Article
Genetics & Heredity
Amy M. Inkster, Martin T. Wong, Allison M. Matthews, Carolyn J. Brown, Wendy P. Robinson
Summary: In this study, the authors analyzed the DNA methylation (DNAme) array data from X and Y chromosomes of 634 placental samples using Illumina Infinium HumanMethylation450 DNAme array. They investigated the effects of probe filtering, normalization, and batch correction on X and Y DNAme data. The study identified key factors to be considered during processing and analysis of sex chromosome data, and proposed two analytical methods for XY chromosome data.
EPIGENETICS & CHROMATIN
(2023)
Review
Cell Biology
Anthony Holland, Neil A. Bradbury
Summary: Cell sex is important in biomedical research, but the sex of cells derived from organs other than reproductive tissue is often overlooked. However, accumulating data show that genes expressed off sex chromosomes have a broad impact on various cells. Moreover, AJP-Cell Physiology requires clear indication of the source of all cells used when submitting an article. Nearly a decade later, it is important to evaluate if improvements have been made in the description of cells and cell lines used in publications submitted to AJP-Cell Physiology.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shahar Shohat, Ethel Vol, Sagiv Shifman
Summary: Sex differences in humans are influenced by gonadal hormones and sex chromosomes. This study explores how sex chromosomes can affect gene expression and the outcome of mutations, using cancer cell lines as a model system. The findings highlight the roles of X and Y chromosomes in sex-specific cell function.
Article
Biochemistry & Molecular Biology
Zeba Sultana, Mathurin Dorel, Bertram Klinger, Anja Sieber, Ilona Dunkel, Nils Bluethgen, Edda G. Schulz
Summary: By combining systematic perturbation experiments with mathematical modeling, it was found that the number of active X chromosomes in mouse embryonic stem cells affects cell signaling and differentiation propensity. The presence of a single active X chromosome makes cells more sensitive to differentiation-promoting pathways and leads to a stronger negative feedback in the MAPK pathway. This may explain the delayed differentiation observed in female mouse embryonic stem cells.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Genetics & Heredity
Kimberly Martin, Pe ' er Dar, Cora MacPherson, Melissa Egbert, Zachary Demko, Sheetal Parmar, Katelyn Hashimoto, Sina Haeri, Fergal Malone, Ronald J. Wapner, Ashley S. Roman, Asma Khalil, Revital Faro, Rajeevi Madankumar, Noel Strong, Robert M. Silver, Nidhi Vohra, Jon Hyett, Matt Rabinowitz, Charlly Kao, Hakon Hakonarson, Bo Jacobsson, Mary E. Norton
Summary: This study aimed to evaluate the performance of cfDNA screening for sex chromosome aneuploidies in an unselected obstetrical population with genetic confirmation. The results showed that cfDNA had comparable performance for detecting sex chromosome aneuploidies as reported in other studies. The accuracy of fetal sex prediction by cfDNA was 100%.
GENETICS IN MEDICINE
(2023)
Review
Pharmacology & Pharmacy
Reegan A. J. Miller, Abigael P. Williams, Susan Kovats
Summary: Epidemiological studies have shown sex differences in the incidence and morbidity of respiratory virus infections, which may be related to differences in the immune response. Animal models also exhibit sex differences in immunity and morbidity, suggesting variations in specific immune mechanisms. Recent research has revealed intrinsic sex differences in immune cell transcriptomes, epigenomes, and proteomes, which may regulate human immunity during viral infections. Understanding the role of sex steroids, X chromosome complement, and immune cell regulation can help explain the significant sex differences in immunity to respiratory pathogens.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Aditya S. Deshpande, Netha Ulahannan, Matthew Pendleton, Xiaoguang Dai, Lynn Ly, Julie M. Behr, Stefan Schwenk, Will Liao, Michael A. Augello, Carly Tyer, Priyesh Rughani, Sarah Kudman, Huasong Tian, Hannah G. Otis, Emily Adney, David Wilkes, Juan Miguel Mosquera, Christopher E. Barbieri, Ari Melnick, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington, Marcin Imielinski
Summary: The study reveals the significance of high-order three-dimensional chromatin interactions in gene regulation. By developing Pore-C and Chromunity, researchers are able to analyze high-order chromatin contacts at the genome scale and find their enrichment in enhancers and promoters in active chromatin as well as highly transcribed and lineage-defining genes.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Evan Gatev, Amy M. Inkster, Gian Luca Negri, Chaini Konwar, Alexandre A. Lussier, Anne Skakkebaek, Marla B. Sokolowski, Claus H. Gravholt, Erin C. Dunn, Michael S. Kobor, Maria J. Aristizabal
Summary: Sex is an important modulator of health that has been historically overlooked in biomedical research; specific autosomal DNAm regions show consistent sex differences and are linked to health conditions; a predictor of sex based on DNAm data can achieve high accuracy.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cell & Tissue Engineering
Atsushi Fukuda, Dane Z. Hazelbaker, Nami Motosugi, Jin Hao, Francesco Limone, Amanda Beccard, Patrizia Mazzucato, Angelica Messana, Chisa Okada, Irune Guerra San Juan, Menglu Qian, Akihiro Umezawa, Hidenori Akutsu, Lindy E. Barrett, Kevin Eggan
Summary: The study found that de novo DNA methyltransferases DNMT3A/3B are crucial for repressing XIST in female hPSCs, and the maintenance of XIST silencing is independent of de novo DNA methylation.
