This document is associated with Part 3 of "On Making the Genome Whole", by Steve Talbott.

In the following text, terms like "H3K9" and "H320" refer to particular locations on histone tails where histone modifications occur. As explained in the main article, these modfications can include methylation (attachment of a methyl group to the indicated location on the tail), acetylation, ubiquitination, phosphorylation, and so on. Mono-, di- and tri-methylation refer to the attachment of one, two or three methyl groups at the given location, indicated, for example, by "H3K9me1", "H3K9me2", or "H3K9me3". Acetylation is indicated by "ac", as in "H3K9ac".

What I offer here is a very limited and briefly summarized selection of findings culled from the technical literature of the past few years. The focus is on mammals and humans, but some of the observations refer to other organisms such as yeast. The aim is simply to provide a general feel for the range and complexity of histone modifications — and, yes, an awareness of how worryingly disconnected the findings are at this stage of our understanding. Don't feel badly if it doesn't add up to a coherent picture for you; neither does it add up for the researchers themselves.

While I have focused here on discoveries relating more or less directly to gene expression, it happens that histone modifications also play a role in such diverse processes as DNA replication, DNA repair, cellular senescence, and genomic instability.

The main sources I have drawn on are Barski et al. (2007), Bártová et al. (2008), Choi and Howe (2009), Kouzarides (2007), Rando and Chang (2009), and Vakoc et al. (2006). (See Part 3 of main article for references.)

