Skip to main content
NCBI home page
Molecular Biology of the Cell logoLink to Molecular Biology of the Cell
. 2026 Jul 23;37(9):re9. doi: 10.1091/mbc.E26-04-0196

Epistemological parameters in the recent era of nuclear organization and function

Thoru Pederson a,*
Editor: Patrick Luskb
PMCID: PMC13525607  PMID: 42489923

Abstract

The sweeping progress in the nuclear organization-function field over the past two decades constitutes a major advance, to be sure. This work significantly impacts molecular, cell, and developmental biology and has uncovered numerous clinical implications. Here I offer perspectives around the epistemological axis in this field of ours, viz. what we knew and when, and what we know (or think we know) now.

  • How both the DNA and other elements of the cell nucleus are spatially and functionally organized was pondered a century ago, with some prescient hints.

  • Over the next 75 years, considerable progress was made and then, in the last two decades, a transformative leap occurred.

  • This review describes this recent major “inflection point”, one that resulted from methodological breakthroughs and new ideas (“in that order” to honor a famous quote) and which now promise to take this field to the tissue and organ level, particularly the brain, and to capitalize on new findings of clinical potential now at hand.

INTRODUCTION

From the time chromosomes were first discovered, in mitotic and meiotic cells (refer to Gall, 1996), how they are organized during interphase was a black box, to the extent it was even pondered. In some cases, the presentation of meiotic chromosomes was so dramatic, for example, the “lampbrush” chromosomes of amphibian oocytes whose investigation was pioneered by H.G. Callan, Oscar Miller, and Joseph Gall, that it seemed inconceivable that this elaborate organization could be accommodated within the confines of the interphase nucleus of typical somatic cells. Electron microscopy enabled visualization of the elementary chromatin fiber (Ris, 1961) but could not, of course, address the larger scale of chromosomal interactions. The same was true in cases where premature chromosome condensation was observed in interphase nuclei after fusion with mitotic cells (Rao and Johnson, 1970) or by exposure of cells to hypertonic medium (Robbins et al., 1970).

And yet all through that era we knew that the location of a genetic locus within the nucleus could influence its expression, as had been most impactfully demonstrated earlier in the phenomenon of Drosophila position-effect variegation (Muller, 1930). That discovery could be rightly viewed as nothing less than the beginning of the entire nuclear organization-function field. Years later, investigation of many other breakage and recombination events added a new question, namely, in cases of reciprocal translocations, how do the ends find one another? The classic case here was, of course, the so-called Philadelphia chromosome (Nowell and Hungerford, 1960), later found to not be a single breakpoint as initially thought but a reciprocal translocation (Rowley, 1973). The fact that this resulted in a fusion protein that is oncogenic was heuristically fortunate in that it catalyzed the cytogenetic frontier of the cancer field. Much later, it was found that the probability of these reciprocal translocations relates to the initial proximity of the two loci (Roix et al., 2003), not entirely unanticipated yet important to be established (Pederson, 2003).

The foregoing was the setting when the subsequent phase of our field that is mainly addressed here got underway. In this review, I summarize what I regard as major features in the evolution of the nuclear structure-function field beginning at about 2000. It is not intended to be a typical comprehensive review article but rather to emphasize trends in our thinking and understanding. My orientation will thus be an epistemological axis, as it has been in many of my other perspectives (e.g., Pederson, 2024a). I had a biochemistry professor who emphasized that we should not only know what is known but also how it came to be known, and I guess his point has stuck with me.

THE BEGINNINGS

The modern era of the local spatial restriction of interphase chromosomes was pioneered by Thomas Cremer and collaborators who elegantly confirmed Boveri's initial observations of “chromosome territories” (Boveri, 1909; Cremer et al., 1982a, 1982b). Another issue that soon arose was whether the interphase chromosomes were tethered in some way or could move about. An important study revealed that the chromosomes of yeast cells display diffusional movements, although within confinement volumes (Marshall et al., 1997). The alternative concept of a “nuclear matrix” had arisen but did not take hold in most quarters (Pederson, 2000). Moreover, at this time many of us in the field recalled the so-called Rabl configuration, named after its first observer (Rabl, 1885), where in at least some cell types the interphase chromosomes are aligned with the telomeres at the nuclear envelope and the centromeres more oriented to the interior. Key subsequent advances included the demonstration of a radial configuration of active and inactive sites in many cell types (Croft et al., 1999) and specific interactions of chromosomal regions with nuclear structures such as the lamina (Pickersgill et al., 2006) and the nucleolus (Nemeth et al., 2010; von Koningsbruggen et al., 2010). These milestones greatly advanced the breadth of our understanding of nuclear organization, and they were made possible by new tools- ones that continued to subsequently be expanded and diversified.