Article
Neurosciences
Sarah R. Ocanas, Victor A. Ansere, Collyn M. Kellogg, Jose V. V. Isola, Ana J. Chucair-Elliott, Willard M. Freeman
Summary: Biological sex influences neurodegenerative diseases through genetic and hormonal mechanisms. Microglial reactivity and the pro-inflammatory environment of the aging brain are influenced by sex, age, and disease state. Further research is needed to understand the regulation of microglial sex effects and develop sex-informed prevention and treatment strategies for brain diseases.
BRAIN RESEARCH BULLETIN
(2023)
Article
Biochemistry & Molecular Biology
Jun Ping, Yun Xia, Jianghong Ran, Xiaomao Zeng
Summary: In contrast to birds and mammals, cold-blooded vertebrates often have homomorphic sex chromosomes. This study on the torrent frog genus Amolops revealed that the homomorphy of sex chromosomes in these frogs is a result of turnover and X-Y recombination. Furthermore, the sex chromosomes in Amolops show heterogeneous evolution, with both homologous and non-homologous chromosomes involved. The turnover rate of non-homologous sex chromosomes is low in these torrent frogs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Chengqing Hu, Jiangcheng Shi, Yujing Chi, Jichun Yang, Qinghua Cui
Summary: The study reveals that X-chromosome-encoded miRNAs have lower expression levels in the left testis of healthy mice, suggesting an imbalanced Y:X ratio between the left and right testis. Additionally, the Y:X ratio is significantly elevated in the left testis but balanced in the right testis according to flow cytometry analysis. This is the first time the biased Y:X ratio in the left testis has been uncovered.
Article
Biochemistry & Molecular Biology
Josselin Gueno, Michael Borg, Simon Bourdareau, Guillaume Cossard, Olivier Godfroy, Agnieszka Lipinska, Leila Tirichine, J. Mark Cock, Susana M. Coelho
Summary: In many eukaryotes, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. The regulation of sex-biased gene expression during sexual differentiation remains unclear. This study investigates the epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, finding that chromatin signatures correlated with gene expression and histone PTMs changes occurred preferentially at sex-specific genes. The chromatin landscape of UV sex chromosomes differs from autosomes, likely driven by evolutionary young genes in the pseudoautosomal regions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Desmond Zeya Chen, Delnaz Roshandel, Zhong Wang, Lei Sun, Andrew D. Paterson
Summary: The UK Biobank has been widely used for genome-wide association studies (GWAS), but the study of the X chromosome has been limited. Recent research has found significant differences in minor allele frequencies on the X chromosome, particularly at the boundaries between the pseudo-autosomal regions and the non-pseudo-autosomal regions. Additionally, a small fraction of sex chromosomes and some autosomal SNPs also showed significant differences in minor allele frequencies.
HUMAN MOLECULAR GENETICS
(2023)
Article
Multidisciplinary Sciences
Charlotte Douglas, Valdone Maciulyte, Jasmin Zohren, Daniel M. Snell, Shantha K. Mahadevaiah, Obah A. Ojarikre, Peter J. Ellis, James M. A. Turner
Summary: In areas such as animal research and agriculture a single sex is often required in abundance, leading to wasted resources and ethical considerations. Here the authors develop a CRISPR/Cas9 mediated synthetic lethal system that enables the production of single sex offspring that can be repurposed for use in multiple organisms.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
Kelsie E. Hunnicutt, Jeffrey M. Good, Erica L. Larson
Summary: Whole tissue RNASeq is a standard method in evolutionary biology for studying gene expression divergence by providing a comprehensive transcriptome profile of a given tissue. However, the diversity of cell types within whole tissues can lead to variations in cellular composition, impacting gene expression profiles. This study investigates the effects of cellular composition differences on gene expression profiles in whole testes samples, comparing them to enriched spermatogenesis populations in two species of house mice. The findings highlight the importance of considering histology in RNASeq and using methods that reduce sample complexity, as differences in cellular composition can modify expression profiles and potentially alter our understanding of gene ontological processes and gene expression evolution.
