Transcriptional regulation and spatial interactions of head-to-head genes

Abstract

Background: In eukaryotic genomes, about 10% of genes are arranged in a head-to-head (H2H) orientation, and the distance between the transcription start sites of each gene pair is closer than 1 kb. Two genes in an H2H pair are prone to co-express and co-function. There have been many studies on bidirectional promoters. However, the mechanism by which H2H genes are regulated at the transcriptional level still needs further clarification, especially with regard to the co-regulation of H2H pairs. In this study, we first used the Hi-C data of chromatin linkages to identify spatially interacting H2H pairs, and then integrated ChIP-seq data to compare H2H gene pairs with and without evidence of spatial interactions in terms of their binding transcription factors (TFs). Using ChIP-seq and DNase-seq data, histones and DNase associated with H2H pairs were identified. Furthermore, we looked into the connections between H2H genes in a human co-expression network.

Results: We found that i) Similar to the behaviour of two genes within an H2H pair (intra-H2H pair), a gene pair involving two distinct H2H pairs (inter-H2H pair) which interact with each other spatially, share common transcription factors (TFs); ii) TFs of intra- and inter-H2H pairs are distributed differently. Factors such as HEY1, GABP, Sin3Ak-20, POL2, E2F6, and c-MYC are essential for the bidirectional transcription of intra-H2H pairs; while factors like CTCF, BDP1, GATA2, RAD21, and POL3 play important roles in coherently regulating inter-H2H pairs; iii) H2H gene blocks are enriched with hypersensitive DNase and modified histones, which participate in active transcriptions; and iv) H2H genes tend to be highly connected compared with non-H2H genes in the human co-expression network.

Conclusions: Our findings shed new light on the mechanism of the transcriptional regulation of H2H genes through their linear and spatial interactions. For intra-H2H gene pairs, transcription factors regulate their transcriptions through bidirectional promoters, whereas for inter-H2H gene pairs, transcription factors are likely to regulate their activities depending on the spatial interaction of H2H gene pairs. In this way, two distinctive groups of transcription factors mediate intra- and inter-H2H gene transcriptions respectively, resulting in a highly compact gene regulatory network.

Figure 1

The definition of head to head (H2H) gene organization and intra/inter-H2H pairs. (A) Head to head (H2H) gene organization. The region between the two transcription start sites is called a bidirectional promoter and the region between the ends of two genes is an H2H block. (B) Intra-H2H pairs and an inter-H2H pair. An inter-H2H pair involves two intra-H2H gene pairs.

Figure 2

The distribution of H2H gene pairs by transcription factors bound to H2H gene pair blocks.

Figure 3

Hierarchical Clustering of TFs bound to H2H gene pairs. Overrepresented TFs are TFs that bind to more than 45% of H2H pairs while other TFs are the non-overrepresented TFs.TFs in the green ellipse are TFs preferring to interact with interacting inter-H2H pairs versus intra-H2H pairs and they all belong to the ‘other TFs’ group.

Figure 4

A co-functional network of H2H gene pair transcription factors. In the network, yellow nodes represent TFs with high degree and green nodes refer to TFs with small degree.

Figure 5

TF similarity distribution of interacting inter-H2H pairs and random inter-gene pairs.

Figure 6

Percentage of gene counts by number of co-expressed neighbors. Non-H2H genes are genes without H2H gene organization.