scholarly journals De novo centromere formation on chromosome fragments with an inactive centromere in maize (Zea mays)

2021 ◽  
Author(s):  
Ryan N. Douglas ◽  
Hua Yang ◽  
Bing Zhang ◽  
Chen Chen ◽  
Fangpu Han ◽  
...  
Keyword(s):  
De Novo ◽  
Low Frequency ◽  
B Chromosome ◽  
Chromosome 9 ◽  
Centromere Region ◽  
Pollen Mitosis ◽  
Accumulation Mechanism ◽  
Chromosome Fragments ◽  
Breakpoint Determination ◽  
Second Pollen Mitosis

AbstractThe B chromosome of maize undergoes nondisjunction at the second pollen mitosis as part of its accumulation mechanism. Previous work identified 9-Bic-1 (9-B inactivated centromere-1), which comprises an epigenetically silenced B chromosome centromere that was translocated to the short arm of chromosome 9(9S). This chromosome is stable in isolation, but when normal B chromosomes are added to the genotype, it will attempt to undergo nondisjunction during the second pollen mitosis and usually fractures the chromosome in 9S. These broken chromosomes allow a test of whether the inactive centromere is reactivated or whether a de novo centromere is formed elsewhere on the chromosome to allow recovery of fragments. Breakpoint determination on the B chromosome and chromosome 9 showed that mini chromosome B1104 has the same breakpoint as 9-Bic-1 in the B centromere region and includes a portion of 9S. CENH3 binding was found on the B centromere region and on 9S, suggesting both centromere reactivation and de novo centromere formation. Another mini chromosome, B496, showed evidence of rearrangement, but it also only showed evidence for a de novo centromere. Other mini chromosome fragments recovered were directly derived from the B chromosome with breakpoints concentrated near the centromeric knob region, which suggests that the B chromosome is broken at a low frequency due to the failure of the sister chromatids to separate at the second pollen mitosis. Our results indicate that both reactivation and de novo centromere formation could occur on fragments derived from the progenitor possessing an inactive centromere.

Unstable inheritance of maize B-type chromosomes that lack centric heterochromatin

Genome ◽  
2006 ◽  
Vol 49 (5) ◽  
pp. 420-431 ◽  
Author(s):  
Wayne R Carlson
Keyword(s):  
B Chromosome ◽  
Chromosome 9 ◽  
Pollen Mitosis ◽  
Genetic Studies ◽  
Telocentric Chromosome ◽  
Deletion Derivative ◽  
Translocation Heterozygote ◽  
Second Pollen Mitosis

The B chromosome of maize undergoes frequent non-disjunction at the second pollen mitosis. In B–A translocations, the B–A chromosome retains the capacity for non-disjunction. We have collected deletion-derivative TB-9Sb stocks. One derivative, the "type 1 telocentric", has a B–9 chromosome that lacks centric heterochromatin. It produces few recessive (non-disjunctional) phenotypes in pollen parent testcrosses of the translocation heterozygote, 9 9–B telo B–9. The finding helped demonstrate the role of centric heterochromatin in non-disjunction. An isochromo some derivative of the type 1 telocentric was also recovered. It was tested in the 9–B 9–B iso B–9 constitution. This is equivalent to 9 9–B telo B–9 in terms of chromosome 9 dosage. Surprisingly, crosses with the isochromosome gave significant levels of recessive phenotypes. In addition, high levels of variegated phenotypes were found. Recently, a circumstance was found that makes inheritance of the type 1 telocentric chromosome somewhat similar to that of the isochromosome. Crosses with hypoploid 9–B 9–B telo B–9 plants showed significant levels of recessive and variegated phenotypes. These crosses were investigated to help explain the source(s) of the phenotypes. Cytological and genetic studies were performed. Centric misdivision was found to account for the variegated phenotypes. A mixture of conventional B non-disjunction and centric misdivision produced the recessive phenotypes. The significance of conventional non-disjunction in the absence of centric heterochromatin is discussed.Key words: cytogenetics, B chromosome, centromere, maize.

Locating a site on the maize B chromosome that controls preferential fertilization

Genome ◽  
2007 ◽  
Vol 50 (6) ◽  
pp. 578-587 ◽  
Author(s):  
Wayne R. Carlson
Keyword(s):  
B Chromosome ◽  
B Chromosomes ◽  
Chromosome 9 ◽  
Chromosome Deletion ◽  
Pollen Mitosis ◽  
Preferential Fertilization ◽  
Second Pollen Mitosis ◽  
A Site ◽  
Derivatives Of

In maize, the B chromosome can undergo nondisjunction at the second pollen mitosis, producing sperm with two B chromosomes and sperm with zero B chromosomes. Preferential fertilization is the ability of the sperm carrying two B chromosomes to transmit more frequently to the embryo of a kernel than the sperm lacking the B chromosome. A translocation involving the B chromosome and chromosome 9, TB-9Sb, has been used to study preferential fertilization. The B-9 chromosome has the same properties of nondisjunction and preferential fertilization as the standard B chromosome. Deletion derivatives of B-9, which lack the centric heterochromatin and possibly some adjacent euchromatin, were tested for their ability to induce preferential fertilization. They were found to lack the capacity for preferential fertilization.

