Allelic Repression Research Articles

Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells

Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica (93-11) and japonica (Nipponbare) inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By contrast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of-origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9ac/H3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Kcnq1ot1 is a long noncoding ribonucleic acid (RNA; lncRNA) that participates in the regulation of genes within the Kcnq1 imprinting domain. Using a novel RNA-guided chromatin conformation capture method, we demonstrate that the 5' region of Kcnq1ot1 RNA orchestrates a long-range intrachromosomal loop between KvDMR1 and the Kcnq1 promoter that is required for maintenance of imprinting. PRC2 (polycomb repressive complex 2), which participates in the allelic repression of Kcnq1, is also recruited by Kcnq1ot1 RNA via EZH2. Targeted suppression of Kcnq1ot1 lncRNA prevents the creation of this long-range intrachromosomal loop and causes loss of Kcnq1 imprinting. These observations delineate a novel mechanism by which an lncRNA directly builds an intrachromosomal interaction complex to establish allele-specific transcriptional gene silencing over a large chromosomal domain.

Non-imprinted allele-specific DNA methylation on human autosomes

Single-nucleotide polymorphisms located within CpG islands are found to cause differences in CpG methylation between alleles, reflecting differences in gene expression.

Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes

Imprinted genes are clustered in domains, and their allelic repression is mediated by imprinting control regions. These imprinting control regions are marked by DNA methylation, which is essential to maintain imprinting in the embryo. To explore how imprinting is regulated in placenta, we studied the Kcnq1 domain on mouse distal chromosome 7. This large domain is controlled by an intronic imprinting control region and comprises multiple genes that are imprinted in placenta, without the involvement of promoter DNA methylation. We found that the paternal repression along the domain involves acquisition of trimethylation at Lys27 and dimethylation at Lys9 of histone H3. Eed-Ezh2 Polycomb complexes are recruited to the paternal chromosome and potentially regulate its repressive histone methylation. Studies on embryonic stem cells and early embryos support our proposal that chromatin repression is established early in development and is maintained in the placenta. In the embryo, however, imprinting is stably maintained only at genes that have promoter DNA methylation. These data underscore the importance of histone methylation in placental imprinting and identify mechanistic similarities with X-chromosome inactivation in extraembryonic tissues, suggesting that the two epigenetic mechanisms are evolutionarily linked.

Expression of the lactate dehydrogenase genes of Xenopus species and interspecies hybrids during early development

1. 1. The expression of LDH genes throughout early development of different Xenopus species, and interspecies hybrids has been compared. 2. 2. In X.1. victorianus oocytes the LDH-B 4 polymer is synthesized exclusively and is stored during early embryonic stages. For the first time at stage 27 is the embryonic LDH gene activity manifest. 3. 3. In other species the situation is somewhat more complicated, in that additional anodal bands appear or, like in X. clivii, even cathodal polymers are formed. 4. 4. In X.1. victorianus ♀ × X. borealis ♂ hybrids only the maternal pattern was expressed throughout the whole embryonic development. This allelic repression persisted up to metamorphosis.

Developmental Genetics of Fishes: Isozymic Analyses of Differential Gene Expression

SYNOPSIS. The fundamental evolutionary position of the fishes and the plasticity of their gene expression render them well suited for developmental genetic analyses. Isozymes, encoded in related loci, have proven to be effective probes of differential gene expression in the fishes. The advanced bony fishes exhibit a higher temporal and spatial specificity of isozyme locus expression than the primitive fishes. Some isozyme loci are limited in their expression to specific developmental periods such as hatching. The more phylogenetically recently derived loci have a more restricted tissue expression, and tend to be expressed later in development than more ancient loci exhibiting a more generalized tissue expression. More closely related isozyme loci tend to overlap more in their cellular expressions than do more distantly related loci. The role of gene and genome relatedness in regulating gene expression also has been studied by the investigation of preferential allele expression in interspecific hybrids. The schedules of gene expression are often perturbed in interspecific fish hybrids. A progressive increase in the severity of developmental abnormalities, at the morphological and enzymatic levels, occurs during embryogenesis of hybrids formed from progressively more distantly related species. In most instances of allelic repression, the paternal allele is preferentially inhibited but occasionally the maternal allele is selectively repressed. A non-reciprocal developmental success is often observed for hybrid embryos derived from reciprocal crosses. These aberrant nucleocytoplasmic interactions have been related to models of gene regulation and the evolutionary divergence of gene regulatory mechanisms.