MEIOSIS, A DISCOVERY LAUNCH PAD

The next major step was in the late 1990s in the laboratory of Nancy Kleckner at Harvard, who had already made major contributions to chromosome biology. How meiotic chromosomes pair had been investigated in the classical era, and key factors had been discovered later, but the details remained a quest for Kleckner and her lab. Her group came up with an ingenious method for capturing interchromosomal interactions in meiosis (Dekker et al., 2002), and it immediately became apparent that it could, in principle, be applied to somatic cells. The first author of this seminal paper, Job Dekker, subsequently joined the faculty of my institution and undertook the refinement of “chromosome conformation capture” (abbreviated “3C”) and its application to genome biology overall (Mirny and Dekker, 2022). The impact was of considerable breadth as to the number of groups that adopted this platform and deployed it in many productive ways. In due course Dekker and collaborators created an array of refinements, the first two of which were branded “4C” and “5C.” Among these advances was the important introduction of the concept of “Topologically Associated Domains (TADs). Then “Hi-C” arrived, a particularly transformative advance led by Erez Lieberman-Aiden in collaboration with Dekker that combined the chromosome capture technology with bioinformatics and computational biology (Lieberman-Aiden et al., 2009).

THE US NATIONAL INSTITUTES OF HEALTH “COMMON FUND”

In 2013, I became aware of this special NIH program when contacted by two colleagues in our field. Administered by the NIH Office of the Director, this special fund seeks ideas from time to time for broad initiatives. Two of my colleagues at the NIH, Tom Misteli and Thomas Reid, informed me that they and others were advancing a proposal for support of a large-scale attack on how the spatial organization of the genome impacts gene expression, development, and human disease. I was invited to support their proposal and enthusiastically did so, as did others. After the various proposals had been reviewed by the NIH Director's advisers, the one for a “4D Nucleome” initiative was approved.

MEETINGS- HERALDS OF A NEW FIELD

As publications in this evolving field appeared in increasing numbers, the typical parallel “signature of promise” occurred when a nascent field takes a forward step, viz. the advent of major meetings. These included the launch in 1998 of a Cold Spring Harbor Laboratory biennial meeting on Nuclear Organization and Function, then a similar EMBO biennial meeting starting in 2005 and held in alternating years with the former. A third, smaller meeting that nonetheless turned out to be important was one at the Jackson Laboratory, Bar Harbor, Maine, launched in 2001 and called the Genome Architecture Consortium, where biophysics and the nanoscale level were emphasized (O'Brien et al., 2003). These three meetings drew together many groups that had not previously been connected. In addition, the nucleus became increasingly included in meetings that would have previously focused exclusively on the cytoplasm, for example, one on molecular machines that included due emphasis on nuclear ones (Bullock et al., 2020).

Maintaining our epistemological theme, another key development was the NIH-funded ENCODE project, launched 12 years before the 4D Nucleome Initiative. Its ambitious goal of mapping the totality of genomic regulatory elements and their chromatin accessibility had been impressively realized by the time the 4D Nucleome launched and was enormously enabling for the latter. We shall return to this important connection between the two endeavors.

Although the genome itself was the focus in the 4D Nucleome Initiative getting underway in this period, there was also a growing awareness of the importance of various nuclear bodies that facilitate gene expression. Through the 1990s and 2000s, there had been considerable progress on these, particularly the nucleolus (Pederson, 2011), and as the 4D Nucleome Initiative got going, the nuclear bodies field continued to thrive and advance. This period of the nuclear bodies field not only benefitted from the 4D Nucleome but contributed to it in certain ways. And, as with the 4D Nucleome, the nuclear bodies field has developed its own community and biennial meeting (Kaufman et al., 2022; Chen et al., 2024), with the next to be held this October.

PHYSICS COMES TO THE NUCLEUS, AND VICE-VERSA

In two of his earliest papers, Francis Crick investigated the viscosity of the cytoplasm (Crick, 1950; Crick and Hughes, 1950). He was unlikely to have considered doing so for the nucleus, as no methods for that were at hand, though ones are today (e.g., Cheng et al., 2025). But more than half a century later, in the period described in this article, the physical and biophysical theater of the nucleus had advanced in parallel with the molecular and genomic dimensions (Pederson, 2014; Pederson and Marko, 2014; Pederson et al., 2015). Key studies revealed that the fluid viscosity of the nucleus is much lower than many had assumed (Wachsmuth et al., 2000) and that RNA traffic in the nucleus is entirely diffusional (Politz et al., 1998, 1999). Important advances were also made on how nuclear structure responds to mechanical stress (Miroshnikova and Wickstrom, 2022; Todorovski et al., 2023; Vahabikashi et al., 2023) as well as on factors that protect against this in certain cases (Alabi et al., 2025). But most transformative as to physics, by now an epochal paradigm shift had occurred.

