| 1. |
- Gonzalez Bosca, Alejandra, et al.
(författare)
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Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila
- 2019
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Ingår i: PloS Computational Biology. - : PUBLIC LIBRARY SCIENCE. - 1553-734X .- 1553-7358. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Complex eukaryotic promoters normally contain multiple cis-regulatory sequences for different transcription factors (TFs). The binding patterns of the TFs to these sites, as well as the way the TFs interact with each other and with the RNA polymerase (RNAp), lead to combinatorial problems rarely understood in detail, especially under varying epigenetic conditions. The aim of this paper is to build a model describing how the main regulatory cluster of the olfactory receptor Or59b drives transcription of this gene in Drosophila. The cluster-driven expression of this gene is represented as the equilibrium probability of RNAp being bound to the promoter region, using a statistical thermodynamic approach. The RNAp equilibrium probability is computed in terms of the occupancy probabilities of the single TFs of the cluster to the corresponding binding sites, and of the interaction rules among TFs and RNAp, using experimental data of Or59b expression to tune the model parameters. The model reproduces correctly the changes in RNAp binding probability induced by various mutation of specific sites and epigenetic modifications. Some of its predictions have also been validated in novel experiments.
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| 2. |
- Zenere, Alberto, 1992-
(författare)
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Integration of epigenetic, transcriptomic and proteomic data
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- One of the scopes of Systems Biology is to propose mathematical models that best capture the dynamic behavior of intra-cellular processes. In this regard, the last two decades have brought up a shift in the field, with technological advances now allowing researchers to access a wide range of high-throughput technologies at an affordable cost. These techniques allow to simultaneously interrogate thousands of variables, such as genome-wide transcriptomics and proteomics. However, parallel to these technological advances, there is a growing need for mathematical models that are suited to integrate measurements obtained from different cellular processes.In this thesis we aim to model combinations of three commonly used high-throughput data: epigenetic (namely ATAC-seq and DNA methylation), transcriptomic (RNA-seq) and proteomic data (MASS-spectrometry). In the first work we analyze paired ATAC-seq and RNA-seq data to integrate measurements of (i) chromatin openness, (ii) transcription factors (TFs) availability and (iii) gene expression. To model these data, we use elementary causal motifs, a class of mathematical models which is suited to represent causal interactions between three nodes. Indeed, our analysis shows that the elementary causal motifs in the data are enriched for biologically relevant TF-gene interactions. Moreover, a significant overlap is observed between the causal motifs identified in datasets representing similar cell stimuli, suggesting that causal motifs represent a robust biological signal.This work is then extended to include another class of high-throughput data: MASS-spectrometry. More precisely, we propose a framework to model the flow of events that goes from chromatin remodeling to splice variants expression, and from splice variants to protein synthesis. As the underlying graph becomes more complex than the previous case, a more general mathematical framework is considered: Bayesian networks. Interestingly, this work shows that most putative associations between chromatin regions, splice variants and proteins that have been gathered by scientific community so far, are supported by the data. Moreover, similarly to the previous work, the causal interactions identified in the data highlight relevant biological features; more precisely, causal chains between chromatin regions, splice variants and proteins are enriched for splice variants that have a major role in protein synthesis.From a technical point of view, causal motifs are characterized by a property known as conditional independence, which can be used to identify causal interactions in the data. However, particularly when the data available is limited, it is challenging to assess conditional independencies in the data. It is therefore of interest to investigate the existence of properties that allow us to predict conditional independence. In particular, in our work we propose two properties: structural balance and inverse balance, which are closely connected to what is known in the literature as positive association and multivariate total positivity of order 2 (MTP2), respectively. Our analysis shows that both heuristics are useful in predicting conditional independence, both from a theoretical perspective and in experimental data.Lastly, a network-based approach is used to integrate DNA methylation and RNA-seq in a case-control study centered around multiple sclerosis, in order to identify common regulatory patterns in DNA methylation and gene expression during the course of pregnancy. The strategy is based on the rationale that proteins that are interconnected in the protein-protein network are more likely to be involved in similar cellular functions. Indeed, the analysis highlights that similar pathways are altered at epigenetic and transcriptomic level, leading to a set of genes that are likely involved in the modification of the disease symptoms that is observed during pregnancy.
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| 3. |
- Zenere, Alberto, 1992-, et al.
(författare)
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Multi-omics protein-coding units as massively parallel Bayesian networks : Empirical validation of causality structure
- 2022
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Ingår i: iScience. - : Cell press. - 2589-0042. ; 25:4
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Tidskriftsartikel (refereegranskat)abstract
- In this article we use high-throughput epigenomics, transcriptomics, and proteomics data to construct fine-graded models of the "protein-coding units"gathering all transcript isoforms and chromatin accessibility peaks associated with more than 4000 genes in humans. Each protein-coding unit has the structure of a directed acyclic graph (DAG) and can be represented as a Bayesian network. The factorization of the joint probability distribution induced by the DAGs imposes a number of conditional independence relationships among the variables forming a protein-coding unit, corresponding to the missing edges in the DAGs. We show that a large fraction of these conditional independencies are indeed verified by the data. Factors driving this verification appear to be the structural and functional annotation of the transcript isoforms, as well as a notion of structural balance (or frustration-free) of the corresponding sample correlation graph, which naturally leads to reduction of correlation (and hence to independence) upon conditioning.
