Chromatin Structure and Transcriptional Activity Shaping Genomic Landscapes in Eukaryotes

Transcription

1 Invisible Cities: Segregated domains in eukaryote genomes Chromatin Structure and Transcriptional Activity Shaping Genomic Landscapes in Eukaryotes Christoforos Nikolaou Computational Genomics Group Dept. of Biology, University of Crete

2 Genomes as Architectures Genomes as Architectures In Zoe the lack of Signs does not allow you to the understand the function of each building: You are lost in an indivisible environment. Italo Calvino, Invisible Cities Left: A 2D live cell DNA dstorm image, adapted from Benke A, Manley S. ChemBioChem Right: Artistic representation of Calvino s city of Zoe by Karina Puente Frantzen

3 Structural Landmarks vs a U-topian Architecture? The lack of landmarks is a characteristic of ultra-designed architectural structures, in which the sense of space is by definition arbitrary. ( ου τόπος = no place) Most urban landscapes have, in contrast, developed through gradual aggregation of distinguishable architectural elements. Top left: Plan for the Ville Radieuse by Le Corbusier, Top Right: CDG International Airport, Paris Bottom Right: Aerial view of Paris

4 The multiple levels of genome organization Gene distribution Gene Regions/Gene Deserts Regulation of gene expression Eu/Hetero-chromatin Chromatin States Topologically Associated Domains (TAD) Transcription Factories Chromosomal Territories RidGE (Caron et al, 2001); Chromatin and Transcription (Jenuwein, 2001); Chromatin States (Ernst & Kellis, 2010); TAD (Bing Ren, 2011); 3D Genome (Fraser et al 2010); Chromosomal Territories (Dekker et al)

5 Can we deduce structural/functional domains in the genome? Structural Entities in the Eukaryotic Genome We are now in the position to dissect the eukaryotic genome in structurally coherent entities (TADs, chromosomal compartments, transcription factories etc) The question: Are there structural properties that distinguish between these entities or are we lost in an indivisible environment? Our goal: To analyze the eukaryote genome in linear space and see if there are attributes that can help us define genomic landmarks and thus grasp a hidden genome architecture. Hi-C map from the data of Duan et al (2009). Adapted from Tsochatzidou et al (2017)

6 Genome Architecture in one dimension Genome segmentation based on co-expression profiles Question: Do up/down-regulated genes tend to cluster in linear dimension? Answer: Yes. Clusters of consistent expression-change under topological stress are longer than expected by chance Tsochatzidou et al, Nucleic Acids Res. 2017

7 Topo-regulated gene clusters are also co-regulated Increased gene co-expression within the topologically defined clusters SPELL Database: >10000 gene expression profiles for yeast Question: Are the defined clusters also co-regulated? Answer: Yes. Topologically defined clusters show higher expression correlation that randomly selected consecutive gene clusters of the same size. Tsochatzidou et al, Nucleic Acids Res. 2017

8 Non-random genomic distribution of gene clusters Gene clusters of different types show clear positional preferences Question: Are gene clusters randomly positioned in the genome? Answer: No. Down-regulated clusters tend to be found close to the centromeres and away from the edges of chromosomes. The opposite is true for Up-regulated gene clusters. Tsochatzidou et al, Nucleic Acids Res. 2017

9 Gene Conservation and TFBS density Down-regulated clusters are more conserved. Up-regulated clusters have more complex regulation patterns. Down-regulated gene clusters are more conserved in terms of sequence than Upregulated ones, which, on the other hand contain more transcription factor binding sites in their promoters. Tsochatzidou et al, Nucleic Acids Res. 2017

10 Spatial preferences of gene clusters Up-regulated gene clusters are more distant from each other In general, expression values under topological stress, increase with increasing distance between adjacent genes. Distance between genes in Up-regulated clusters is significantly higher than the genome average, while Downregulated genes are placed closer than the expected mean. Distance preferences are not related to length of genes. Tsochatzidou et al, Nucleic Acids Res. 2017

11 Transcriptional directionality matters Patterns of transcriptional direction differ between clusters Down-regulated clusters have more common changes in transcriptional direction compared to Up-regulated ones where genes tend to be transcribed in the same direction. Tsochatzidou et al, Nucleic Acids Res. 2017

12 Genome Architecture in one dimension Co-directional transcription is buffering topological stress Genes transcribed in the same direction (and with greater intergenic space) can dissipate (or even harness) the accumulation of topological stress. Conservation of directionality is apparent in up-regulated genes even at low sequence conservation. Tsochatzidou et al, Nucleic Acids Res. 2017

13 Genome Urbanization Genome Organization reminiscent of urban landscapes Tsochatzidou et al, Nucleic Acids Res. 2017

14 The multiple levels of genome organization How can elements from one level associate/define the next one? Gene distribution Gene Regions/Gene Deserts Regulation of gene expression Eu/Hetero-chromatin Chromatin States? Topologically Associated Domains (TAD) Transcription Factories Chromosomal Territories RidGE (Caron et al, 2001); Chromatin and Transcription (Jenuwein, 2001); Chromatin States (Ernst & Kellis, 2010); TAD (Bing Ren, 2011); 3D Genome (Fraser et al 2010); Chromosomal Territories (Dekker et al)