Time Course Study of the Chromosome-Type Breakage-Fusion-Bridge Cycle in Maize

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1435-1444
Author(s):  
Yin-Zhou Zheng ◽  
Robin R Roseman ◽  
Wayne R Carlson
Keyword(s):  
Time Course ◽  
B Chromosome ◽  
Developmental Time ◽  
Chromosome 9 ◽  
Pollen Mitosis ◽  
Chromosome Type ◽  
Root Cells ◽  
Wide Range ◽  
Time Course Study ◽  
Second Pollen Mitosis

Abstract The B chromosome of maize has been used in a study of dicentric chromosomes. TB-9Sb is a translocation between the B and chromosome 9. The B-9 of TB-9Sb carries 60% of the short arm of 9. For construction of dicentrics, a modified B-9 chromosome was used, B-9-Dp9. It consists of the B-9 chromosome plus a duplicated 9S region attached to the distal end. In meiosis, fold-back pairing and crossing over in the duplicated region gives a chromatid-type dicentric B-9 that subsequently initiates a chromatid-type breakage-fusion-bridge cycle. In the male, it forms a single bridge in anaphase II of meiosis and at the first pollen mitosis. However, the cycle is interrupted by nondisjunction of the B centromere at the second pollen mitosis, which sends the B-9 dicentric to one pole and converts it from a chromatid dicentric to a chromosome dicentric. As expected, the new dicentric undergoes the chromosome-type breakage-fusion-bridge cycle and produces double bridges. A large number of plants with chromosome dicentrics were produced in this way. The presence of double bridges in the root cells of plants with a chromosome dicentric was studied during the first 10 wk of development. It was found that the number of plants and cells showing double bridges declined steadily over the 10-wk period. Several lines of evidence indicate that there was no specific developmental time for dicentric loss. “Healing” of broken chromosomes produced by dicentric breakage accounted for much of the dicentric loss. Healing produced a wide range of derived B-9 chromosomes, some large and some small. A group of minichromosomes found in these experiments probably represents the small end of the scale for B-9 derivatives.

A new method for producing homozygous duplications in maize

1986 ◽  
Vol 28 (6) ◽  
pp. 1034-1040 ◽  
Author(s):  
W. R. Carlson ◽  
C. Curtis
Keyword(s):  
Gene Dosage ◽  
B Chromosome ◽  
Chromosome 9 ◽  
New Method ◽  
Maize Genome ◽  
Pollen Mitosis ◽  
Normal Pattern ◽  
Key Words Maize ◽  
Second Pollen Mitosis ◽  
Chromosome Segments

Translocations between the B chromosomes of maize and standard (A) chromosomes have been widely used to manipulate the dosage of A chromosome segments. The B chromosome frequently undergoes nondisjunction at the second pollen mitosis as part of its normal pattern of inheritance. BA chromosomes also undergo nondisjunction and, therefore, are used to produce duplications and deficiencies of A-chromatin. Duplications are useful in gene dosage studies and some may have agronomic value if they are associated with useful phenotypes. However, duplications produced by BA nondisjunction cannot be easily maintained during propagation. The BA undergoes nondisjunction each generation, destabilizing its inheritance. A new method is presented here for systematically duplicating segments of the maize genome using B–A translocations. The method uses meiotic segregation rather than nondisjunction to produce duplications. It employs AB chromosomes instead of BA chromosomes. As a test of the method, homozygous duplications (segmental tetrasomics) were constructed for a region on chromosome 3 and for another region on chromosome 9.Key words: maize, B chromosome, duplication.

scholarly journals Sequential de novo centromere formation and inactivation on a chromosomal fragment in maize

2015 ◽  
Vol 112 (11) ◽  
pp. E1263-E1271 ◽  
Author(s):  
Yalin Liu ◽  
Handong Su ◽  
Junling Pang ◽  
Zhi Gao ◽  
Xiu-Jie Wang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
De Novo ◽  
B Chromosome ◽  
Chromosome 9 ◽  
Centromeric Dna ◽  
Repeat Sequences ◽  
Centromeric Repeat ◽  
And Function ◽  
Centromere Assembly ◽  
Derivatives Of

The ability of centromeres to alternate between active and inactive states indicates significant epigenetic aspects controlling centromere assembly and function. In maize (Zea mays), misdivision of the B chromosome centromere on a translocation with the short arm of chromosome 9 (TB-9Sb) can produce many variants with varying centromere sizes and centromeric DNA sequences. In such derivatives of TB-9Sb, we found a de novo centromere on chromosome derivative 3-3, which has no canonical centromeric repeat sequences. This centromere is derived from a 288-kb region on the short arm of chromosome 9, and is 19 megabases (Mb) removed from the translocation breakpoint of chromosome 9 in TB-9Sb. The functional B centromere in progenitor telo2-2 is deleted from derivative 3-3, but some B-repeat sequences remain. The de novo centromere of derivative 3-3 becomes inactive in three further derivatives with new centromeres being formed elsewhere on each chromosome. Our results suggest that de novo centromere initiation is quite common and can persist on chromosomal fragments without a canonical centromere. However, we hypothesize that when de novo centromeres are initiated in opposition to a larger normal centromere, they are cleared from the chromosome by inactivation, thus maintaining karyotype integrity.

