bioRxiv preprint doi: https://doi.org/10.1101/2020.10.05.326009; this version posted October 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Chromosomes distribute randomly to, but not within, human neutrophil nuclear lobes 2 3 Christine R Keenan1,2 *, Michael J Mlodzianoski 1,2 *, Hannah D Coughlan1,2, Naiara G Bediaga1,2, 4 Gaetano Naselli1,2, Erin C Lucas1,2, Qike Wang1,2, Carolyn A de Graaf1,2, Douglas J Hilton1,2, Leonard 5 C Harrison1,2, Gordon K Smyth1,3, Kelly L Rogers1,2, Thomas Boudier1,2, 4, Rhys S Allan1,2 * and 6 Timothy M Johanson1,2 * 7 8 Affiliations: 1The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, 9 Australia. 2Department of Medical Biology, 3School of Mathematics and Statistics, The University of 10 Melbourne, Parkville, Victoria, 3010, Australia. 4 Institute of Biology Paris-Seine, Sorbonne Université, 11 Paris 12 13 Corresponding author: Timothy Johanson ([email protected]) 14 15 16 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.05.326009; this version posted October 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 17 Abstract 18 19 The proximity pattern and radial distribution of chromosome territories within spherical nuclei are 20 well understood to be random and non-random, respectively. Whether this distribution pattern is 21 conserved in the partitioned or lobed nuclei of polymorphonuclear cells is unclear. Here we use 22 chromosome paint technology and a novel high-throughput imaging analysis pipeline to examine the 23 chromosome territories of all 46 chromosomes in hundreds of single human neutrophils – an abundant 24 and famously polymorphonuclear immune cell. 25 26 By comparing the distribution of chromosomes to randomly shuffled controls, and validating with 27 orthogonal chromosome conformation capture technology, we show for the first time that all human 28 chromosomes randomly distribute to neutrophil nuclear lobes, while maintaining a non-random radial 29 distribution within these lobes. Furthermore, by leveraging the power of this vast dataset, we are able 30 to reveal characteristics of chromosome territories not detected previously. For example, we 31 demonstrate that chromosome length correlates with three-dimensional volume not only in 32 neutrophils but other human immune cells. 33 34 This work demonstrates that chromosomes are largely passive passengers during the neutrophil lobing 35 process, but are able to maintain their macro-level organisation within lobes. Furthermore, the random 36 distribution of chromosomes to the naturally partitioned nuclear lobes suggests that specific 37 transchromosomal interactions are unimportant in mature neutrophils. 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.05.326009; this version posted October 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 38 Introduction 39 40 First proposed in 1885 (1), interphase chromosomes maintaining a territorial organisation is now a 41 widely accepted principle of nuclear organisation in most eukaryotes (2). This is unsurprising given 42 the importance of this organisation to functions as fundamental as gene expression and DNA repair. 43 For example, the radial position of a chromosome within the nucleus is strongly correlated with its 44 transcriptional activity (3, 4). Furthermore, the proximity of chromosomes to one another (both 45 homologous and non-homologous) is thought to be important during DNA repair (5) and potentially 46 even in direct gene regulation (6-10). 47 48 While the radial distribution of chromosomes is well understood to be non-random (2), the position of 49 chromosomes relative to each other, or proximity pattern, is contentious, with reports of both non- 50 random (11-15) and random distributions (16). In the absence of being able to observe interphase 51 chromosome movements in live cells over long periods of time, combined with the absence of 52 physical barriers to restrict chromosome movement, it is possible that these studies simply differ in 53 their detection of transient or infrequent interphase chromosomal interactions or movements. 54 55 Human neutrophils constitute approximately two thirds of the immune cells in human blood. They are 56 readily identifiable by their polymorphonuclear nature with their nuclei being segmented into 2-6 57 lobes joined only by thin filaments of nucleoplasm (17). Here we exploit this natural nuclear 58 segmentation to examine the importance of interphase chromosome distribution. We hypothesise that 59 if interactions between chromosomes are biologically important these chromosomes would 60 preferentially locate together into neutrophil nuclear lobes, enabling continuing interaction. 