• H3K9 acetylation (H3K9ac) correlates broadly with uncondensed chromatin regions, chromosome looping, and, in general, active gene expression, as does H3K4 di-methylation (H3K4me2). These two modifications can also characterize inactive regions that are poised and ready for transcription.
• Other marks generally associated with uncondensed, active chromatin include H3K4me3, H3K36me3, H3K79me3, H4K20me1, and H4K20me2. Note, however: a modification can be repressive even though it is associated with (generally) open and active chromatin. That is, it can play a role in silencing particular genes in such a context. Thus, H3K79me3, despite being listed here, is often associated with gene repression. In general, each mark can have its own distinctive distribution. For example, H3K4me3 occurs predominantly at point locations near transcription start sites, whereas H3K36me3 is distributed across the transcribed region of genes, peaking at the downstream end.
• Methylation of H3K4 prevents the deacetylation of H3.
• Marks generally associated with condensed chromatin (heterochromatin) include H3K9me2, H3K9me3, H3K27me3, and H4K20me3.
• Methylated H3K9 provides a binding site for heterochromatin protein 1 (HP1), which leads to formation of heterochromatin and repression of transcription. However, phosphorylation of of the neighboring H3S10 prevents the binding of HP1 to methylated H3K9 or causes its ejection.
• Also, while H3K9 methylation is broadly associated with condensed chromatin, it is found to be enriched at many active gene promoters.
• The histone tail of H4 makes contact with the histones on a neighboring nucleosome, and in this way is thought to facilitate the formation of the 30-nanometer chromatin fiber. Acetylation of H4K16 inhibits this interaction, and therefore helps to prevent the compaction of chromatin into a 30-naonometer fiber.
• It's also been found that H4K16 acetylation reduces the activity of some chromatin remodeling complexes.
• While acetylation in general is associated with open chromatin and gene transcription, acetylation of some sites on H4 inversely correlates with transcription (in yeast). "Thus it is possible that, when [experimental procedures are based on] tetra-acetylated histone H4, positive effects from one modification are negated by acetylation at other sites" (Choi and Howe).
• In vitro experiments with single nucleosomes show tetra-acetylation of H3 resulting in a 2-fold increase in the rate of nucleosome sliding.
• The same processes that remove (gene-activating) acetyl groups from, for example, H3K9, recruit methyltransferases that methylate H3K9. Thus, on the promoters of active genes, antagonistic distributions are observed for H3K9ac and H3K9me3: that is, the histone location shows heavy acetylation when the associated gene is active, and heavy tri-methylation when it is silent. In such cases it is thought that acetylation at a transcription start site (associated with gene expression) may impose a boundary beyond which the methylation of the transcribed region of the gene cannot pass. Such methylation, if it were to "leak over" onto the transcription start site, would be a repressive mark.
• One researcher's summary of the histone modifications at active and inactive genes: "Active genes are characterized by high levels of H3K4me1, H3K4me2, H3K4me3, H3K9me1, and [variant histone] H2A.Z surrounding TSSs [transcription start sites] and elevated levels of H2BK5me1, H3K36me3, H3K27me1, and H4K20me1 downstream of TSSs and throughout the entire transcribed region. In contrast, inactive genes are characterized by low or negligible levels of H3K4 methylation at promoter regions, high levels of H3K27me3 and H3K79me3 in promoter and gene-body regions; low or negligible levels of H3K36me3, H3K27me1, H3K9me1, and H4K20me1 in gene-body regions; and uniformly distributed and low levels of H2A.Z" (Barski et al. 2007).
• Histone acetylation tends to peak in the neighborhood of a gene's promoter. However, H3K14ac, H3K23ac, H4K12ac, and H4K16ac occur on histone tails throughout the body of genes and seem to be necessary for nucleosome eviction and for the continuation of RNA Polymerase transcribing activity after initiation.
• "What is the difference between an active enhancer and an active promoter? Though both the promoters and enhancers are associated with H3K4 methylation, H2A.Z, and H3K9me1, active promoters are characterized by high levels of H3K27me1, H3K36me3, H3K9me1, H4K20me1, and H2BK5me1 downstream of TSSs" (Barski et al. 2007).
• H3K79me3 is associated with actively transcribed genes in yeast. But in humans it "modestly correlates with gene silencing in human T cells except for a small group of the most active genes that were associated with higher levels of H3K79me3" (Barski et al. 2007).
• Heterochromatin near centromeres (roughly: near the center of chromosomes) is enriched for H3K9me3 and H3K20me3, but not for H3K9me2, H3K9me1, H3K27me2, or H3K27me3.
• H3K27me1, too, is enriched at heterochromatin near centromeres, but it is also "present at all euchromatic regions examined; however this modification is selectively removed in the vicinity of the transcription sites at active genes. This suggests that H3K27me1 removal may be a general prerequisite for the initiation of high-level transcription" (Vakoc et al. 2006).
• "H3K36 methylation can have a repressive effect on promoter activity; however, this modification is distributed in the coding regions of active genes, where it serves to suppress aberrant transcription initiation..." (Vakoc et al. 2006).
• Nucleosomes with tetra-acetylation of histone H3 are enabled to slide spontaneously.
• "Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation" [title of paper published in 2007].
• "Mono-ubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells" [another article title].
• There are so-called "bivalent domains" associated with the genes for differentiation in stem cells. These are DNA regions displaying "contradictory" histone modifications. There are large regions of H3K27 methylation, a repressive mark, but within these regions the promoters show H3K4 methylation, an activating mark. This bivalence is thought to play a role in keeping the genes for differentiation temporarily repressed, but poised and ready for expression once cellular differentiation begins, at which time the repressive marks are removed (Gan et al. 2007; Bernstein et al. 2006; Azuara et al 2006). In this way the bivalence may help the stem cells remain in the pluripotent state.
• A change in levels of histone acetylation in cells of the nervous system is associated with both memory formation and addictive behaviors.
• The inactive X chromosome in females has its own distinctive pattern of methylation, including H4K20me1, H3K27me3, and H3K9me2, and reduction of H3K4 methylation. This pattern occurs in combination with a complex of other features, including recruitment of the "macro-H2A" histone variant, DNA methylation, and reduced H4 acetylation.
• In yeast, histone H2BK123 ubiquitylation is required for di- and tri-methylation of H3K4 and H3K79, but not for mono-methylation.
• A typical report on an investigation of a particular gene: "We observe two distinct patterns of lysine methylation. H3K4me3 and H3K79me3 are similarly enriched near the transcription start site, whereas H3K9me3, H3K36me3, and surprisingly H4K20me1 colocalize and are maintained across the entire transcribed region" (Vakoc et al. 2006).
• Activating marks such as H3K4me3 and K3K79me3 are considerably reduced on the promoters of genes showing variable expression (as opposed to genes showing more constant levels of expression).
• Chromosome translocations, involving the transfer of a section of one chromosome to a different chromosome, are heavily implicated in some cancers. They commonly occur at certain points on the chromosome, known as "break points". "We found that the breakpoint associated with T cell lymphoma at the IGHA1 locus is located within peaks of activating histone modifications, such as H3K4me1, H3K4me2, H3K4me3, and H3K9me1, whereas the breakpoints at this locus in non-T cell cancers are not associated with these activating modifications" (Barski et al. 2007).
• In one particular disease (Hutchinson-Gilford progeria syndrome), "heterochromatin markers, such as H3K9 tri-methylation and heterochromatin protein HP1-gamma, are reduced in the diseased cells", while "H4K20 tri-methylation is increased".
• Consistent with the elaborate spatial organization of the nucleus (see Part 2 of the main article), there is evidence that histone modifications are organized in distinct nuclear layers. For example, H3K9me1 marks chromatin in the nuclear interior, while H3K9me2 occurs preferentially at the periphery.
• Likewise, H3K9me2 is mainly associated with DNA that replicates during the middle of the period of DNA replication, whereas H3K9me3 marks late-replicating heterochromatin.
• Finally, for the die-hard enthusiast, here's the abstract from Altaf et al. 2007: "Dot1 (Disruptor of telomeric silencing-1) is a histone H3 lysine 79 methyltransferase that contributes to the establishment of heterochromatin boundary and has been linked to transcription elongation. We found that histone H4 N-terminal domain, unlike other histone tails, interacts with Dot1 and is essential for H3 K79 methylation. Furthermore, we show that the heterochromatin protein Sir3 inhibits Dot1-mediated methylation and that this inhibition is dependent on lysine 16 of H4. Sir3 and Dot1 bind the same short basic patch of histone H4 tail, and Sir3 also associates with the residues surrounding H3 K79 in a methylation-sensitive manner. Thus, Sir3 and Dot1 compete for the same molecular target on chromatin. ChIP analyses support a model in which acetylation of H4 lysine 16 displaces Sir3, allowing Dot1 to bind and methylate H3 lysine 79, which in turn further blocks Sir3 binding/spreading. This draws a detailed picture of the succession of molecular events occurring during the establishment of telomeric heterochromatin boundaries."

If you would like to see some impressive graphs showing the distribution of individual histone marks relative to transcription start sites in the human genome, go to this article by Barski et al. (2007), scroll down to Figure 2, and click on the figure. For a PDF version of the file, click here and just scroll down to Figure 2.