scholarly journals A Game of Thrones at Human Centromeres II. A new molecular/evolutionary model

2019 ◽  
Author(s):  
William R. Rice
Keyword(s):  
Tandem Repeats ◽  
Position Effect ◽  
Rapid Evolution ◽  
Evolutionary Model ◽  
Elevated Concentration ◽  
Position Effect Variegation ◽  
Repeat Array ◽  
Centromeric Repeat ◽  
New Form ◽  
Game Of Thrones

Human centromeres are remarkable in four ways: they are i) defined epigenetically by an elevated concentration of the histone H3 variant CENP-A, ii) inherited epigenetically by trans-generational cary-over of nucleosomes containing CENP-A, iii) formed over unusually long and complex tandem repeats (Higher Order Repeats, HORs) that extend over exceptionally long arrays of DNA (up to 8 Mb), and iv) evolve in such a rapid and punctuated manner that most HORs on orthologous chimp and human chromosomes are in different clades. What molecular and evolutionary processes generated these distinctive characteristics? Here I motivate and construct a new model for the formation, expansion/contraction, homogenization and rapid evolution of human centromeric repeat arrays that is based on fork-collapse during DNA replication (in response to proteins bound to DNA and/or collisions between DNA and RNA polymerases) followed by out-of-register re-initiation of replication via Break-Induced Repair (BIR). The model represents a new form of molecular drive. It predicts rapid and sometimes punctuated evolution of centromeric HORs due to a new form of intragenomic competition that is based on two features: i) the rate of tandem copy number expansion, and ii) resistance to invasion by pericentric heterochromatin within a centromere’s HOR array. These features determine which variant array elements will eventually occupy a pivotal region within a centromeric repeat array (switch-point) that gradually expands to populate the entire array. In humans, continuous HOR turnover is predicted due to intra-array competition between three repeat types with an intransitive hierarchy: A < B < C < A, where A = short, single-dimer HORs containing one monomer that binds centromere protein-B (CENP-B) and another that does not, B = moderately longer HORs composed of ≥ 2 dimers, and C = substantially longer HORs that lose their dimeric modular structure. Continuous turnover of proteins that bind centromeric DNA (but these proteins are not constituents of the kinetochore) and polygenic variation influencing position-effect variegation are predicted to cause rapid turnover of centromeric repeats in species lacking HORs and/or CENP-B binding at centromeres. Evolution at centromeres is a molecular ‘Game-of-Thrones’ because centromeric sequences ‘reign’ due to an epigenetic ‘crown’ of CENP-A that is perpetually ‘usurped’ by new sequences that more rapidly assemble large ‘armies’ of tandem repeats and/or resist ‘invasion’ from a surrounding ‘frontier’ of percentric heterochromatin. These ‘regal transitions’ occur in a backdrop of slashing and decapitation (fork-collapse generating truncated sister chromatids) in the context of promiscuous sex that is frequently incestuous (out-of-register BIR between sibling chromatids).

scholarly journals Transgene Repeat Arrays Interact With Distant Heterochromatin and Cause Silencing in cis and trans

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1181-1190 ◽  
Author(s):  
Douglas R Dorer ◽  
Steven Henikoff
Keyword(s):  
Transgene Expression ◽  
Tandem Repeats ◽  
Position Effect ◽  
Position Effect Variegation ◽  
Dependent Manner ◽  
Repeat Array ◽  
Naturally Occurring ◽  
Homologous Position ◽  
Cis And Trans ◽  
In Cis