CONDENSATES ARRIVE ON THE NUCLEAR SCENE

When I was a first-year graduate student, three molecular biologists had recently been appointed to the faculty, and they quickly populated the weekly seminar schedule with their like. I vividly recall the visits by the likes of Jean-Pierre Changeux, Arthur Pardee and Gordon Tomkins (they were really more biochemists than molecular biologists, but this was a period of great synergy between the two disciplines). Their seminars on the catalytic versus regulatory subunits of the enzymes they were studying. I paid no attention to how these stuck together, nor, frankly, did they—it was these enzymes’ feedback regulation that was on the wing. But, as we now know, heterotypic protein complexes can form in other ways, ones that were unanticipated back then.

In a study that will always be regarded as a milestone in our field, the amplified nucleoli in Xenopus oocytes were revealed to undergo a dynamic liquid-like phase transition (Brangwynne et al., 2011). This phenomenon had been reported earlier for a type of cytoplasmic granules, and, both for the nucleus and cytoplasm, these findings set off a major “course correction.” To date, this physical attribute has been defined for the nucleolus, transcription sites, nuclear speckles, Cajal bodies and heterochromatin. Its basis was discovered to reside in low complexity domains of participating proteins.

FISHING EXPEDITIONS

Many of us have had a review committee label a grant application as such, and there are surely kinder and more constructive ways. But a different kind of FISHing expedition occurred in 1969–1970, and it was anything but a pejorative term but rather, a revolutionary method in molecular cell biology (Gall and Pardue, 1969; Pardue and Gall, 1969; John et al., 1969; Pardue et al., 1970). In due course it underwent three advances. The first was the replacement of radioactive probes by fluorescent ones (Langer et al., 1982; Matera and Ward, 1992), with F thus added to In Situ Hybridization to give FISH. The second was the advent of ever more facile chemical synthesis of oligos and the third was extraordinary innovation arising in the period covered here, one of which was “Oligopaint” (Beliveau et al., 2015; Reboul et al., 2025). These and related advances contributed mightily to the ability to image the 3D organization of chromosomal loci at enhanced scale.

CRISPR- IN ITS OTHER DEPLOYMENT

The enormous breakthrough of CRISPR-based gene editing can never be overstated. But a group at UCSF had the idea that it could also be turned to the localization and dynamics of specific chromosomal loci in live cells (Chen et al., 2013). This had been achieved previously in pioneering advances by Andrew Belmont and colleagues using GFP-tagged lac operator arrays (Robinett et al., 1996), and later by others who deployed fluorescent TALE's (Ma et al., 2013; Miyanari, Ziegler-Birling and Torres-Padilla, 2013; Thanisch et al., 2013). But the CRISPR-based approach (Chen et al., 2013) had advantages in terms of its ease. My group and collaborators subsequently expanded CRISPR-based tracking of genomic loci to achieve greater spectral range (Ma et al., 2015, 2016a) and sensitivity (Ma et al., 2018), as well as to reveal new insights into the live cell kinetics of CRISPR action (Ma et al., 2016b) and interphase chromosome dynamics (Ma et al., 2019).

TODAY AND BEYOND

Now I turn to some of the most recent developments, offering thoughts on new dimensions and directions in our field that seem particularly promising and/or provocative to me.

A NEW ERA OF SYNERGY: THE ENCODE-4D NUCLEOME NEXUS

The completion of the decade-long 4D Nucleome Initiative in August of 2025 as an NIH Common Fund program has not meant that these investigators have turned their attention elsewhere- few, if any, have. There is, for example, significant momentum on neurobiological aspects as well as an increasing disease focus-both of which were getting underway in the 4D Nucleome Initiative by 2024. As just one of many examples, the human congenital malformation known as pulmonary agenesis has been associated with a complex set of genomic rearrangements including the de novo formation of a TAD at a particular genomic locus (Melo et al., 2021). Additional directions emerging from the 4D Nucleome Initiative can also be sensed in the recent summary of its decade of many accomplishments (Dekker et al., 2025). These advances synergize with the recently reported 2.5-fold expansion of the human cis-regulatory elements identified previously in ENCODE, as well as a three-fold expansion of the murine ones (Moore et al., 2026). Moreover, this all comes at a time when we increasingly understand how transcriptional enhancers’ cooperativity is based on their propinquity in the folded genome (Friman and Bickmore, 2026; Hansen et al., 2026) and are raising ideas about enhancers sometimes looping to ones nearby, instead of to promoters- the latter having been accepted as the “standard model” (Struhl, 2025).

