Molecular cloning, expression, and functional features of IGF1 splice variants in sheep

Insulin-like growth factor 1 (IGF1),also known as somatomedin C, is essential for the regulation of animal growth and development. In many species, the IGF1 gene can be alternatively spliced into multiple transcripts, encoding different pre-pro-IGF1 proteins. However, the exact alternative splicing patterns of IGF1 and the sequence information of different splice variants in sheep are still unclear. In this study, four splice variants (class 1-Ea, class 1-Eb, class 2-Ea, and class 2-Eb) were obtained, but no IGF1 Ec, similar to that found in other species, was discovered. Bioinformatics analysis showed that the four splice variants shared the same mature peptide (70 amino acids) and possessed distinct signal peptides and E peptides. Tissue expression analysis indicated that the four splice variants were broadly expressed in all tested tissues and were most abundantly expressed in the liver. In most tissues and stages, the expression of class 1-Ea was highest, and the expression of other splice variants was low. Overall, levels of the four IGF1 splice variants at the fetal and lamb stages were higher than those at the adult stage. Overexpression of the four splice variants significantly increased fibroblast proliferation and inhibited apoptosis (P < 0.05). In contrast, silencing IGF1 Ea or IGF1 Eb with siRNA significantly inhibited proliferation and promoted apoptosis (P < 0.05). Among the four splice variants, class 1-Ea had a more evident effect on cell proliferation and apoptosis. In summary, the four ovine IGF1 splice variants have different structures and expression patterns and might have different biological functions.

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Genomic-Wide Analysis of the PLC Family and Detection of GmPI-PLC7 Responses to Drought and Salt Stresses in Soybean

Frontiers in Plant Science ◽

10.3389/fpls.2021.631470 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhi-Feng Chen ◽

Jing-Na Ru ◽

Guo-Zhong Sun ◽

Yan Du ◽

Jun Chen ◽

...

Keyword(s):

Abiotic Stresses ◽

Nadh Oxidase ◽

Expression Patterns ◽

Tissue Expression ◽

Oxygen Free Radical ◽

Relationship Analysis ◽

Tissue Expression Analysis ◽

Drought And Salt Tolerance ◽

Drought And Salt Stresses ◽

Series Of Experiments

Phospholipase C (PLC) performs significant functions in a variety of biological processes, including plant growth and development. The PLC family of enzymes principally catalyze the hydrolysis of phospholipids in organisms. This exhaustive exploration of soybean GmPLC members using genome databases resulted in the identification of 15 phosphatidylinositol-specific PLC (GmPI-PLC) and 9 phosphatidylcholine-hydrolyzing PLC (GmNPC) genes. Chromosomal location analysis indicated that GmPLC genes mapped to 10 of the 20 soybean chromosomes. Phylogenetic relationship analysis revealed that GmPLC genes distributed into two groups in soybean, the PI-PLC and NPC groups. The expression patterns and tissue expression analysis showed that GmPLCs were differentially expressed in response to abiotic stresses. GmPI-PLC7 was selected to further explore the role of PLC in soybean response to drought and salt stresses by a series of experiments. Compared with the transgenic empty vector (EV) control lines, over-expression of GmPI-PLC7 (OE) conferred higher drought and salt tolerance in soybean, while the GmPI-PLC7-RNAi (RNAi) lines exhibited the opposite phenotypes. Plant tissue staining and physiological parameters observed from drought- and salt-stressed plants showed that stress increased the contents of chlorophyll, oxygen free radical (O2–), hydrogen peroxide (H2O2) and NADH oxidase (NOX) to amounts higher than those observed in non-stressed plants. This study provides new insights in the functional analysis of GmPLC genes in response to abiotic stresses.

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Large and small splice variants of collagen XII: differential expression and ligand binding.

The Journal of Cell Biology ◽

10.1083/jcb.130.4.1005 ◽

1995 ◽

Vol 130 (4) ◽

pp. 1005-1014 ◽

Cited By ~ 77

Author(s):

M Koch ◽

B Bohrmann ◽

M Matthison ◽

C Hagios ◽

B Trueb ◽

...