Tandem repeats of Drosophila transgenes can cause heterochromatic variegation for transgene expression in a copy-number and orientation-dependent manner. Here, we demonstrate different ways in which these transgene repeat arrays interact with other sequences at a distance, displaying properties identical to those of a naturally occurring block of interstitial heterochromatin. Arrays consisting of tandemly repeated white transgenes are strongly affected by proximity to constitutive heterochromatin. Moving an array closer to heterochromatin enhanced variegation, and enhancement was reverted by recombination of the array onto a normal sequence chromosome. Rearrangements that lack the array enhanced variegation of white on a homologue bearing the array. Therefore, silencing of white genes within a repeat array depends on its distance from heterochromatin of the same chromosome or of its paired homologue. In addition, white transgene arrays cause variegation of a nearby gene in cis, a hallmark of classical position-effect variegation. Such spreading of heterochromatic silencing correlates with array size. Finally, white transgene arrays cause pairing-dependent silencing of a non-variegating white insertion at the homologous position.

scholarly journals A Sex-Influenced Modifier in Drosophila That Affects a Broad Spectrum of Target Loci Including the Histone Repeats

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 903-917 ◽  
Author(s):  
Utpal Bhadra ◽  
Manika Pal-Bhadra ◽  
James A Birchler
Keyword(s):  
Broad Spectrum ◽  
Tandem Repeats ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Position Effect ◽  
Blot Hybridization ◽  
Phenotypic Expression ◽  
Northern Blot Hybridization ◽  
Position Effect Variegation ◽  
Effect Variegation

A second chromosomal trans-acting modifier, Lightener of white (Low), modulates the phenotypic expression of various alleles of the white eye color gene. This modifier has an unusually broad spectrum of affected genes including white, brown, scarlet and the eye developmental genes, Bar and Lobe. In addition, Low weakly suppresses position effect variegation. Northern blot hybridization with different X and autosomal probes reveals that Low modulates genes of independent expression patterns. Interestingly, many of the modulations of gene expression are developmentally restricted and differ in intensity between the sexes. Low also elevates the expression of the histone tandem repeats in three distinct developmental stages. A deficiency encompassing the histone cluster reduces their transcript levels and significantly alters the expression of some of the tested genes. Thus, Low is a modifier that plays a role in modulating the expression of genes governing various processes including pigment deposition, eye development, chromosomal proteins and position effect variegation.

scholarly journals A Game of Thrones at Human Centromeres I. Multifarious structure necessitates a new molecular/evolutionary model

2019 ◽  
Author(s):  
William R. Rice
Keyword(s):  
Spatial Organization ◽  
Repeat Unit ◽  
Rapid Evolution ◽  
Evolutionary Model ◽  
Generic Model ◽  
Crossing Over ◽  
Unequal Crossing Over ◽  
Centromeric Repeat ◽  
Repeat Units ◽  
Protein Binding Sequence

Human centromeres form over arrays of tandemly repeated DNA that are exceptionally complex (repeats of repeats) and long (spanning up to 8 Mbp). They also have an exceptionally rapid rate of evolution. The generally accepted model for the expansion/contraction, homogenization and evolution of human centromeric repeat arrays is a generic model for the evolution of satellite DNA that is based on unequal crossing over between sister chromatids. This selectively neutral model predicts that the sequences of centromeric repeat units will be effectively random and lack functional constraint. Here I used shotgun PacBio SMRT reads from a homozygous human fetal genome (female) to determine and compare the consensus sequences (and levels of intra-array variation) for the active centromeric repeats of all the chromosomes. To include the Y chromosome using the same technology, I used the same type of reads from a diploid male. I found many different forms and levels of conserved structure that are not predicted by –and sometimes contradictory to– the unequal crossing over model. Much of this structure is based on spatial organization of three types of ~170 bp monomeric repeat units that are predicted to influence centromere strength (i.e., the level of outer kinetochore proteins): one with a protein-binding sequence at its 5’ end (a 17 bp b-box that binds CENP-B), a second that is identical to the first except that the b-box is mutated so that it no longer binds CENP-B, and a third lacking a b-box but containing a 19 bp conserved “n-box” sequence near its 5’ end. The frequency and organization of these monomer types change markedly as the number of monomers per repeat unit increases, and also differs between inactive and active arrays. Active arrays are also much longer than flanking, inactive arrays, and far longer than required for cellular functioning. The diverse forms of structure motivate a new hypothesis for the lifecycle of human centromeric sequences. These multifarious levels of structures, and other lines of evidence, collectively indicate that a new model is needed to explain the form, function, expansion/contraction, homogenization and rapid evolution of centromeric sequences.

