Genomic Insights into the Different Layers of Gene Regulation in Yeast

The model organism Saccharomyces cerevisiae has allowed the development of new functional genomics techniques devoted to the study of transcription in all its stages. With these techniques, it has been possible to find interesting new mechanisms to control gene expression that act at different levels and for different gene sets apart from the known cis-trans regulation in the transcription initiation step. Here we discuss a method developed in our laboratory, Genomic Run-On, and other new methods that have recently appeared with distinct technical features. A comparison between the datasets generated by them provides interesting genomic insights into the different layers of gene regulation in eukaryotes.

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Mechanisms of Nucleosome Reorganization by PARP1

International Journal of Molecular Sciences ◽

10.3390/ijms222212127 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12127

Author(s):

Natalya V. Maluchenko ◽

Dmitry K. Nilov ◽

Sergey V. Pushkarev ◽

Elena Y. Kotova ◽

Nadezhda S. Gerasimova ◽

...

Keyword(s):

Molecular Dynamics ◽

Dna Repair ◽

Gene Regulation ◽

Transcription Initiation ◽

Histone H1 ◽

Linker Histone ◽

Gene Promoters ◽

Linker Histone H1 ◽

Nucleosomal Dna ◽

Dna Ends

Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair, chromatin organization and transcription. During transcription initiation, PARP1 interacts with gene promoters where it binds to nucleosomes, replaces linker histone H1 and participates in gene regulation. However, the mechanisms of PARP1-nucleosome interaction remain unknown. Here, using spFRET microscopy, molecular dynamics and biochemical approaches we identified several different PARP1-nucleosome complexes and two types of PARP1 binding to mononucleosomes: at DNA ends and end-independent. Two or three molecules of PARP1 can bind to a nucleosome depending on the presence of linker DNA and can induce reorganization of the entire nucleosome that is independent of catalytic activity of PARP1. Nucleosome reorganization depends upon binding of PARP1 to nucleosomal DNA, likely near the binding site of linker histone H1. The data suggest that PARP1 can induce the formation of an alternative nucleosome state that is likely involved in gene regulation and DNA repair.

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Geomorphometric analysis of cave ceiling channels mapped with 3-D terrestrial laser scanning

Hydrology and Earth System Sciences ◽

10.5194/hess-20-1827-2016 ◽

2016 ◽

Vol 20 (5) ◽

pp. 1827-1849 ◽

Cited By ~ 14

Author(s):

Michal Gallay ◽

Zdenko Hochmuth ◽

Ján Kaňuk ◽

Jaroslav Hofierka

Keyword(s):

Laser Scanning ◽

Methodological Approach ◽

Terrestrial Laser Scanning ◽

Scalar Fields ◽

Complex Environments ◽

New Methods ◽

Digital Elevation ◽

Unique Manner ◽

Elevation Model ◽

Different Levels

Abstract. The change of hydrological conditions during the evolution of caves in carbonate rocks often results in a complex subterranean geomorphology, which comprises specific landforms such as ceiling channels, anastomosing half tubes, or speleothems organized vertically in different levels. Studying such complex environments traditionally requires tedious mapping; however, this is being replaced with terrestrial laser scanning technology. Laser scanning overcomes the problem of reaching high ceilings, providing new options to map underground landscapes with unprecedented level of detail and accuracy. The acquired point cloud can be handled conveniently with dedicated software, but applying traditional geomorphometry to analyse the cave surface is limited. This is because geomorphometry has been focused on parameterization and analysis of surficial terrain. The theoretical and methodological concept has been based on two-dimensional (2-D) scalar fields, which are sufficient for most cases of the surficial terrain. The terrain surface is modelled with a bivariate function of altitude (elevation) and represented by a raster digital elevation model. However, the cave is a 3-D entity; therefore, a different approach is required for geomorphometric analysis. In this paper, we demonstrate the benefits of high-resolution cave mapping and 3-D modelling to better understand the palaeohydrography of the Domica cave in Slovakia. This methodological approach adopted traditional geomorphometric methods in a unique manner and also new methods used in 3-D computer graphics, which can be applied to study other 3-D geomorphological forms.

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PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping

GigaScience ◽

10.1093/gigascience/giz088 ◽

2019 ◽

Vol 8 (8) ◽

Author(s):

Luis Francisco Hernández Sánchez ◽

Bram Burger ◽

Carlos Horro ◽

Antonio Fabregat ◽

Stefan Johansson ◽

...

