bao, Mona A. Kirby, Yulin Jin, Monica L. Wood, Brian Scheffler, Sheron Simpson, Ramey C. Youngblood, Mary V. Duke, Linda Ballard, Adam Phillippy, Sergey Koren, Zhanjiang Liu
Summary: This study generated high-quality chromosome level reference genome sequences for channel catfish and blue catfish in the US, and identified three major pericentric inversions on their chromosomes. These reference genome sequences, along with the contrasting chromosomal architecture, can provide guidance for interspecific breeding programs.
Review
Biotechnology & Applied Microbiology
Haifei Hu, Armin Scheben, Jian Wang, Fangping Li, Chengdao Li, David Edwards, Junliang Zhao
Summary: Inversions significantly impact plant adaptation and gene functions. This review highlights advancements in technology and methodology that allow a better understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Ronald J. Nowling, Fabian Fallas-Moya, Amir Sadovnik, Scott Emrich, Matthew Aleck, Daniel Leskiewicz, John G. Peters
Summary: This study proposes using feature hashing to construct a feature matrix from SNP VCF files, reducing memory usage by 97% while maintaining minimal reductions in accuracy for inversion detection and localization tasks. This allows for easy and efficient analysis of inversions in larger data sets on common laptop and desktop computers.
Article
Multidisciplinary Sciences
Max Lundberg, Alexander Mackintosh, Anna Petri, Staffan Bensch
Summary: The authors used a combination of long reads, linked reads, and optical mapping to characterize three chromosomal regions in the willow warbler that are associated with migration differences and environmental gradients. They found inversions in each of the regions and similar divergence times between inverted and non-inverted haplotypes across the regions. The improved genomes allowed them to identify candidate genes for migration and adaptations to environmental gradients.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Zhibin Zhang, Ruili Lv, Bin Wang, Hongwei Xun, Bao Liu, Chunming Xu
Summary: Allopolyploidy is a powerful genetic and evolutionary force that combines divergent genomes into a common nucleus. One of its striking features is the ability to generate rapid and saltational biological consequences through 'genome shock'. In this study, we analyzed the changes in genome-wide gene expression under diverse environmental conditions in a synthetic allotetraploid wheat, revealing that allopolyploidy caused large-scale changes in gene expression that were variable across conditions and exacerbated by stresses and chromosomal exchanges. Our results provide new insights into the direct impacts of allopolyploidy on condition-dependent changes in subgenome expression.
Article
Multidisciplinary Sciences
Krishan Gupta, Guangyu Wang, Shuo Zhang, Xinlei Gao, Rongbin Zheng, Yanchun Zhang, Qingshu Meng, Lili Zhang, Qi Cao, Kaifu Chen
Summary: Recent studies have found stripes as architectural features of three-dimensional chromatin and their connection to epigenetic regulation of transcription. While there are tools available to define stripes in a single sample, there is no reported method to quantitatively measure the dynamic change of each stripe between samples. In this study, a bioinformatics tool called StripeDiff was developed to detect differential stripes between samples. StripeDiff showed optimal performance in both simulation data analysis and real Hi-C data analysis. Applying StripeDiff to Hi-C data revealed new insights into the connection between change of chromatin stripe and change of chromatin modification, transcriptional regulation, and cell differentiation.
Article
Biochemistry & Molecular Biology
Noora Poikela, Dominik R. Laetsch, Maaria Kankare, Anneli Hoikkala, Konrad Lohse
Summary: Interspecific gene flow is a source of genetic variation, but selection against it strengthens reproductive barriers between species. We used an experimental approach to investigate the role of chromosomal inversions and incompatibility genes in preventing gene flow between Drosophila virilis group species. Our findings suggest that genetic incompatibilities within chromosomal inversions play an important role in speciation.