Article
Cell Biology
Chun-Yi Cho, James P. Kemp, Robert J. Duronio, Patrick H. O'Farrell
Summary: Collisions between DNA replication forks and transcribing RNA polymerases disrupt gene transcription, especially during the rapid cell cycles of early embryonic development. Replication dependency defers the onset of transcription to maintain orderly progression and avoid conflicts between transcription and replication.
Article
Biochemistry & Molecular Biology
Olga V. Andreenkova, Olga D. Shishkina, Alexandra I. Klimenko, Aleksandra E. Korenskaia, Margarita A. Bobrovskikh, Natalja V. Shatskaya, Gennady V. Vasiliev, Nataly E. Gruntenko
Summary: Several methods for extracting Wolbachia DNA from insect hosts have been described, but the low quantity of the bacteria made these techniques labor-intensive. This paper proposes a simplified and accelerated method for isolating high-purity Wolbachia DNA from Drosophila melanogaster, using centrifugation, filtration, and a modified version of the Livak buffer protocol. The proportion of Wolbachia DNA in total DNA was quantified using sequencing and bioinformatic analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Taotao Li, Duo Du, Dandan Zhang, Yicheng Lin, Jiakang Ma, Mengyu Zhou, Weida Meng, Zelin Jin, Ziqiang Chen, Haozhe Yuan, Jue Wang, Shulong Dong, Shaoyang Sun, Wenjing Ye, Bosen Li, Houbao Liu, Zhao Zhang, Yuchen Jiao, Zhi Xie, Wenqing Qiu, Yun Liu
Summary: Constructing high-quality haplotype-resolved genome assemblies has improved the ability to detect genetic variants. The authors demonstrated a targeted approach using CRISPR-based enrichment to assemble MHC haplotypes, enabling population genetic studies and disease mechanism elucidation.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Balaji Sundararaman, Alisa O. Vershinina, Samantha Hershauer, Joshua D. Kapp, Shelby Dunn, Beth Shapiro, Richard E. Green
Summary: Hybridization capture approaches are cost-effective for targeted high-throughput sequencing analysis in low-content, fragmented DNA samples. This study introduces a DNA bait synthesis method called CNER, which combines rolling-circle amplification and restriction digestion to generate discrete hybridization probes. The CNER method is successfully applied to capture and sequence a panel of ancient horse DNA libraries, outperforming a commercially available approach in terms of target coverage and depth.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Kevin S. Kuchinski, Kara D. Loos, Danae M. Suchan, Jennifer N. Russell, Ashton N. Sies, Charles Kumakamba, Francisca Muyembe, Placide Mbala Kingebeni, Ipos Ngay Lukusa, Frida N'Kawa, Joseph Atibu Losoma, Maria Makuwa, Amethyst Gillis, Matthew LeBreton, James A. Ayukekbong, Nicole A. Lerminiaux, Corina Monagin, Damien O. Joly, Karen Saylors, Nathan D. Wolfe, Edward M. Rubin, Jean J. Muyembe Tamfum, Natalie A. Prystajecky, David J. McIver, Christian E. Lange, Andrew D. S. Cameron
Summary: This study evaluated the feasibility of using hybridization probe capture technique to recover more extensive genomic information from specimens. The results showed that probe capture achieved more genome sequence compared to standard amplicon sequencing protocols, and identified new coronaviruses. The study suggests that probe capture can be effectively used alongside other sequencing technologies for high-throughput discovery and surveillance of coronaviruses.
Article
Food Science & Technology
Khalid Sedeek, Andrea Zuccolo, Alice Fornasiero, Annika M. Weber, Krishnaveni Sanikommu, Sangeetha Sampathkumar, Luis F. Rivera, Haroon Butt, Saule Mussurova, Abdulrahman Alhabsi, Nurmansyah Nurmansyah, Elizabeth P. Ryan, Rod A. Wing, Magdy M. Mahfouz
Summary: In this study, genome assemblies of 5 pigmented rice varieties were generated and the genetic variation among 51 pigmented rice varieties was evaluated. Phylogenetic analysis divided the pigmented varieties into four groups. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. A regeneration and transformation system was established and CRISPR-Cas9 was used to create an early maturing, shorter-stature black rice variety. This study provides a multi-omics resource for understanding and improving Asian pigmented rice.
Article
Evolutionary Biology
Leonardo G. de Lima, Francisco J. Ruiz-Ruano
Summary: This study conducted a comprehensive analysis of SatDNA in 37 species from the genus Drosophila, revealing the diversity and variation of SatDNA sequences in the genome. The study also identified shared SatDNA families among closely related species and the emergence of species-specific SatDNA families. Additionally, the study found a positive correlation between genome size and the category of repetitive elements.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Gastroenterology & Hepatology
Camille Peneau, Sandrine Imbeaud, Tiziana La Bella, Theo Z. Hirsch, Stefano Caruso, Julien Calderaro, Valerie Paradis, Jean-Frederic Blanc, Eric Letouze, Jean-Charles Nault, Giuliana Amaddeo, Jessica Zucman-Rossi
Summary: This study aimed to characterize HBV integrations in liver tissues of HCC patients and revealed new mechanisms of HBV-associated oncogenesis. HBV integrations have direct oncogenic consequences, posing a challenge for the monitoring of HBV-infected patients.
