Investigations led to the demonstration of very striking similarities in chromatin-related events between sporulation and spermatogenesis.
A collaborative effort between researchers from the University of Pennsylvania (Penn), School of Medicine (PA, USA) and Inserm (Grenoble, France) have recently published their findings in the journal, Genes and Development, involving their study that used a yeast model to map epigenetic processes in cells during gametogenesis. The team consisted of Dr Shelley Berger, the Daniel S Och University Professor, and director of the Epigenetics Program at Penn, along with postdoctoral fellow Dr Jérôme Govin and colleague Dr Saadi Khochbin, Centre national de la recherche scientifique senior researcher at the Institut Albert Bonniot (Inserm/Université Joseph Fourrier in Grenoble).
“In the paper, we show that first, histone H4 hyperacetylation occurs during spore genome compaction, and second, that Bdf1, a paralog of Brdt, is involved. This will allow us to use the strength of the yeast system to dissect the molecular basis of acetylation-dependent chromatin compaction by Brdt/Bdf1”, enthused Dr Khochbin.
The team set out by screening yeast to find mutants that were unable to form spores – an analogous process to sperm formation in mammals. Dr Khochbin described their investigation.
“Since nucleosomes are the fundamental units of genome organization, we hypothesized that all the alterations of the (highly) conserved histone H3 and H4 specifically affecting sporulation, would give us important information on the fundamental molecular events directing these dramatic genomic rearrangements. The mutational screen of histones H3 and H4 revealed structural determinants specifically important for sporulation. Among other things, a meiotic-specific phosphorylation of H3, at T11, was uncovered. From there, we started a cross-exanimation strategy to test the idea of a molecular parallelism between sporulation and spermatogenesis regarding the organization of the genome. We have tested the occurrence of the new histone modifications found during sporulation, in spermatogenic cells. At the same time, we have transposed our knowledge of chromatin modifications during spermatogenesis to sporulation and examined their validity in this system”.
Dr Khochin explained that conceptually these results support the idea that spermatogenesis has evolved from sporulation and has conserved some the basic mechanisms directing not only meiosis, but also the compaction of the genome.
Several years ago, Dr Khochin and colleagues discovered a double bromodomain-containing factor capable of compacting hyperacetylated chromatin and its subsequent structural studies, revealed that Brdt‘s chromatin compacting activity depends on the simultaneous recognition of H4K5ac and H4K8ac.
“Future investigations should exploit the conclusion reached here that the postmeiotic phases of sporulation could be used to understand mechanisms controlling genome compaction during spermatogenesis”, concluded Khochbin.
Source: Govin J, Dorsey J, Gaucher J, Rousseaux S, Khochbin S, Berger SL: Systematic screen reveals new functional dynamics of histones H3 and H4 during gametogenesis. Genes Dev. 24(16), 1772–1786 (2010).
Acknowledgements
With thanks to Dr Saadi Khochbin for the comments regarding the paper.
The biology of addiction is a very complex matter with the molecular basis proving to be even more complicated as revealed by a study in the journal, Nature Neuroscience, that investigated the role of the X-linked transcriptional repressor methyl CpG binding protein 2 (MeCP2) in cocaine addiction in rats. Since cocaine addiction is commonly viewed as a disorder of neuroplasticity, MeCP2, which is already known for its role in the neurodevelopmental disorder Rett syndrome, was identified by the investigators as possibly a key player in the regulation of neuroplasticity in postmitotic neurons.
Dr Paul Kenny and his team from The Scripps Research Institute–Scripps Florida (FL, USA) used rats to study cocaine use in an attempt to further elucidate our understanding of the molecular mechanisms behind addiction. In the study, the rats were allowed to dose themselves with the drug for 6 h a day, and the investigators found that the rats seemed to increase their dosage daily – just the same as human addicts do. The main objective of the team was to try to identify the potential involvement of MeCP2 in addition since its relationship to addiction has not been previously explored.
In their experiments, the investigators specifically focused on the relationship between MeCP2 and addiction in the rats. From their research, they uncovered a novel interaction between MeCP2 and miR-212, where each were demonstrated to regulate the other. They also discovered that the MeCP2 and miR-212 seem to ‘fight‘ for control of the brain-derived neurotrophic factor (BDNF) known to play a role in psychostimulant reward, and caused an increase the rats‘ desire for cocaine.
This led the investigators to hypothesize that when levels of MeCP2 and BDNF in the dorsal striatum are increased, the rats are more vulnerable to addiction; while the knocking down of MeCP2 by miR-212 reversed the desire to have more cocaine. Therefore, it could be understood that the microRNA exerts its influence through MeCP2 itself, since there is no evidence of a direct interaction between miR-212 and BDNF.
The authors concluded by stating that: “These data suggest that homeostatic interactions between MeCP2 and miR-212 in dorsal striatum may be important in regulating vulnerability to cocaine addiction”.
