51
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Cody JP, Graham ND, Birchler JA. BiBAC Modification and Stable Transfer into Maize (
Zea mays)
Hi‐II Immature Embryos via
Agrobacterium‐
Mediated Transformation. ACTA ACUST UNITED AC 2018; 2:350-369. [DOI: 10.1002/cppb.20061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jon P. Cody
- Division of Biological Sciences, Tucker Hall, University of Missouri Columbia Missouri
| | - Nathaniel D. Graham
- Division of Biological Sciences, Tucker Hall, University of Missouri Columbia Missouri
| | - James A. Birchler
- Division of Biological Sciences, Tucker Hall, University of Missouri Columbia Missouri
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52
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Nani TF, Schnable JC, Washburn JD, Albert P, Pereira WA, Sobrinho FS, Birchler JA, Techio VH. Location of low copy genes in chromosomes of Brachiaria spp. Mol Biol Rep 2018; 45:109-118. [PMID: 29330722 DOI: 10.1007/s11033-018-4144-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/27/2017] [Indexed: 01/09/2023]
Abstract
Repetitive DNA sequences have been widely used in cytogenetic analyses. The use of gene sequences with a low-copy-number, however, is little explored especially in plants. To date, the karyotype details in Brachiaria spp. are limited to the location of rDNA sites. The challenge lies in developing new probes based on incomplete sequencing data for the genus or complete sequencing of related species, since there are no model species with a sequenced genome in Brachiaria spp. The present study aimed at the physical location of conserved genes in chromosomes of Brachiaria ruziziensis, Brachiaria brizantha, and Brachiaria decumbens using RNAseq data, as well as sequences of Setaria italica and Sorghum bicolor through the fluorescent in situ hybridization technique. Five out of approximately 90 selected sequences generated clusters in the chromosomes of the species of Brachiaria studied. We identified genes in synteny with 5S and 45S rDNA sites, which contributed to the identification of chromosome pairs carrying these genes. In some cases, the species of Brachiaria evaluated had syntenic segments conserved across the chromosomes. The use of genomic sequencing data is essential for the enhancement of cytogenetic analyses.
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Affiliation(s)
- Thaís Furtado Nani
- Department of Biology, Federal University of Lavras, Lavras, Minas Gerais State, Brazil
| | | | - Jacob D Washburn
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Patrice Albert
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | | | - Fausto Souza Sobrinho
- Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Embrapa Gado de Leite (CNPGL), Juiz de Fora, Minas Gerais State, Brazil
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Vânia Helena Techio
- Department of Biology, Federal University of Lavras, Lavras, Minas Gerais State, Brazil.
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53
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Liu Y, Su H, Liu Y, Zhang J, Dong Q, Birchler JA, Han F. Cohesion and centromere activity are required for phosphorylation of histone H3 in maize. Plant J 2017; 92:1121-1131. [PMID: 29032586 DOI: 10.1111/tpj.13748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/03/2017] [Accepted: 10/10/2017] [Indexed: 05/03/2023]
Abstract
Haspin-mediated phosphorylation of histone H3 at threonine 3 (H3T3ph) promotes proper deposition of Aurora B at the inner centromere to ensure faithful chromosome segregation in metazoans. However, the function of H3T3ph remains relatively unexplored in plants. Here, we show that in maize (Zea mays L.) mitotic cells, H3T3ph is concentrated at pericentromeric and centromeric regions. Additional weak H3T3ph signals occur between cohered sister chromatids at prometaphase. Immunostaining on dicentric chromosomes reveals that an inactive centromere cannot maintain H3T3ph at metaphase, indicating that a functional centromere is required for H3T3 phosphorylation. H3T3ph locates at a newly formed centromeric region that lacks detectable CentC sequences and strongly reduced CRM and ZmBs repeat sequences at metaphase II. These results suggest that centromeric localization of H3T3ph is not dependent on centromeric sequences. In maize meiocytes, H3T3 phosphorylation occurs at the late diakinesis and extends to the entire chromosome at metaphase I, but is exclusively limited to the centromere at metaphase II. The H3T3ph signals are absent in the afd1 (absence of first division) and sgo1 (shugoshin) mutants during meiosis II when the sister chromatids exhibit random distribution. Further, we show that H3T3ph is mainly located at the pericentromere during meiotic prophase II but is restricted to the inner centromere at metaphase II. We propose that this relocation of H3T3ph depends on tension at the centromere and is required to promote bi-orientation of sister chromatids.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qianhua Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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54
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Abstract
Quantitative trait genes have been difficult to analyze because of the subtle effects of their natural variation. Rodríguez-Leal et al. now develop a promoter-editing approach to generate a range of effective alleles for analysis, providing an avenue to investigate complex interactions among such genes.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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55
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Abstract
Genetic dominance has long been considered as a qualitative reflection of interallelic interactions. Dominance arises from many multiple sources whose unifying theme is the existence of non-linear relationships between the genotypic and phenotypic values. One of the clearest examples are dominant negative mutations (DNMs) in which a defective subunit poisons a macromolecular complex. Dominance can also be due to the presence of a heterozygous null allele, as is the case of haploinsufficiency. Dominance can also be influenced by epistatic (interloci) interactions. For instance, a pre-existing genetic variant can make possible the expression of a pathogenic variant in a seemingly "dominant" fashion. Such interactions, which can make an individual more or less sensitive to a particular pathogenic variant, will also be discussed here.
