Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions

Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.

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CLUSTERING BIOLOGICAL ANNOTATIONS AND GENE EXPRESSION DATA TO IDENTIFY PUTATIVELY CO-REGULATED BIOLOGICAL PROCESSES

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720006002181 ◽

2006 ◽

Vol 04 (04) ◽

pp. 833-852 ◽

Cited By ~ 16

Author(s):

CORNELIU HENEGAR ◽

RAFFAELLA CANCELLO ◽

SOPHIE ROME ◽

HUBERT VIDAL ◽

KARINE CLÉMENT ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Data ◽

Regulation Of Gene Expression ◽

Muscular Contraction ◽

Supplementary Information ◽

Biological Processes ◽

Expression Data ◽

Biological Interactions ◽

Microarray Gene Expression ◽

Data Set

Motivation: Functional profiling is a key step of microarray gene expression data analysis. Identifying co-regulated biological processes could help for better understanding of underlying biological interactions within the studied biological frame. Results: We present herein an original approach designed to search for putatively co-regulated biological processes sharing a significant number of co-expressed genes. An R language implementation named "FunCluster" was built and tested on two gene expression data sets. A discriminatory functional analysis of the first data set, related to experiments performed on separated adipocytes and stroma vascular fraction cells of human white adipose tissue, highlighted the prevalent role of nonadipose cells in the synthesis of inflammatory and immunity molecules in human adiposity. On the second data set, resulting from a model investigating insulin coordinated regulation of gene expression in human skeletal muscle, FunCluster analysis spotlighted novel functional classes of putatively co-regulated biological processes related to protein metabolism and the regulation of muscular contraction. Availability: Supplementary information about the FunCluster tool is available on-line at .

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Review of Progress in Predicting Protein Methylation Sites

Current Organic Chemistry ◽

10.2174/1385272823666190723141347 ◽

2019 ◽

Vol 23 (15) ◽

pp. 1663-1670 ◽

Cited By ~ 1

Author(s):

Chunyan Ao ◽

Shunshan Jin ◽

Yuan Lin ◽

Quan Zou

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Transcriptional Activity ◽

Regulation Of Gene Expression ◽

Protein Methylation ◽

Biological Processes ◽

Post Translational Modification ◽

Regulatory Enzymes ◽

Lysine Residues ◽

Arginine Residues

Protein methylation is an important and reversible post-translational modification that regulates many biological processes in cells. It occurs mainly on lysine and arginine residues and involves many important biological processes, including transcriptional activity, signal transduction, and the regulation of gene expression. Protein methylation and its regulatory enzymes are related to a variety of human diseases, so improved identification of methylation sites is useful for designing drugs for a variety of related diseases. In this review, we systematically summarize and analyze the tools used for the prediction of protein methylation sites on arginine and lysine residues over the last decade.

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Hypoxia Transcriptomic Modifications Induced by Proton Irradiation in U87 Glioblastoma Multiforme Cell Line

Journal of Personalized Medicine ◽

10.3390/jpm11040308 ◽

2021 ◽

Vol 11 (4) ◽

pp. 308

Author(s):

Valentina Bravatà ◽

Walter Tinganelli ◽

Francesco P. Cammarata ◽

Luigi Minafra ◽

Marco Calvaruso ◽

...

Keyword(s):