Keyword(s):

Ligand Binding ◽

Splice Variants ◽

Expression Patterns ◽

Collagen I ◽

Heparin Binding ◽

Fibronectin Type Iii ◽

Alternatively Spliced ◽

Collagenous Domain ◽

Fibronectin Type

Collagen XII has a short collagenous tail and a very large, three-armed NC3 domains consisting primarily of fibronectin type III repeats. Differential splicing within this domain gives rise to a large (320 kD) and a small (220 kD) subunit; the large but not the small can carry glycosaminoglycan. To investigate whether collagen XII variants have distinct expression patterns and functions, we generated antibody and cDNA probes specific for the alternatively spliced domain. We report here that the large variant has a more restricted expression in embryonic tissue than the small. For example, whereas the small variant is widespread in the dermis, the large is limited to the base of feather buds. Distinct proportions of mRNA for the two variants were detected depending on the tissue. Monoclonal antibodies allowed us to separate collagen XII variants, and to show that homo- and heterotrimers exist. Collagen XII variants differ in ligand binding. Small subunits interact weakly with heparin via their COOH-terminal domain. Large subunits have additional, stronger heparin-binding site(s) in their NH2-terminal extra domain. In vivo, both large and small collagen XII are associated with interstitial collagen. Here we show biochemically and ultrastructurally that collagen XII can be incorporated into collagen I fibrils when it is present during, but not after, fibril formation. Removal of the collagenous domain of collagen XII reduces its coprecipitation with collagen I. Our results indicate that collagen XII is specifically associated with fibrillar collagen, and that the large variant has binding sites for extracellular ligands not present in the small variant.

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Genome-wide Identification and Characterization of the DELLA Subfamily in Prunus mume

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.140.3.223 ◽

2015 ◽

Vol 140 (3) ◽

pp. 223-232 ◽

Cited By ~ 1

Author(s):

Jiuxing Lu ◽

Weiru Yang ◽

Qixiang Zhang

Keyword(s):

Expression Patterns ◽

Ornamental Plants ◽

Fruit Trees ◽

Tissue Expression ◽

Prunus Mume ◽

Tissue Expression Analysis ◽

Della Proteins ◽

Genes Encoding ◽

Positive Regulators ◽

Delayed Flowering

Control of development is an important issue in the production of ornamental plants. Gibberellins (GAs) play a key role in regulating plant growth and development. DELLA is nuclear negative regulators of GA signaling. We identified two DELLA homologous genes, PmDELLA1 and PmDELLA2, in the genome of mei (Prunus mume) genome. We analyzed the structure, expression patterns and molecular functions of both genes. Tissue expression analysis showed that both genes were transcriptionally active. PmDELLA1 showed higher expression in seeds than PmDELLA2. This indicated that PmDELLA2 plays different roles from PmDELLA1 in seed germination. The expressions of both genes at various flowering stages were relatively low. We speculated that PmDELLAs might be positive regulators of flowering by releasing the repression of GA during floral blooming. Transgenic arabidopsis (Arabidopsis thaliana) lines overexpressing the two genes showed dwarf and delayed flowering. We confirmed that the two PmDELLAs were partially conserved with genes encoding DELLA proteins in arabidopsis. Our bioinformatics and functional analyses provide information that may be valuable to improve the economic, agronomic and ecological properties of mei and other Rosaceae fruit trees.

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Molecular cloning and tissue expression analysis of immunoglobulin light k chain cDNA from cobia Rachycentron canadium Linnaeus

Journal of Fishery Sciences of China ◽

10.3724/sp.j.1118.2011.00048 ◽

2013 ◽

Vol 18 (1) ◽

pp. 48-58

Author(s):

Yue’e HOU ◽

Juan FENG ◽

Zhangyong NING ◽

Lina MAO ◽

Zhixun GUO ◽

...