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Affiliation(s)
- R A Veitia
- Institut Jacques Monod, CNRS-UMR 7592, Paris Cedex 13, France.,Université Paris Diderot, Paris, France
| | - S Caburet
- Institut Jacques Monod, CNRS-UMR 7592, Paris Cedex 13, France.,Université Paris Diderot, Paris, France
| | - J A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
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56
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Zhao H, Zeng Z, Koo DH, Gill BS, Birchler JA, Jiang J. Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3. Chromosome Res 2017; 25:299-311. [PMID: 28831743 DOI: 10.1007/s10577-017-9564-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 01/01/2023]
Abstract
Centromeres can arise de novo from non-centromeric regions, which are often called "neocentromeres." Neocentromere formation provides the best evidence for the concept that centromere function is not determined by the underlying DNA sequences, but controlled by poorly understood epigenetic mechanisms. Numerous neocentromeres have been reported in several plant and animal species. However, it has been elusive how and why a specific chromosomal region is chosen to be a new centromere during the neocentromere activation events. We report recurrent establishment of neocentromeres in a pericentromeric region of chromosome 3 in maize (Zea mays). This latent region is located in the short arm and is only 2 Mb away from the centromere (Cen3) of chromosome 3. At least three independent neocentromere activation events, which were likely induced by different mechanisms, occurred within this latent region. We mapped the binding domains of CENH3, the centromere-specific H3 histone variant, of the three neocentromeres and analyzed the genomic and epigenomic features associated with Cen3, the de novo centromeres and an inactivated centromere derived from an ancestral chromosome. Our results indicate that lack of genes and transcription and a relatively high level of DNA methylation in this pericentromeric region may provide a favorable chromatin environment for neocentromere activation.
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Affiliation(s)
- Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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57
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Veitia RA, Govindaraju DR, Bottani S, Birchler JA. Aging: Somatic Mutations, Epigenetic Drift and Gene Dosage Imbalance. Trends Cell Biol 2017; 27:299-310. [DOI: 10.1016/j.tcb.2016.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
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58
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Su H, Liu Y, Dong Q, Feng C, Zhang J, Liu Y, Birchler JA, Han F. Dynamic location changes of Bub1-phosphorylated-H2AThr133 with CENH3 nucleosome in maize centromeric regions. New Phytol 2017; 214:682-694. [PMID: 28079247 DOI: 10.1111/nph.14415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 11/27/2016] [Indexed: 05/03/2023]
Abstract
The genomic stability of all organisms requires precise cell division with proper chromosome orientation. The Bub1-H2Aph-Sgo1 pathway and spindle assembly checkpoint (SAC) components have been identified in yeast and mammals that are important for sister centromere orientation and chromosome segregation. However, their roles in plants are not clear. Maize meiotic mutants and minichromosomes were used to study the role of H2AThr133 phosphorylation and SAC components in sister centromere orientation and chromosome segregation. Unlike previously reported, SAC protein Bub1-Sgo1 recruitment was independent of Rec8 in maize and did not play a role in centromere protection in meiosis I. Chromatin immunoprecipitation sequencing analysis with immnolocalization results indicate most CENH3 nucleosomes contain phosphorylated H2AThr133 in centromeric regions. H2AThr133ph spreads to encompass centromeric regions including the inner centromeric and pericentromeric regions during (pro)metaphase. The presence and localization of SAC components and H2AThr133ph on maize lines containing sister chromatids separate precociously in anaphase I revealed no direct role of these proteins on centromere orientation in meiosis I . This work sheds light on the relationship between H2AThr133ph and CENH3 nucleosome in plants, and the phosphorylation with dynamic location changes in centomeric regions suggests temporal and spatial regulation roles for H2A phosphorylation in chromosome segregation.
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Affiliation(s)
- Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianhua Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao Feng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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59
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Abstract
This unit presents a highly reliable protocol to produce and screen metaphase chromosome spreads from root tip cell suspensions of soybean (Glycine max), or other legumes. The procedures represent soybean-optimized versions of protocols developed for maize. The use of pressurized nitrous oxide to reliably generate metaphase-arrested chromosomes is crucial to overcoming one of the challenges of working with tiny and numerous soybean chromosomes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Seth D Findley
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Gary Stacey
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
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60
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Abstract
This article presents protocols for fluorescence in situ hybridization (FISH) in the cultivated soybean, Glycine max. The protocols represent soybean-optimized versions developed for maize. We describe the use of two different probes types: genomic-repeat-based fluorescently-tagged oligonucleotides and bacterial artificial chromosomes (BACs). The two probe types can be used either individually or together, depending on the experimental questions. The article also includes starting points for executing FISH in additional legume species. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Seth D Findley
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Gary Stacey
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
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61
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Su H, Liu Y, Liu YX, Lv Z, Li H, Xie S, Gao Z, Pang J, Wang XJ, Lai J, Birchler JA, Han F. Dynamic chromatin changes associated with de novo centromere formation in maize euchromatin. Plant J 2016; 88:854-866. [PMID: 27531446 DOI: 10.1111/tpj.13305] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 07/21/2016] [Accepted: 08/11/2016] [Indexed: 05/25/2023]
Abstract
The inheritance and function of centromeres are not strictly dependent on any specific DNA sequence, but involve an epigenetic component in most species. CENH3, a centromere histone H3 variant, is one of the best-described epigenetic factors in centromere identity, but the chromatin features required during centromere formation have not yet been revealed. We previously identified two de novo centromeres on Zea mays (maize) minichromosomes derived from euchromatic sites with high-density gene distributions but low-density transposon distributions. The distribution of gene location and gene expression in these sites indicates that transcriptionally active regions can initiate de novo centromere formation, and CENH3 seeding shows a preference for gene-free regions or regions with no gene expression. The locations of the expressed genes detected were at relatively hypomethylated loci, and the altered gene expression resulted from de novo centromere formation, but not from the additional copy of the minichromosome. The initial overall DNA methylation level of the two de novo regions was at a low level, but increased substantially to that of native centromeres after centromere formation. These results illustrate the dynamic chromatin changes during euchromatin-originated de novo centromere formation, which provides insight into the mechanism of de novo centromere formation and regulation of subsequent consequences.