Source: Im HI, Hollander JA, Bali P, Kenny PJ: MeCP2 controls BDNF expression and cocaine intake through homeostatic interactions with microRNA-212. Nat. Neurosci. 13(9), 1120–1127 (2010).
A paper recently published in Nature by Joseph Costello and colleagues at the University of California, San Francisco (CA, USA) suggests that intragenic DNA methylation helps genes determine transcription start sites. To explore the role of intragenic methylation, the researchers generated a high-resolution DNA methylation map of 24.7 million of the 28 million CpG sites in the human brain.
Costello commented that, “Recent work from Zilberman (published in Science) and Jacobsen (published in Proceedings of the National Academy of Science) show gene body methylation is ancient in evolutionary terms, suggesting an important, conserved but undisclosed function. Our study picks up from there, and shows conservation of gene body methylation (limited to two species) is tissue and cell-type specific. Further, we identify a major function, regulation of alternative promoters embedded in gene body”.
The dense map revealed that of all CpG islands, 34% of those lying in intragenic regions contained a methyl group, compared with only 3% of those within 5´ promoters. In addition, intragenic CpG islands were shown to be more likely than 5´ promoters to be the site of tissue-specific methylation. The team found that whereas unmethylated CpG islands overlapped with trimethylated H3K4 (found in abundance at promoters), intragenic CpG islands coincided with RNA markers of transcription initiation.
In a discovery that could support the role of intragenic methylation in managing cell context-specific alternative promoters in gene bodies, the human SHANK3 locus (which encodes the synaptic protein SHANK3) and its mouse counterpart exhibited tissue-specific methylation. This in turn regulated intragenic promoter activity in vitro and in vivo.
Costello concluded, “The question that remains is what is being made from alternative promoters … noncoding RNA, protein isoforms? Probably some of both”.
Source: Maunakea A, Nagarajan R, Bilenky M et al.: Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466, 253–257 (2010).
A collaborative effort between Harvard (MA, USA), Johns Hopkins (MA, USA) and Stanford (MA, USA) scientists has produced the first ever epigenetic landscape map of tissue differentiation. Published in Nature, the study offers a comprehensive map of methylation and transcriptional changes that accompany myeloid versus lymphoid fate decisions.
“It wasn‘t a boring linear process”, remarked Prof Andrew Feinberg, King Fahd Professor of Molecular Medicine and director of the Center for Epigenetics at Johns Hopkins‘ Institute for Basic Biomedical Sciences (MD, USA). “Instead, we saw these waves of change during the development of these cell types”.
Using genome-wide methylation-profiling system comprehensive high-throughput arrays for relative methylation (CHARM), the team analyzed 4.6 million CpG sites throughout the genome in order to find the DNA methylation ‘hotspots‘ during hematopoiesis. They searched multipotent progenitors, common lymphoid progenitors, common myeloid progenitors, granulocyte/macrophage progenitors and thymocyte progenitors (DN1, DN2, DN3).
Asked whether there were any unexpected findings, Feinberg highlighted “the dynamic plasticity that accompanies lineage-specific differentiation and the marked difference in DNA methylation between myeloid and lymphoid cells”, as an important finding.
Indeed, a higher rate of global DNA methylation was seen in lymphoid restriction as opposed to myeloid. This was supported functionally by myeloid skewing of progenitors after DNA methyltransferase inhibitor treatment. The higher methylation rates in lymphocytes resulted from a wave of DNA methylation loss early on in development and a subsequent regain. By contrast, the myeloid cells experienced an early burst of methylation and an erasure later on during development. Differential DNA methylation correlated with gene expression more strongly at CpG island shores than CpG islands.
In addition, a plethora of pathways and genes not previously associated with blood cell differentiation, such as Arl4c and Jdp2, were unearthed in the study. Hematopoietic differentiation caused numerous transcription factors to be silenced (including Meis 1), and modifiers of the epigenome to be altered.
The first epigenetic landscape map can also be used to predict which types of stem cells the blood cells stem from as they still retain marks characteristic of their lineage.
As for the implications of the study, Feinberg suggested that, “We‘re studying differences in leukemic stem cells, and it will be important to see whether any of the epigenetic modifiers that were themselves modified by DNA methylation, regulate hematopoietic differentiation”.
“Furthermore, the discreet stages of cell differentiation indicated by the study could lead to a redefining of cell types based on epigenetic marks – therefore, from this study, we seem to be edging closer to understanding the epigenetic basis of disease”, he continued.
Feinberg concluded, “Genes themselves aren‘t going to tell us what‘s really responsible for the great diversity in cell types in a complex organism like ourselves, but I think epigenetics – and how it controls genes – can. That‘s why we wanted to know what was happening generally to the levels of DNA methylation as cells differentiate”.
Source: Ji H, Ehrlich LI, Murakami P et al.: Comprehensive methylome map of lineage commitment from hematopoietic progenitors. Nature 467(7313), 338–3342 (2010).
Acknowledgements
With thanks to Dr Andrew Feinberg for his comments regarding the paper.