Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modu...Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes(trans)with both the addition or subtraction of chromosome arms.Transposable elements(TEs)comprise a substantial fraction of the genome,and their reaction to genomic imbalance is therefore of interest.Here,we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs,but reductions in monosomy and increases in disomy and trisomy were also common.By contrast,the ploidy series showed little TE modulation.The modulation of TEs and genes in the same experimental group were compared,and TEs showed greater modulation than genes,especially in disomy.Class Ⅰ and Ⅱ TEs were differentially modulated in most aneuploidies,and some superfamilies in each TE class also showed differential modulation.Finally,the significantly upregulated TEs in three disomies(TB-7Lb,TB9Lc,and TB-10L19)did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs,indicating that modulations of TEs do not compound the effect on genes.These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs,similar to the response of core genes to genomic imbalance.展开更多
It has been known for decades that the maize B chromosome undergoes nondisjunction at the second pollen mitosis.Fluorescence in-situ hybridization (FISH) was used to undertake a quantitative study of maize plants wi...It has been known for decades that the maize B chromosome undergoes nondisjunction at the second pollen mitosis.Fluorescence in-situ hybridization (FISH) was used to undertake a quantitative study of maize plants with differing numbers of B chromosomes to observe if instability increases by increasing B dosage in root tip tissue.B chromosome nondisjunction was basically absent at low copy number,but increased at higher B numbers.Thus,B nondisjunction rates are dependent on the dosage of B's in the sporophyte.Differences in nondisjunction were also documented between odd and even doses of the B.In plants that have inherited odd numbered doses of the B chromosome,B loss is nearly twice as likely as B gain in a somatic division.When comparing plants with even doses of B's to plants with odd doses of B's,plants with even numbers had a significantly higher chance to increase in number.Therefore,the B's nondisjunctive capacity,previously thought to be primarily restricted to the gametophyte,is present in sporophytic cells.展开更多
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 chrom...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.展开更多
Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa,potato, and ...Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa,potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated fieldbased phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally,whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype,its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.展开更多
The centromere is an essential chromosome site at which the kinetochore forms and loads proteins needed for faithful segregation during the cell cycle and meiosis(Houben et al., 1999;Cleveland et al.,2003;Ma et al.,2...The centromere is an essential chromosome site at which the kinetochore forms and loads proteins needed for faithful segregation during the cell cycle and meiosis(Houben et al., 1999;Cleveland et al.,2003;Ma et al.,2007;Birchler and Han,2009).Centromere specific sequences such as tandem repeats or transposable elements evolve quickly both within and between the species but have conserved kinetochore proteins(Henikoff and Furuyama,2010).展开更多
Congratulations to the Genetics Society of China on their 40;anniversary! Genetics has expanded in scope in that time frame and has penetrated into many areas of biology, medicine and agriculture. Genetics is poised t...Congratulations to the Genetics Society of China on their 40;anniversary! Genetics has expanded in scope in that time frame and has penetrated into many areas of biology, medicine and agriculture. Genetics is poised to continue that trajectory into the future with promises of new understanding and new technologies for the benefit to society. Here, we will highlight some of the展开更多
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 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 upregula-tion.Although some support for Ohno's hypothesis has been provided through the years,recent genomic studies testing this hypoth-esis 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 con-firmed 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.展开更多
The centromere is a highly organized structure mainly composed of repeat sequences,which make this region extremely difficult for sequencing and other analyses.It plays a conserved role in equal division of chromosome...The centromere is a highly organized structure mainly composed of repeat sequences,which make this region extremely difficult for sequencing and other analyses.It plays a conserved role in equal division of chromosomes into daughter cells in both mitosis and meiosis.However,centromere sequences show notable plasticity.In a dicentric chromosome,one of the centromeres can become inactivated with the underlying DNA unchanged.Furthermore,formerly inactive centromeres can regain activity under certain conditions.In addition,neocentromeres without centromeric repeats have been found in a wide spectrum of species.This evidence indicates that epigenetic mechanisms together with centromeric sequences are associated with centromere specification.展开更多
Dosage compensation refers to the equal expression between the sexes despite the fact that the dosage of the X chromosome is different in males and females.In Drosophila there is a twofold upregulation of the single m...Dosage compensation refers to the equal expression between the sexes despite the fact that the dosage of the X chromosome is different in males and females.In Drosophila there is a twofold upregulation of the single male X.In triple X metafemales,there is also dosage compensation,which occurs by a two-thirds downregulation.There is a concomitant reduction in expression of many autosomal genes in metafemales.The male specific lethal(MSL)complex is present on the male X chromosome.Evidence is discussed showing that the MSL complex sequesters a histone acetyltransferase to the X chromosome to mute an otherwise increased expression by diminishing the histone acetylation on the autosomes.Several lines of evidence indicate that a constraining activity occurs from the MSL complex to prevent overcompensation on the X that might otherwise occur from the high level of acetylation present.Together,the evidence suggests that dosage compensation is a modification of a regulatory inverse dosage effect that is a reflection of intrinsic gene regulatory mechanisms and that the MSL complex has evolved in reaction in order to equalize the expression on both the X and autosomes of males and females.展开更多
基金supported by National Science Foundation USA grant IOS-1545780Computation for this work was performed on the highperformance computing infrastructure provided by Research Computing Support Services and in part by the National Science Foundation USA under grant number CNS-1429294 at the University of Missouri,Columbia,MO,https://doi.org/10.32469/10355/69802.