scholarly journals Mutational Analysis of a Histone Deacetylase in Drosophila melanogaster: Missense Mutations Suppress Gene Silencing Associated With Position Effect Variegation

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 657-668 ◽  
Author(s):  
Randy Mottus ◽  
Richard E Sobel ◽  
Thomas A Grigliatti
Keyword(s):  
Drosophila Melanogaster ◽  
Histone Deacetylase ◽  
Transcriptional Activity ◽  
Mutational Analysis ◽  
Position Effect ◽  
Transcriptional Regulator ◽  
Position Effect Variegation ◽  
Missense Mutations ◽  
Effect Variegation ◽  
New Mutations

Abstract For many years it has been noted that there is a correlation between acetylation of histones and an increase in transcriptional activity. One prediction, based on this correlation, is that hypomorphic or null mutations in histone deacetylase genes should lead to increased levels of histone acetylation and result in increased levels of transcription. It was therefore surprising when it was reported, in both yeast and fruit flies, that mutations that reduced or eliminated a histone deacetylase resulted in transcriptional silencing of genes subject to telomeric and heterochromatic position effect variegation (PEV). Here we report the first mutational analysis of a histone deacetylase in a multicellular eukaryote by examining six new mutations in HDAC1 of Drosophila melanogaster. We observed a suite of phenotypes accompanying the mutations consistent with the notion that HDAC1 acts as a global transcriptional regulator. However, in contrast to recent findings, here we report that specific missense mutations in the structural gene of HDAC1 suppress the silencing of genes subject to PEV. We propose that the missense mutations reported here are acting as antimorphic mutations that “poison” the deacetylase complex and propose a model that accounts for the various phenotypes associated with lesions in the deacetylase locus.

scholarly journals Mutual Correction of Faulty PCNA Subunits in Temperature-Sensitive Lethal mus209 Mutants of Drosophila melanogaster

Genetics ◽  
2000 ◽  
Vol 154 (4) ◽  
pp. 1721-1733
Author(s):  
Daryl S Henderson ◽  
Ulrich K Wiegand ◽  
David G Norman ◽  
David M Glover
Keyword(s):  
Germ Line ◽  
Position Effect ◽  
Three Dimensional ◽  
Nuclear Antigen ◽  
Dimensional Structure ◽  
Female Sterility ◽  
Temperature Sensitive ◽  
Position Effect Variegation ◽  
Dna Double Strand Breaks ◽  
Mutant Genotype

Abstract Proliferating cell nuclear antigen (PCNA) functions in DNA replication as a processivity factor for polymerases δ and ε, and in multiple DNA repair processes. We describe two temperature-sensitive lethal alleles (mus209B1 and mus2092735) of the Drosophila PCNA gene that, at temperatures permissive for growth, result in hypersensitivity to DNA-damaging agents, suppression of position-effect variegation, and female sterility in which ovaries are underdeveloped and do not produce eggs. We show by mosaic analysis that the sterility of mus209B1 is partly due to a failure of germ-line cells to proliferate. Strikingly, mus209B1 and mus2092735 interact to restore partial fertility to heteroallelic females, revealing additional roles for PCNA in ovarian development, meiotic recombination, and embryogenesis. We further show that, although mus209B1 and mus2092735 homozygotes are each defective in repair of transposase-induced DNA double-strand breaks in somatic cells, this defect is substantially reversed in the heteroallelic mutant genotype. These novel mutations map to adjacent sites on the three-dimensional structure of PCNA, which was unexpected in the context of this observed interallelic complementation. These mutations, as well as four others we describe, reveal new relationships between the structure and function of PCNA.