Mapping the nuclear proteomic landscape

The initial proteomics analyses of the nucleolus (Andersen et al., 2002) and interchromatin granule clusters (Mintz et al., 1999; Saitoh et al., 2004) were important first steps and were followed during the period covered here by proximity labeling methods to capture proteins within 10–20 nm of a given nuclear body or specific genomic site (Kaewsapsak et al., 2017; Chen et al., 2018; Gao et al., 2018; Fazi et al., 2019; Dopie et al., 2020; Liu et al., 2024; Tsue et al., 2024). Another version of these methods, developed by Wei Zhang and colleagues at Synthcell, Taipei, Taiwan, and termed “Microscoop,” involves training a light beam on a very small, desired site within the nucleus and thus spatially limiting the reporter's activation (refer to Chen et al., 2024). Other key advances include ways to restrict or eliminate rogue free radical behavior, previously looming from the photochemistry of these methods. And the recent extraordinary revolution in cryo-electron tomography has also found application to the nucleus (Kechagia and Medalia, 2026). All these emerging methods are ushering in a bold new frontier of subnuclear proteomics at the nanoscopic scale.

CONDENSATES, REDUX

Adding up the nucleolus, certain transcription sites, almost all the nuclear bodies, and heterochromatin, it emerges that a substantial part of the intranuclear mass behaves in this way. It is also possible that we do not yet completely understand the full dimension of condensate physical chemistry (in the nucleus or anywhere in the cell). There are recent findings that suggest this might be the case (e.g., Shinn et al., 2026), as do recent studies of unanticipated capillary effects at the edges of these bodies, which change the equations of state (Gouveia et al., 2022). Integrating these new aspects into the nuclear condensates field constitutes a new frontier, beyond the initial liquid-liquid phase separation views- as heuristically catalytic as they were.

PUSHING THE GENOME AROUND

I have been surprised that Hi-C has not been more intensively applied to ask how transgenes adjust the 3D-nucleome. Small insertions might not be expected to appreciably alter the Hi-C map, for example moving a locus across a TAD boundary, and it is perfectly possible that even with larger insertions (i.e., transgenic experiments with cells or mice), deleterious effects may have passed unnoticed. But as clinical applications of AAV-based gene therapy advance, this issue becomes pressing. This technology often involves non-integrating vectors, but not always. Indeed, in the latter cases, transcriptionally active sites are selectively targeted (Russell, 2003). I don't think anyone knows why and, after all, we do know that transcriptionally inactive sites are by no means buried. As always, when a puzzle like this arises, it is a place on which to drill down.

HYPERMUTATION, GENOME STABILITY AND MEMORY

Like the other aspects of our field listed above, here is one that again has seen tremendous progress. Nonetheless, there remain cases of promising potential. For example, somatic hypermutation, long known as the basis of B-lymphocyte-mediated immunity, has recently been connected to intranuclear chromatin organization (Schoeberl et al., 2025), and this beckons further pursuit. Another recent finding is that DNA double-strand breaks leave a heritable genomic mark at the site of their repair (Bantele et al., 2025). This is as intriguing a recent finding as any in our field and, like the somatic hypermutation finding, has obvious clinical potential. A third area ripe for investigation is a longstanding mystery in reproductive biology, namely that mammalian oocytes display paradoxically low mutation rates. There is increasing evidence that this may relate to unique features of oocyte genome organization (Dudko et al., 2025). A fourth area of great importance is around the fourth “D” in the term “4D Nucleome”, viz. how this organization is stably inherited in dividing cell populations (when it is, and why when it is not) and locked in non-mitotic ones. The latter seem to get “special treatment.” What is it? Histone marks have been implicated (Paldi and Cavalli, 2026; Paldi et al., 2026), but is there something more going on?

LET'S NOT FORGET THE LAMINA

Not to push Paul Simon's song “Mother and Child Reunion” too far as metaphor, but I think of the telophase-reforming lamina and the subsequently organizing G1 genome in this way, the latter finding its “remembered footing,” as it were. The heritability of genome-lamina contacts is on the one hand known, and on the other a mystery as to how it works. I think this is as important a frontier as any in our field. In what safe is the early G1operating manual, to soon be deployed, kept for those 30–45 min. of mitosis? Could a clue lie in how the cytoplasm senses the disassembly and reassembly of the nucleus? After all, we know that the nuclear lamina and the cytoplasmic intermediate filament system are not exactly “unaware” of one another (e.g., Vahabikashi et al., 2022).

