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The work described in this book is an excellent example of interdisciplinary research in systems biology. It shows how concepts and approaches from the field of physics can be efficiently used to answer biological questions, and reports on a novel methodology involving creative computer-based analyses of high-throughput biological data. Many of the findings described in the book, which are the result of collaborations between the author (a theoretical scientist) and experimental biologists, and between different laboratories, have been published in high-quality peer-reviewed journals such as Molecular Cell and Nature. However, while those publications address different aspects of post-transcriptional gene regulation, this book provides readers with a complete, coherent and logical view of the research project as a whole. The introduction presents post-transcriptional gene regulation from a distinct angle, highlighting aspects of information theory and evolution, and laying the groundwork for the questions addressed in the subsequent chapters, which concern the regulation of the transcriptome as the primary functional carrier of active genetic information.

Engineering. --- Gene expression. --- Biochemistry. --- Systems biology. --- Biological systems. --- Computational intelligence. --- Computational Intelligence. --- Biological Networks, Systems Biology. --- Gene Expression. --- Biochemistry, general. --- Intelligence, Computational --- Artificial intelligence --- Soft computing --- Biosystems --- Systems, Biological --- Biology --- System theory --- Systems biology --- Computational biology --- Bioinformatics --- Biological systems --- Molecular biology --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Medical sciences --- Genes --- Genetic regulation --- Construction --- Industrial arts --- Technology --- Philosophy --- Composition --- Expression --- RNA-protein interactions. --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Protein binding --- Systems Biology.

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The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel ‘protein occupancy profiling’ technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3’ UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universität Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.  .

Engineering. --- Biomedical Engineering. --- Systems Biology. --- Computational Biology/Bioinformatics. --- Bioinformatics. --- Biological models. --- Biomedical engineering. --- Ingénierie --- Bio-informatique --- Modèles biologiques --- Génie biomédical --- Health & Biological Sciences --- Biomedical Engineering --- RNA-protein interactions. --- RNA polymerases. --- DNA-dependent RNA polymerases --- DNA-directed RNA polymerases --- Polymerases, RNA --- Ribonucleate nucleotidyltransferases --- RNA nucleotidyltransferases --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Systems biology. --- Protein binding --- Transferases --- Biomedical Engineering and Bioengineering. --- Bio-informatics --- Biological informatics --- Biology --- Information science --- Computational biology --- Systems biology --- Models, Biological --- Clinical engineering --- Medical engineering --- Bioengineering --- Biophysics --- Engineering --- Medicine --- Data processing --- Bioinformatics --- Biological systems --- Molecular biology

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This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and other quantitative tools. This emerging field has begun to unravel the molecular underpinnings of how RNAs fulfill their multitude of roles in sustaining cellular life. The physical and chemical understanding of RNA biology that results from biophysical studies is critical to our ability to harness RNAs for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.

Biochemistry. --- Bioinformatics. --- Biomedical Engineering. --- Cytology. --- Medicine. --- Non-coding RNA. --- Physics. --- RNA-protein interactions. --- Molecular Probe Techniques --- Amino Acids, Peptides, and Proteins --- RNA --- Investigative Techniques --- Nucleic Acids --- Chemicals and Drugs --- Nucleic Acids, Nucleotides, and Nucleosides --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Proteins --- Protein Interaction Mapping --- RNA, Untranslated --- Human Anatomy & Physiology --- Biology --- Health & Biological Sciences --- Animal Biochemistry --- Biophysics --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- fRNA --- Functional RNA --- ncRNA --- nmRNA --- Non-messenger RNA --- Non-translated RNA --- Noncoding RNA --- Nontranslated RNA --- Small non-messenger RNA --- Small RNA --- snmRNA --- sRNA --- Untranslated RNA --- Life sciences. --- Human physiology. --- Molecular biology. --- Cell biology. --- Biophysics. --- Biological physics. --- Life Sciences. --- Biochemistry, general. --- Biophysics and Biological Physics. --- Human Physiology. --- Cell Biology. --- Molecular Medicine. --- Protein binding --- Biological and Medical Physics, Biophysics. --- Clinical sciences --- Medical profession --- Human biology --- Life sciences --- Medical sciences --- Pathology --- Physicians --- Cell biology --- Cellular biology --- Cells --- Cytologists --- Bio-informatics --- Biological informatics --- Information science --- Computational biology --- Systems biology --- Physiology --- Human body --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Data processing --- Composition --- Health Workforce --- Molecular biochemistry --- Molecular biophysics --- Biochemistry --- Biomolecules --- Biological physics --- Physics

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Disordered proteins are relatively recent newcomers in protein science. They were first described in detail by Wright and Dyson, in their J. Mol. Biol. paper in 1999. First, it was generally thought for more than a decade that disordered proteins or disordered parts of proteins have different amino acid compositions than folded proteins, and various prediction methods were developed based on this principle. These methods were suitable for distinguishing between the disordered (unstructured) and structured proteins known at that time. In addition, they could predict the site where a folded protein binds to the disordered part of a protein, shaping the latter into a well-defined 3D structure. Recently, however, evidence has emerged for a new type of disordered protein family whose members can undergo coupled folding and binding without the involvement of any folded proteins. Instead, they interact with each other, stabilizing their structure via “mutual synergistic folding” and, surprisingly, they exhibit the same residue composition as the folded protein. Increasingly more examples have been found where disordered proteins interact with non-protein macromolecules, adding to the already large variety of protein–protein interactions. There is also a very new phenomenon when proteins are involved in phase separation, which can represent a weak but functionally important macromolecular interaction. These phenomena are presented and discussed in the chapters of this book.

