Multiple transcription factors contribute to inter-chromosomal interaction in yeast

Revealing Potential Genes Affecting Flocculation and/or Viability of Saccharomyces pastorianus by Comparative Genomic Analysis

Yeast flocculation and viability are critical factors in beer production. Adequate flocculation of yeast at the end of fermentation helps to reduce off-flavors and cell separation, while high viability is beneficial for yeast reuse. In this study, we used comparative genomics to analyze the genome information on Saccharomyces pastorianus W01, and its spontaneous mutant W02 with appropriate weakened flocculation ability (better off-flavor reduction performance) and unwanted decreased viability, to investigate the effect of different gene expressions on yeast flocculation or/and viability. Our results indicate that knockout of CNE1, CIN5, SIN3, HP-3, YPR170W-B, and SCEPF1_0274000100 and overexpression of CNE1 and ALD2 significantly decreased the flocculation ability of W01, while knockout of EPL1 increased the flocculation ability of W01. Meanwhile, knockout of CIN5, YPR170W-B, OST5, SFT1, SCEPF1_0274000100, and EPL1 and overexpression of SWC3, ALD2, and HP-2 decreased the viability of W01. CIN5, EPL1, SCEPF1_0274000100, ALD2, and YPR170W-B have all been shown to affect yeast flocculation ability and viability.

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

MOTIVATION

A growing amount of noncoding genetic variants, including single-nucleotide polymorphisms, are found to be associated with complex human traits and diseases. Their mechanistic interpretation is relatively limited and can use the help from computational prediction of their effects on epigenetic profiles. However, current models often focus on local, 1D genome sequence determinants and disregard global, 3D chromatin structure that critically affects epigenetic events.

RESULTS

We find that noncoding variants of unexpected high similarity in epigenetic profiles, with regards to their relatively low similarity in local sequences, can be largely attributed to their proximity in chromatin structure. Accordingly, we have developed a multimodal deep learning scheme that incorporates both data of 1D genome sequence and 3D chromatin structure for predicting noncoding variant effects. Specifically, we have integrated convolutional and recurrent neural networks for sequence embedding and graph neural networks for structure embedding despite the resolution gap between the two types of data, while utilizing recent DNA language models. Numerical results show that our models outperform competing sequence-only models in predicting epigenetic profiles and their use of long-range interactions complement sequence-only models in extracting regulatory motifs. They prove to be excellent predictors for noncoding variant effects in gene expression and pathogenicity, whether in unsupervised "zero-shot" learning or supervised "few-shot" learning.

AVAILABILITY AND IMPLEMENTATION

Codes and data can be accessed at https://github.com/Shen-Lab/ncVarPred-1D3D and https://zenodo.org/record/7975777.

Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica

Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions. To investigate the potential importance of distant contacts, we performed high-throughput chromatin conformation capture (Hi-C) experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea. We then combined our results with published Hi-C data from Arabidopsis thaliana. We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene. Genes with higher numbers of conserved noncoding sequences (CNSs) nearby were more likely to have contact with distant genes. With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity. In addition, for the genes we studied, distant contacting genes with CNSs were more likely to be transcriptionally coordinated. These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors, correlating with distant contacts to ensure coordinated expression. This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.

Three-Dimensional Genome Map of the Filamentous Fungus Penicillium oxalicum

Higher-order spatial organization of the chromatin in the nucleus plays crucial roles in the maintenance of cell functions and the regulation of gene expression. Three-dimensional (3D) genome sequencing has been used to great effect in mammal and plants, but the availability of 3D genomes of filamentous fungi is severely limited. Here, we performed a chromosome-level genome assembly of Penicillium oxalicum through single-molecule real-time sequencing (Pacific Biosciences) and chromatin interaction mapping (Hi-C), with a scaffold N50 of 4.07 Mb and a contig N50 of 3.81 Mb, and further elucidated the 3D genome architecture of P. oxalicum. High-frequency interchromosomal contacts occurred within the centromeres and telomeres, as well as within individual chromosomes. There were 12,203 cis-interactions and 7,884 trans-interactions detected at a resolution of 1 kb. Moreover, a total of 1,099 topologically associated domains (or globules) were found, ranging in size from 2.0 to 76.0 kb. Interestingly, transcription factor-bound motifs were enriched in the globule boundaries. All the cellulase and xylanase genes were discretely distributed in the 3D model of the P. oxalicum genome as a result of few cis- and trans-interactions. Our results from this study provide a global view of chromatin interactions in the P. oxalicum genome and will act as a resource for studying spatial regulation of gene expression in filamentous fungi. IMPORTANCE The spatial structure of chromatin plays important roles in normal cell functions and the regulation of gene expression. The three-dimensional (3D) architectures of the genomes of many mammals and plants have been elucidated, but corresponding studies on filamentous fungi, which play vital roles as decomposers of organic matter in the soil, are very limited. Penicillium oxalicum is one of the predominant cellulolytic aerobic fungi in subtropical and tropical forest soils and can secrete integrative cellulase and xylanase under integrated regulatory control, degrading plant biomass highly efficiently. In the present study, we employed Hi-C technology to construct the 3D genome model of P. oxalicum strain HP7-1 and to further investigate cellulase and xylanase as well as transcription factor genes in 3D genome. These results provide a resource to achieve a deeper understanding of cell function and the regulation of gene expression in filamentous fungi.

Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates inter-chromosomal movement

Hundreds of genes interact with the yeast nuclear pore complex (NPC), localizing at the nuclear periphery and clustering with co-regulated genes. Dynamic tracking of peripheral genes shows that they cycle on and off the NPC and that interaction with the NPC slows their sub-diffusive movement. Furthermore, NPC-dependent inter-chromosomal clustering leads to coordinated movement of pairs of loci separated by hundreds of nanometers. We developed fractional Brownian motion simulations for chromosomal loci in the nucleoplasm and interacting with NPCs. These simulations predict the rate and nature of random sub-diffusion during repositioning from nucleoplasm to periphery and match measurements from two different experimental models, arguing that recruitment to the nuclear periphery is due to random sub-diffusion and transient capture by NPCs. Finally, the simulations do not lead to inter-chromosomal clustering or coordinated movement, suggesting that interaction with the NPC is necessary, but not sufficient, to cause clustering.

RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture

Three-dimensional (3D) genome organization has emerged as an important layer of gene regulation in development and disease. The functional properties of chromatin folding within individual chromosomes (i.e., intra-chromosomal or in cis) have been studied extensively. On the other hand, interactions across different chromosomes (i.e., inter-chromosomal or in trans) have received less attention, being often regarded as background noise or technical artifacts. This viewpoint has been challenged by emerging evidence of functional relationships between specific trans chromatin interactions and epigenetic control, transcription, and splicing. Therefore, it is an intriguing possibility that the key processes involved in the biogenesis of RNAs may both shape and be in turn influenced by inter-chromosomal genome architecture. Here I present the rationale behind this hypothesis, and discuss a potential experimental framework aimed at its formal testing. I present a specific example in the cardiac myocyte, a well-studied post-mitotic cell whose development and response to stress are associated with marked rearrangements of chromatin topology both in cis and in trans. I argue that RNA polymerase II clusters (i.e., transcription factories) and foci of the cardiac-specific splicing regulator RBM20 (i.e., splicing factories) exemplify the existence of trans-interacting chromatin domains (TIDs) with important roles in cellular homeostasis. Overall, I propose that inter-molecular 3D proximity between co-regulated nucleic acids may be a pervasive functional mechanism in biology.

Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution

BACKGROUND

Chromosome conformation capture-based methods, especially Hi-C, enable scientists to detect genome-wide chromatin interactions and study the spatial organization of chromatin, which plays important roles in gene expression regulation, DNA replication and repair etc. Thus, developing computational methods to unravel patterns behind the data becomes critical. Existing computational methods focus on intrachromosomal interactions and ignore interchromosomal interactions partly because there is no prior knowledge for interchromosomal interactions and the frequency of interchromosomal interactions is much lower while the search space is much larger. With the development of single-cell technologies, the advent of single-cell Hi-C makes interrogating the spatial structure of chromatin at single-cell resolution possible. It also brings a new type of frequency information, the number of single cells with chromatin interactions between two disjoint chromosome regions.

RESULTS

Considering the lack of computational methods on interchromosomal interactions and the unsurprisingly frequent intrachromosomal interactions along the diagonal of a chromatin contact map, we propose a computational method dedicated to analyzing interchromosomal interactions of single-cell Hi-C with this new frequency information. To the best of our knowledge, our proposed tool is the first to identify regions with statistically frequent interchromosomal interactions at single-cell resolution. We demonstrate that the tool utilizing networks and binomial statistical tests can identify interesting structural regions through visualization, comparison and enrichment analysis and it also supports different configurations to provide users with flexibility.

CONCLUSIONS

It will be a useful tool for analyzing single-cell Hi-C interchromosomal interactions.

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: systems biology on diverse data types

Between June 10–12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics in 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics and systems biology. Systems biology has been a main theme in ICIBM 2018, with exciting advances presented in many areas of systems biology, covering various different data types such as gene regulation, circular RNAs expression, single-cell RNA-Seq, inter-chromosomal interactions, metabolomics, proteomics and phosphoproteomics. Here, we describe ten high quality papers to be published in BMC Systems Biology.