IN CLOSING

In these latter sections I have, of course, only touched on the many new avenues unfolding in our field, and readers will have their own favorites. And let's face it, there are likely to be new developments that come out of the blue. I recall from high school Latin that the word science comes from the verb “to know” (scire), but years later it dawned on me that our word “science” descends from the Latin verb's present participle, sciens = knowing. And so, just because we have proudly learned so much over the past decade in our field and possess some insight into how we got to know it, we must humbly admit that we most certainly don't know everything. That is our ticket for the future, in both meanings of “admission.”

ACKNOWLEDGMENTS

I am grateful to Job Dekker and Paul Kaufman at UMass Chan not only for our collaboration in the 4D Nucleome but for their supportive collegial interactions with me over the years. It is no accident that the first citation in this piece is Joe Gall's masterful book. He knew more about both the history and modern era of the nucleus than anyone I can think of and contributed to it in so many ways (Pederson, 2024b). His longstanding kindness to me and support of my work were treasured. I dedicate this article to his memory and legacy. This article was not constructed as a comprehensive review of the field but instead as a compilation of personal perspectives and thus, by definition, is selective in coverage. I was not, for this reason, able to include the work of many other important contributors in our field. During the period covered here, my laboratory was funded by grants from the NIH (GM-60551), the National Science Foundation (MCB-0445841), and the NIH 4D Nucleome (U01 DA-040588, with Job Dekker and Paul Kaufman). From 1998 to the present, I have also received financial support as the UMass Medical School's Vitold Arnett Professor in Cell Biology.

Abbreviations used:

AAV

adenovirus-associated virus

ENCODE

encyclopedia of DNA elements.

Footnotes

This article was published online ahead of print in MBoC in Press (http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E26-04-0196) on July 23, 2026.

Disclosure

From 2021 to 2025, I served as an External Adviser to the NIH 4D Nucleome Initiative. This was after the above-cited grant from the 4D Nucleome had ended, and it came with no financial compensation.