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Affiliation(s)
- Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Xin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenling Lv
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongyao Li
- Chinese Agriculture University, Beijing, 100193, China
| | - Shaojun Xie
- Chinese Agriculture University, Beijing, 100193, China
| | - Zhi Gao
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, 65211-7400, USA
| | - Junling Pang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinsheng Lai
- Chinese Agriculture University, Beijing, 100193, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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62
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
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63
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Swyers NC, Cody JP, McCaw ME, Graham ND, Zhao C, Gaeta RT, Birchler JA. Telomere-Mediated Chromosomal Truncation for Generating Engineered Minichromosomes in Maize. Curr Protoc Plant Biol 2016; 1:488-500. [PMID: 31725959 DOI: 10.1002/cppb.20031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Minichromosomes have been generated in maize using telomere-mediated truncation. Telomere DNA, because of its repetitive nature, can be difficult to manipulate. The protocols in this unit describe two methods for generating the telomere DNA required for the initiation of telomere-mediated truncation. The resulting DNA can then be used with truncation cassettes for introduction into maize via transformation. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nathan C Swyers
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Jon P Cody
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Morgan E McCaw
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Nathaniel D Graham
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Changzeng Zhao
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - Robert T Gaeta
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
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64
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Birchler JA. Parallel Universes for Models of X Chromosome Dosage Compensation in Drosophila: A Review. Cytogenet Genome Res 2016; 148:52-67. [PMID: 27166165 DOI: 10.1159/000445924] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Dosage compensation in Drosophila involves an approximately 2-fold increase in expression of the single X chromosome in males compared to the per gene expression in females with 2 X chromosomes. Two models have been considered for an explanation. One proposes that the male-specific lethal (MSL) complex that is associated with the male X chromosome brings histone modifiers to the sex chromosome to increase its expression. The other proposes that the inverse effect which results from genomic imbalance would tend to upregulate the genome approximately 2-fold, but the MSL complex sequesters histone modifiers from the autosomes to the X to mute this autosomal male-biased expression. On the X, the MSL complex must override the high level of resulting histone modifications to prevent overcompensation of the X chromosome. Each model is evaluated in terms of fitting classical genetic and recent molecular data. Potential paths toward resolving the models are suggested.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Mo., USA
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65
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Yu W, Yau YY, Birchler JA. Plant artificial chromosome technology and its potential application in genetic engineering. Plant Biotechnol J 2016; 14:1175-1182. [PMID: 26369910 DOI: 10.1111/pbi.12466] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/16/2015] [Accepted: 08/07/2015] [Indexed: 06/05/2023]
Abstract
Genetic engineering with just a few genes has changed agriculture in the last 20 years. The most frequently used transgenes are the herbicide resistance genes for efficient weed control and the Bt toxin genes for insect resistance. The adoption of the first-generation genetically engineered crops has been very successful in improving farming practices, reducing the application of pesticides that are harmful to both human health and the environment, and producing more profit for farmers. However, there is more potential for genetic engineering to be realized by technical advances. The recent development of plant artificial chromosome technology provides a super vector platform, which allows the management of a large number of genes for the next generation of genetic engineering. With the development of other tools such as gene assembly, genome editing, gene targeting and chromosome delivery systems, it should become possible to engineer crops with multiple genes to produce more agricultural products with less input of natural resources to meet future demands.
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Affiliation(s)
- Weichang Yu
- Shenzhen Research Institute, Chinese University of Hong Kong, Shenzhen, China
| | - Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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66
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Abstract
Plant centromeres are generally composed of tandem arrays of simple repeats that are typical of a particular species, but that evolve rapidly. Centromere specific retroelements are also present. These arrays associate with a centromere specific variant of histone H3 that anchors the site of the kinetochore. Although such DNA arrays are typical of the centromere, the specification of centromere activity has an epigenetic component as shown by the fact that centromeres are formed in the absence of such repeats and that centromeres in dicentric chromosomes regularly undergo inactivation.
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Affiliation(s)
- J C Lamb
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Mo., USA
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67
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Birchler JA, Johnson AF, Veitia RA. Kinetics genetics: Incorporating the concept of genomic balance into an understanding of quantitative traits. Plant Sci 2016; 245:128-34. [PMID: 26940497 DOI: 10.1016/j.plantsci.2016.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 05/21/2023]
Abstract
While most mutations are recessive, variants that affect quantitative traits are largely semi-dominant in their action making hybrids between divergent genotypes intermediate. In parallel, changes in chromosomal dosage (aneuploidy) for multiple regions of the genome modulate quantitative characters. We have previously argued that these observations are a reflection of a common process, originating from the more or less subtle effects of changes in dosage on the action of multi-subunit regulatory machineries. Kinetic analyses that vary the amount of one subunit of a complex while holding others constant do not always predict a linear response for the production of the whole. Indeed, in many instances, strong non-linear effects are expected. Here, we advocate that these kinetic observations and predictions should be incorporated into quantitative genetics thought.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
| | - Adam F Johnson
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Reiner A Veitia
- Institut Jacques Monod, 15 rue Helene Brion, 75013 Paris, France; Universite Paris Diderot, Paris, France
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68
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Wolfgruber TK, Nakashima MM, Schneider KL, Sharma A, Xie Z, Albert PS, Xu R, Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting GG. High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events. Front Plant Sci 2016; 7:308. [PMID: 27047500 PMCID: PMC4806543 DOI: 10.3389/fpls.2016.00308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/27/2016] [Indexed: 05/02/2023]
Abstract
The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR) has presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here, we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 × 10(-6) and 5 × 10(-5) for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb from the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length CR from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB) repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. In many cases examined here, DSB repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to efficiently repair frequent DSBs in centromeres.