Keyword(s):

Protein Interactions ◽

Posttranslational Modifications ◽

Knowledge Bases ◽

Protein Isoforms ◽

Biomedical Data ◽

Protein Protein Interactions ◽

Gene Sets ◽

Functional Knowledge ◽

Pathway Analyses ◽

Different Levels

Abstract Background Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and posttranslational modification states of proteins are lost when converting input and pathways into gene-centric lists. Findings Based on the Reactome knowledge base, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input and outputs the possibly affected biochemical reactions, subnetworks, and pathways. Conclusions PathwayMatcher enables refining the network representation of pathways by including proteoforms defined as protein isoforms with posttranslational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity, and it becomes possible to distinguish interactions between different forms of the same protein.

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σIfromBacillus subtilis: Impact on Gene Expression and Characterization of σI-Dependent Transcription That Requires New Types of Promoters with Extended −35 and −10 Elements

Journal of Bacteriology ◽

10.1128/jb.00251-18 ◽

2018 ◽

Vol 200 (17) ◽

Cited By ~ 4

Author(s):

Olga Ramaniuk ◽

Martin Převorovský ◽

Jiří Pospíšil ◽

Dragana Vítovská ◽

Olga Kofroňová ◽

...

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Iron Metabolism ◽

Transcription Initiation ◽

Iron Homeostasis ◽

Model Organism ◽

Content Type ◽

Σ Factor

ABSTRACTThe σIsigma factor fromBacillus subtilisis a σ factor associated with RNA polymerase (RNAP) that was previously implicated in adaptation of the cell to elevated temperature. Here, we provide a comprehensive characterization of this transcriptional regulator. By transcriptome sequencing (RNA-seq) of wild-type (wt) and σI-null strains at 37°C and 52°C, we identified ∼130 genes affected by the absence of σI. Further analysis revealed that the majority of these genes were affected indirectly by σI. The σIregulon, i.e., the genes directly regulated by σI, consists of 16 genes, of which eight (thedhbandykuoperons) are involved in iron metabolism. The involvement of σIin iron metabolism was confirmed phenotypically. Next, we set up anin vitrotranscription system and defined and experimentally validated the promoter sequence logo that, in addition to −35 and −10 regions, also contains extended −35 and −10 motifs. Thus, σI-dependent promoters are relatively information rich in comparison with most other promoters. In summary, this study supplies information about the least-explored σ factor from the industrially important model organismB. subtilis.IMPORTANCEIn bacteria, σ factors are essential for transcription initiation. Knowledge about their regulons (i.e., genes transcribed from promoters dependent on these σ factors) is the key for understanding how bacteria cope with the changing environment and could be instrumental for biotechnologically motivated rewiring of gene expression. Here, we characterize the σIregulon from the industrially important model Gram-positive bacteriumBacillus subtilis. We reveal that σIaffects expression of ∼130 genes, of which 16 are directly regulated by σI, including genes encoding proteins involved in iron homeostasis. Detailed analysis of promoter elements then identifies unique sequences important for σI-dependent transcription. This study thus provides a comprehensive view on this underexplored component of theB. subtilistranscription machinery.

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PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping

10.1101/375097 ◽

2018 ◽

Author(s):

Luis Francisco Hernández Sánchez ◽

Bram Burger ◽

Carlos Horro ◽

Antonio Fabregat ◽

Stefan Johansson ◽

...

Keyword(s):

Protein Interactions ◽

Biomedical Data ◽

Protein Protein Interactions ◽

Post Translational Modification ◽

Post Translational Modifications ◽

Network Construction ◽

Gene Sets ◽

Functional Knowledge ◽

Pathway Analyses ◽

Different Levels

AbstractBackgroundMapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers, e.g. gene sets, in pathway knowledgebases. However, the isoform and post-translational modification states of proteins are lost when converting input and pathways into gene-centric lists.FindingsBased on the Reactome knowledgebase, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input, and outputs the possibly affected biochemical reactions, subnetworks, and pathways.ConclusionsPathwayMatcher enables refining the network-representation of pathways by including isoform and post-translational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity and it becomes possible to distinguish interactions between different forms of the same protein.

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A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments

10.7287/peerj.preprints.934v1 ◽

2015 ◽

Cited By ~ 1

Author(s):

Nicholas A Bokulich ◽

Jai Ram Rideout ◽

Evguenia Kopylova ◽

Evan Bolyen ◽

Jessica Patnode ◽

...

Keyword(s):

Marker Gene ◽

Amplicon Sequencing ◽

Evaluation Framework ◽

Taxonomic Resolution ◽

Marker Genes ◽

Classification Methods ◽

New Methods ◽

Taxonomic Assignments ◽

Different Levels

Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms. Results: We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtime up to two-fold and achieve high precision genus-level assignments; an evaluation of classification methods that highlights differences in performance with different marker genes and at different levels of taxonomic resolution; and an extensible framework for evaluating and optimizing new classification methods, which we hope will serve as a model for standardized and reproducible bioinformatics methods evaluations. Conclusions: Our new methods are accessible in QIIME 1.9.0, and our evaluation framework will support ongoing optimization of classification methods to complement rapidly evolving short-amplicon sequencing and bioinformatics technologies. Static versions of all of the analysis notebooks generated with this framework, which contain all code and analysis results, can be viewed at http://bit.ly/srta-010.