scholarly journals B CHROMOSOME NONDISJUNCTION IN CORN: CONTROL BY FACTORS NEAR THE CENTROMERE

Genetics ◽  
1981 ◽  
Vol 97 (2) ◽  
pp. 379-389
Author(s):  
Wayne R Carlson ◽  
Tau-San Chou
Keyword(s):  
B Chromosome ◽  
B Chromosomes ◽  
Translocation Chromosome ◽  
Pollen Mitosis ◽  
Second Pollen Mitosis ◽  
Chromosome Nondisjunction

ABSTRACT B chromosomes of corn are stable at all mitotic and meiotic divisions of the plant except the second pollen mitosis. In the latter division, B chromosomes undego mitotic nondisjunction at rates as high as 98%. Studies by several workers on B-A translocation chromosomes have provided evidence for the existence of four factors on the B chromosome that control nondisjunction and are separable from the centromere. Two of these factors, referred to here as factors 3 and 4, flank the B chromosome centromere. Factor 3 is the centromere-adjacent heterochromatin in the long arm of the B chromosome; factor 4 is located in the minute short arm. Evidence is presented here supporting the existence of factors 3 and 4. Deficiencies that include each factor were identified following centromeric misdivision events, with breaks at or near the centromere of a B-translocation chromosome. B chromosomes lacking factors 3 or 4 show much less nondisjunction than do chromosomes containing them. The possible function of factor 4 in nondisjuntion is also discussed.

scholarly journals The Behavior of the Maize B Chromosome and Centromere

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 476 ◽  
Author(s):  
Handong Su ◽  
Yalin Liu ◽  
Yang Liu ◽  
James Birchler ◽  
Fangpu Han
Keyword(s):  
De Novo ◽  
B Chromosome ◽  
B Chromosomes ◽  
Genetic Studies ◽  
Accumulation Mechanism

The maize B chromosome is a non-essential chromosome with an accumulation mechanism. The dispensable nature of the B chromosome facilitates many types of genetic studies in maize. Maize lines with B chromosomes have been widely used in studies of centromere functions. Here, we discuss the maize B chromosome alongside the latest progress of B centromere activities, including centromere misdivision, inactivation, reactivation, and de novo centromere formation. The meiotic features of the B centromere, related to mini-chromosomes and the control of the size of the maize centromere, are also discussed.

scholarly journals Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
A. Rose Brannon ◽  
Gowtham Jayakumaran ◽  
Monica Diosdado ◽  
Juber Patel ◽  
Anna Razumova ◽  
...  
Keyword(s):  
Cancer Patients ◽  
De Novo ◽  
Low Frequency ◽  
High Sensitivity ◽  
Clinical Analysis ◽  
De Novo Mutation ◽  
Cell Free Dna ◽  
Free Dna ◽  
Somatic Alterations ◽  
Mutation Profiling

AbstractCirculating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.

scholarly journals De Novo Evolution of Satellite DNA on the Rye B Chromosome

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 869-884 ◽  
Author(s):  
Tim Langdon ◽  
Charlotte Seago ◽  
R Neil Jones ◽  
Helen Ougham ◽  
Howard Thomas ◽  
...  
Keyword(s):  
De Novo ◽  
Indirect Evidence ◽  
Heterochromatic Region ◽  
B Chromosome ◽  
Transient Stage ◽  
Sequence Elements ◽  
Complex Sequences ◽  
Strand Annealing ◽  
Single Sequence ◽  
Specific Sequences

Abstract The most distinctive region of the rye B chromosome is a subtelomeric domain that contains an exceptional concentration of B-chromosome-specific sequences. At metaphase this domain appears to be the physical counterpart of the subtelomeric heterochromatic regions present on standard rye chromosomes, but its conformation at interphase is less condensed. In this report we show that the two sequence families that have been previously found to make up the bulk of the domain have been assembled from fragments of a variety of sequence elements, giving rise to their ostensibly foreign origin. A single mechanism, probably based on synthesis-dependent strand annealing (SDSA), is responsible for their assembly. We provide evidence for sequential evolution of one family on the B chromosome itself. The extent of these rearrangements and the complexity of the higher-order organization of the B-chromosome-specific families indicate that instability is a property of the domain itself, rather than of any single sequence. Indirect evidence suggests that particular fragments may have been selected to confer different properties on the domain and that rearrangements are frequently selected for their effect on DNA structure. The current organization appears to represent a transient stage in the evolution of a conventional heterochromatic region from complex sequences.

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