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Affiliation(s)
- Thomas K. Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Megan M. Nakashima
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Kevin L. Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Anupma Sharma
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Zidian Xie
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Patrice S. Albert
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Ronghui Xu
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Paul Bilinski
- Department of Plant Sciences, University of California DavisDavis, CA, USA
| | - R. Kelly Dawe
- Department of Plant Biology, University of GeorgiaAthens, GA, USA
| | | | - James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Gernot G. Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
- *Correspondence: Gernot G. Presting
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Feng C, Yuan J, Wang R, Liu Y, Birchler JA, Han F. Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System. J Genet Genomics 2015; 43:37-43. [PMID: 26842992 DOI: 10.1016/j.jgg.2015.10.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/14/2015] [Accepted: 10/20/2015] [Indexed: 12/18/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system, which is a newly developed technology for targeted genome modification, has been successfully used in a number of species. In this study, we applied this technology to carry out targeted genome modification in maize. A marker gene Zmzb7 was chosen for targeting. The sgRNA-Cas9 construct was transformed into maize protoplasts, and indel (insertion and deletion) mutations could be detected. A mutant seedling with an expected albino phenotype was obtained from screening 120 seedlings generated from 10 callus events. Mutation efficiency in maize heterochromatic regions was also investigated. Twelve sites with different expression levels in maize centromeres or pericentromere regions were selected. The sgRNA-Cas9 constructs were transformed into protoplasts followed by sequencing the transformed protoplast genomic DNA. The results show that the genes in heterochromatic regions could be targeted by the CRISPR/Cas9 system efficiently, no matter whether they are expressed or not. Meanwhile, off-target mutations were not found in the similar sites having no PAM (protospacer adjacent motif) or having more than two mismatches. Together, our results show that the CRISPR/Cas9 system is a robust and efficient tool for genome modification in both euchromatic and heterochromatic regions in maize.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Abstract
This year marks the 150(th) anniversary of the presentation by Gregor Mendel of his studies of plant hybridization to the Brunn Natural History Society. Their nature and meaning have been discussed many times. However, on this occasion, we reflect on the scientific enterprise and the perception of new discoveries.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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71
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Abstract
Background Stoichiometric imbalances in macromolecular complexes can lead to altered function. Such imbalances stem from under- or over-expression of a subunit of a complex consequent to a deletion, duplication or regulatory mutation of an allele encoding the relevant protein. In some cases, the phenotypic perturbations induced by such alterations can be subtle or be lacking because nonlinearities in the process of protein complex assembly can provide some degree of buffering. Results We explore with biochemical models of increasing plausibility how buffering can be elicited. Specifically, we analyze the formation of a dimer AB and show that there are particular sets of parameters so that decreasing/increasing the input amount of either A or B translates into a non proportional (buffered) change of AB. The buffer effect also appears in higher-order structures provided that there are intermediate subcomplexes in the assembly process. Conclusions We highlight the importance of protein degradation and/or conformational inactivation for buffering to appear. The models sketched here have experimental support but can be further tested with existing biological resources. Reviewers This article was reviewed by Eugene Koonin, Berend Snel and Csaba Pal.
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Affiliation(s)
- Reiner A Veitia
- Institut Jacques Monod, 15 rue Hélène Brion, 75013, Paris, France. .,Université Paris Diderot, Paris, France.
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, MO, 65211, USA.
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72
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Li J, Hou J, Sun L, Wilkins JM, Lu Y, Niederhuth CE, Merideth BR, Mawhinney TP, Mossine VV, Greenlief CM, Walker JC, Folk WR, Hannink M, Lubahn DB, Birchler JA, Cheng J. From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data. PLoS One 2015; 10:e0125000. [PMID: 25902288 PMCID: PMC4406561 DOI: 10.1371/journal.pone.0125000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 03/19/2015] [Indexed: 01/31/2023] Open
Abstract
RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS). These RNA reads can be mapped to reference genomes to investigate changes of gene expression but improved procedures for mining large RNA-Seq datasets to extract valuable biological knowledge are needed. RNAMiner--a multi-level bioinformatics protocol and pipeline--has been developed for such datasets. It includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed genes, predicting gene functions, and constructing gene regulatory networks. To demonstrate its utility, we applied RNAMiner to datasets generated from Human, Mouse, Arabidopsis thaliana, and Drosophila melanogaster cells, and successfully identified differentially expressed genes, clustered them into cohesive functional groups, and constructed novel gene regulatory networks. The RNAMiner web service is available at http://calla.rnet.missouri.edu/rnaminer/index.html.
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Affiliation(s)
- Jilong Li
- Computer Science Department, University of Missouri, Columbia, Missouri, United States of America
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
| | - Jie Hou
- Computer Science Department, University of Missouri, Columbia, Missouri, United States of America
| | - Lin Sun
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | | | - Yuan Lu
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Chad E. Niederhuth
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Benjamin Ryan Merideth
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Thomas P. Mawhinney
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Valeri V. Mossine
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - C. Michael Greenlief
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America
| | - John C. Walker
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - William R. Folk
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Mark Hannink
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Dennis B. Lubahn
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jianlin Cheng
- Computer Science Department, University of Missouri, Columbia, Missouri, United States of America
- MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America
- Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
- C. Bond Life Science Center, University of Missouri, Columbia, Missouri, United States of America
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73
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, Tucker Hall, University of Missouri, Columbia, Missouri 65211, USA
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Veitia RA, Veyrunes F, Bottani S, Birchler JA. X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses. J Mol Cell Biol 2015; 7:2-11. [PMID: 25564545 DOI: 10.1093/jmcb/mjv001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
X chromosome inactivation is a mechanism that modulates the expression of X-linked genes in eutherian females (XX). Ohno proposed that to achieve a proper balance between X-linked and autosomal genes, those on the active X should also undergo a 2-fold upregulation. Although some support for Ohno's hypothesis has been provided through the years, recent genomic studies testing this hypothesis have brought contradictory results and fueled debate. Thus far, there are as many results in favor as against Ohno's hypothesis, depending on the nature of the datasets and the various assumptions and thresholds involved in the analyses. However, they have confirmed the importance of dosage balance between X-linked and autosomal genes involved in stoichiometric relationships. These facts as well as questions and hypotheses are discussed below.