Étude électrophorétique de l'hybride expérimental entre Papio anubis et P. cynocephalus

Hybrids between Papio anubis and P. cynocephalus occur in nature. We have studied laboratory bred hybrids, together with their backcrossed offspring. Electrophoretic experiments on the proteins, serum enzymes and erythrocytes obtained from both hybrids and parents lead to three conclusions. First, both parents and hybrids possess proteins having identical mobilities; this case is the most frequent in the 23 loci studied. Second, individual polymorphism caused by, for example, carbonic anhydrase I or transferrin in one or both parents results in the appearance of a codominant phenotype in the hybrid, when the parental components are distinguishable. Third, when other enzymes such as albumin, alkaline phosphatase, haemoglobin and the serum esterases have particular electrophoretic mobilities in the parents, then the hybrid is again codominant; a particularly interesting case among the esterases is that of pseudocholinesterase, where the paternal component is partially repressed in the hybrid. The hybrid than exhibits the phenomenon of allelic repression of at least one gene, which confirms the taxonomic position of species of the two forms of Papio studied.

Mus musculus x Mus caroli hybrids: mouse mules.

Analysis of six enzymes using starch gel electrophoresis indicates that autosomal and X-linked genes of both parental species are expressed normally in M. musculus X M. caroli hybrids. There is no evidence for allelic repression for the four autosomally inherited enzymes. Banding patterns for G6PD and PGK-1 indicate that X-chromosome inactivation occurs and that the maternally derived M. musculus X-chromosome is preferentially expressed in the yolk sac. Despite normal genetic expression none of the four adult female hybrids was fertile and the male hybrids tended to be retarded during fetal development. The routine production of fetal M. musculus X M. caroli hybrids, heterozygous for three X-linked genes coding for G6PD, PGK-1, and HPRT, should provide an excellent system for the analysis of X-chromosome expression and an alternative to the mule for studies of hybrid reproduction and development.

Allelic expression and genetic distance in hybrid macaque monkeys

Levels of structural genic divergence at 21 loci encoding blood proteins were quantified in six macaque (Macaca) species, using standard techniques of starch-gel electrophoresis. Genetic distances between all pairs of species fall within a narrow range (0.080 less than or equal to D less than or equal to 0.250; D = 0.164) which is near the lower limit of genetic distances typically observed between other congeneric organisms. In an effort to measure levels of regulatory gene differences between these species, we have examined the patterns of allelic expression in their F1, F2, and backcross hybrids. Nine of the 21 loci examined encode allelic forms of the proteins with different electrophoretic mobilities in at least some of the individual parents of the hybrids. In all cases where expected, hybrids express fully both maternal and paternal allelic products, thus providing no strong evidence ofr a breakdown in the regulatory mechanisms responsible for proper expression of these genes. Results are compared to degrees of allelic repression previously observed in other hybrids, and are discussed within the context of current ideas about rates of regulatory gene evolution in mammals.

Repression of nucleolar organizer activity in an interspecific hybrid of the genux Xenopus

Nucleolar expression in reciprocal hybrids between African frogs of the species Xenopus laevis and X. mulleri has been examined throughout ontogeny. Evidence is presented for the stagespecific regulation of nucleolar expression in these hybrids, and for a maternal effect that operates during the early development. Advantage has been taken of the nucleolar organizer deletion in X. laevis to demonstrate that the uninucleolate conditions of hybrid nuclei at certain developmental stages is the result of an allelic repression of the mulleri nucleolar organizer region by the laevis genome. Differences in nucleolar expression between the reciprocal hybrids and the parental species have been put on a quantitative basis for several selected tissues.

Preferential inhibition of allelic isozyme synthesis in an interspecific sunfish hybrid

AbstractInterspecific hybrids were produced in the laboratory by crossing male redear sunfish (Lepomis microlophus) with female warmouth (Lepomis gulosus). Approximately three‐fourths of the F1 hybrids were morphologically normal, whereas the remainder possessed a deformity of the lower jaw. This deformity may have been due to a failure of nucleocytoplasmic interactions during development. The reciprocal cross of male warmouth × female redear was subject to complete mortality at the free‐swimming stage.Enzymes, the parental allelic isozymes of which are electrophoretically distinguishable, were chosen as genetic markers. Both of the parentally derived allelic isozymes for malate dehydrogenase and tetrazolium oxidase were synthesized in the adult F1 hybrid. Heteropolymers containing both types of subunits were formed for these two enzymes. Thus, both parental alleles were functional in the hybrid.An esterase isozyme observed only in the redear was absent in the adult F1 hybrid. This result suggests that the synthesis of this paternal isozyme may have been repressed because the egg cytoplasm was incompatible with the paternally derived allele. Maternal allelic repression was apparently observed at the lactate dehydrogenase E locus. The warmouth E locus functioned in the heart tissue so that the two heteropolymers B3E1 and A3E1 were synthesized, but these two heteropolymers were not detected in the redear cardiac tissue or in the heart tissue of the adult F1 hybrid. These results suggest the repression of this maternally derived gene function in the F1 hybrid. The morphologically normal and abnormal F1 hybrids possessed identical isozyme patterns for all four enzyme systems.