Glioblastoma Multiforme ◽

Cell Line ◽

Acute Hypoxia ◽

Hypoxic Condition ◽

Biological Processes ◽

Microarray Gene Expression ◽

Hypoxic Conditions ◽

Gene Expression Analyses ◽

Shed Light ◽

New Strategies

In Glioblastoma Multiforme (GBM), hypoxia is associated with radioresistance and poor prognosis. Since standard GBM treatments are not always effective, new strategies are needed to overcome resistance to therapeutic treatments, including radiotherapy (RT). Our study aims to shed light on the biomarker network involved in a hypoxic (0.2% oxygen) GBM cell line that is radioresistant after proton therapy (PT). For cultivating cells in acute hypoxia, GSI’s hypoxic chambers were used. Cells were irradiated in the middle of a spread-out Bragg peak with increasing PT doses to verify the greater radioresistance in hypoxic conditions. Whole-genome cDNA microarray gene expression analyses were performed for samples treated with 2 and 10 Gy to highlight biological processes activated in GBM following PT in the hypoxic condition. We describe cell survival response and significant deregulated pathways responsible for the cell death/survival balance and gene signatures linked to the PT/hypoxia configurations assayed. Highlighting the molecular pathways involved in GBM resistance following hypoxia and ionizing radiation (IR), this work could suggest new molecular targets, allowing the development of targeted drugs to be suggested in association with PT.

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Transcription Factors as the “Blitzkrieg” of Plant Defense: A Pragmatic View of Nitric Oxide’s Role in Gene Regulation

International Journal of Molecular Sciences ◽

10.3390/ijms22020522 ◽

2021 ◽

Vol 22 (2) ◽

pp. 522

Author(s):

Noreen Falak ◽

Qari Muhammad Imran ◽

Adil Hussain ◽

Byung-Wook Yun

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Plant Defense ◽

Systemic Acquired Resistance ◽

Defense Mechanism ◽

Regulation Of Gene Expression ◽

Acquired Resistance ◽

Biological Processes ◽

Genetic Components ◽

Transcriptional Changes

Plants are in continuous conflict with the environmental constraints and their sessile nature demands a fine-tuned, well-designed defense mechanism that can cope with a multitude of biotic and abiotic assaults. Therefore, plants have developed innate immunity, R-gene-mediated resistance, and systemic acquired resistance to ensure their survival. Transcription factors (TFs) are among the most important genetic components for the regulation of gene expression and several other biological processes. They bind to specific sequences in the DNA called transcription factor binding sites (TFBSs) that are present in the regulatory regions of genes. Depending on the environmental conditions, TFs can either enhance or suppress transcriptional processes. In the last couple of decades, nitric oxide (NO) emerged as a crucial molecule for signaling and regulating biological processes. Here, we have overviewed the plant defense system, the role of TFs in mediating the defense response, and that how NO can manipulate transcriptional changes including direct post-translational modifications of TFs. We also propose that NO might regulate gene expression by regulating the recruitment of RNA polymerase during transcription.

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Function of cofactor Akirin2 in the regulation of gene expression in model human Caucasian neutrophil-like HL60 cells

Bioscience Reports ◽

10.1042/bcj20210294 ◽

2021 ◽

Author(s):

Sara Artigas-Jerónimo ◽

Margarita Villar ◽

Agustín Estrada-Peña ◽

Adrián Velázquez-Campoy ◽

Pilar Alberdi ◽

...

Keyword(s):

Gene Expression ◽

Neural Development ◽

Transcriptional Activation ◽

Regulation Of Gene Expression ◽

Regulatory Function ◽

Biological Processes ◽

Protein Targets ◽

Chromatin Remodelers ◽

Hl60 Cells ◽

Associated Proteins

The Akirin family of transcription cofactors are involved throughout the metazoan in the regulation of different biological processes such as immunity, interdigital regression, muscle and neural development. Akirin do not have catalytic or DNA-binding capability and exert its regulatory function primarily through interacting proteins such as transcription factors, chromatin remodelers, and RNA-associated proteins. In this study, we focused on the human Akirin2 regulome and interactome in neutrophil-like model human Caucasian promyelocytic leukemia HL60 cells. Our hypothesis is that metazoan evolved to have Akirin2 functional complements and different Akirin2-mediated mechanisms for the regulation of gene expression. To address this hypothesis, experiments were conducted using transcriptomics, proteomics and systems biology approaches in akirin2 knockdown and wildtype HL60 cells to characterize Akirin2 gene/protein targets, functional complements and to provide evidence of different mechanisms that may be involved in Akirin2-mediated regulation of gene expression. The results revealed Akirin2 gene/protein targets in multiple biological processes with higher representation of immunity and identified immune response genes as candidate Akirin2 functional complements. In addition to linking chromatin remodelers with transcriptional activation, Akirin2 also interacts with histone H3.1 for regulation of gene expression.