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Affiliation(s)
- Reiner A Veitia
- Institut Jacques Monod, Paris, France Université Paris Diderot, Paris, France
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, CNRS/Université Montpellier II, Montpellier, France
| | - Samuel Bottani
- Université Paris Diderot, Paris, France Matière et Systèmes Complexes, Paris, France
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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75
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Liu Y, Su H, Zhang J, Liu Y, Han F, Birchler JA. Dynamic epigenetic states of maize centromeres. Front Plant Sci 2015; 6:904. [PMID: 26579154 PMCID: PMC4620398 DOI: 10.3389/fpls.2015.00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/10/2015] [Indexed: 05/03/2023]
Abstract
The centromere is a specialized chromosomal region identified as the major constriction, upon which the kinetochore complex is formed, ensuring accurate chromosome orientation and segregation during cell division. The rapid evolution of centromere DNA sequence and the conserved centromere function are two contradictory aspects of centromere biology. Indeed, the sole presence of genetic sequence is not sufficient for centromere formation. Various dicentric chromosomes with one inactive centromere have been recognized. It has also been found that de novo centromere formation is common on fragments in which centromeric DNA sequences are lost. Epigenetic factors play important roles in centromeric chromatin assembly and maintenance. Non-disjunction of the supernumerary B chromosome centromere is independent of centromere function, but centromere pairing during early prophase of meiosis I requires an active centromere. This review discusses recent studies in maize about genetic and epigenetic elements regulating formation and maintenance of centromere chromatin, as well as centromere behavior in meiosis.
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Affiliation(s)
- Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri at Columbia, ColumbiaMO, USA
- *Correspondence: James A. Birchler,
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76
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Birchler JA. Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 2014; 123:459-69. [DOI: 10.1007/s00412-014-0478-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
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77
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Abstract
Platforms for the development of synthetic chromosomes in plants have been produced in several species using telomere mediated chromosomal truncation with the simultaneous inclusion of sites that facilitate further additions to the newly generated minichromosome. By utilizing truncated supernumerary or B chromosomes, the output of the genes on the minichromosome can be amplified. Proof of concept experiments have been successful illustrating that minichromosome platforms can be modified in vivo. Engineered minichromosomes can likely be combined with haploid breeding if they are incorporated into inducer lines given that the observations that basically inert chromosomes from haploid inducer lines can be recovered at workable frequencies in otherwise haploid plants. Future needs of synthetic chromosome development are discussed.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
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78
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Conant GC, Birchler JA, Pires JC. Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Curr Opin Plant Biol 2014; 19:91-8. [PMID: 24907529 DOI: 10.1016/j.pbi.2014.05.008] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/06/2014] [Accepted: 05/08/2014] [Indexed: 05/04/2023]
Abstract
Requirements to maintain dosage balance shape many genome-scale patterns in organisms, including the resolution of whole genome duplications (WGD), as well as the varied effects of aneuploidy, segmental duplications, tandem duplications, gene copy number variations (CNV), and epigenetic marks. Like neofunctionalization and subfunctionalization, the impact of absolute and relative dosage varies over time. These variations are of particular importance in understanding the role of dosage in the evolution of polyploid organisms. Numerous investigations have found the consequences of polyploidy remain distinct from small-scale duplications (SSD). This observation is significant as all flowering plants have experienced at least two ancient polyploid events, and many angiosperm lineages have undergone additional rounds of polyploidy. Intriguingly, recent studies indicate a link between how epigenetic marks in recent allopolyploids may induce immediate changes in gene expression and the longer-term patterns of biased fractionation and chromosomal evolution. We argue that dosage effects represent one aspect of an emerging pluralistic framework, a framework that will use biophysics, genomic technologies, and systems-level models of cells to broaden our view of how genomes evolve.
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Affiliation(s)
- Gavin C Conant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; Informatics Institute, University of Missouri, Columbia, MO 65211, United States.
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
| | - J Chris Pires
- Informatics Institute, University of Missouri, Columbia, MO 65211, United States; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
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79
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Zhang B, Dong Q, Su H, Birchler JA, Han F. Histone phosphorylation: its role during cell cycle and centromere identity in plants. Cytogenet Genome Res 2014; 143:144-9. [PMID: 24713809 DOI: 10.1159/000360435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
As the main protein components of chromatin, histones can alter the structural/functional capabilities of chromatin by undergoing extensive post-translational modifications (PTMs) such as phosphorylation, methylation, acetylation, ubiquitination, sumoylation, and so on. These PTMs are thought to transmit signals from the chromatin to the cell machinery to regulate various processes. Histone phosphorylation is associated with chromosome condensation/segregation, activation of transcription, and DNA damage repair. In this review, we focus on how different histone phosphorylations mark for chromatin change during the cell cycle, the relationship between histone phosphorylation and functional centromeres, and the candidate kinases that trigger and the phosphatase or kinase inhibitors that alter histone phosphorylation. Finally, we review the crosstalk between different PTMs.
