Topologically associating domain (TAD) boundaries stable across diverse cell types are evolutionarily constrained and enriched for heritability

Abstract

14 15 Background: Topologically associating domains (TADs) are fundamental units of three-16 dimensional (3D) nuclear organization. The regions bordering TADs-TAD boundaries-17 regulate gene expression by restricting interactions of cis-regulatory sequences to their target 18genes. TAD and TAD boundary disruption have been implicated in rare disease pathogenesis; 19 however, we have a limited framework for integrating cross-cell-type TAD maps into the study of 20 genome evolution and interpretation of common trait-associated variants. Here, we investigate 21 an unexplored attribute of 3D genome architecture-the stability of TAD boundaries across cell 22 types-and demonstrate its relevance to understanding how genetic variation in TADs 23 contributes to complex disease. 24Results: By synthesizing TAD maps across 37 diverse cell types with multiple annotations and 25 41 genome-wide association studies (GWAS), we investigate the differences in function and 26 evolutionary constraint between TADs versus TAD boundaries. We demonstrate that TAD 27 boundaries are more evolutionarily constrained than TADs. We find that boundaries are 28 enriched for disease heritability, especially for immunologic, hematologic, and metabolic traits. 29 Next, we stratify boundaries by their stability across cell types and show that more than 30% of 30 boundaries are unique to a specific tissue. Compared to these unique boundaries, cell-type-31 stable boundaries are enriched for CTCF binding, evolutionary constraint, housekeeping genes, 32 and trait heritability, suggesting greater functional importance. 33 Conclusions: Cell-type-stable TAD boundaries have greater sequence-level constraint and 34 complex trait heritability enrichment than cell-type-unique boundaries and TADs overall. Thus, 35 considering TAD and boundary stability across cell types provides valuable context for 36 understanding the genome's functional landscape and enabling 3D-structural aware variant 37 interpretation. 38 39 2 BACKGROUND 40 41 The three-dimensional (3D) conformation of the genome facilitates the regulation of gene 42 expression. 1-4 Using chromosome conformation capture technologies (3C, 4C, 5C, Hi-C), 5-7 43recent studies have demonstrated that modulation of gene expression via 3D chromatin 44 structure is important for many physiologic and pathologic cellular functions, including cell type 45 identity, cellular differentiation, and risk for multiple rare diseases and cancer. [8][9][10][11][12][13] Nonetheless, 46 many fundamental questions remain about the functions of and evolutionary constraints on 3D 47 74 associating" TADs and the "insulatory" boundaries. For example, in cross-species multiple 75 sequence alignments, syntenic break enrichment at TAD boundaries suggests a long-term 76 evolutionary preference for rearrangements that "shuffle" intact TADs, rather than "break" 77 them. 25,26 Additionally, TADs often contain clusters of co-regulated genes-e.g., cytochrome 78 genes and olfactory receptors. 7,20,27 Intra-TAD structural variation...

Novel genetic variants associated with mortality after unrelated donor allogeneic hematopoietic cell transplantation

“…CTCF functions as an insulator, preventing the influence of CIS-acting enhancers on gene activation and defines TAD boundaries. A conserved TAD boundary (75,100,000À75,260,000) encompasses this region [38] and is adjacent to a TAD containing CXCL (1,2,3,5,6,8,9,11). Interestingly, this region has been previously identified in a GWAS of vaccine response.…”

Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies

“…Unfortunately, Hi-C data is still not available for either human NCC or NC-derived embryonic tissues. This will be hopefully solved in the near future because TADs might be more variable among cell types/tissues than previously anticipated ( Dixon et al, 2012 ; McArthur and Capra, 2020 ). Furthermore, smaller topological domains with important regulatory functions (e.g., sub-TADs) tend to show higher tissue specificity ( Berlivet et al, 2013 ; Kragesteen et al, 2018 ; Beagan and Phillips-Cremins, 2020 ).…”

“…This last observation, together with another report in which the regulatory elements controlling Xist expression have been dissected (Galupa et al, 2020), suggest that TAD boundaries are not impenetrable, but rather partially permeable barriers that do not completely insulate genes from regulatory elements located in neighboring TADs. Moreover, TAD boundary positions are not strictly conserved among all cell types, and thus, future efforts should include obtaining Hi-C maps in additional cell types and tissues (Dixon et al, 2012;McArthur and Capra, 2020). Together with cell type-specific gene-expression data, these additional Hi-C maps would help improve the predictions of how SV might affect gene expression through long-range regulatory mechanisms.…”

Super-enhancers: a new frontier for epigenetic modifiers in cancer chemoresistance

“…TADs, regions enriched in chromatin interactions, are composed of contact domains and multiple subTADs containing dense genes and inhibitory and activating chromatin signatures [76]. TADs are chromatin loop architectures formed in the process of genome organization, and are basic units of 3D nuclear organization, the properties and functions of which are affected by the 3D conformation of chromatin [77][78][79]. Architectural proteins, architectural protein binding sites, tRNAs, short interspersed nuclear elements and housekeeping genes form the boundaries of TADs that play a role of insulator and guarantee the interactions of distant elements [77,80].…”