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Use of SciDBMaker as Tool for the Design of Specialized Biological Databases

Visual Analytics and Interactive Technologies ◽

10.4018/978-1-60960-102-7.ch015 ◽

2011 ◽

pp. 251-265 ◽

Cited By ~ 1

Author(s):

Riadh Hammami ◽

Ismail Fliss

Keyword(s):

Molecular Biology ◽

Best Practices ◽

Exponential Growth ◽

Protein Sequence ◽

Knowledge Bases ◽

Biological Processes ◽

Biological Databases ◽

Experimental Findings ◽

Biology Research

The exponential growth of molecular biology research in recent decades has brought concomitant growth in the number and size of genomic and proteomic databases used to interpret experimental findings. Particularly, growth of protein sequence records created the need for smaller and manually annotated databases. Since scientists are continually developing new specific databases to enhance their understanding of biological processes, the authors created SciDBMaker to provide a tool for easy building of new specialized protein knowledge bases. This chapter also suggests best practices for specialized biological databases design, and provides examples for the implementation of these practices.

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Redox Homeostasis and Metabolism in Cancer: A Complex Mechanism and Potential Targeted Therapeutics

International Journal of Molecular Sciences ◽

10.3390/ijms21093100 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3100 ◽

Cited By ~ 1

Author(s):

Alia Ghoneum ◽

Ammar Yasser Abdulfattah ◽

Bailey Olivia Warren ◽

Junjun Shu ◽

Neveen Said

Keyword(s):

Cancer Cells ◽

Cancer Progression ◽

Metabolic Pathways ◽

Redox Homeostasis ◽

Ros Production ◽

Biological Processes ◽

Survival Pathways ◽

Oncogenic Mutations ◽

And Oxidative Stress ◽

Shed Light

Reactive Oxygen Species or “ROS” encompass several molecules derived from oxygen that can oxidize other molecules and subsequently transition rapidly between species. The key roles of ROS in biological processes are cell signaling, biosynthetic processes, and host defense. In cancer cells, increased ROS production and oxidative stress are instigated by carcinogens, oncogenic mutations, and importantly, metabolic reprograming of the rapidly proliferating cancer cells. Increased ROS production activates myriad downstream survival pathways that further cancer progression and metastasis. In this review, we highlight the relation between ROS, the metabolic programing of cancer, and stromal and immune cells with emphasis on and the transcription machinery involved in redox homeostasis, metabolic programing and malignant phenotype. We also shed light on the therapeutic targeting of metabolic pathways generating ROS as we investigate: Orlistat, Biguandes, AICAR, 2 Deoxyglucose, CPI-613, and Etomoxir.

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Patterns of Locomotor Drive to Motoneurons and Last-Order Interneurons: Clues to the Structure of the CPG

Journal of Neurophysiology ◽

10.1152/jn.2001.86.1.447 ◽

2001 ◽

Vol 86 (1) ◽

pp. 447-462 ◽

Cited By ~ 105

Author(s):

R. E. Burke ◽

A. M. Degtyarenko ◽

E. S. Simon

Keyword(s):