Research & information: general --- Biology, life sciences --- intrinsically disordered proteins --- epiproteome --- disordered protein platform --- molecular recognition feature --- post-translational modifications --- physiological homeostasis --- stress response --- RIN4 --- p53 --- molecular machines --- intrinsically disordered protein --- membrane-less organelle --- neurodegenerative disease --- p300 HAT acetylation --- post-translational modification --- protein aggregation --- Tau fibrillation --- intrinsically disorder proteins --- disorder-to-order regions --- protein–RNA interactions --- unstructured proteins --- conformational plasticity --- disordered protein --- folding --- ribosomal protein --- spectroscopy --- protein stability --- temperature response --- protein thermostability --- salt bridges --- meta strategy --- dual threshold --- significance voting --- decision tree based artificial neural network --- protein intrinsic disorder --- intrinsic disorder --- intrinsic disorder prediction --- intrinsically disordered region --- protein conformation --- transcriptome --- RNA sequencing --- Microarray --- differentially regulated genes --- gene ontology analysis --- functional analysis --- intrinsically disordered --- structural disorder --- correlated mutations --- co-evolution --- evolutionary couplings --- residue co-variation --- interaction surface --- residue contact network --- dehydron --- homodimer --- hydrogen bond --- inter-subunit interaction --- ion pair --- mutual synergistic folding --- solvent-accessible surface area --- stabilization center --- MLL proteins --- MLL4 --- lncRNA --- HOTAIR --- MEG3 --- leukemia --- histone lysine methyltransferase --- RNA binding --- protein --- hydration --- wide-line 1H NMR --- secretion --- immune --- extracellular --- protein-protein interaction --- structural domain --- evolution --- transcription factors --- DNA-protein interactions --- Sox2 sequential DNA loading --- smFRET --- DNA conformational landscape --- sequential DNA bending --- transcription factor dosage --- oligomer --- N-terminal prion protein --- copper binding --- prion disease mutations --- Nuclear pore complex --- FG-Nups --- phosphorylation --- coarse-grained --- CABS model --- MC simulations --- statistical force fields --- protein structure --- intrinsically disordered proteins (IDPs) --- neurodegenerative diseases --- aggregation --- drugs --- drug discovery --- plant virus --- eIF4E --- VPg --- potyvirus --- molten globule --- fluorescence anisotropy --- protein hydrodynamics --- intrinsically disordered proteins --- epiproteome --- disordered protein platform --- molecular recognition feature --- post-translational modifications --- physiological homeostasis --- stress response --- RIN4 --- p53 --- molecular machines --- intrinsically disordered protein --- membrane-less organelle --- neurodegenerative disease --- p300 HAT acetylation --- post-translational modification --- protein aggregation --- Tau fibrillation --- intrinsically disorder proteins --- disorder-to-order regions --- protein–RNA interactions --- unstructured proteins --- conformational plasticity --- disordered protein --- folding --- ribosomal protein --- spectroscopy --- protein stability --- temperature response --- protein thermostability --- salt bridges --- meta strategy --- dual threshold --- significance voting --- decision tree based artificial neural network --- protein intrinsic disorder --- intrinsic disorder --- intrinsic disorder prediction --- intrinsically disordered region --- protein conformation --- transcriptome --- RNA sequencing --- Microarray --- differentially regulated genes --- gene ontology analysis --- functional analysis --- intrinsically disordered --- structural disorder --- correlated mutations --- co-evolution --- evolutionary couplings --- residue co-variation --- interaction surface --- residue contact network --- dehydron --- homodimer --- hydrogen bond --- inter-subunit interaction --- ion pair --- mutual synergistic folding --- solvent-accessible surface area --- stabilization center --- MLL proteins --- MLL4 --- lncRNA --- HOTAIR --- MEG3 --- leukemia --- histone lysine methyltransferase --- RNA binding --- protein --- hydration --- wide-line 1H NMR --- secretion --- immune --- extracellular --- protein-protein interaction --- structural domain --- evolution --- transcription factors --- DNA-protein interactions --- Sox2 sequential DNA loading --- smFRET --- DNA conformational landscape --- sequential DNA bending --- transcription factor dosage --- oligomer --- N-terminal prion protein --- copper binding --- prion disease mutations --- Nuclear pore complex --- FG-Nups --- phosphorylation --- coarse-grained --- CABS model --- MC simulations --- statistical force fields --- protein structure --- intrinsically disordered proteins (IDPs) --- neurodegenerative diseases --- aggregation --- drugs --- drug discovery --- plant virus --- eIF4E --- VPg --- potyvirus --- molten globule --- fluorescence anisotropy --- protein hydrodynamics