Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat

Yi, Congyang; Liu, Qian; Huang, Yuhong; Liu, Chang; Guo, Xianrui; Fan, Chaolan; Zhang, Kaibiao; Liu, Yang; Han, Fangpu

doi:10.1007/s11427-023-2513-9

Cited by 3 publications

References 69 publications

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Non-canonical DNA in human and other ape telomere-to-telomere genomes

Smeds,

Kamali,

Kejnovská

et al. 2024

Preprint

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Non-canonical (non-B) DNA structures (e.g., bent DNA, hairpins, G-quadruplexes, Z-DNA, etc.), which form at certain sequence motifs (e.g., A-phased repeats, inverted repeats, etc.), have emerged as important regulators of cellular processes and drivers of genome evolution. Yet, they have been understudied due to their repetitive nature and potentially inaccurate sequences generated with short-read technologies. Here we comprehensively characterize such motifs in the long-read telomere-to-telomere (T2T) genomes of human, bonobo, chimpanzee, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. Non-B DNA motifs are enriched at the genomic regions added to T2T assemblies, and occupy 9-15%, 9-11%, and 12-38% of autosomes, and chromosomes X and Y, respectively. Functional regions (e.g., promoters and enhancers) and repetitive sequences are enriched in non-B DNA motifs. Non-B DNA motifs concentrate at short arms of acrocentric chromosomes in a pattern reflecting their satellite repeat content and might contribute to satellite dynamics in these regions. Most centromeres and/or their flanking regions are enriched in at least one non-B DNA motif type, consistent with a potential role of non-B structures in determining centromeres. Our results highlight the uneven distribution of predicted non-B DNA structures across ape genomes and suggest their novel functions in previously inaccessible genomic regions.

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Non-canonical DNA in human and other ape telomere-to-telomere genomes

Smeds,

Kamali,

Kejnovská

et al. 2024

Preprint

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Stable minichromosome and functional neocentromere derived from rye 7R chromosome arm

Tang,

Liu,

Pan

et al. 2024

BMC Plant Biol

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Background The study of newly formed centromere with stable transmission ability can provide theoretical guidance for the construction of artificial chromosomes. More neocentromeres are needed to study the mechanisms of their formation. Results In this study, a minichromosome 7RLmini was derived from the progeny of wheat-rye 7R monosomic addition line. The minichromosome 7RLmini contained subtelomeric tandem repeats pSc119.2 and rye-specific pSc200, and it came from the distal region of the long arm of 7R chromosome. A neocentromere was formed in this minichromosome, and it did not contain centromeric repetitive sequences CCS1 and pAWRC.1. CENH3 ChIP-seq and ssDRIP-seq data confirmed that a 2.4 Mb segment from the rye 7R chromosome was involved in the neocentromere formation and enrichment of R-loops in this region. Within the 2.4 Mb segment, the GC content was higher that of AT, and a major binding position of CENH3 nucleosomes was identified on a 6 kb unknown LTR retrotransposon TE00002448. This unknown LTR retrotransposon was rye-specific and distributed through all the arms of rye chromosomes. The minichromosome exhibited stable generational transmission. Conclusion A minichromosome from rye 7R with neocentromere was obtained in this study and the neocentromere was formed at the position far away from its native equivalent. This minichromosome provides additional material for the research on the mechanism of neocentromere formation. We theorize that R-loops and transposable element might be involved in the positioning of CENH3 nucleosomes in a functional neocentromere.

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Evolution, Gene Duplication, and Expression Pattern Analysis of CrRLK1L Gene Family in Zea mays (L.)

Wang,

Xue,

et al. 2024

IJMS

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Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) plays pivotal roles in regulating plant growth and development, mediating intercellular signal transduction, and modulating responses to environmental stresses. However, a comprehensive genome-wide identification and analysis of the CrRLK1L gene family in maize remains elusive. In this study, a total of 24 CrRLK1L genes were identified in the maize whole genome. A phylogenetic analysis further revealed that CrRLK1L proteins from Arabidopsis, rice, and maize were grouped into nine distinct subgroups, with subgroup IV being unique to maize. Gene structure analysis demonstrated that the number of introns varied greatly among ZmCrRLK1L genes. Notably, the genome-wide duplication (WGD) events promoted the expansion of the ZmCrRLK1L gene family. Compared with Arabidopsis, there were more collinear gene pairs between maize and rice. Tissue expression patterns indicated that ZmCrRLK1L genes are widely expressed in various tissues, with ZmCrRLK1L5/9 specifically highly expressed in roots, and ZmCrRLK1L8/14/16/21/22 expressed in anthers. Additionally, RNA-seq and RT-qPCR analyses revealed that the expression of ZmCrRLK1L1/2/20/22 genes exhibited different expression patterns under drought and salt stresses. In summary, our study lays a foundation for elucidating the biological roles of ZmCrRLK1L genes in maize growth and development, reproductive development, and stress responses.

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Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat

Cited by 3 publications

References 69 publications

Non-canonical DNA in human and other ape telomere-to-telomere genomes

Non-canonical DNA in human and other ape telomere-to-telomere genomes

Stable minichromosome and functional neocentromere derived from rye 7R chromosome arm

Evolution, Gene Duplication, and Expression Pattern Analysis of CrRLK1L Gene Family in Zea mays (L.)

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