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| 4. |
- Zenere, Alberto, et al.
(författare)
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On the coupling of model predictive control and robust Kalman filtering
- 2018
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Ingår i: IET Control Theory & Applications. - : INST ENGINEERING TECHNOLOGY-IET. - 1751-8644 .- 1751-8652. ; 12:13, s. 1873-1881
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Tidskriftsartikel (refereegranskat)abstract
- Model predictive control (MPC) represents nowadays one of the main methods employed for process control in industry. Its strong suits comprise a simple algorithm based on a straightforward formulation and the flexibility to deal with constraints. On the other hand, it can be questioned its robustness regarding model uncertainties and external noises. Thus, a lot of efforts have been spent in the past years into the search of methods to address these shortcomings. In this study, the authors propose a robust MPC controller which stems from the idea of adding robustness in the prediction phase of the algorithm while leaving the core of MPC untouched. More precisely, they consider a robust Kalman filter that has been recently introduced and they further extend its usability to feedback control systems. Overall the proposed control algorithm allows to maintain all of the advantages of MPC with an additional improvement in performance and without any drawbacks in terms of computational complexity. To test the actual reliability of the algorithm, they apply it to control a servomechanism system characterised by non-linear dynamics.
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| 5. |
- Zenere, Alberto, et al.
(författare)
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Prominent epigenetic and transcriptomic changes in CD4(+) and CD8(+) T cells during and after pregnancy in women with multiple sclerosis and controls
- 2023
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Ingår i: Journal of Neuroinflammation. - : BMC. - 1742-2094. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundMultiple sclerosis (MS) is a neuroinflammatory disease in which pregnancy leads to a temporary amelioration in disease activity as indicated by the profound decrease in relapses rate during the 3rd trimester of pregnancy. CD4(+) and CD8(+) T cells are implicated in MS pathogenesis as being key regulators of inflammation and brain lesion formation. Although Tcells are prime candidates for the pregnancy-associated improvement of MS, the precise mechanisms are yet unclear, and in particular, a deep characterization of the epigenetic and transcriptomic events that occur in peripheral T cells during pregnancy in MS is lacking.MethodsWomen with MS and healthy controls were longitudinally sampled before, during (1st, 2nd and 3rd trimesters) and after pregnancy. DNA methylation array and RNA sequencing were performed on paired CD4(+) and CD8(+) T cells samples. Differential analysis and network-based approaches were used to analyze the global dynamics of epigenetic and transcriptomic changes.ResultsBoth DNA methylation and RNA sequencing revealed a prominent regulation, mostly peaking in the 3rd trimester and reversing post-partum, thus mirroring the clinical course with improvement followed by a worsening in disease activity. This rebound pattern was found to represent a general adaptation of the maternal immune system, with only minor differences between MS and controls. By using a network-based approach, we highlighted several genes at the core of this pregnancy-induced regulation, which were found to be enriched for genes and pathways previously reported to be involved in MS. Moreover, these pathways were enriched for in vitro stimulated genes and pregnancy hormones targets.ConclusionThis study represents, to our knowledge, the first in-depth investigation of the methylation and expression changes in peripheral CD4(+) and CD8(+) T cells during pregnancy in MS. Our findings indicate that pregnancy induces profound changes in peripheral T cells, in both MS and healthy controls, which are associated with the modulation of inflammation and MS activity.
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| 6. |
- Zenere, Alberto, et al.
(författare)
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Relating balance and conditional independence in graphical models
- 2022
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Ingår i: Physical review. E. - : American Physical Society. - 2470-0045 .- 2470-0053. ; 106:4
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Tidskriftsartikel (refereegranskat)abstract
- When data are available for all nodes of a Gaussian graphical model, then, it is possible to use sample correlations and partial correlations to test to what extent the conditional independencies that encode the structure of the model are indeed verified by the data. In this paper, we give a heuristic rule useful in such a validation process: When the correlation subgraph involved in a conditional independence is balanced (i.e., all its cycles have an even number of negative edges), then a partial correlation is usually a contraction of the corresponding correlation, which often leads to conditional independence. In particular, the contraction rule can be made rigorous if we look at concentration subgraphs rather than correlation subgraphs. The rule is applied to real data for elementary gene regulatory motifs.
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| 7. |
- Zenere, Alberto, et al.
(författare)
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Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs
- 2022
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 38:1, s. 173-178
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: The simultaneous availability of ATAC-seq and RNA-seq experiments allows to obtain a more in-depth knowledge on the regulatory mechanisms occurring in gene regulatory networks. In this article, we highlight and analyze two novel aspects that leverage on the possibility of pairing RNA-seq and ATAC-seq data. Namely we investigate the causality of the relationships between transcription factors, chromatin and target genes and the internal consistency between the two omics, here measured in terms of structural balance in the sample correlations along elementary length-3 cycles. Results: We propose a framework that uses the a priori knowledge on the data to infer elementary causal regulatory motifs (namely chains and forks) in the network. It is based on the notions of conditional independence and partial correlation, and can be applied to both longitudinal and non-longitudinal data. Our analysis highlights a strong connection between the causal regulatory motifs that are selected by the data and the structural balance of the underlying sample correlation graphs: strikingly, >97% of the selected regulatory motifs belong to a balanced subgraph. This result shows that internal consistency, as measured by structural balance, is close to a necessary condition for 3-node regulatory motifs to satisfy causality rules.
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