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New Approaches for Quantitative Reconstruction of Radiation Dose in Human Blood Cells

10.1101/640052 ◽

2019 ◽

Cited By ~ 2

Author(s):

Shanaz A. Ghandhi ◽

Igor Shuryak ◽

Shad R. Morton ◽

Sally A. Amundson ◽

David J. Brenner

Keyword(s):

Radiation Dose ◽

Mean Squared Error ◽

Data Sets ◽

Reconstruction Method ◽

Dose Reconstruction ◽

New Methods ◽

Rapid Assays ◽

Squared Error ◽

Gene Sets ◽

Human Blood Cells

AbstractIn the event of a nuclear attack or radiation event, there would be an urgent need for assessing and reconstructing the dose to which hundreds or thousands of individuals were exposed. These measurements would need a rapid assay to facilitate triage and medical management for individuals based on dose. Our approaches to development of rapid assays for reconstructing dose, using transcriptomics, have led to identification of gene sets that have potential to be used in the field; but need further testing. This was a proof-of-principle study for new methods using radiation-responsive genes to generate quantitative, rather than categorical, radiation-dose reconstructions based on a blood sample. We used a new normalization method to reduce effects of variability of gene signals in unirradiated samples across studies; developed a quantitative dose-reconstruction method that is generally under-utilized compared to categorical methods; and combined these to determine a gene-set as a reconstructor. Our dose-reconstruction biomarker was trained on two data sets and tested on two independent ones. It was able to predict dose up to 4.5 Gy with root mean squared error (RMSE) of ± 0.35 Gy on test datasets (same platform), and up to 6.0 Gy with RMSE of 1.74 Gy on another (different platform).

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Enhancers predominantly regulate gene expression in vivo via transcription initiation

10.1101/844191 ◽

2019 ◽

Author(s):

Martin S. C. Larke ◽

Takayuki Nojima ◽

Jelena Telenius ◽

Jacqueline A. Sharpe ◽

Jacqueline A. Sloane-Stanley ◽

...

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Transcription Initiation ◽

Genetically Engineered ◽

Control Gene ◽

Transcriptional Initiation ◽

Pol Ii ◽

Rna Molecules ◽

Control Gene Expression

ABSTRACTGene transcription occurs via a cycle of linked events including initiation, promoter proximal pausing and elongation of RNA polymerase II (Pol II). A key question is how do transcriptional enhancers influence these events to control gene expression? Here we have used a new approach to quantify transcriptional initiation and pausing in vivo, while simultaneously identifying transcription start sites (TSSs) and pause-sites (TPSs) from single RNA molecules. When analyzed in parallel with nascent RNA-seq, these data show that differential gene expression is achieved predominantly via changes in transcription initiation rather than Pol II pausing. Using genetically engineered mouse models deleted for specific enhancers we show that these elements control gene expression via Pol II recruitment and/or initiation rather than via promoter proximal pause release. Together, our data show that enhancers, in general, control gene expression predominantly by Pol II recruitment and initiation rather than via pausing.

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Spatial Organization of the Gene Regulatory Program: An Information Theoretical Approach to Breast Cancer Transcriptomics

Entropy ◽

10.3390/e21020195 ◽

2019 ◽

Vol 21 (2) ◽

pp. 195 ◽

Cited By ~ 5

Author(s):

Guillermo de Anda-Jáuregui ◽

Jesús Espinal-Enriquez ◽

Enrique Hernández-Lemus

Keyword(s):

Breast Cancer ◽

Gene Regulation ◽

Spatial Organization ◽

Spatial Relationship ◽

Information Theoretic ◽

Gene Regulatory ◽

Trans Regulation ◽

Cis And Trans ◽

Biological State ◽

Trans Gene

Gene regulation may be studied from an information-theoretic perspective. Gene regulatory programs are representations of the complete regulatory phenomenon associated to each biological state. In diseases such as cancer, these programs exhibit major alterations, which have been associated with the spatial organization of the genome into chromosomes. In this work, we analyze intrachromosomal, or cis-, and interchromosomal, or trans-gene regulatory programs in order to assess the differences that arise in the context of breast cancer. We find that using information theoretic approaches, it is possible to differentiate cis-and trans-regulatory programs in terms of the changes that they exhibit in the breast cancer context, indicating that in breast cancer there is a loss of trans-regulation. Finally, we use these programs to reconstruct a possible spatial relationship between chromosomes.

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