15 Genome Architecture three dimensions Three-dimensional preferences for gene clusters. Up-regulated clusters tend to overlap TAD insulators Overlap with Insulators TADs defined on the basis of an insulation score. Insulator regions called on the basis of TAD separation. Up-regulated gene clusters are enriched in insulating regions. No apparent tendency was observed for down-regulated ones. Tsochatzidou et al, Nucleic Acids Res. 2017

16 From structure to function and back to structure How is the compartmentalization linked to the finer chromatin structure? Chromatin structure is stratified in hierarchical levels from local, nucleosomal patterns to global 3D topology. How are the two levels linked? Can broader genomic domains differ in their nucleosome positioning patterns? Left: Definition of TAD-like domains in yeast chriv. Nikolaou C. Current Genetics, 2017 Right: Different nucleosomal occupancy patterns for different gene groups. Nikolaou et al, NAR 2012

17 The Plan What we did We divided the yeast genome in TAD-like domains based on an insulation analysis of Hi-C maps We obtained the average nucleosome occupancy profile for the genes in each TAD-like domain We clustered the domains according to their average nucleosome occupancy pattern We wanted to see differences in the functional and structural properties of the different TAD-like clusters, such as: Genomic localization Gene conservation Transcription factor binding enrichment Chromosomal distribution

18 Nucleosome occupancy patterns delineate gene neighborhoods Strikingly different nucleosome occupancy profiles in the yeast genome Closed-chromatin pattern: Shallow Nucleosome Free Region (NFR) upstream of the TSS. Fuzzy nucleosomes upstream and downstream Open Chromatin pattern: A clear Nucleosome Free Region (NFR) upstream of the TSS. Periodically positioned nucleosomes downstream of the TSS. Very Open Chromatin pattern: Clear and very deep Nucleosome Free Region (NFR) upstream of the TSS. Periodically positioned nucleosomes downstream of the TSS. Wellpositioned -1 nucleosome upstream of the NFR. C. Nikolaou, Current Genetics, 2017

19 Nucleosome occupancy patterns delineate gene neighborhoods Open Chromatin Clusters. Deep NFR, Nucleosome Periodicity Closed Chromatin Clusters: Shallow or no NFR, lack of periodicity C. Nikolaou, Current Genetics, 2017

20 Some classes are different than others Different nucleosome occupancy is linked to various genomic aspects Different classes of TAD-like domains based on their nucleosome occupancy patterns also differ in a number of aspects such as size, sequence conservation and chromosomal localization. C. Nikolaou, Current Genetics, 2017

21 Regulatory compartmentalization between classes Strikingly different Regulatory potential among the TAD-like Classes Open/Closed Chromatin classes are recaptured at the level of transcription factor binding enrichment (Classes 1,2,4 vs 3,5 and 6). Differences between classes of the same type are also indicative of an additional level of complexity. (e.g. Class 2 shares a few factors with Class 5) Insulating Regions have predominantly characteristics of open chromatin. Cluster 3 appears to be the more depleted in transcription factor binding despite its apparently open nucleosome occupancy profile. C. Nikolaou, Current Genetics, 2017

22 Genome Compartmentalization in structural neighborhoods Uneven chromosomal distribution of TAD-like domain structural classes Unequal distribution of the different classes along the yeast genome and among chromosomes points towards a particular compartmentalization of structurally coherent genomic domains. C. Nikolaou, Current Genetics, 2017

23 Genome Segregation in non-interacting genomic neighborhoods Lack of inter-chromosomal interactions between classes Different classes tend to be isolated in terms of inter-chromosomal interactions. (Abundance of blue boxes) Overall lack of inter-chromosomal interactions is more pronounced between different classes than within them Classes that show increased interaction tendency belong to similar categories (red boxes) Insulating regions show the greatest tendency for inter-chromosomal interactions with themselves. C. Nikolaou, Current Genetics, 2017

24 Invisible Cities: Segregated domains in the yeast genome Part #1: Conclusions The architecture of the yeast genome contains structural landmarks instead of a uniform indivisible environment. The yeast genome is compartmentalized in TAD-like domains that differ in the nucleosome occupancy patterns of their contained genes. The different structural classes of genomic domains are associated with different chromatin structure (open/closed nucleosomal patterns), linear chromosomal localization (proximity to telomeres or ARS), sequence conservation and transcription factor binding enrichments. The yeast genome appears to be not only compartmentalized but also segregated in the sense that different classes tend to be isolated, lacking interactions in 3D space. Our observations support the evolution of the genome s architecture through self-organization of chromatin structural elements.

25 End credits Our collaborators Our Group Maria Tsochatzidou Analysis of GRO seq data Roderic Guigo, (CRG, Barcelona) Maria Malliarou Genome compartmentalization Antonis Klonizakis Transcription factor enrichment analysis Antonis Papadakis Regulatory Networks Vassilis Ntassis Genome Segregation Stelios Mavropoulos, Labrina Bondi Bipartite Networks Joaquim Roca, (CSIC, Barcelona) George Kollias (BSRC Alexander Fleming, Athens) Eleni Lianoudaki Position-dependent Gene Expression Nefely Paschou Nina Koukourikou