文摘Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes(trans)with both the addition or subtraction of chromosome arms.Transposable elements(TEs)comprise a substantial fraction of the genome,and their reaction to genomic imbalance is therefore of interest.Here,we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs,but reductions in monosomy and increases in disomy and trisomy were also common.By contrast,the ploidy series showed little TE modulation.The modulation of TEs and genes in the same experimental group were compared,and TEs showed greater modulation than genes,especially in disomy.Class Ⅰ and Ⅱ TEs were differentially modulated in most aneuploidies,and some superfamilies in each TE class also showed differential modulation.Finally,the significantly upregulated TEs in three disomies(TB-7Lb,TB9Lc,and TB-10L19)did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs,indicating that modulations of TEs do not compound the effect on genes.These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs,similar to the response of core genes to genomic imbalance.
基金supported by the National Science Foundation grant of USA (No. DBI0701297)
文摘It has been known for decades that the maize B chromosome undergoes nondisjunction at the second pollen mitosis.Fluorescence in-situ hybridization (FISH) was used to undertake a quantitative study of maize plants with differing numbers of B chromosomes to observe if instability increases by increasing B dosage in root tip tissue.B chromosome nondisjunction was basically absent at low copy number,but increased at higher B numbers.Thus,B nondisjunction rates are dependent on the dosage of B's in the sporophyte.Differences in nondisjunction were also documented between odd and even doses of the B.In plants that have inherited odd numbered doses of the B chromosome,B loss is nearly twice as likely as B gain in a somatic division.When comparing plants with even doses of B's to plants with odd doses of B's,plants with even numbers had a significantly higher chance to increase in number.Therefore,the B's nondisjunctive capacity,previously thought to be primarily restricted to the gametophyte,is present in sporophytic cells.
基金supported by the National Basic Research Program of China(973 Program)(Grant No.2011CB944601)the National Natural Science Foundation of China(Grant No.31320103912)USA National Science Foundation(Grant No.DBI 0922703)
文摘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.
基金supported by the National Science Foundation (USA) grant IOS-1545780
文摘Progressive heterosis, i.e., the additional hybrid vigor in double-cross tetraploid hybrids not found in their single-cross tetraploid parents, has been documented in a number of species including alfalfa,potato, and maize. In this study, four artificially induced maize tetraploids, directly derived from standard inbred lines, were crossed in pairs to create two single-cross hybrids. These hybrids were then crossed to create double-cross hybrids containing genetic material from all four original lines. Replicated fieldbased phenotyping of the materials over four years indicated a strong progressive heterosis phenotype in tetraploids but not in their diploid counterparts. In particular, the above ground dry weight phenotype of double-cross tetraploid hybrids was on average 34% and 56% heavier than that of the single-cross tetraploid hybrids and the double-cross diploid counterparts, respectively. Additionally,whole-genome resequencing of the original inbred lines and further analysis of these data did not show the expected spectrum of alleles to explain tetraploid progressive heterosis under the complementation of complete recessive model. These results underscore the reality of the progressive heterosis phenotype,its potential utility for increasing crop biomass production, and the need for exploring alternative hypothesis to explain it at a molecular level.
文摘The centromere is an essential chromosome site at which the kinetochore forms and loads proteins needed for faithful segregation during the cell cycle and meiosis(Houben et al., 1999;Cleveland et al.,2003;Ma et al.,2007;Birchler and Han,2009).Centromere specific sequences such as tandem repeats or transposable elements evolve quickly both within and between the species but have conserved kinetochore proteins(Henikoff and Furuyama,2010).
文摘Congratulations to the Genetics Society of China on their 40;anniversary! Genetics has expanded in scope in that time frame and has penetrated into many areas of biology, medicine and agriculture. Genetics is poised to continue that trajectory into the future with promises of new understanding and new technologies for the benefit to society. Here, we will highlight some of the
基金This work was supported by the Centre Nationalde la R echerche Scientifique(CN RS,France),Paris Diderot-Paris7 University,and the Agence Nationale de la Recherche(ANR,lceberg Project).
文摘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 upregula-tion.Although some support for Ohno's hypothesis has been provided through the years,recent genomic studies testing this hypoth-esis 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 con-firmed 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.
基金supported by the National Natural Science Foundation of China(Grant No.31071083)National Science Foundation(No.DBI0922703).
文摘The centromere is a highly organized structure mainly composed of repeat sequences,which make this region extremely difficult for sequencing and other analyses.It plays a conserved role in equal division of chromosomes into daughter cells in both mitosis and meiosis.However,centromere sequences show notable plasticity.In a dicentric chromosome,one of the centromeres can become inactivated with the underlying DNA unchanged.Furthermore,formerly inactive centromeres can regain activity under certain conditions.In addition,neocentromeres without centromeric repeats have been found in a wide spectrum of species.This evidence indicates that epigenetic mechanisms together with centromeric sequences are associated with centromere specification.
基金supported by National Institutes of Health grant RO1GM068042-05.
文摘Dosage compensation refers to the equal expression between the sexes despite the fact that the dosage of the X chromosome is different in males and females.In Drosophila there is a twofold upregulation of the single male X.In triple X metafemales,there is also dosage compensation,which occurs by a two-thirds downregulation.There is a concomitant reduction in expression of many autosomal genes in metafemales.The male specific lethal(MSL)complex is present on the male X chromosome.Evidence is discussed showing that the MSL complex sequesters a histone acetyltransferase to the X chromosome to mute an otherwise increased expression by diminishing the histone acetylation on the autosomes.Several lines of evidence indicate that a constraining activity occurs from the MSL complex to prevent overcompensation on the X that might otherwise occur from the high level of acetylation present.Together,the evidence suggests that dosage compensation is a modification of a regulatory inverse dosage effect that is a reflection of intrinsic gene regulatory mechanisms and that the MSL complex has evolved in reaction in order to equalize the expression on both the X and autosomes of males and females.