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Affiliation(s)
- B Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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80
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Zhang J, Zhang B, Su H, Birchler JA, Han F. Molecular mechanisms of homologous chromosome pairing and segregation in plants. J Genet Genomics 2014; 41:117-23. [PMID: 24656232 DOI: 10.1016/j.jgg.2013.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/09/2013] [Accepted: 12/09/2013] [Indexed: 11/18/2022]
Abstract
In most eukaryotic species, three basic steps of pairing, recombination and synapsis occur during prophase of meiosis I. Homologous chromosomal pairing and recombination are essential for accurate segregation of chromosomes. In contrast to the well-studied processes such as recombination and synapsis, many aspects of chromosome pairing are still obscure. Recent progress in several species indicates that the telomere bouquet formation can facilitate homologous chromosome pairing by bringing chromosome ends into close proximity, but the sole presence of telomere clustering is not sufficient for recognizing homologous pairs. On the other hand, accurate segregation of the genetic material from parent to offspring during meiosis is dependent on the segregation of homologs in the reductional meiotic division (MI) with sister kinetochores exhibiting mono-orientation from the same pole, and the segregation of sister chromatids during the equational meiotic division (MII) with kinetochores showing bi-orientation from the two poles. The underlying mechanism of orientation and segregation is still unclear. Here we focus on recent studies in plants and other species that provide insight into how chromosomes find their partners and mechanisms mediating chromosomal segregation.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James A Birchler
- Division of Biological Sciences, 311 Tucker Hall, University of Missouri, Columbia, MO 65211, USA.
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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81
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Abstract
Heterosis research over the past century has focused primarily on diploid plants and animals. This is despite the fact that most heterotic organisms contain polyploid events in their recent and/or ancient past and various important crop species are heterotic polyploids. We present an argument for the study of heterosis within polyploid systems and give examples of how their study can improve current hypotheses and generate new ones. Polyploid systems allow experiments not possible in diploids but the insights gained must be incorporated into models to explain heterosis at all levels.
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Affiliation(s)
- Jacob D Washburn
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO, 65211, USA
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82
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Birchler JA. Interploidy hybridization barrier of endosperm as a dosage interaction. Front Plant Sci 2014; 5:281. [PMID: 25018757 PMCID: PMC4071978 DOI: 10.3389/fpls.2014.00281] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/29/2014] [Indexed: 05/06/2023]
Abstract
Crosses between plants at different ploidy levels will often result in failure of endosperm development. The basis of this phenomenon has been attributed to parental gene imprinting of genes involved with endosperm development but a review of the data from maize indicates a dosage interaction between the contributions of the female gametophyte and the primary endosperm nucleus to early endosperm development. However, it is noted that parental imprinting is a non-mutational means that can alter dosage sensitive factors and therefore can contribute to this effect. Operationally, the genes determining ploidy hybridization barrier would qualify for Dobzhansky-Muller incompatibilities that prevent gene flow between species.
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Affiliation(s)
- James A. Birchler
- *Correspondence: James A. Birchler, Division of Biological Science, University of Missouri-Columbia, 311 Tucker Hall, Columbia, MO 65211-7400, USA e-mail:
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83
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Birchler JA. Does ectopic cell death cause somatic mutations in the neighboring cells by activating transposons? Mob Genet Elements 2014; 4:e28040. [PMID: 24567848 DOI: 10.4161/mge.28040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 11/19/2022] Open
Abstract
Ectopic cell death in Drosophila produces a nonautonomous inhibition of RNA interference (RNAi) in neighboring normal cells. The expression of transposable elements (TE) is increased due to this reduction in the silencing mechanism. New insertions of TE have been documented in mutants for RNAi functions. These observations raise the possibility that persistent environmental insults that produce cell death might increase the frequency of somatic mutations, which might trigger somatic genetic disease.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences; University of Missouri; Columbia, MO USA
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84
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Abstract
The typical behavior of chromosomes in meiosis is that homologous pairs synapse, recombine, and then separate at anaphase I. At anaphase II, sister chromatids separate. However, studies of small chromosomes in maize derived from a variety of sources typically have failure of sister chromatid cohesion at anaphase I. This failure occurs whether there is pairing of two copies of a minichromosome or not. These characteristics have implications for managing the transmission of the first generation artificial chromosomes in plants. Procedures to address these issues of minichromosomes are discussed.
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Affiliation(s)
- James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
- *Correspondence: James A. Birchler, Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO 65211-7400, USA e-mail:
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
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85
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Xie W, Donohue RC, Birchler JA. Quantitatively increased somatic transposition of transposable elements in Drosophila strains compromised for RNAi. PLoS One 2013; 8:e72163. [PMID: 23940807 PMCID: PMC3733903 DOI: 10.1371/journal.pone.0072163] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/07/2013] [Indexed: 11/19/2022] Open
Abstract
In Drosophila melanogaster, small RNAs homologous to transposable elements (TEs) are of two types: piRNA (piwi-interacting RNA) with size 23-29nt and siRNA (small interfering RNA) with size 19-22nt. The siRNA pathway is suggested to silence TE activities in somatic tissues based on TE expression profiles, but direct evidence of transposition is lacking. Here we developed an efficient FISH (fluorescence in Situ hybridization) based method for polytene chromosomes from larval salivary glands to reveal new TE insertions. Analysis of the LTR-retrotransposon 297 and the non-LTR retroposon DOC shows that in the argonaut 2 (Ago2) and Dicer 2 (Dcr2) mutant strains, new transposition events are much more frequent than in heterozygous strains or wild type strains. The data demonstrate that the siRNA pathway represses TE transposition in somatic cells. Nevertheless, we found that loss of one functional copy of Ago2 or Dcr2 increases somatic transpositions of the elements at a lower level depending on the genetic background, suggesting a quantitative role for RNAi core components on mutation frequency.