white+ Transgene Insertions Presenting a Dorsal/Ventral Pattern Define a Single Cluster of Homeobox Genes That Is Silenced by the Polycomb-group Proteins in Drosophila melanogaster

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 257-275 ◽  
Author(s):  
Sophie Netter ◽  
Marie-Odile Fauvarque ◽  
Ruth Diez del Corral ◽  
Jean-Maurice Dura ◽  
Dario Coen
Keyword(s):  
Chromatin Structure ◽  
Target Genes ◽  
Position Effect ◽  
Phenotypic Expression ◽  
Positional Information ◽  
Genomic Region ◽  
Polycomb Group ◽  
Position Effect Variegation ◽  
Trithorax Group ◽  
Clear Cut

AbstractWe used the white gene as an enhancer trap and reporter of chromatin structure. We collected white+ transgene insertions presenting a peculiar pigmentation pattern in the eye: white expression is restricted to the dorsal half of the eye, with a clear-cut dorsal/ventral (D/V) border. This D/V pattern is stable and heritable, indicating that phenotypic expression of the white reporter reflects positional information in the developing eye. Localization of these transgenes led us to identify a unique genomic region encompassing 140 kb in 69D1–3 subject to this D/V effect. This region contains at least three closely related homeobox-containing genes that are constituents of the iroquois complex (IRO-C). IRO-C genes are coordinately regulated and implicated in similar developmental processes. Expression of these genes in the eye is regulated by the products of the Polycomb -group (Pc-G) and trithorax-group (trx-G) genes but is not modified by classical modifiers of position-effect variegation. Our results, together with the report of a Pc -G binding site in 69D, suggest that we have identified a novel cluster of target genes for the Pc-G and trx-G products. We thus propose that ventral silencing of the whole IRO-C in the eye occurs at the level of chromatin structure in a manner similar to that of the homeotic gene complexes, perhaps by local compaction of the region into a heterochromatin-like structure involving the Pc-G products.

scholarly journals Characterization of the Genomic Xist Locus in Rodents Reveals Conservation of Overall Gene Structure and Tandem Repeats but Rapid Evolution of Unique Sequence

2001 ◽  
Vol 11 (5) ◽  
pp. 833-849 ◽  
Author(s):  
T. B. Nesterova ◽  
S. Ya. Slobodyanyuk ◽  
E. A. Elisaphenko ◽  
A. I. Shevchenko ◽  
C. Johnston ◽  
...  
Keyword(s):  
Gene Structure ◽  
Tandem Repeats ◽  
Rapid Evolution ◽  
Unique Sequence ◽  
Xist Locus

pitkinD, a Novel Gain-of-Function Enhancer of Position-Effect Variegation, Affects Chromatin Regulation During Oogenesis and Early Embryogenesis in Drosophila

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1227-1244 ◽  
Author(s):  
Steffi Kuhfittig ◽  
János Szabad ◽  
Gunnar Schotta ◽  
Jan Hoffmann ◽  
Endre Máthé ◽  
...  
Keyword(s):  
Germ Line ◽  
Position Effect ◽  
Early Embryogenesis ◽  
Position Effect Variegation ◽  
Chromatin Regulation ◽  
Gain Of Function ◽  
Position Effects ◽  
Dominant Female ◽  
Effect Variegation ◽  
Female Germ Line

Abstract The vast majority of the &gt;100 modifier genes of position-effect variegation (PEV) in Drosophila have been identified genetically as haplo-insufficient loci. Here, we describe pitkinDominant (ptnD), a gain-of-function enhancer mutation of PEV. Its exceptionally strong enhancer effect is evident as elevated spreading of heterochromatin-induced gene silencing along euchromatic regions in variegating rearrangements. The ptnD mutation causes ectopic binding of the SU(VAR)3-9 heterochromatin protein at many euchromatic sites and, unlike other modifiers of PEV, it also affects stable position effects. Specifically, it induces silencing of white+ transgenes inserted at a wide variety of euchromatic sites. ptnD is associated with dominant female sterility. +/+ embryos produced by ptnD/+ females mated with wild-type males die at the end of embryogenesis, whereas the ptnD/+ sibling embryos arrest development at cleavage cycle 1-3, due to a combined effect of maternally provided mutant product and an early zygotic lethal effect of ptnD. This is the earliest zygotic effect of a mutation so far reported in Drosophila. Germ-line mosaics show that ptn+ function is required for normal development in the female germ line. These results, together with effects on PEV and white+ transgenes, are consistent with the hypothesis that the ptn gene plays an important role in chromatin regulation during development of the female germ line and in early embryogenesis.

