Is the Y chromosome disappearing?--both sides of the argument

On August 31, 2011 at the 18th International Chromosome Conference in Manchester, Jenny Graves took on Jenn Hughes to debate the demise (or otherwise) of the mammalian Y chromosome. Sex chromosome evolution is an example of convergence; there are numerous examples of XY and ZW systems with varying degrees of differentiation and isolated examples of the Y disappearing in some lineages. It is agreed that the Y was once genetically identical to its partner and that the present-day human sex chromosomes retain only traces of their shared ancestry. The euchromatic portion of the male-specific region of the Y is ~1/6 of the size of the X and has only ~1/12 the number of genes. The big question however is whether this degradation will continue or whether it has reached a point of equilibrium. Jenny Graves argued that the Y chromosome is subject to higher rates of variation and inefficient selection and that Ys (and Ws) degrade inexorably. She argued that there is evidence that the Y in other mammals has undergone lineage-specific degradation and already disappeared in some rodent lineages. She also pointed out that there is practically nothing left of the original human Y and the added part of the human Y is degrading rapidly. Jenn Hughes on the other hand argued that the Y has not disappeared yet and it has been around for hundreds of millions of years. She stated that it has shown that it can outsmart genetic decay in the absence of "normal" recombination and that most of its genes on the human Y exhibit signs of purifying selection. She noted that it has added at least eight different genes, many of which have subsequently expanded in copy number, and that it has not lost any genes since the human and chimpanzee diverged ~6 million years ago. The issue was put to the vote with an exact 50/50 split among the opinion of the audience; an interesting (though perhaps not entirely unexpected) skew however was noted in the sex ratio of those for and against the notion.

[Distorted heterochromatin replication in Drosophila melanogaster polytene chromosomes as a result of euchromatin-heterochromatin rearrangements]

Studies of the position effect resulting from chromosome rearrangements in Drosophila melanogaster have shown that replication distortions in polytene chromosomes correlate with heritable gene silencing in mitotic cells. Earlier studies mostly focused on the effects of euchromatin--heterochromatin rearrangements on replication and silencing of euchromatic regions adjacent to the heterochromatin breakpoint. This review is based on published original data and considers the effect of rearrangements on heterochromatin: heterochromatin blocks that are normally underrepresented or underreplicated in polytene chromosomes are restored. Euchromatin proved to affect heterochromatin, preventing its underreplication. The effect is opposite to the known inactivation effect, which extends from heterochromatin to euchromatin. The trans-action of heterochromatin blocks on replication of heterochromatin placed within euchromatin is discussed. Distortions of heterochromatin replication in polytene chromosomes are considered to be an important characteristic associated with the functional role of the corresponding genome regions.

Oxymoron no more: the expanding world of heterochromatic genes

Heterochromatin has been oversimplified and even misunderstood. In particular, the existence of heterochromatic genes is often overlooked. Diverse types of genes reside within regions classified as constitutive heterochromatin and activating influences of heterochromatin on gene expression in Drosophila are well documented. These properties are usually considered paradoxical because heterochromatin is commonly portrayed as "silent chromatin". In the past, studies of heterochromatic genes were limited to a few Drosophila genes. However, the recent discovery of several hundred heterochromatic genes in Drosophila, plants and mammals through sequencing projects offers new opportunities to examine the variety of ways in which heterochromatin influences gene expression. Comparative genomics is revealing diverse origins of heterochromatic genes and remarkable evolutionary fluidity between heterochromatic and euchromatic domains. These features justify a broader view of heterochromatin, one that accommodates repressive, permissive and activating effects on gene expression, and recognizes chromosomal and evolutionary transitional states between heterochromatin and euchromatin.

SCN- binding to the charged lysines of histones end domains mimics acetylation and shows the major histone-DNA interactions involved in eu and heterochromatin stabilization

SCN- binds to the charged amino group of lysines, inducing local changes in the electrostatic free energy of histones. We exploited this property to selectively perturb the histone-DNA interactions involved in the stabilization of eu and heterochromatin. Differential scanning calorimetry (DSC) was used as leading technique in combination with trypsin digestion that selectively cleaves the histone end domains. Euchromatin undergoes progressive destabilization with increasing KSCN concentration from 0 to 0.3 M. Trypsin digestion in the presence of 0.2 M KSCN show that the stability of the linker decreases as a consequence of the competitive binding of SCN- to the amino groups located in the C and N-terminal domain of H1 and H3, respectively; likewise, the release of the N-terminal domain of H4 induces an appreciable depression in both the temperature and enthalpy of melting of core particle DNA. Unfolding of heterochromatin requires, in addition to further cleavage of H4, extensive digestion of H2A and H2B, strongly suggesting that these histones stabilize the higher order structure by forming a protein network which extends throughout the heterochromatin domain.

The contradictory definitions of heterochromatin: transcription and silencing

Eukaryotic genomes are packaged in two general varieties of chromatin: gene-rich euchromatin and gene-poor heterochromatin. Each type of chromatin has been defined by the presence of distinct chromosomal proteins and posttranslational histone modifications. This review addresses recent findings that appear to blur the definitions of euchromatin and heterochromatin by pointing to the presence of typically heterochromatic modifications (including H3K9me) in euchromatin and typically euchromatic enzymes (including RNA polymerases) in heterochromatin. We discuss the implications of these new findings for the current definition of heterochromatin.

Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin

Histone posttranslational modifications mediate establishment of structurally and functionally distinct chromatin compartments of eukaryotic nuclei. The association of different histone modifications with euchromatic and heterochromatic compartments is relatively conserved in highly divergent model organisms such as Drosophila and mammals. However, some differences between these model systems have been uncovered while limited data are available from organisms nearer the invertebrate-vertebrate transition. We identified a chromatin compartment in both diploid and endocycling cells of the urochordate, Oikopleura dioica, enriched in heterochromatic histone modifications and DNA methylation. Surprisingly, this compartment also contained high levels of histone H3 trimethylated at lysine 4 (H3 Me(3)K4), a modification thus far associated with actively transcribed sequences. Although in Drosophila and mouse cells, H3 Me(3)K4 was prevalently associated with euchromatin, we also detected it in their pericentromeric heterochromatin. We further showed that H3 Me(3)K4 abundance was not necessarily proportional to local levels of transcriptional activity in either euchromatin or heterochromatin. Our data indicate greater plasticity across evolution in the association of histone lysine methylation with functionally distinct chromatin domains than previously thought and suggest that H3 Me(3)K4 participates in additional processes beyond marking transcriptionally active chromatin.

Heterochromatin structure and function

Although heterochromatin has long been used as a model for studying chromatin condensation and heritable gene silencing, it is only relatively recently that detailed information has become available on the mechanisms that underlie its structure. Current evidence suggests that these operate on at least three different levels. A regular nucleosome array may facilitate packaging of the chromatin into a highly condensed configuration. Methylation of histone H3 lysine 9 and lysine 27 generates heterochromatin marks that are recognised through binding of heterochromatin proteins such as HP1. Finally, very recent studies using genetic and biochemical approaches have indicated that the RNAi machinery plays an important role in the formation of heterochromatin.

Euchromatinization of mammalian nuclei

This paper discusses a mechanism for converting heterochromatin into the more relaxed state of euchromatin. Actuation of such state conversion stems from disassembly of internal vesicles that are incapable of surviving when trapped within the inner chamber of mammalian nuclei.

Programming off and on states in chromatin: mechanisms of Polycomb and trithorax group complexes

Polycomb and trithorax group proteins are evolutionarily conserved chromatin components that maintain stable states of gene expression. Recent studies have identified and characterized several multiprotein complexes containing these transcriptional regulators. Advances in understanding molecular activities of these complexes in vitro, and functional domains present in their subunits, suggest that they control transcription through multistep mechanisms that involve nucleosome modification, chromatin remodeling, and interaction with general transcription factors.

Recombinogenic effects of suppressors of position-effect variegation in Drosophila

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-p(p) region of chromosome 3. Su(var)2-2(01) and Su(var)2-14(01) 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.

On the roles of heterochromatin and euchromatin in meiosis in drosophila: mapping chromosomal pairing sites and testing candidate mutations for effects on X-Y nondisjunction and meiotic drive in male meiosis

Mapping of pairing sites involved in meiotic homolog disjunction in Drosophila has led to conflicting hypotheses about the nature of such sites and the role of heterochromatin in meiotic pairing. In the female-specific distributive system, pairing regions appear to be exclusively heterochromatic and map to broad regions encompassing many different sequences. In male meiosis, autosomal pairing sites appear to be distributed broadly within euchromatin but to be absent from heterochromatin, whereas the X-pairing site maps in the centric heterochromatin. The X site has been shown to coincide with the intergenic spacer (IGS) repeats within the rDNA arrays shared between the X and Y. It has not been clear whether the heterochromatic location of this pairing site has any significance. A novel assay for genic modifiers of X-Y chromosome pairing was developed based on the intermediate nondisjunction levels observed in males whose X chromosome lacks the native pairing site but contains two transgenic insertions of single rDNA genes. This assay was used to test several mutations in Su(var) (Suppressor of position effect variegation), PcG (Polycomb-Group) recombination defective, and repair-defective genes. No strong effects on disjunction were seen. However, the tests did uncover several mutations that suppress or enhance the meiotic drive (distorted X-Y recovery ratio) that accompanies X-Y pairing failure.

Centromeres are specialized replication domains in heterochromatin

The properties that define centromeres in complex eukaryotes are poorly understood because the underlying DNA is normally repetitive and indistinguishable from surrounding noncentromeric sequences. However, centromeric chromatin contains variant H3-like histones that may specify centromeric regions. Nucleosomes are normally assembled during DNA replication; therefore, we examined replication and chromatin assembly at centromeres in Drosophila cells. DNA in pericentric heterochromatin replicates late in S phase, and so centromeres are also thought to replicate late. In contrast to expectation, we show that centromeres replicate as isolated domains early in S phase. These domains do not appear to assemble conventional H3-containing nucleosomes, and deposition of the Cid centromeric H3-like variant proceeds by a replication-independent pathway. We suggest that late-replicating pericentric heterochromatin helps to maintain embedded centromeres by blocking conventional nucleosome assembly early in S phase, thereby allowing the deposition of centromeric histones.