Chromatin is a complicated scene. Staying on top of who’s who in residue and degree-specific histone modifications and chromatin modifying proteins is more than a full time job. So, if you’re looking to jump start your investigations and pull down some quick hitting data, you’ll want to consider picking up on some quality antibodies targeting these influential marks and proteins.
Gutless Disclaimer: These following modifications and proteins represent a subset that EpiGenie has seen in the literature recently. We do not favor any one histone, modification, variant etc., anymore than any other, but we understand if you do (and that’s cool with us) so please accept our sincerest apologies if we left your favorite mark off our shortlist.
It will silence expression quicker than a ruthless dictator. It’s more repressive than the summertime heat in Texas. Trimethylation of lysine 27 on H3 has been closely linked to transcriptional repression in a number of key processes in plants and animals and is one of the most frequently interrogated histone modifications.
This post-translation mod is frequently delivered by EZH2, a key member of the polycomb gang, and can be stripped by lysine demethylases like JMJD3. H3k27me3 presence is on the move during development and disease, swaying gene expression along with it.
Despite its well-documented association with silenced genes, there’s still a lot to learn about how H3K27 methylation operates and interacts with the other players in epigenetics and gene regulation. Just last summer, a team of researchers taking a focused approach combed through the imprinted Rasgrf1 locus and found an interesting relationship between H3K27me3 and DNA methylation where the two were not only mutually exclusive, but antagonistic.
But it’s not always all or nothing with H3K27me3. This histone mod put the “bi” in bivalent domains, where it shares space with the activating mark, H3K4me3. As bivalent domains continue to grab the attention of the research community, we see H3K27me3 “poised” for the lab-light, which is why antibodies for this mark should be in every fridge.
ChIP happens frequently in epigenetics research, so be prepared and check out new antibodies for H3K27me3 at Invitrogen.
The yin to H3K27me3’s yang, H3K4me3 lets it all hang out. Far from being a repressed, uptight goody-two-shoes, this mod is quite the party animal, activating the transcription of a smorgasbord of genes and marking meiotic and V(D)J recombination sites.
All this activity isn’t happening willy-nilly. It has direction. Well, it has a COMPASS, anyway. The complex known as COMPASS in yeast (aka MLL/hSet1A and B complexes in mammals) can mono-, di-, or trimethylate histone H3 at lysine 4. And once H3K4 is trimethylated, it can grab onto the plant homeodomain finger of TAF3 to bind TFIID and get the transcription party started.
But other mods, such as H3K27me3 and H3K9me3, can really throw cold water on things. For example, in a paper published just last month, researchers scanned the entire genomes of naïve and memory CD8+ T cells. Though not too surprising, they found that H3K4me3 positively correlated with gene expression, whereas H3K27me3 correlated with reduced expression. But they also showed that the relative abundance of these histone mods created four distinct relationships with gene expression: repressed, active, poised, and bivalent. When genes were “poised” for quick activation in resting T cells, they had lots of H3K4me3, but less H3K27me3. “Bivalent” genes in resting T cells had lots of both mods. These associations laid the ground work for differential regulation of these genes. To further unravel this tangled web, you’ll need specific Abs at hand.
Like a wild west outlaw, when histone deacetylase 1 (HDAC1) rolls into town, almost everything shuts down. HDAC1 rips acetyl groups off of histones, causing the DNA wound around them to shrivel up and condense. Even if the sheriffs (transcription factors) come by, they can’t get in to the DNA to help start expression.
HDAC1 is most often associated with transcription repression during cell proliferation and cancer development, and because of this, it is a “wanted” enzyme. Scores of labs around the world are looking for inhibitors that can stop HDAC1 and its posse (HDAC2–11 and SIRT1–7) in their tracks. In fact, researchers recently figured out that HDAC inhibitors and DNA methylation inhibitors get rid of gastric cancer cells through an miRNA mechanism. But HDAC1 Abs could go a long way toward working out the details of how exactly the protein does its dirty work.
Check out Invitrogen’s new ChIP Abs. HDACs will have nowhere to hide!
Sure, methyltransferases put methyl groups onto histones in the first place, but who slaves away during every cell cycle to maintain that repression? Division after division—it’s got to be back-breaking work. Who’s behind it all? Why, it’s Suz12 and her buddies in the Polycomb Repressive Complex 2 (PRC2).
Sometimes, though, Suz12 and friends get a little tired and drift away. In a paper out last fall, scientists reported that as prostate cancer gathers steam, some developmental genes lose their PRC marks and get methylated on DNA instead using the old “epigenetic switch” trick. Another autumn foray into Suz12 territory revealed more info on the repressing protein’s M.O. A team at the University of Copenhagen showed that Suz12 and other PRC2 members maintain repression by landing on H3K27me3 sites while DNA is being copied. But is Suz12 doing all the work or are her PRC partners shouldering most of the burden? Abs sure would help answer that question…
RNA Pol II
The Big Kahuna. The Big Cheese. The Grand Poohbah. Yes, it’s RNA Pol II, the master transcriber. In our world, transcription may be a tiresome chore, but in the cell, it’s how the magic starts. Without RNA Pol II, the cell would just be a greasy water balloon. Nothing’s gonna happen within those plasma membranes unless RNA Pol II is around to turn the famous DNA instructions into RNA.
It’s impressive, really. Single-handedly, RNA Pol II (OK, it’s really a gang of 12 subunits) can unwind DNA, paste together complementary RNA strands, and make sure the result is correct.
But like many top celebrities, however, RNA Pol II looks to assistants for direction. Transcription factors, “Polly’s” own posttranslational mods, and chromatin structure all tell RNA Pol II where to stand and when to arrive, radioing in from the red carpet of the genome. Recently, researchers showed that various heterochromatin proteins (HP1s) drag an HDAC complex and other proteins to heterochromatin to save RNA Pol II from a potentially embarrassing situation, avoiding the scandal of plopping down in a region of heterochromatin near centromeres. Where is Polly now? Abs could clue you in to a Polly sighting near you.
We hear a lot about two-faced politicians in the news, but two-faced histone mods? All this time, we thought that H3K9me3 was a repressive mark, shunning RNA Pol II and other parts of the transcription machinery. “Go away; nothing to see here,” was H3K9me3’s refrain. But all along, it turns out that this mod was leading a double life. Sometimes, H3K9me3 can activate transcription.
In research published in spring 2008, researchers saw that H3K9me3 was lurking with actively expressed genes in some human cancer cell lines. So, what’s the deal? Is H3K9me3 really activating and repressing? How does it know to do one function as opposed to the other? Hmm, maybe some Abs would clear up the issue.
The Abs Scene
Antibodies continue to be a staple for most epigenetic sample prep processes. As insanely powerful techniques like ChIP-Seq continue to crank out massive data sets, our view of the roles of these marks will continue to change, so stay tuned as we continue to cover the top mods, proteins and emerging players. Think we missed a good one? Tell us at email@example.com and we’ll throw it in the hopper for the next review!