Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster

Apoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The large diversity of regulators of apoptosis in mammalian cells and their numerous interactions complicate the analysis of their individual functions, particularly in development. The remarkable conservation of apoptotic mechanisms across species has allowed the genetic pathways of apoptosis determined in lower species, such as the nematode Caenorhabditis elegans and the fruitfly Drosophila melanogaster, to act as models for understanding the biology of apoptosis in mammalian cells. Though many components of the apoptotic pathway are conserved between species, the use of additional model organisms has revealed several important differences and supports the use of model organisms in deciphering complex biological processes such as apoptosis.

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Sex and tissue‐specific evolution of developmental plasticity in Drosophila melanogaster

Ecology and Evolution ◽

10.1002/ece3.7136 ◽

2020 ◽

Author(s):

Didem P. Sarikaya ◽

Katherine Rickelton ◽

Julie M. Cridland ◽

Ryan Hatmaker ◽

Hayley K. Sheehy ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Developmental Plasticity ◽

Tissue Specific

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Three-dimensional organization of Drosophila melanogaster interphase nuclei. I. Tissue-specific aspects of polytene nuclear architecture.

The Journal of Cell Biology ◽

10.1083/jcb.104.6.1455 ◽

1987 ◽

Vol 104 (6) ◽

pp. 1455-1470 ◽

Cited By ~ 78

Author(s):

M Hochstrasser ◽

J W Sedat

Keyword(s):

Drosophila Melanogaster ◽

Three Dimensional ◽

Nuclear Architecture ◽

Close Packing ◽

Prothoracic Gland ◽

Cell Type ◽

Interphase Chromosome ◽

Tissue Specific ◽

Spatial Domains ◽

Four Levels

Interphase chromosome organization in four different Drosophila melanogaster tissues, covering three to four levels of polyteny, has been analyzed. The results are based primarily on three-dimensional reconstructions from unfixed tissues using a computer-based data collection and modeling system. A characteristic organization of chromosomes in each cell type is observed, independent of polyteny, with some packing motifs common to several or all tissues and others tissue-specific. All chromosomes display a right-handed coiling chirality, despite large differences in size and degree of coiling. Conversely, in each cell type, the heterochromatic centromeric regions have a unique structure, tendency to associate, and intranuclear location. The organization of condensed nucleolar chromatin is also tissue-specific. The tightly coiled prothoracic gland chromosomes are arrayed in a similar fashion to the much larger salivary gland chromosomes described previously, having polarized orientations, nonintertwined spatial domains, and close packing of the arms of each autosome, whereas hindgut and especially the unusually straight midgut chromosomes display striking departures from these regularities. Surprisingly, gut chromosomes often appear to be broken in the centric heterochromatin. Severe deformations of midgut nuclei observed during gut contractions in living larvae may account for their unusual properties. Finally, morphometric measurements of chromosome and nuclear dimensions provide insights into chromosome growth and substructure and also suggest an unexpected parallel with diploid chromatin organization.

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Classification of topological domains based on gene expression and regulation

Genome ◽

10.1139/gen-2013-0111 ◽

2013 ◽

Vol 56 (7) ◽

pp. 415-423 ◽

Cited By ~ 2

Author(s):

Jingjing Zhao ◽

Hongbo Shi ◽

Nadav Ahituv

Keyword(s):

Gene Expression ◽

Gene Ontology ◽

Tissue Type ◽

Specific Gene ◽

Gene Expression And Regulation ◽

Genome Chromosome ◽

Chromosome Conformation ◽

Topological Domains ◽

Tissue Specific ◽

Mouse Tissues

Tissue-specific gene expression is thought to be one of the major forces shaping mammalian gene order. A recent study that used whole-genome chromosome conformation assays has shown that the mammalian genome is divided into specific topological domains that are shared between different tissues and organisms. Here, we wanted to assess whether gene expression and regulation are involved in shaping these domains and can be used to classify them. We analyzed gene expression and regulation levels in these domains by using RNA-seq and enhancer-associated ChIP-seq datasets for 17 different mouse tissues. We found 162 domains that are active (high gene expression and regulation) in all 17 tissues. These domains are significantly shorter, contain less repeats, and have more housekeeping genes. In contrast, we found 29 domains that are inactive (low gene expression and regulation) in all analyzed tissues and are significantly longer, have more repeats, and gene deserts. Tissue-specific active domains showed some correlation with tissue-type and gene ontology. Domain temporal gene regulation and expression differences also displayed some gene ontology terms fitting their temporal function. Combined, our results provide a catalog of shared and tissue-specific topological domains and suggest that gene expression and regulation could have a role in shaping them.