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Affiliation(s)
- Weiwu Xie
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Ryan C. Donohue
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
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86
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87
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Gao Z, Han F, Danilova TV, Lamb JC, Albert PS, Birchler JA. Labeling meiotic chromosomes in maize with fluorescence in situ hybridization. Methods Mol Biol 2013; 990:35-43. [PMID: 23559200 DOI: 10.1007/978-1-62703-333-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Fluorescence in situ hybridization (FISH) can be used to visualize chromosomal features using repetitive or single gene probes above a minimum target size. When applied to meiosis, each chromosome of the karyotypic complement can be identified, which can facilitate an understanding of the interrelationship of different chromosomes during this process. On the other hand, the pachytene stage of early meiosis is characterized by slightly but not strongly condensed chromosomes that permit more detailed analyses of adjacent features than can be achieved with somatic metaphase chromosomes.
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Affiliation(s)
- Zhi Gao
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO, USA
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88
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Birchler JA. Aneuploidy in plants and flies: The origin of studies of genomic imbalance. Semin Cell Dev Biol 2013; 24:315-9. [DOI: 10.1016/j.semcdb.2013.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 02/11/2013] [Indexed: 12/18/2022]
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Masonbrink RE, Fu S, Han F, Birchler JA. Heritable loss of replication control of a minichromosome derived from the B chromosome of maize. Genetics 2013; 193:77-84. [PMID: 23114381 PMCID: PMC3527256 DOI: 10.1534/genetics.112.146126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 10/29/2012] [Indexed: 01/24/2023] Open
Abstract
During an accumulation regime of a small telomere-truncated B chromosome, a derivative with large variations in size and multiple punctate centromere loci exhibiting amplified copy numbers was discovered. Multiple centromere satellite loci or transgene signals were documented in amplified chromosomes, suggesting over-replication. Immunolocalization studies revealed multiple foci of biochemical markers characteristic of active centromeres such as CENP-C and phosphorylation of histones H3S10 and H2AThr133. The amplified chromosomes exhibit an absence of chromosome disjunction in meiosis I and an infrequent chromosome disjunction in meiosis II. Despite their unusual structure and behavior these chromosomes were observed in the lineage for seven generations during the course of this study. While severely truncated relative to a normal B chromosome, the progenitor minichromosome is estimated to be at least several megabases in size. Given that the centromere and transgene signals at opposite ends of the chromosome generally match in copy number, the replication control is apparently lost over several megabases.
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Affiliation(s)
- Rick E. Masonbrink
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Shulan Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese National Academy of Sciences, Beijing, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese National Academy of Sciences, Beijing, China
| | - James A. Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
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Birchler JA. Insights from paleogenomic and population studies into the consequences of dosage sensitive gene expression in plants. Curr Opin Plant Biol 2012; 15:544-548. [PMID: 22939251 DOI: 10.1016/j.pbi.2012.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 08/16/2012] [Indexed: 06/01/2023]
Abstract
Classical studies of plant phenotypes of individuals with whole or partial genome dosage changes led to the concept of genomic balance. Subsequent studies of gene expression in ploidy and aneuploidy series showed a greater number of modulations in aneuploid plants than with whole genome changes leading to the idea that gene expression processes were modulated by stoichiometric changes of interacting regulatory factors. Recent studies of genomic sequences and copy number variants in populations reveal different fates of duplicate genes depending on whole genome or segmental duplication. Following polyploidy formation, members of macromolecular complexes persist in the evolutionary lineage longer than random genes and a complementary pattern is found for segmental duplications in that there is an underrepresentation of members of macromolecular complexes. These and other studies described suggest there are negative fitness consequences when an imbalance occurs for members of macromolecular complexes including regulatory functions.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO 65211, United States.
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91
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Abstract
Paramutation, a phenomenon of epigenetic switching that violates Mendel's Law of Segregation, was first discovered in maize and later observed in other plants. In a recent report in Nature, de Vanssay and colleagues (2012) describe in Drosophila an operationally analogous phenomenon to paramutation that is mediated by piwi-interacting RNAs.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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92
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Abstract
Multiple copies of B chromosomes in maize (Zea mays) can accumulate in the genome using the B chromosome's accumulation mechanism, specifically nondisjunction at the second pollen mitosis and preferential fertilization of the egg. Using this mechanism, we accumulated 4 different-sized minichromosomes derived from the B chromosome to test the chromosome limits of the cell. The accumulation of normal B chromosomes is associated with multiple phenotypes including white stripes and asymmetric leaf blades, but when minichromosomes are accumulated these symptoms are absent. We also found that multiple B chromosome-derived minichromosomes can coexist with A chromosome-derived minichromosomes. During the years that these experiments were conducted, we found many B chromosome rearrangements and fragments, 2 recoverable A chromosome fragments, and observed a minichromosome breakage-fusion-bridge cycle in roots.
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Affiliation(s)
- R E Masonbrink
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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93
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Birchler JA, Presting GG. Retrotransposon insertion targeting: a mechanism for homogenization of centromere sequences on nonhomologous chromosomes. Genes Dev 2012; 26:638-40. [PMID: 22474258 DOI: 10.1101/gad.191049.112] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The centromeres of most eukaryotic organisms consist of highly repetitive arrays that are similar across nonhomologous chromosomes. These sequences evolve rapidly, thus posing a mystery as to how such arrays can be homogenized. Recent work in species in which centromere-enriched retrotransposons occur indicates that these elements preferentially insert into the centromeric regions. In two different Arabidopsis species, a related element was recognized in which the specificity for such targeting was altered. These observations provide a partial explanation for how homogenization of centromere DNA sequences occurs.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri at Columbia, Columbia, Missouri 65211, USA.
