EPD meeting, September 2016

Short talk Abstracts

A booklet with the short talk abstractsin can be downloaded here.

Poster Abstracts

1. Promoter-proximal transcripts: a genome-wide prediction and functional validation study

Sarah Natalia Mapelli, Sara Napoli, Giuseppina Pisignano, Giuseppina M. Carbone and Carlo V. Catapano

Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), and USI

Long noncoding RNAs (lncRNAs) are emerging as important players in the epigenetic machinery with key roles in development and diseases. Recent RNA-sequencing studies have revealed frequent low-abundance transcripts in the promoter regions that might act as cis-regulatory elements of the adjacent genes. However, the frequency and function of these promoter-proximal noncoding transcripts remain largely unknown. In this study we applied transcripts prediction strategies to a collection of global nuclear run-on sequencing (GRO-seq) datasets from human cell lines to perform a survey of promoter-proximal transcripts in the human genome. We discovered several promoters with promoter-proximal transcripts (≤2 kb from the gene transcription start site) and highly dynamic patterns of transcription both in the sense and antisense orientation relative to the neighboring genes in the cell lines examined. The diversity of the relationships between promoter-proximal transcripts and expression of the neighboring genes suggested their possible involvement in both transcriptional activation and silencing depending on the promoter and cell context. For selected genes the presence and orientation of the predicted promoter-proximal transcripts were confirmed by qRT-PCR and strand-specific RT-PCR in human prostate cell lines. Small interfering RNAs (siRNAs) were used next to target the promoter-proximal transcripts and assess their functional impact on the neighboring gene expression. Modulation of the adjacent genes was observed in a promoter transcript-dependent and cell-specific manner leading to either transcriptional activation or repression. Collectively, these findings demonstrate the widespread presence of sense and antisense promoter-proximal transcripts and provide evidence of their involvement in transcriptional gene regulation in a cell context dependent fashion. Understanding the contribution of promoter-proximal transcripts to epigenetic regulatory networks may uncover novel mechanisms of disease and provide the basis for novel epigenetic drug discovery.

2. Comparative analysis of transcriptomes and modular integrated networks across distant species reveal conserved biomarkers of physiological aging

Andrea Komljenovic and Marc Robinson-Rechavi

University of Lausanne

Despite abundant experiments and diverse data available to study aging, finding the robust pathways and networks involved in aging remains challenging. To tackle this, we are interested in evolutionarily conserved marks associated with aging, from short-lived model organisms to long-lived species. We combine cross-species and dietary restriction analyses, to study the level and mechanisms of conserved age-related co-expression changes. We performed comparative and network analysis of publicly available transcriptomes related to aging and dietary restriction from four species: H. sapiens, M. musculus, C. elegans and D. melanogaster. Meta-analysis across experiments of these species showed an overall down-regulation of gene expression profiles in old age. We found that age-related expression patterns across species occurred in oxidative-reduction, lipid metabolic process, catalytic activities and proteolysis. The aging effects at a single-gene levels showed weak positive correlation across species, but a stronger correlation at the gene-set level. We extended our gene-set level analysis by cross-species gene-set prioritization method in order to obtain more robust up- and down-regulated aging mechanisms. The prioritized gene-sets that are up-regulated in aging were related to centrosome, kinetochore and many types of junction regulation, while down-regulated confirmed previous results on mitochondrial-related gene-sets. We integrated different layers of biological information into networks and characterized the modules. These results implicate evolutionarily conserved mitochondrion and immune system related modules, and show consistent inverse effects of diet on aging across species.

3. Transcriptional regulatory mechanisms underlying rhythmic gene expression in mouse tissues

Jake Yeung, Jerome Mermet and Felix Naef


Mammalian organs schedule distinct functions at specific times of the day. This synchrony with the external environment uses the circadian clock, which ticks in nearly all cells of the body. Although distinct tissues share a common core clock circuitry, studies have shown that rhythmic gene expression is highly tissue-specific, the regulation of which is poorly understood. We used large-scale data integration and modeling to identify transcriptional regulators orchestrating tissue-wide and tissue-specific oscillations. This approach predicted a tissue-wide module of TF binding motifs whose oscillating activities were phase-coherent across tissues. Moreover, this module significantly extended the expected repertoire of known core clock regulators. Next, we predicted TF motifs with distinct temporal activity in different tissues, suggesting that single TFs binding at promoters could differentially regulate the same gene to generate tissue-specific rhythms. By contrast, we identified a subset of liver-rhythmic genes where concerted action between core clock and liver-specific TFs regulate rhythms at distal enhancers. Using 4C-Seq, we found that these enhancers can form dynamic chromatin loops with the promoter to output liver-specific rhythms. Our analysis suggests distinct roles in which promoters can play to regulate rhythmic gene expression.

4. The DNA pattern methodology for gene promoters

Paul Gagniuc

Institute of Diabetes, Nutrition and Metabolic Diseases ”N.C. Paulescu”, Romania

Promoter research may lead us to the edge of understanding the intimate and fundamental mechanisms of life. The observable effects of promoters in the overall homeostasis of the body are given by the expression of genes. However, the cause of gene expression is directly related to the promoter structure and the relationship between these short regions inside the cell nucleus. Unfortunately, today the trend of scientific investigations is more focused on the effect (gene expression) and less focused on the cause (structure and relationship between promoters inside the cell nucleus). Here, a novel approach for promoter research is brought to the scene, namely the DNA pattern method. One of the most fundamental observations made by using this method, concerned the gene promoters from Eukaryotic Promoter Database (EPD). This observation strongly suggested that many gene promoters which differ in the nucleotide arrangement, can accommodate the same genetic information (observation made by pattern similarity). New methods of analysis may be crucial in the near future. In terms of DNA analysis, a paradigm shift is waiting to happen, yet in a genomic era which has no end.

