Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome

DNA Research, 2016, 23(2), 155–169 doi: 10.1093/dnares/dsw005 Advance Access Publication Date: 29 February 2016 Full Paper Full Paper Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome Arashdeep Singh, Meenakshi Bagadia, and Kuljeet Singh Sandhu* Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, SAS Nagar 140306, India *To whom correspondence should be addressed. Tel. +91 172-2293182. Fax. +91 172-2240266. E-mail: Edited by Prof. Takashi Ito Received 4 November 2015; Accepted 31 January 2016 Abstract Despite recent advances, the underlying functional constraints that shape the three-dimensional organization of eukaryotic genome are not entirely clear. Through comprehensive multivariate analyses of genome-wide datasets, we show that cis and trans interactions in yeast genome have significantly distinct functional associations. In particular, (i) the trans interactions are constrained by coordinated replication and co-varying mutation rates of early replicating domains through interactions among early origins, while cis interactions are constrained by coordination of late replication through interactions among late origins; (ii) cis and trans interactions exhibit differential preference for nucleosome occupancy; (iii) cis interactions are also constrained by the essentiality and co-fitness of interacting genes. Essential gene clusters associate with high average interaction frequency, relatively short-range interactions of low variance, and exhibit less fluctuations in chromatin conformation, marking a physically restrained state of engaged loci that, we suggest, is important to mitigate the epigenetic errors by restricting the spatial mobility of loci. Indeed, the genes with lower expression noise associate with relatively short-range interactions of lower variance and exhibit relatively higher average interaction frequency, a property that is conserved across Escherichia coli, yeast, and mESCs. Altogether, our observations highlight the coordination of replication and the minimization of expression noise, not necessarily co-expression of genes, as potent evolutionary constraints shaping the spatial organization of yeast genome. Key words: 3D genome organization, long-range chromatin interactions, replication, expression noise, evolutionary constraints, essential genes 1. Introduction Eukaryotic genes and their regulatory elements communicate with each other through a complex wiring of long-range interactions.1 It is now well established that distal enhancers can physically juxtapose to their cognate promoters for transcriptional regulation.2–8 Interestingly, distant genes can also co-localize in nuclear space.9,10 The prevailing view is that the genes spatially cluster at concentrated foci of RNA polymerase II, also known as transcription factories.11–16 It is suggested that the spatial convergence of genes at transcription factories provide a topological basis of co-expression of engaged genes; however, such proposals have not been subjected to proper scrutiny. Recent advent of high throughput derivatives of Chromosome Conformation Capture (3C) has availed genome-wide quantitative data of long-range chromatin interactions across diverse spectra of model systems. 17–26 Briefly, in 3C-derived techniques, the chromatin is cross-linked with formaldehyde, restriction © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any 155 medium, provided the original work is properly cited. For commercial re-use, please contact 156 Functional constraints of spatial genome organization digested, and the open ends of cross-linked products are ligated in diluted conditions to prefer intra-molecular ligation over intermolecular. In HiC, the ligated junctions are then pulled down and sequenced using deep sequencing to unravel all-to-all chromatin interactions.21 HiC has revealed large topologically associated domains (TADs) that exhibit high density of intra-connectivity of chromatin and are largely conserved across cell lineages.27,28 TADs are tightly associated with the chromatin type and replication timing, and are marked by CTCF on boundaries. 27,29,30 Widespread enhancer-to-promoter interactions, that are mostly cell-type specific, have been uncovered across several systems.28,31–33 Zhang et al.31 have suggested differential usage of enhancers during embryonic stem cell differentiation. Some studies have also revealed promoter-to-terminator interactions commonly found for housekeeping genes,34 possibly ascribing a circular template for recurrent transcription. Most interesting of all is the widespread promoter-topromoter interactions among genes impinging from neighbouring regions to form discrete multi-gene complexes.34,35 However, what functional and evolutionary constraints might have shaped the large-scale organization of promoter–promoter interactions is not entirely clear. Although the genes within multi-gene complexes are shown to be co-expressed,34,36 whether or not co-expression of engaged genes is dependent on their spatial, but not the linear, proximity remains to be seen. Moreover, it is hypothesized that interacting promoters can influence transcriptional states of each other and that the promoter of one gene can function as an enhancer of other gene.34 Nevertheless, these proposals are yet not established as fact. Importantly, most of these studies have primarily focussed on intra-chromosomal (referred as ‘cis’ in this study) interactions and whether or not distant genes converging from different chromosomes (referred as trans interactions) have functional association is yet not clear. Comprehensive statistical analyses of accumulated HiC like datasets can answer several questions pertaining to non-random genome organization. Here, we ask whether we can delineate evolutionary constraints of three-dimensional organization of genome. Multivariate analyses provide a statistical platform to assess the association of several different functional variables in an unbiased manner. Availability of various genome-wide datasets and highresolution data of cis as well as trans chromatin interactions makes budding yeast an ideal candidate for multivariate analysis to identify the potential functional constraints shaping the nonrandom spatial organization of genome. The article by Duan et al.22 suggested following key features of three-dimensional organization of budding yeast genome: (i) interactions among the centromeres, (ii) interactions among the sites of early origin and not the late origins, and (iii) interactions among t-RNA genes. A few followup studies suggest (...truncated)