61 62 Using chromosome paint technology alongside novel high-throughput image analysis pipelines, we 63 have examined all 46 human chromosomes in 240 single neutrophils. We reveal that while the radial 64 distribution of chromosomes within neutrophil nuclear lobes is non-random, the distribution of 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.05.326009; this version posted October 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 65 chromosomes to lobes is in fact random, suggesting that gene regulatory interactions between specific 66 chromosomes are highly unlikely to occur in human blood neutrophils. 67 68 Results 69 70 Novel analysis pipeline detects the position and characteristics of all human chromosomes in 71 three-dimensions 72 73 Given the complexity of examining all 46 human chromosomes in hundreds of single, segmented 74 neutrophil nuclei, we developed a bespoke image analysis pipeline to detect the position and three- 75 dimensional characteristics of all chromosomes in images generated using chromosome paint. 76 77 In brief, each of the 22 autosome pairs and the X and Y chromosomes within fixed healthy male 78 human blood neutrophil nuclei (Supp Fig 1A) is “painted” with a specific combination of fluorescent 79 oligonucleotides within the chromosome paint mix (Fig 1A, B). The whole nucleus is then imaged 80 and analysed using our analysis pipeline (Fig 1C). First, the intensity of each of the five channels in 81 each individual image is normalised. A malleable grid with lines that flex to incorporate nearby 82 voxels of similar channel intensity patterns is then applied to each image. This flexibility allows the 83 grid to capture the highly variable three-dimensional shapes formed by chromosomes. Adjacent cubes 84 of the grid that share channel intensities are then combined to create “objects”. Based upon the 85 expected spectral combinations for each chromosome (Fig 1 B) these objects are then assigned as 86 chromosomes. To avoid the common pitfall of arbitrary thresholding to define genuine signal from 87 background (2), here every image has an individually determined threshold. This threshold is 88 calculated by automated sequential testing of various thresholds to determine the value which 89 maximises the number of objects with genuine chromosome channel combinations, while minimizing 90 spectrally spurious objects (e.g. detected objects that have a channel combination differing from the 91 24 specific chromosome combinations). 92 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.05.326009; this version posted October 5, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 93 Importantly, chromosome paint and our image analysis pipeline detect the majority of the 22 human 94 autosomes and the sex chromosomes at approximately the expected proportions (Fig 1 D, Supp Fig 95 1B). While some chromosomes appear more difficult to define or detect (e.g. chromosome 13, 15, 21 96 and 22), the proportions of chromosomes detected are similar across human immune cell types (CD4+ 97 and CD8+ T cells) (Supp Fig 1C, D), suggesting that the variation in detection frequency observed is 98 technical, not biological. 99 100 We next examine the three-dimensional character of all 46 chromosomes, including volume (Fig 1 E) 101 and surface area (Fig 1 F), among others (Supp Fig 1E, F). While the physical characteristics of the 102 chromosome territories varies greatly across neutrophil nuclei, the volume and surface area of the Y 103 chromosomes are, as expected, consistently and significantly (P=0.02 and P= 0.04, respectively) 104 smaller than the X chromosome (Fig 1 E, F). 105 106 While the differences in the three-dimensional character of the chromosomes are subtle, the ability to 107 examine all chromosomes (as opposed to between 2-7 chromosomes (18-20)) in large numbers of 108 cells affords the power to reveal correlations previously missed. For example, contrary to previous 109 studies suggesting that there is no relationship between chromosome linear length and three- 110 dimensional volume (18, 20), our analysis reveals a significant linear relationship between the two (r2 111 = 0.359, P = 0.001), not only in neutrophils (Fig 1G), but other human immune cells (Supp Fig 1G). 112 113 Thus, while chromosome paint data contains variance in both chromosome detection and three- 114 dimensional parameters, the scale of our dataset allows elucidation of biologically important 115 correlations and phenomena that were undetectable using previous methods.