5. A functional genomics explorer for visualizing and comparing large amounts of ChIP-seq and related datasets retrieved in the public domain

Marco Antonio Mendoza Parra, Pierre-Etienne Cholley, Matthias Blum and Hinrich Gronemeyer


With the democratization of high throughput approaches, interrogating genome functions in a comprehensive manner will constitute in the following years the driving force for the development of personalized / predictive medicine. In fact, while data assessment is becoming largely accessible thanks to the democratization of massive parallel sequencing, the major challenge in the present big genomics data era resides in the necessity of developing computational solutions for interrogating huge numbers of datasets in a comparative manner. We have previously developed a quality control system dedicated to ChIP-sequencing and related datasets, which has been used for qualifying more than 38,000 publicly available data (www.ngs-qc.org). More recently, we have expanded the concept of quality assessment to long-range chromatin interaction assays, such that more than 250 publicly available HiC (including several variants of the original protocol, like in situ or capture HiC), but also several ChIA-PET (>50) and 4C-seq (>900) datasets were qualified and made available via a dedicated database: www.ngs-qc.org/logiqa. Here we present a functional genomics datasets explorer providing a large flexibility for the retrieval of publicly available datasets; access to their quality grades in a global and local manner, as well as to visualize their associated enrichment patterns. Furthermore, it provides computational solutions for multiple dataset comparisons in a large scale manner (several hundreds) and in either a global or local genomic context, such that datasets retrieved in a variety of studies could suddenly be integrated. For the first time, users may have the possibility of using the large amounts of public data as a resource for inferring predictions without requiring to download and preprocess the available raw data.

6. Predicting Zinc Finger Proteins Specificity

Alexandra Styliani Kalantzi, Alina Isakova, Bart Deplancke and Matteo Dal Peraro


DNA recognition by Zinc Finger Proteins (ZFPs) belonging to the KRAB (Krüppel Associated Box) family plays an important role in gene silencing. However, the molecular determinants defining the recognition of specific DNA nucleotides by the critical amino acids of the ZFP domains is not decoded. Here we propose a method that can predict (i) how ZFP repeats bind on their DNA consensus sequence and (ii) what is the most probable DNA target sequence. Our method is based on the analysis of the binding network of resolved structures of protein/DNA complexes, and is validated on a benchmark set of known solved ZFP/DNA complexes. We finally used our method to characterize the binding specificity of a set of KRAB-ZFPs integrating our predictions with new SMiLE-seq (Selective Microfluidics-based Ligand Enrichment - sequencing) data.

7. The regulatory complexity of the genome: The enhancer-promoter interaction model encoded by the transcription factors AP-1 and NF -Y

Martin Haubrock, Fabian Hartmann and Edgar Wingender

Institute of Bioformatics, University Medical Center Gottingen (UMG)

Transcription factors (TFs) are proteins that control gene expression through a variety of mechanisms such as enhancing the efficiency of the basal transcription complex to assemble or re-model chromatin. Most of them act by recognizing cis-regulatory elements or TF binding sites (TFBS) in gene proximal (promoter) or distal (enhancer) regions in a sequence-specific way. The ChIP-seq technology is widely used to systematically identify gene regulatory regions interacting with a known TF. In this work we show a novel regulatory relationship between the transcription factors c- Fos/AP-1 and NF-Y. We observe a clear distinction between c-Fos-bound enhancers, which exhibit a canonical AP-1 motif, and c-Fos-bound promoter regions, which are characterized by NF-Y-bound CCAAT boxes, preferably as a direct dimer with a distinct distance distribution. We believe that this particular promoter class can be found in ChIP-seq experiments because of a specific cross-linking between these interacting distal and proximal regions (enhanceosome structure).

8. Tandem repeats in promoters confer gene expression divergence

Tugce Bilgin Sonay and Andreas Wagner


Tandem Repeats (TRs) are repetetive DNA tracts, which are among the most variable loci. They experience much frequent mutations than point mutations, which makes them an important source of genetic variation. This also made genomic analyses of TRs challenging, which could be overcome only with recent advances in the sequencing and genotyping approaches. Many studies suggested that TR mutations can effect gene expression in a gradual and reversible manner, which raised the question whether TRs could be seen as evolutionary tuning knobs in gene regulation. To answer this question, we explored the impact of TRs on gene expression evolution in 13,035 one-to-one othologous genes in three species, human, chimpanzee and rhesus macaque (repeat unit length 2-50 base pairs). We found that on average 30% of these genes harbored TRs in their 5 kb upstream of transcription start sites, which were also significantly enriched for DNase hypersensitive sites. We used publicly available RNA-seq gene expression data to assess whether genes that contain TRs in their promoters have higher expression divergence than those that do not with a phylogenetic approach. We observed a significant association between repeats in gene promoters and increased expression divergence, an observation that was not explained by relaxed selection of those sequences. When changing the distance of the upstream regions considered, we found that repeat-containing genes diverged more rapidly in their expression, and this difference was most pronounced for repeats within 1 kbp upstream of the transcription start site. Our work showed for the first time in eukaryotes that TRs, a type of sequence with unusually high mutability, are a relevant class of regulatory mutations that might contribute to such species differences.