REFERENCES

  1. Alabi Y, Aksenova V, Arnaoutov A, Marin H, Dasso M, Buchwalter A (2025). Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity. Mol Biol Cell 36, 1–16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI (2002). Directed proteomic analysis of the human nucleolus. Curr Biol 12, 1–11. [DOI] [PubMed] [Google Scholar]
  3. Bantele S, Mordini I, Biran A, Alcaraz N, Zonderland G, Wenger A, Krietenstein N, Groth A, Lukas J (2025). Repair of DNA double-stranded breaks leaves heritable impairment to genome function. Science 390, eadk6662. [DOI] [PubMed] [Google Scholar]
  4. Beliveau BJ, Boettinger AN, Avendano MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignes F, Fonseka CY, Erceg J, et al. (2015). Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using oligopaint FISH probes. Nat Commun 6, 7147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Boveri T (1909), Die Blastomerenkerne von Ascaris megalocephala und dir Theorie der Chromosomeindividualitat. Arch Zellforsch 3, 181–268. [Google Scholar]
  6. Brangwynne CP, Mitchison TJ, Hyman AA (2011) Active, liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc Natl Acad Sci USA 108, 4334–4439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bullock S, Visa N, Pederson T (2020). Meeting report- nuclear and cytoplasmic machines at work. J Cell Sci 133, jcs 245134. [DOI] [PubMed] [Google Scholar]
  8. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, W Zhang, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B (2013). Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479–1491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chen LL, Larschan E, Matera AG, Strom A, Pederson T (2024) Nuclear bodies: concentrating at an aqueous site, with momentum. Nucleus 15, 2404677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Chen Y, Zhang Y, Wang Y, Brinkman EK, Adam SA, Goldman RD, van Steensel B, Ma J, Belmont AS (2018). Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. J Cell Biol 217, 4025–4048. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cheng H, Roggeveen JV, Wang H, Stone HA, Shi Z, Brangwynne CP (2025). Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments. Proc Natl Acad Sci USA 122, e2407423122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cremer T, Cremer C, Baumann H, Luedtke EK, Sperling K, Tueber V, Zorn Z (1982a). Rabl's model of interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation laser-UV-microbeam experiments. Hum Genet 60, 46–56. [DOI] [PubMed] [Google Scholar]
  13. Cremer T, Cremer C, Schneider T, Baumann H, Hens L, Kirsch-Volders M (1982b). Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments. Hum Genet 62, 201–209. [DOI] [PubMed] [Google Scholar]
  14. Crick FHC (1950). The physical properties of cytoplasm. A study by means of the magnetic particle method. II. Theoretical treatment. Exp Cell Res 1, 505–533. [Google Scholar]
  15. Crick FHC, Hughes AFW (1950). The physical properties of cytoplasm. A study by means of the magnetic particle method I Experimental. Exp Cell Res 1, 37–60. [Google Scholar]
  16. Croft JA, Bridger JM, Boyle S, Perry P, Teague P, Bickmore WA (1999). Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145, 1119–1131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Dekker J, Rippe K, Dekker M, Kleckner N (2002). Capturing chromosome conformation. Science 295, 1306–1311. [DOI] [PubMed] [Google Scholar]
  18. Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, et al. (2025). An integrated view of the structure and function of the human 4D nucleome. Nature 649, 759–776. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Dopie J, Sweredoski MJ, Mordian A, Belmont AS (2020). Tryamide signal amplification mass spectrometry (TSA-MS) ratio defines nuclear speckle proteins. J Cell Biol 219, e201910207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Dudko N, Dobrucki JW, Fulka H (2025). Mechanisms underlying low mutation rates in mammalian oocytes and preimplantation embryos. Nucl Acids Res 53, gkaf760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Fazi FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettinger AN, Chang HY, Ting AY (2019). Atlas of subcellular RNA localization revealed by APEX-seq. Cell 178, 473–490. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Friman ET, Bickmore WA (2026). Enhancer cooperativity in the folded genome. Curr Opin Genet Dev 96, 102416. [DOI] [PubMed] [Google Scholar]
  23. Gall JG (1996). A pictorial history. Views of the cell. Bethesda, MD: American Society for Cell Biology. [Google Scholar]
  24. Gall JG, Pardue ML (1969). Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 63, 378–383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Gao XD, Tu L-C, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu LJ, Wolfe SA, Sontheimer EJ (2018). C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Nat Meth 15, 433–436. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Gouveia B, Kim Y, Shaevitz JW, Petry S, Stone HA, Brangwynne CP (2022). Capillary forces generated by biomolecular condensates. Nature 609, 253–264. [DOI] [PubMed] [Google Scholar]
  27. Hansen KL, Adachi AS, Braccioli L, Kadvani S, Boileau RM, Martinovic M, Pokorny B, Shah RS, Anderson EC, Zhang K, et al. (2026) Syngery between regulatory elements can render cohesion dispensable for distal enhancer function. Science 391, eadt4221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. John HA, Birnstiel ML, Jones KW (1969). RNA-DNA hybrids at the cytological level. Nature 223, 582–587. [DOI] [PubMed] [Google Scholar]
