Article
Plant Sciences
Xiaowen Shi, Hua Yang, Chen Chen, Jie Hou, Tieming Ji, Jianlin Cheng, James A. Birchler
Summary: By studying maize plants with varying numbers of B chromosomes, it was found that the B chromosome can affect the expression of A-located genes and the copy number of B chromosome is positively correlated with the expression of B-located genes. Additionally, the B chromosome leads to increased expression of A-located miRNAs and affects the expression of A-located and B-located transposable elements.
Editorial Material
Biochemistry & Molecular Biology
Nancy A. Eckardt, James A. Birchler, Blake C. Meyers
Article
Multidisciplinary Sciences
Xiaowen Shi, Hua Yang, Chen Chen, Jie Hou, Tieming Ji, Jianlin Cheng, James A. Birchler
Summary: miRNAs play a crucial role in genome imbalance, with cis miRNAs showing a predominant gene-dosage effect in aneuploids, while trans miRNAs tend towards an inverse level of regulation.
NATURE COMMUNICATIONS
(2022)
Review
Biotechnology & Applied Microbiology
Jingwei Zhou, Yang Liu, Xianrui Guo, James A. Birchler, Fangpu Han, Handong Su
Summary: This article systematically summarizes the current knowledge of centromere biology, discussing the relationship between DNA compositions and the histone H3 variant in centromere establishment and identity. The roles of centromeres in cell division and three-dimensional genomic architecture are explored, along with potential applications in plant breeding and chromosome engineering. The challenges and strategies for de novo design and synthesis of centromeres are also assessed.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Review
Biochemistry & Molecular Biology
Xiaowen Shi, Hua Yang, James A. Birchler
Summary: Classic genetic studies have found that changing the dosage of part of the genome (aneuploidy) has more detrimental effects on gene expression compared to altering the dosage of the whole genome (ploidy). miRNAs, a class of small RNAs involved in gene expression regulation, are likely to be dosage-sensitive and play a role in genomic balance networks.
Article
Multidisciplinary Sciences
Qian Liu, Congyang Yi, Zeyan Zhang, Handong Su, Chang Liu, Yuhong Huang, Wei Li, Xiaojun Hu, Cheng Liu, James A. Birchler, Yang Liu, Fangpu Han
Summary: Non-B-form DNA plays a crucial role in the oat genome, specifically in centromeres. Through systematic studies using the oat system, the presence and structural characteristics of non-B-form DNA in centromeres were identified and its potential role was revealed.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Editorial Material
Genetics & Heredity
Thomas E. Juenger, Andrea L. Sweigart, Jianming Yu, James Birchler
Article
Biochemistry & Molecular Biology
Hua Yang, Xiaowen Shi, Chen Chen, Jie Hou, Tieming Ji, Jianlin Cheng, James A. Birchler
Summary: Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set. Studies have found that aneuploidy often shows an inverse modulation of transposable elements (TEs), while reductions in monosomy and increases in disomy and trisomy are also common. The ploidy series, on the other hand, showed little TE modulation. The modulation of TEs and genes in the same experimental group were compared, and TEs showed greater modulation than genes, especially in disomy.
PLANT COMMUNICATIONS
(2023)
Article
Cell Biology
Vincent A. Brennan, Hua Yang, Zhi Gao, James A. Birchler
Summary: The B chromosome in maize is a supernumerary chromosome that has developed a drive mechanism to ensure its presence in maize populations. Different maize lines exhibit varying responses to B chromosome fertilization, with one inbred line (B73) showing a preference for the sperm with the B chromosome.
Article
Biochemistry & Molecular Biology
James A. Birchler, Hua Yang
Summary: Gene duplication is a contributor to the evolution of genes with new functions. Different mechanisms, such as tandem duplication, transposition, and whole-genome duplication, can give rise to multiple copies of genes. The fate of duplicate genes can involve deletion, reduced expression, splitting functions, or divergence for new functions. The balance of interactors plays a role in determining the fate of duplicated genes. Different mechanisms can maintain duplicated genes, which may change over time and intersect.