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94
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Masonbrink RE, Gaeta RT, Birchler JA. Multiple maize minichromosomes in meiosis. Chromosome Res 2012; 20:395-402. [DOI: 10.1007/s10577-012-9283-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/09/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
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95
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96
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Abstract
Synthetic chromosomes provide the means to stack transgenes independently of the remainder of the genome. Combining them with haploid breeding could provide the means to transfer many transgenes more easily among varieties of the same species. The epigenetic nature of centromere formation complicates the production of synthetic chromosomes. However, telomere-mediated truncation coupled with the introduction of site-specific recombination cassettes has been used to produce minichromosomes consisting of little more than a centromere. Methods that have been developed to modify genes in vivo could be applied to minichromosomes to improve their utility and to continue to increase their length and genic content. Synthetic chromosomes establish the means to add or subtract multiple transgenes, multigene complexes, or whole biochemical pathways to plants to change their properties for agricultural applications or to use plants as factories for the production of foreign proteins or metabolites.
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Affiliation(s)
- Robert T Gaeta
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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97
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Gao Z, Fu S, Dong Q, Han F, Birchler JA. Inactivation of a centromere during the formation of a translocation in maize. Chromosome Res 2011; 19:755-61. [PMID: 21947957 DOI: 10.1007/s10577-011-9240-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/24/2011] [Accepted: 08/25/2011] [Indexed: 11/25/2022]
Abstract
Fluorescence in situ hybridization analysis of a reciprocal translocation in maize between chromosomes 1 and 5 that has been used extensively in maize genetics revealed the presence of an inactive centromere at or near the breakpoints of the two chromosomes. This centromere contains both the satellite repeat, CentC, and the centromeric retrotransposon family, CRM, that are typical of centromere regions in maize. This site does not exhibit any of the tested biochemical features of active centromeres such as association with CENP-C and phosphorylation of serine-10 on histone H3. The most likely scenario for this chromosome arrangement is that a centromere was included in the repair process that formed the translocation but became inactive and has been inherited in this state for several decades. The documentation of an inactive A chromosome centromere in maize extends the evidence for an epigenetic component to centromere function in plants. This case provides an experimental example of how karyotype evolution might proceed via changes in centromere inactivation.
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Affiliation(s)
- Zhi Gao
- Division of Biological Sciences, University of Missouri, 311 Tucker Hall, Columbia, MO 65211, USA
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98
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Abstract
Mutations and most transgenes that induce ectopic cell death in Drosophila will produce an inhibitory effect on RNA interference (RNAi) in adjacent cells. When extensive cell death is sporadically induced using a heat shock promoted-head involution defective (hs-hid) transgene, molecular attributes of this inhibition can be studied. For a Green Fluorescent Protein (GFP) RNAi construct, cell death causes a greater accumulation of the mature mRNA and the double stranded RNA with an accompanying reduction in the homologous siRNAs. Endogenous transposable element expression is increased and there is an overall reduction in their corresponding siRNAs. The implications of this finding for the conduct of RNAi and potential reasons for its existence are discussed.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO USA.
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99
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Gaeta RT, Danilova TV, Zhao C, Masonbrink RE, McCaw ME, Birchler JA. Recovery of a telomere-truncated chromosome via a compensating translocation in maize. Genome 2011; 54:184-95. [PMID: 21423281 DOI: 10.1139/g10-108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Maize-engineered minichromosomes are easily recovered from telomere-truncated B chromosomes but are rarely recovered from A chromosomes. B chromosomes lack known genes, and their truncation products are tolerated and transmitted during meiosis. In contrast, deficiency gametes resulting from truncated A chromosomes prevent their transmission. We report here a de novo compensating translocation that permitted recovery of a large truncation of chromosome 1 in maize. The truncation (trunc-1) and translocation with chromosome 6 (super-6) occurred during telomere-mediated truncation experiments and were characterized using single-gene fluorescent in situ hybridization (FISH) probes. The truncation contained a transgene signal near the end of the broken chromosome and transmitted together with the compensating translocation as a heterozygote to approximately 41%-55% of progeny. Transmission as an addition chromosome occurred in ~15% of progeny. Neither chromosome transmitted through pollen. Transgene expression (Bar) cosegregated with trunc-1 transcriptionally and phenotypically. Meiosis in T1 plants revealed eight bivalents and one tetravalent chain composed of chromosome 1, trunc-1, chromosome 6, and super-6 in diplotene and diakinesis. Our data suggest that de novo compensating translocations allow recovery of truncated A chromosomes by compensating deficiency in female gametes and by affecting chromosome pairing and segregation. The truncated chromosome can be maintained as an extra chromosome or together with the super-6 as a heterozygote.
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Affiliation(s)
- Robert T Gaeta
- Department of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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100
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Findley SD, Pappas AL, Cui Y, Birchler JA, Palmer RG, Stacey G. Fluorescence in situ hybridization-based karyotyping of soybean translocation lines. G3 (Bethesda) 2011; 1:117-29. [PMID: 22384324 PMCID: PMC3276125 DOI: 10.1534/g3.111.000034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 05/07/2011] [Indexed: 01/06/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is a major crop species and, therefore, a major target of genomic and genetic research. However, in contrast to other plant species, relatively few chromosomal aberrations have been identified and characterized in soybean. This is due in part to the difficulty of cytogenetic analysis of its small, morphologically homogeneous chromosomes. The recent development of a fluorescence in situ hybridization -based karyotyping system for soybean has enabled our characterization of most of the chromosomal translocation lines identified to date. Utilizing genetic data from existing translocation studies in soybean, we identified the chromosomes and approximate breakpoints involved in five translocation lines.
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