  29. Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY (2017) Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. eLife 5, e29224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Kaufman PD, Huang S, Pederson T (2022). The nuclear bodies conference: hubs of genomic activity, July 24–28, Western Shore, Nova Scotia, Canada. FASEB J 36, e22588. [DOI] [PubMed] [Google Scholar]
  31. Kechagia Z, Madalia O (2026). High-resolution nuclear cell biology by cryo-electron tomography. Nucleus 17, 2675754. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Langer-Safer PR, Levine M, Ward D (1982). Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Natl Acad Sci USA 79, 4381–4385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Leiberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. (2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Liu Y, McGann CD, Krebs M, Perkins A, Fields R, Camplisson CK, Nwizugbo DZ, Hsu ASC, Tsue AF, Kania EE, et al. (2024). O-MAP uncovers the molecular neighborhoods associated with specific genomic loci. eLife 13, RP102489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Ma H, Naseri A, Reyes-Gutierrez P, Wolfe SA, Zhang S, Pederson T (2015). Multicolor CRISPR labeling of chromosomal loci in human cells. Proc Natl Acad Sci USA 112, 3002–3007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Ma H, Reyes-Gutierrez P, Pederson T (2013). Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. Proc Natl Acad Sci USA 110, 21048–21053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ma H, Tu L-C, Naseri A, Huisman ZS, Grunwald D, Pederson T (2016). Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotech 34, 528–530. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Ma H, Tu L-C, Naseri A, Chung Y-C, Grunwald D, Zhang S, Pederson T (2018). CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Meth 15, 928–931. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Ma H, Tu L-C, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016). CRISPR-Cas9 nuclear dynamics and target recognition in living cells. J Cell Biol 214, 529–537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Ma H, Tu L-C, Chung Y-C, Naseri A, Grunwald D, S Zhang, Pederson T (2019). Cell cycle- and genome distance-dependent dynamics of a discrete chromosomal region. J Cell Biol 218, 1467–1477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Marshall WF, Straight A, Marko J, Swedlow J, Dernberg A, Belmont A, Murray AW, Agard DA, Sedat JW (1997). Interphase chromosomes undergo constrained diffusional motion in living cells. Curr Biol 7, 930–939. [DOI] [PubMed] [Google Scholar]
  42. Matera AG, Ward D (1992). Oligonucleotide probes for the analysis of specific repetitive DNA sequences by fluorescence in situ hybridization. Hum Mol Genet 1, 535–539. [DOI] [PubMed] [Google Scholar]
  43. Melo US, Piard J, Fischer-Zirnsak B, Marius-Konstantin K, Schopflin R, Menash MA, Holtgrewe M, Arbez-Gindre F, Martin A, Guigue V, et al. (2021). Complete lung agenesis caused by complex genomic rearrangements with neo-TAD formation at the SHH locus. Hum Genet 140, 1459–1469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Mintz PJ, Patterson SD, Neuwald AF, Spahr CS, Spector DL (1999). Purification and biochemical characterization of interchromatin granule clusters. EMBO J 18, 4308–4320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Mirny L, Dekker J (2022). Mechanisms of chromosome folding and nuclear organization. In The Nucleus, 2nd ed., ed. Pombo A, Hetzer MW, Misteli T, Cold Spring Harbor NY: Cold Spring Harbor Laboratory Press, 189–208. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Miroshnikova YA, Wickstrom AA (2022). Mechanical forces in nuclear organization. In The Nucleus, 2nd ed., ed Pombo A, Hetzer MW, Misteli T, Cold Spring Harbor Laboratory Press, Cold Spring Harbor NY, 93–108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Miyanari Y, Ziegler-Birling C, Torres-Padilla ME (2013). Live visualization of chromatin dynamics with fluorescent TALEs. Nat Struc Mol Biol 20, 1321–1324. [DOI] [PubMed] [Google Scholar]
  48. Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, et al. (2026). An expanded registry of cis-regulatory elements. Nature. 10.1038/s41586-025-09909-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Muller HJ (1930). Types of visible variations induced by X-rays in Drosophila. J Genet 22, 299–334. [Google Scholar]
  50. Nemeth A, Conseca A, Santoyo-Lopez J, Medina I, Montaner D, Peterfia B, Solovei I, Cremer T, Dopazo J, Langst G (2010). Initial genomics of the human nucleolus. PLoS Genetics 6, e1000889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Nowell PS, Hungerford DA (1960). A minute chromosome in human chronic myelogenous leukemia. Science 132, 1497–1500. [Google Scholar]
  52. O'Brien TP, Bult CJ, Cremer C, Grunze M, Knowles BB, Langowski J, McNally J, Pederson T, Politz JC, Pombo A, et al. (2003) Genome function and nuclear organization: from gene expression to nanoscience. Genome Res 13, 1029–1041. [DOI] [PubMed] [Google Scholar]
  53. Paldi F, Cavalli G (2026). 3D genome folding in epigenetic regulation and cellular memory. Trends Cell Biol 36, 28–41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Paldi F, Szalay M-F, Dufau S, DiStefano M, Reboul H, Jost D, Bantignies F, Cavalli G (2026). Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding. Nat Genet 58, 404–417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Pardue ML, Gall JG (1969). Molecular hybridization of radioactive DNA to the DNA of cytological preparations. Proc Natl Acad Sci USA 64, 600–604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Pardue ML, Gerbi SA, Eckhardt RA, Gall JG (1970). Cytological localization of DNA complementary to ribosomal RNA in polytene chromosomes of Diptera. Chromosoma 29, 268–290. [DOI] [PubMed] [Google Scholar]
