New & Noteworthy

HIR Complex Influences Transcription Interference

May 27, 2022

Eukaryotic transcription is most often initiated by RNA polymerase II (RNAPII) and regulated by several factors, including epigenetic factors, histone modification, DNA methylation, and non-coding antisense transcripts. Non-coding antisense transcripts, produced from the strand opposite to the sense strand, use transcription interference (TI) to regulate gene expression. TI is a phenomenon where one transcription activity negatively impacts the other in cis. One such example is when transcription of long non-coding RNAs (lncRNAs) overlaps with coding gene promoters, causing repression of that gene. Antisense transcripts are involved in several biological processes and show dysregulation in different diseases; however, the mechanisms underlying the antisense mediated transcription interference (AMTI) are not well understood. 

An exciting study by Soudet J et al. in Nucleic Acid Res has identified new components in budding yeast to be involved in AMTI. The authors highlight a strong connection between HIR histone chaperone complex binding and antisense transcription in context with SAGA or TFIID-dependent gene regulation. Likewise, the study shows that induction of antisense transcription influences HIR binding, nucleosome repositioning, and (de novo) histone deposition. 

Soudet J et al., 2022

Furthermore, data show that antisense transcription into promoters at SAGA-dependent genes restricts the access of the transcription factor binding sites (TBSs) and transcription factors (TFs) by closing the promoter nucleosome depleted regions (NDRs) with nucleosomes, thus repressing the genes. When antisense elongation begins, nucleosomes are randomly lost from the promoters, and chromatin has a chance to reopen again before new nucleosomes are incorporated. In the absence of HIR complex, the promoters stay open and upregulate the SAGA-dependent genes. 

The study confirms that SAGA-dependent genes are associated with higher HIR binding and antisense transcription into promoters. Interestingly, TFIID-dependent genes do not show the same effect even in the presence of high antisense transcription levels. Although SAGA and TFIID-dependent gene classes share a high level of antisense transcription as a common feature, the authors propose that genes can interchange these classes when the balance between TF binding and nucleosome incorporation is changed.

Thus, the study sheds light on the mechanism of the antisense mediated transcription interference and emphasizes the role of the HIR histone chaperone complex in gene regulation.

Categories: Research Spotlight

Tags: Antisense transcription, gene regulation, HIR Complex, Saccharomyces cerevisiae, SAGA, Transcription Interference

Cheerio Containment

September 11, 2017

In the store the other day I saw a kid in a stroller covered in Cheerios, an opened, near empty Ziploc-type plastic bag next to him. It looked like one of those cheap, knock off brands that are much harder to close properly.


Just like a poorly closed zipper means more spilled Cheerios, a looser H1 clamp means more transcripts. Image from

Other than keeping the Cheerios out of reach, his parents had two options here. The first was to use two bags, putting the cheaper re-sealable bag into another one. The odds are much better that at least one of them would be closed properly.

The second option was to get a re-sealable bag with a better zipper, like an actual Ziploc. With a better baggie, the parents had a much better chance of making sure that the bag was sealed.

In a new study out in GENETICS, Lawrence and coworkers show that yeast cells go for the second approach when it comes to the histone H1 and gene expression regulation. Rather than regulating gene expression by controlling the number of molecules of H1 in a cell, the yeast instead regulates transcription by controlling how well H1 can bind DNA. And it looks like the strength of binding is influenced by the acetylation of H1’s more famous histone cousins—the histones found in the nucleosome.

Almost everyone has heard of the histones that make up the nucleosome, that structure of DNA wrapped around a core of eight histone proteins. H1 is a bit less famous. It binds the linker DNA, or the DNA between some of the nucleosomes.

When bound, H1 tends to repress nearby genes. It acts like a clamp that keeps the nucleosome in place.

This gene repression is probably why our friend Saccharomyces cerevisiae has only one H1 per 4-37 nucleosomes as compared to the one H1 per nucleosome in vertebrates. After all, S. cerevisiae’s genome has a much higher gene density. If it had one H1 for every nucleosome it might not have any genes turned on!

You may have noticed that scientists don’t have a good handle on an exact number of H1 molecules in a yeast cell. One of the first things these authors did was a careful study to try to nail down just what that number is. They came up with 18.9 +/- 1 nucleosomes/H1.

The next step was to figure out how a yeast cell controls H1 to regulate gene expression. There are two general ideas about how a cell might go about this.

In the first, the cell controls the amount of H1 it makes. The more H1, the more genes get repressed.

In the second, H1 is controlled by the acetylation of the core histone proteins. The acetylation loosens the core histone’s grip on the DNA making it harder for H1 to bind.

It would be very hard to do experiments in most beasts to try to tell which model is correct. For example, mammals have 11 genes for H1 proteins. This makes changing the overall amount of H1 nontrivial to say the least.

This is where the ultimate model organism, S. cerevisiae, can come in and save the day yet again (#APOYG). Since this yeast has only one H1 gene, HHO1, it is much simpler to tweak the amount of H1 protein in a cell.

Lawrence and coworkers put HHO1 under the control of the GAL promoter and found that in the presence of galactose, the extra H1 had a severe effect on growth. These yeast were unhappy with around three times as much H1 protein, even though there was not much of an effect on chromosomal structure as measured by micrococcal nuclease assays.


Low acetylation on this Ziploc. Image from General Mills.

The researchers next looked for genes which when deleted, rescued the growth defect of yeast making too much H1. They did this by transforming their GAL-HHO1 plasmid into the collection of ~4700 nonessential gene knockout strains.

Histone deacetylases (HDACs) were the most interesting class of genes they found that could rescue the growth defect. By deleting an HDAC gene, histone acetylation increases (because the deacetylation decreases), implying that H1 can be regulated by the acetylation status of histones. The loss of the HDAC increased the amount of acetylation, which made it harder for H1 to bind, and so repress transcription.

They confirmed this finding in a couple of ways with the most interesting one using a couple of different mutants of histone H3. One mutant had its acetylation sites in the H3 tail changed to glutamines, which mimics a histone in a perpetual state of acetylation. This mimic of an acetylated H3 tail partially rescued the growth defect of too much H1.

So it looks like the effect of H1 can be regulated by the acetylation status of its more famous histone kin. More acetylation results in a looser grip, which makes for more transcription. Like a cheap plastic baggie with a zipper with a looser grip making Cheerios more likely to spill, H1’s looser grip due to more acetylation results in more transcription and more transcripts being let loose into the cell.

by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: gene regulation, H1, HHO1, histones, nucleosome