Article
Biochemistry & Molecular Biology
Emily E. K. Kopania, Erica L. Larson, Colin Callahan, Sara Keeble, Jeffrey M. Good
Summary: This study used FACS technology to analyze the expression data of spermatogenesis in mice, and found that expression differences and protein coding sequence evolution were faster in late spermatogenesis. The protein evolution rate on the X chromosome was also faster. Different regulatory mechanisms varied between different cell types, cis-regulatory changes were more common in late spermatogenesis, while trans-acting changes were more common in early spermatogenesis and more conserved across species.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Correction
Genetics & Heredity
Erica L. Larson, Emily E. K. Kopania, Kelsie E. Hunnicutt, Dan Vanderpool, Sara Keeble, Jeffrey M. Good
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Erica L. Larson, Emily E. K. Kopania, Kelsie E. Hunnicutt, Dan Vanderpool, Sara Keeble, Jeffrey M. Good
Summary: This study investigates the mechanisms of hybrid male sterility in house mice and finds that disruption of gene expression during meiosis and postmeiotic development is associated with specific genotypes and X-linked genes. The results support the hypothesis that X-linked hybrid sterility has a variable genetic basis and highlight the importance of epigenetic regulation of the X chromosome during spermatogenesis.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Elizabeth J. Beckman, Felipe Martins, Taichi A. Suzuki, Ke Bi, Sara Keeble, Jeffrey M. Good, Andreas S. Chavez, Mallory A. Ballinger, Kennedy Agwamba, Michael W. Nachman
Summary: Researchers sequenced the genomes of house mice in the Andes and found that mice in Ecuador and Bolivia independently adapted to high elevation. The response to selection at high elevation varied between transects, with only a few genes showing parallel selection. They also discovered hypoxia-associated genes that experienced a significant allele frequency change at the highest elevations.
Article
Evolutionary Biology
Emily C. Moore, Gregg W. C. Thomas, Sebastian Mortimer, Emily E. K. Kopania, Kelsie E. Hunnicutt, Zachary J. Clare-Salzler, Erica L. Larson, Jeffrey M. Good
Summary: This study constructed a chromosome-scale de novo genome assembly for the Siberian dwarf hamster and revealed widespread female recombination suppression across approximately 65% of the Phodopus X chromosome. The suppressed Xp arm was enriched for transposable element families and lacked genes primarily expressed in placenta, showing similar gene densities, expression patterns, and rates of molecular evolution when compared to the recombinant Xq arm.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Nathanael D. Herrera, Kayce C. Bell, Colin M. Callahan, Erin Nordquist, Brice A. J. Sarver, Jack Sullivan, John R. Demboski, Jeffrey M. Good
Summary: Discovery of cryptic species within western chipmunks using genomic data highlights the presence of a new species and two subspecies, with evidence of hybridization with other species.
Article
Medicine, Research & Experimental
Meng Zhou, Minjeong Ko, Anna C. H. Hoge, Kelsey Luu, Yuzhen Liu, Magdalena L. Russell, William W. Hannon, Zhenwei Zhang, Jian Carrot-Zhang, Rameen Beroukhim, Eliezer M. Van Allen, Atish D. Choudhury, Peter S. Nelson, Matthew L. Freedman, Mary -Ellen Taplin, Matthew Meyerson, Srinivas R. Viswanathan, Gavin Ha
Summary: This study systematically investigates the impact of structural variation on the genomic landscape of prostate cancer in different disease states using whole genome sequencing. The results reveal distinct recurrent breakpoints in localized and metastatic castration-resistant prostate cancers, with different patterns of structural variation and associated genes in mCRPC and localized prostate cancer. By defining mCRPC subtypes based on structural variation, this study provides insights into the clinical outcomes and genetic features of different subgroups.
Article
Multidisciplinary Sciences
Kathryn Wilsterman, Emily C. Moore, Rena M. Schweizer, Kirksey Cunningham, Jeffrey M. Good, Zachary A. Cheviron
Summary: Adaptation to high elevation can reduce the impact of hypoxia-related gestational complications in placental mammals. By studying deer mice, researchers found that highland mice can maintain normal fetal growth under hypoxic conditions by expanding a specific compartment of the placenta. They also discovered significant overlap between genes associated with fetal growth in deer mice and genes involved in human placental development, indicating conserved or convergent pathways.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Microbiology
John W. Terbot, Parul Johri, Schuyler W. Liphardt, Vivak Soni, Susanne P. Pfeifer, Brandon S. Cooper, Jeffrey M. Good, Jeffrey D. Jensen
Summary: In the past 3 years, the SARS-CoV-2 virus has caused a global health crisis with multiple waves of spread. Genomic surveillance efforts have increased to track and anticipate the virus's evolution, resulting in a large number of patient isolates available in public databases. However, accurately quantifying the emergence of adaptive viral variants is challenging due to various co-occurring and interacting evolutionary processes. This study outlines the critical components of an evolutionary baseline model for SARS-CoV-2, including mutation rates, recombination rates, fitness effects, infection dynamics, and compartmentalization, and discusses the current understanding of these parameters. Recommendations for future clinical sampling, model construction, and statistical analysis are also provided.
Article
Cell Biology
Thomas J. Firneno Jr, Georgy Semenov, Erik B. Dopman, Scott A. Taylor, Erica L. Larson, Zachariah Gompert
Summary: This study characterizes the relationship between the coupling coefficient and genetic loci across hybrid zones, showing a smooth continuum from high variance and weak coupling to low variance and strong coupling. The results suggest low hybridization rates and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2023)