Fictive Locomotion ◽

Cutaneous Reflex ◽

Reflex Pathways ◽

Locomotor Control ◽

Low Threshold ◽

Experimental Findings ◽

Differential Control ◽

Flexor Digitorum ◽

First Time ◽

Shed Light

We have examined the linkage between patterns of activity in several hindlimb motor pools and the modulation of oligosynaptic cutaneous reflex pathways during fictive locomotion in decerebrate unanesthetized cats to assess the notion that such linkages can shed light on the structure of the central pattern generator (CPG) for locomotion. We have concentrated attention on the cutaneous reflex pathways that project to the flexor digitorum longus (FDL) motor pool because of that muscle's unique variable behavior during normal and fictive locomotion in the cat. Differential locomotor control of last-order excitatory interneurons in pathways from low-threshold cutaneous afferents in the superficial peroneal and medial plantar afferents to FDL motoneurons is fully documented for the first time. The qualitative patterns of differential control are shown to remain the same whether the FDL muscle is active in early flexion, as usually found, or during the extension phase of fictive locomotion, which is less common during fictive stepping. The patterns of motor pool activity and of reflex pathway modulation indicate that the flexion phase of fictive locomotion has distinct early versus late components. Observations during “normal” and unusual patterns of fictive stepping suggest that some aspects of locomotor pattern formation can be separated from rhythm generation, implying that these two CPG functions may be embodied, at least in part, in distinct neural organizations. The results are discussed in relation to a provisional circuit diagram that could explain the experimental findings.

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Hydrodynamics of flagellated microswimmers near free-slip interfaces

Journal of Fluid Mechanics ◽

10.1017/jfm.2015.738 ◽

2016 ◽

Vol 789 ◽

pp. 514-533 ◽

Cited By ~ 27

Author(s):

D. Pimponi ◽

M. Chinappi ◽

P. Gualtieri ◽

C. M. Casciola

Keyword(s):

Numerical Solutions ◽

Stokes Equations ◽

Slip Surface ◽

Initial Conditions ◽

Aerobic Bacteria ◽

Slip Boundary ◽

Experimental Findings ◽

Micro Organisms ◽

Air Interfaces ◽

Shed Light

The hydrodynamics of a flagellated micro-organism is investigated when swimming close to a planar free-slip surface by means of numerical solutions of the Stokes equations obtained via a boundary element method. Depending on the initial conditions, the swimmer can either escape from the free-slip surface or collide with the boundary. Interestingly, the micro-organism does not exhibit a stable orbit. Independently of escape or attraction to the interface, close to a free-slip surface, the swimmer follows a counter-clockwise trajectory, in agreement with experimental findings (Di Leonardo et al., Phys. Rev. Lett., vol. 106 (3), 2011, 038101). The hydrodynamics is indeed modified by the free surface. In fact, when the same swimmer moves close to a no-slip wall, a set of initial conditions exists which result in stable orbits. Moreover, when moving close to a free-slip or a no-slip boundary, the swimmer assumes a different orientation with respect to its trajectory. Taken together, these results contribute to shed light on the hydrodynamical behaviour of micro-organisms close to liquid–air interfaces which are relevant for the formation of interfacial biofilms of aerobic bacteria.

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The chicken model organism for epigenomic research

Genome ◽

10.1139/gen-2020-0129 ◽

2020 ◽

Author(s):

Tasnim H. BEACON ◽

James R DAVIE

Keyword(s):

High Throughput Sequencing ◽

Chicken Genome ◽

Regulation Of Gene Expression ◽

Model Organism ◽

Bioinformatic Tools ◽

Sequencing Technologies ◽

Trace Back ◽

Human Orthologs ◽

Genomic Studies ◽

Chicken Model

The chicken model organism has advanced the areas of developmental biology, virology, immunology, oncology, epigenetic regulation of gene expression, conservation biology, and genomics of domestication. Further, the chicken model organism has aided in our understanding of human disease. Through the recent advances in high-throughput sequencing and bioinformatic tools, researchers have successfully identified sequences in the chicken genome that have human orthologs, improving mammalian genome annotation. In this review, we highlight the importance of chicken as an animal model in basic and pre-clinical research. We will present the importance of chicken in poultry epigenetics and in genomic studies that trace back to their ancestor, the last link between human and chicken tree of life. There are still many genes of unknown function in the chicken genome yet to be characterized. By taking advantage of recent sequencing technologies, it is possible to gain further insight into the chicken epigenome.

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