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Highly Tissue Specific Expression of Sphinx Supports Its Male Courtship Related Role in Drosophila melanogaster

PLoS ONE ◽

10.1371/journal.pone.0018853 ◽

2011 ◽

Vol 6 (4) ◽

pp. e18853 ◽

Cited By ~ 17

Author(s):

Ying Chen ◽

Hongzheng Dai ◽

Sidi Chen ◽

Luoying Zhang ◽

Manyuan Long

Keyword(s):

Drosophila Melanogaster ◽

Male Courtship ◽

Specific Expression ◽

Tissue Specific ◽

Tissue Specific Expression

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Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

10.1101/469569 ◽

2018 ◽

Author(s):

Valerie Wood ◽

Antonia Lock ◽

Midori A. Harris ◽

Kim Rutherford ◽

Jürg Bähler ◽

...

Keyword(s):

Gene Ontology ◽

Fission Yeast ◽

Genome Sequencing ◽

Large Scale ◽

Biological Process ◽

Blind Spot ◽

Model Organisms ◽

Biological Processes ◽

Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

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A novel, tissue-specific integrin subunit, beta nu, expressed in the midgut of Drosophila melanogaster

Development ◽

10.1242/dev.118.3.845 ◽

1993 ◽

Vol 118 (3) ◽

pp. 845-858 ◽

Cited By ~ 7

Author(s):

G.H. Yee ◽

R.O. Hynes

Keyword(s):

Drosophila Melanogaster ◽

Matrix Proteins ◽

Beta Subunits ◽

Integrin Subunit ◽

Integrin Receptor ◽

Tissue Specific ◽

Surface Receptors ◽

Polymerase Chain ◽

Maximal Expression

The integrins are a family of cell surface receptors for extracellular matrix proteins and counter-receptors on other cells. We have used the polymerase chain reaction to identify a novel integrin receptor beta subunit in Drosophila melanogaster. The deduced amino acid sequence of this subunit, which we have termed beta v (beta-neu), indicates that it has several unusual properties. The beta v subunit is roughly 33% identical with each of the previously sequenced vertebrate and Drosophila beta subunits and is lacking four of the 56 cysteine residues characteristic of most members of this protein family. The expression of the beta v gene is strikingly restricted. It is temporally regulated, with maximal expression occurring at 12–15 hours of embryonic development. In situ hybridization analyses and antibody localization on whole-mount embryos reveal that beta v expression is tissue-specific and confined to the developing midgut endoderm and its precursors during embryogenesis. Tissue specificity of expression is maintained through later stages of development as beta v transcripts are found exclusively in the larval midgut. Within this structure, beta v transcripts are especially concentrated in the cells of the midgut imaginal islands which give rise to the adult midgut.

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Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Open Biology ◽

10.1098/rsob.200149 ◽

2020 ◽

Vol 10 (9) ◽

pp. 200149 ◽

Cited By ~ 1

Author(s):

Valerie Wood ◽

Seth Carbon ◽

Midori A. Harris ◽

Antonia Lock ◽

Stacia R. Engel ◽

...

Keyword(s):

Quality Control ◽

Gene Ontology ◽

Biological Processes ◽

Gene Products ◽

Model Species ◽

Ontology Term ◽

Protein Coding ◽

Ontology Structure ◽

Exclusive Processes ◽

Annotation Quality

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

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Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00017-10 ◽

2010 ◽

Vol 74 (4) ◽

pp. 479-503 ◽

Cited By ~ 37

Author(s):

Trudy Torto-Alalibo ◽

Candace W. Collmer ◽

Michelle Gwinn-Giglio ◽

Magdalen Lindeberg ◽

Shaowu Meng ◽

...

Keyword(s):

Gene Ontology ◽

Effector Proteins ◽

Biological Processes ◽

Gene Products ◽

Host Defenses ◽

Host Interactions ◽

Microbial Associations ◽

Bioinformatic Approaches ◽

Go Terms ◽

Diverse Plant

SUMMARY Microbes form intimate relationships with hosts (symbioses) that range from mutualism to parasitism. Common microbial mechanisms involved in a successful host association include adhesion, entry of the microbe or its effector proteins into the host cell, mitigation of host defenses, and nutrient acquisition. Genes associated with these microbial mechanisms are known for a broad range of symbioses, revealing both divergent and convergent strategies. Effective comparisons among these symbioses, however, are hampered by inconsistent descriptive terms in the literature for functionally similar genes. Bioinformatic approaches that use homology-based tools are limited to identifying functionally similar genes based on similarities in their sequences. An effective solution to these limitations is provided by the Gene Ontology (GO), which provides a standardized language to describe gene products from all organisms. The GO comprises three ontologies that enable one to describe the molecular function(s) of gene products, the biological processes to which they contribute, and their cellular locations. Beginning in 2004, the Plant-Associated Microbe Gene Ontology (PAMGO) interest group collaborated with the GO consortium to extend the GO to accommodate terms for describing gene products associated with microbe-host interactions. Currently, over 900 terms that describe biological processes common to diverse plant- and animal-associated microbes are incorporated into the GO database. Here we review some unifying themes common to diverse host-microbe associations and illustrate how the new GO terms facilitate a standardized description of the gene products involved. We also highlight areas where new terms need to be developed, an ongoing process that should involve the whole community.

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