Serotype expression and transformation in Tetrahymena pyriformis.

SYNOPSIS. Of the 4 serotypes of Tetrahymena pyriformis, syngen 1, the H (expressed at 20–35 C) and T (expressed at 36–40 C) serotypes and their genetic bases have received the most attention. The present study describes the L and I serotypes, considers their transformations to and from the H serotype, and compares inter‐locus repression with allelic repression.The L serotype occurs below 20 C. No strain differences have been found between L antigens. However, the rate of transformation between H and L varies in the families, which can be ranked according to their preference for the H or L serotype. A3 is strongly L; D1 is strongly H; the other families form a continuum between these extremes. Preference for the H or L serotype is not correlated with the H allele present.Serotype differences may be hereditary, by the “dilution” test for hereditary differences. Altho the environment largely determines which serotype will be expressed, sublines can maintain established H and L serotypes for more than 40 fissions in a common environment. Crosses between H and L cells suggest macronuclear control of serotype determination and a cytoplasmic influence on macronuclear differentiation. Evidence for the cytoplasmic influence comes from both conjugants and nonconjugants.The I serotype is induced from the H serotype at room temperature by treatment with specific H antibodies, which are also necessary for I maintenance. The I serotype consists of a series of unstable serotypes which transform among themselves. Clones go thru an initial I type one day after induction and then diversify to express secondary types. The initial type and the secondary types are characteristic of the family but are not related to the H genotype. Family C1 lacks 2 secondary types found in other families studied.The differences between inter‐locus repression and allelic repression are marked. Altho inter‐locus repression is labile, all efforts to reverse allelic differentiations have failed. H heterozygotes maintained for long periods of time in the I or L state showed no reversal of H allelic repression.

Sequential nuclear differentiation in Tetrahymena.

UCLEAR differentiation is often responsible for phenotypic differences among genically identical lines in ciliates and is demonstrated by patterns of assortment in vegetative pedigrees. The first example of such a nuclear differentiation ( SONNEBORN 1937, 1939) was the “caryonidal inheritance” of mating types in syngen 1 of Paramecium aurelia. In this case, macronuclei usually differentiate in an “all-or-none” fashion early in their development, and mating types are distributed at the cell divisions at which whole new macronuclei are assorted. Macronuclear differentiation is also the basis for mating type determination in the Group B syngens of P. aurelia, which appeared initially to manifest “cytoplasmic inheritance” (SONNEBORN 1954; NANNEY 1957). In syngen 1 of Tetrahymena pyriformis, macronuclear differentiation is again responsible for intraclonal mating type differences, but the diploid subunits of a single compound macronucleus often differentiate to express different mating types and then continue to assort for many cell divisions (NANNEY 1956; ALLEN and NANNEY 1958). Submacronuclear differentiation and vegetative assortment have also been demonstrated to underlie intraclonal variations in the H-immobilization antigens (NANNEY and DUBERT 1960) and the esterase and acid phosphatase isozymes (ALLEN 1960,1961 ; ALLEN, MISCH and MORRISON 1963). The specificity of the H-immobilization antigens is controlled by alleles at the H locus. Within each of the 11 inbred strains of syngen 1, T. pyriformis, one of four alleles (HA, HC, HD, and HE) is found in homozygous condition. Heterozygotes at the H locus initially express both antigenic types, but in the course of cellular proliferation produce sublines expressing only one or the other serotype. This intraclonal differentiation is interpreted as due to the repression or inactivation of one of the two alleles in each subnucleus. The probabilities of repression of the two alleles determine the ratio of the two kinds of pure subclones, which is characteristic of the allelic combination. An analysis of the distribution of this “output ratio” in vegetative pedigrees shows that the H antigenic determination occurs either before or soon after the first macronuclear division, as an uncoordinated event among the subnuclei (NANNEY, NAGEL and TOUCHBERRY 1964). The timing of allelic repression has been studied in three of the possible six heterozygotes at the H locus. The objective of the present study was to extend and complete the analysis of the remaining allelic combinations. The distributions within