Tributaries of the 2023 Nobel Prize in Physiology or Medicine, and lessons learned

Almost without exception, scientific breakthroughs are not epistemological orphans. Historians of science have developed a body of scholarship on this, and the cases arising in our era continue to confirm the phenomenon. The work by Katalin Karikó and Drew Weissman that proved foundational for the subsequent development of mRNA vaccines for COVID-19 had its antecedent roots yet is also a striking example of both serendipity and their persistence. Their receipt of the 2023 Nobel Prize in Physiology or Medicine was greatly deserved and, as Alfred Nobel likely envisioned the broad impact to be for all the prizes, affirms to the public at large that there is such a thing as the scientific method, and that there are such things as facts. The importance of society recognizing this has always been critically important, perhaps never more so than now.

Nucleolar structure connects with global nuclear organization

The nucleolus is a multifunctional nuclear body. To tease out the roles of nucleolar structure without resorting to the use of multi-action drugs, we knocked down the RNA polymerase I subunit RPA194 in HeLa cells by siRNA. Loss of RPA194 resulted in nucleolar-structural segregation and effects on both nucleolus-proximal and distal-nuclear components. The perinucleolar compartment was disrupted, centromere clustering around nucleoli was significantly reduced, and the intranuclear locations of specific genomic loci were altered. Moreover, Cajal bodies, distal from nucleoli, underwent morphological and some compositional changes. In comparison, when the preribosomal RNA-processing factor, UTP4, was knocked down, neither nucleolar segregation nor the intranuclear effects were observed, demonstrating that the changes of nucleolar proximal and distal nuclear domains in RPA194 knockdown cells unlikely arise from a cessation of ribosome synthesis, rather from the consequence of nucleolar-structure alteration. These findings point to a commutative system that links nucleolar structure to the maintenance and spatial organization of certain nuclear domains and genomic loci.

An Intermittent Cytochemist

I wanted to be a cytochemist but encountered detours and then, in some of my work, became one of a different kind than classically defined. I recount this here to discourage young scientists from regarding cytochemistry as something that peaked in the past, but rather to be viewed as an entirely new form of the discipline, and so rich with opportunities. (J Histochem Cytochem 71: 475-480, 2023).

Nucleolar structure connects with global nuclear organization

The nucleolus is a multi-functional nuclear body. To tease out the roles of nucleolar structure without resorting to multi-action drugs, we knocked down RNA polymerase I subunit RPA194 in HeLa cells by siRNA. Loss of RPA194 resulted in nucleolar structural segregation and effects on both nucleolus-proximal and distal nuclear components. The perinucleolar compartment was disrupted, centromere-nucleolus interactions were significantly reduced, and the intranuclear locations of specific genomic loci were altered. Moreover, Cajal bodies, distal from nucleoli, underwent morphological and compositional changes. To distinguish whether these global reorganizations are the results of nucleolar structural disruption or inhibition of ribosome synthesis, the pre-ribosomal RNA processing factor, UTP4, was also knocked down, which did not lead to nucleolar segregation, nor the intranuclear effects seen with RPA195A knockdown, demonstrating that they do not arise from a cessation of ribosome synthesis. These findings point to a commutative system that links nucleolar structure to the maintenance and spatial organization of certain nuclear bodies and genomic loci.

"Mechanism"-a misused term?

Many of us use the term "mechanism" when we shouldn't. Here I offer some thoughts, especially as guidance for young scientists.

A conundrum in 3-D genome organization and expression?

Recent advances in our understanding of how the genome is folded within the nucleus have included cases in which this positioning correlates with gene expression, either positively or negatively. But is the 3-D location of a gene a cause or an effect of its expression? In this Perspective I articulate the problem and then cite as guideposts recent cases where causation has indeed been arguably established. The hope is to critically illuminate this issue for continued consideration in this important, evolving field.

The nuclear bodies conference: Hubs of genomic activity, June 24-28, Western Shore, Nova Scotia, Canada

This conference brought together leaders in the investigation of various bodies that populate the nucleus, a field that complements research on chromosome biology. These nuclear bodies had been receiving increasing attention as hubs of genome activity and the new findings reported at the conference strongly confirmed and significantly expanded this principle.

Sheldon Penman: Visionary of cell form and function

Sheldon Penman made major contributions to the field of RNA synthesis and, more broadly, the nexus between cellular form and gene readout. He will be remembered for his creativity and breadth of expertise, as well as his opposition to what he believed were threatening incursions into science by corporate interests.

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription

INTRODUCTION

Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cells remains unclear.

RESULT

Here, we develop EpiGo (Epigenetic perturbation induced Genome organization)-KRAB to introduce H3K9me3 at hundreds of loci spanning megabases on human chromosome 19 and simultaneously track genome organization. EpiGo-KRAB is sufficient to induce genomic clustering and de novo heterochromatin-like domain formation, which requires SETDB1, a methyltransferase of H3K9me3. Unexpectedly, EpiGo-KRAB-induced heterochromatin-like domain does not result in widespread gene repression except a small set of genes with concurrent loss of H3K4me3 and H3K27ac. Ectopic H3K9me3 appears to spread in inactive regions but is largely restricted from transcriptional initiation sites in active regions. Finally, Hi-C analysis showed that EpiGo-KRAB reshapes existing compartments mainly at compartment boundaries.

CONCLUSIONS

These results reveal the role of H3K9me3 in genome organization could be partially separated from its function in gene repression.

Genome architecture and expression 2019-2020: the transition phase

To set the stage for this collection, let us reflect on how the field of genome architecture and expression is undergoing current movement including, inter alia, the adoption of physico-chemical approaches of which the article's subtitle is a pun. This field had gained powerful new momentum 5-7 years ago and now one senses certain tipping points, as the foundational elements of the field are being refined and expanded.

A 20-year encounter with the imposter syndrome

Both in their formative years and later careers, some scientists suffer from something more than occasional self-doubts. There is a more severe affliction that strikes many more than was once realized. Here I reflect on my encounter, in the hope that sharing it can be of some value.

The Centriole Mystique

Centrioles organize the microtubule network and mitotic spindle and, as basal bodies, nucleate cilia and flagella. They undergo a beguiling process in which one appears to give rise to another and at a baffling orthogonal geometry. Nucleic acid-based replication has been pondered during cycles of zeniths and nadirs of plausibility, the latter now the state. Centrioles can also arise de novo, and thus the longstanding focus on centriole 'replication' may have led us astray from ground truth. We are in an era in which the assembly pathways of most intracellular machines are becoming understood in considerable detail. But apart from knowing the structure and parts list, little in our extant knowledge conveys how centrioles arise. Here the matters at hand are summarized, and a siren call is sounded.