  57. Pederson T (2000). Half a century of “the nuclear matrix. Mol Biol Cell 11, 799–805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Pederson T (2003). Gene territories and cancer. Nat Genet 34, 242–243. [DOI] [PubMed] [Google Scholar]
  59. Pederson T (2011). The nucleolus. In The Nucleus, ed. Misteli T., Spector DL, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 209–223. [Google Scholar]
  60. Pederson T (2014). The nuclear physique. Intl Rev Cell Mol Biol 307, 1–13. [DOI] [PubMed] [Google Scholar]
  61. Pederson T (2024a). Tributaries of the 2023 Nobel Prize in Physiology and Medicine and lessons learned. RNA 30, 101–104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Pederson T (2024b). Remembrance: Joseph Gall. Nucleus 15, 2426552. [Google Scholar]
  63. Pederson T, King MC, Marko JF (2015). Forces, fluctuations and self-organization in the nucleus. Mol Biol Cell 26, 3915–3919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Pederson T, Marko JF (2014). Nuclear physics (of the cell, not the atom). Mol Biol Cell 25, 3466–3469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, van Steensel B (2006). Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38, 1005–1014. [DOI] [PubMed] [Google Scholar]
  66. Politz JCR, Browne ES, Wolf DE, Pederson T (1998) Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc Natl Acad Sci USA 95, 6043–6048. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Politz JCR, Tuft RA, Pederson T, Singer RH (1999). Movement of nuclear poly(A) RNA throughout the interchromatin space of living cells. Curr Biol 9, 285–289. [DOI] [PubMed] [Google Scholar]
  68. Rabl C (1885). Uber Zelltheilung. Morph Jb 10, 214–330. [Google Scholar]
  69. Rao P, Johnson RT (1970). Mammalian cell fusion studies on the regulation of DNA synthesis and mitosis. Nature 225, 159–164. [DOI] [PubMed] [Google Scholar]
  70. Reboul H, Normanno D, Szabo Q, Jerkovic I, Cavalli G, Bantignies F (2025). Oligopaint FISH to study chromosomal architecture and structural variations. Meth Mol Biol 2968, 465–484. [DOI] [PubMed] [Google Scholar]
  71. Ris H (1961). Ultrastructural and molecular organization of genetic systems. Can J Genet Cytol 3, 95–120. [DOI] [PubMed] [Google Scholar]
  72. Robbins E, Pederson T, Klein P (1970). Comparison of mitotic phenomena and effects induced by hypertonic solutions in HeLa cells. J Cell Biol 44, 400–416. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Robinett CC, Straight A, Li G, Wilhelm C, Sudlow G, Murray A, Belmont AS (1996). In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J Cell Biol 135, 1685–1700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T (2003). Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet 34, 287–291. [DOI] [PubMed] [Google Scholar]
  75. Rowley JD (1973). A new consistent chromosomal abnormality in chronic myelogenous leukemia identified by quinacrine fluorescence and Giemsa staining. Nature 243, 290–293. [DOI] [PubMed] [Google Scholar]
  76. Russell DW (2003). AAV loves an active genome. Nat Genet 34, 241–242. [DOI] [PubMed] [Google Scholar]
  77. Saitoh N, Spah CS, Patterson SD, Bubulya P, Neuwald AF, Spector DL (2004). Proteomic analysis of interchromatin granule clusters. Mol Biol Cell 15, 3876–3890. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Schoeberl UE, Fitz J, von der Linde M, Valieris R, Bauer B, Malzl D, Frussios K, Costea J, Schmidt F, Pflaum J, et al. (2025). Regulation of somatic hypermutation by higher-order chromatin structure. Mol Cell 85, 2701–2717. [DOI] [PubMed] [Google Scholar]
  79. Shinn MK, Tomares DT, Liu V, Pant A, Qiu Y, Vitalis A, Song YJ, Ayala Y, Ruff KM, Strout GW, et al. (2026). Nuclear speckle proteins form intrinsic and MALAT1-dependent microphases. Cell 189, 832–852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  80. Struhl K (2025). Distal enhancers loop to proximal enhancers, not to promoters. Nat Rev Mol Cell Biol 26, 730–713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Thanisch K, Schneider K, Morbitzer R, Solovei I, Lahaye T, Bultmann S, Leonhardt H (2013). Targeting and tracing of specific DNA sequences in human chromosomes with transcription activator-like effectors. Nucl Acids Res 42, e38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Todorovski V, McCluggage F, Li Y, Meid A, Spatz JP, Holle AW, Fox AH, Choi YS (2023), Confined environments induce polarized paraspeckle condensates. Commun Biol 6, 145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Tsue AF, Kania EE, Lei DQ, Fields R, McGann C, Marciniak DM, Hershberg EA, Deng X, Kihiu M, Ong S-E, et al. (2024). Oligonucleotide-mediated proximity-interactome mapping (O-MAP): a unified method for discovering RNA-interacting proteins and genomic loci in situ. Nat Meth 21, 2058–2071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Vahabikashi A, Sivagurunathan S, Nicado FAS, Han YL, Park CY, Kittissopikul M, Wong X, Tran JP, Gundersen GG, Reddy KL, et al. (2022) Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleoskeletal coupling and whole-cell mechanics. Proc Natl Acad Sci USA 119, e21211816119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. von Koningsbruggen S, Gierliński M, Schofield P, Martin D, Barton GJ, Ariyurek Y, den Dunnen JT, Lamond AI, (2010). High-resolution whole genomic sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Mol Biol Cell 21, 3735–3748. [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Wachsmuth M, Waldeck W, Langowski J (2000). Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy. J Mol Biol 298, 677–689. [DOI] [PubMed] [Google Scholar]

Articles from Molecular Biology of the Cell are provided here courtesy of American Society for Cell Biology

RESOURCES