Article
Multidisciplinary Sciences
Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: Transgenic reporters are valuable tools for studying enhancers, but they may inhibit the expression of other genes. Competition for transcription factors is thought to be partially responsible for this inhibition of gene expression.
Article
Biochemistry & Molecular Biology
Alison H. Nguyen, Weixiang Wang, Emily Chong, Kamalakar Chatla, Doris Bachtrog
Summary: By studying the Y chromosomes in fruit flies, it was found that the differences between Y chromosomes are mainly caused by a few active transposable elements, which have recently expanded on the largest Y chromosome. Different elements are responsible for the expansion of Y on differently sized chromosomes.
Article
Biochemistry & Molecular Biology
Oriol Fornes, Tamar Av-Shalom, Andrea J. Korecki, Rachelle A. Farkas, David J. Arenillas, Anthony Mathelier, Elizabeth M. Simpson, Wyeth W. Wasserman
Summary: MiniPromoters are short DNA sequences that can drive gene expression in specific cells and tissues. OnTarget is a webserver that simplifies the process of designing MiniPromoters by combining user-provided data with internal data to identify candidate promoters and enhancers.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Shahin Eghbalsaied, Wilfried A. Kues
Summary: In this study, large plasmids containing the CRISPR/Cas9 system and a puromycin transgene were used to evaluate the efficiency of targeted integration. The inclusion of nocodazole and RNase HII during electroporation significantly improved the rate of high-fidelity repair events.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Adriana Adolfi, Amy Lynd, Gareth J. Lycett, Anthony A. James
Summary: The phi C31 system is a crucial genetic tool for the transgenic manipulation of malaria mosquitoes and other insect vectors, enabling precise modification of the Anopheles genome to achieve genetic control of malaria.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Cell Biology
Ruoying Chen, Micheala A. Aldred, Weiling Xu, Joe Zein, Peter Bazeley, Suzy A. A. Comhair, Deborah A. Meyers, Eugene R. Bleecker, Chunyu Liu, Serpil C. Erzurum, Bo Hu
Summary: The study found that targeted-sequencing and WGS have comparable capacity to determine genotypes and call mtDNA haplogroups and homoplasmies, but show large variability in identifying heteroplasmies, especially low-frequency ones. Investigators should exercise caution when dealing with heteroplasmies acquired from different sequencing methods, and further research is needed to improve variant detection methods for mitochondrial DNA.
Article
Multidisciplinary Sciences
Sebastien Levesque, Diana Mayorga, Jean-Philippe Fiset, Claudia Goupil, Alexis Duringer, Andreanne Loiselle, Eva Bouchard, Daniel Agudelo, Yannick Doyon
Summary: Prime editing allows precise genetic modifications without the need for donor DNA templates, but its efficiency remains a challenge. In this study, a robust co-selection strategy was designed by co-editing the Na+/K+ ATPase, enabling easy genetic modifications and revealing certain patterns in the editing process. This lays the foundation for creating cellular models and developing cell-type specific co-selection strategies.
NATURE COMMUNICATIONS
(2022)
Letter
Biochemistry & Molecular Biology
Haowei Cao, Rui Xu, Qiping Shi, Dandan Zhang, Juan Huang, Yang Hong
JOURNAL OF GENETICS AND GENOMICS
(2017)
Article
Neurosciences
Song Wu, Guangming Gan, Zhiping Zhang, Jie Sun, Qifu Wang, Zhongbao Gao, Meixiang Li, Shan Jin, Juan Huang, Ulrich Thomas, Yong-hui Jiang, Yan Li, Rui Tian, Yong Q. Zhang
JOURNAL OF NEUROSCIENCE
(2017)
Article
Cell Biology
Weihui Xu, Juan Huang, Baohua Li, Jiayang Li, Yonghong Wang
Article
Genetics & Heredity
Juan Huang, Wenke Zhou, Annie M. Watson, Yuh-Nung Jan, Yang Hong
Article
Cell Biology
Juan Huang, Lynn Huang, Yi-Jiun Chen, Erin Austin, Caitlin E. Devor, Fabrice Roegiers, Yang Hong
JOURNAL OF CELL SCIENCE
(2011)
Article
Multidisciplinary Sciences
Juan Huang, Wenke Zhou, Wei Dong, Annie M. Watson, Yang Hong
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2009)
Article
Biochemistry & Molecular Biology
Ya Wang, Rui Xu, Yiwei Cheng, Haowei Cao, Zibin Wang, Tianyu Zhu, Jiayin Jiang, Hao Zhang, Chang Wang, Lin Qi, Mingxi Liu, Xuejiang Guo, Juan Huang, Jiahao Sha
JOURNAL OF GENETICS AND GENOMICS
(2019)
Article
Multidisciplinary Sciences
Liuze Gao, Shuhui Chang, Wenjuan Xia, Xiaolin Wang, Chenwang Zhang, Liping Cheng, Xu Liu, Liang Chen, Qinghua Shi, Juan Huang, Eugene Yujun Xu, Ge Shan