scholarly journals Multiple Effects of Genetic Background on Variegated Transgene Expression in Mice

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1107-1112
Author(s):  
Margaret L Opsahl ◽  
Margaret McClenaghan ◽  
Anthea Springbett ◽  
Sarah Reid ◽  
Richard Lathe ◽  
...  
Keyword(s):  
Transgene Expression ◽  
Milk Protein ◽  
Position Effect ◽  
Position Effect Variegation ◽  
Parental Population ◽  
Expression Levels ◽  
Variable Expression ◽  
Specific Effects ◽  
Milk Protein Genes ◽  
Β Lactoglobulin

Abstract BLG/7 transgenic mice express an ovine β-lactoglobulin transgene during lactation. Unusually, transgene expression levels in milk differ between siblings. This variable expression is due to variegated transgene expression in the mammary gland and is reminiscent of position-effect variegation. The BLG/7 line was created and maintained on a mixed CBA × C57BL/6 background. We have investigated the effect on transgene expression of backcrossing for 13 generations into these backgrounds. Variable transgene expression was observed in all populations examined, confirming that it is an inherent property of the transgene array at its site of integration. There were also strain-specific effects on transgene expression that appear to be independent of the inherent variegation. The transgene, compared to endogenous milk protein genes, is specifically susceptible to inbreeding depression. Outcrossing restored transgene expression levels to that of the parental population; thus suppression was not inherited. Finally, no generation-dependent decrease in mean expression levels was observed in the parental population. Thus, although the BLG/7 transgene is expressed in a variegated manner, there was no generation-associated accumulated silencing of transgene expression.

scholarly journals Recombinogenic Effects of Suppressors of Position-Effect Variegation in Drosophila

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 609-621
Author(s):  
Thomas Westphal ◽  
Gunter Reuter
Keyword(s):  
Chromatin Structure ◽  
Position Effect ◽  
Heterochromatic Region ◽  
Crossing Over ◽  
Position Effect Variegation ◽  
Chromosome 2 ◽  
Additive Effects ◽  
Suppressor Mutations ◽  
Effect Variegation ◽  
Meiotic Nondisjunction

Abstract Compact chromatin structure, induction of gene silencing in position-effect variegation (PEV), and crossing-over suppression are typical features of heterochromatin. To identify genes affecting crossing-over suppression by heterochromatin we tested PEV suppressor mutations for their effects on crossing over in pericentromeric regions of Drosophila autosomes. From the 46 mutations (28 loci) studied, 16 Su(var) mutations of the nine genes Su(var)2-1, Su(var)2-2, Su(var)2-5, Su(var)2-10, Su(var)2-14, Su(var) 2-15, Su(var)3-3, Su(var)3-7, and Su(var)3-9 significantly increase in heterozygotes or by additive effects in double and triple heterozygotes crossing over in the ri-pp region of chromosome 3. Su(var)2-201 and Su(var) 2-1401 display the strongest recombinogenic effects and were also shown to enhance recombination within the light-rolled heterochromatic region of chromosome 2. The dominant recombinogenic effects of Su(var) mutations are most pronounced in proximal euchromatin and are accompanied with significant reduction of meiotic nondisjunction. Our data suggest that crossing-over suppression by heterochromatin is controlled at chromatin structure as well as illustrate the possible effects of heterochromatin on total crossing-over frequencies in the genome.

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