Keyword(s):

Molecular Cloning ◽

Expression Analysis ◽

Tissue Expression ◽

Tissue Expression Analysis

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Differential Expression of BARD1 Isoforms in Melanoma

Genes ◽

10.3390/genes12020320 ◽

2021 ◽

Vol 12 (2) ◽

pp. 320

Author(s):

Lorissa I. McDougall ◽

Ryan M. Powell ◽

Magdalena Ratajska ◽

Chi F. Lynch-Sutherland ◽

Sultana Mehbuba Hossain ◽

...

Keyword(s):

Long Range ◽

Patient Outcomes ◽

Splice Variants ◽

Significant Proportion ◽

Nanopore Sequencing ◽

Rna Seq ◽

Splice Isoforms ◽

Tissue Samples ◽

Multiple Transcripts ◽

Mrna Variants

Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified BARD1 splice variants in melanoma are warranted.

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Cloning and mapping of human PKIB and PKIG, and comparison of tissue expression patterns of three members of the protein kinase inhibitor family, including PKIA

Biochemical Journal ◽

10.1042/bj3490403 ◽

2000 ◽

Vol 349 (2) ◽

pp. 403-407 ◽

Cited By ~ 9

Author(s):

Lihua ZHENG ◽

Long YU ◽

Qiang TU ◽

Min ZHANG ◽

Hua HE ◽

...

Keyword(s):

Skeletal Muscle ◽

Protein Kinase ◽

Nuclear Export ◽

Kinase Inhibitor ◽

Expression Patterns ◽

Nuclear Export Signal ◽

Tissue Expression ◽

Protein Kinase Inhibitor ◽

The Other ◽

Dependent Protein

Two novel members of the human cAMP-dependent protein kinase inhibitor (PKI) gene family, PKIB and PKIG, were cloned. The deduced proteins showed 70% and 90% identity with mouse PKIβ and PKIγ respectively. Both the already identified pseudosubstrate site and leucine-rich nuclear export signal motifs were defined from the 11 PKIs of different species. The PKIB and PKIG genes were mapped respectively to chromosome 6q21-22.1, using a radiation hybrid GB4 panel, and to chromosome 20q13.12-13.13, using a Stanford G3 panel. Northern-blot analysis of three PKI isoforms, including the PKIA identified previously, revealed significant differences in their expression patterns. PKIB had two transcripts of 1.9 kb and 1.4 kb. The former transcript was abundant in both placenta and brain and the latter was expressed most abundantly in placenta, highly in brain, heart, liver, pancreas, moderately in kidney, skeletal muscle and colon, and very little in the other eight tissues tested. PKIG was widely expressed as a 1.5-kb transcript with the highest level in heart, hardly detectable in thymus and peripheral blood leucocytes and was moderately expressed in the other tissues, with slightly different levels. However, PKIA was specifically expressed as two transcripts of 3.3 kb and 1.5 kb in heart and skeletal muscle. The distinct expression patterns of the three PKIs suggest that their roles in various tissues are probably different.

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Protein structure-based gene expression signatures

10.1101/2020.06.03.133066 ◽

2020 ◽

Author(s):

R. Rahman ◽

Y. Xiong ◽

J. G. C. van Hasselt ◽

J. Hansen ◽

E. A. Sobie ◽

...

Keyword(s):

Gene Expression ◽

Protein Structure ◽

Mrna Expression ◽

Expression Patterns ◽

Drug Effects ◽

Tissue Expression ◽

Structural Features ◽

Biological Phenomena ◽

Gene Expression Signatures ◽

Cellular Phenotypes

AbstractGene expression signatures (GES) connect phenotypes to mRNA expression patterns, providing a powerful approach to define cellular identity, function, and the effects of perturbations. However, the use of GES has suffered from vague assessment criteria and limited reproducibility. The structure of proteins defines the functional capability of genes, and hence, we hypothesized that enrichment of structural features could be a generalizable representation of gene sets. We derive structural gene expression signatures (sGES) using features from various levels of protein structure (e.g. domain, fold) encoded by the transcribed genes in GES, to describe cellular phenotypes. Comprehensive analyses of data from the Genotype-Tissue Expression Project (GTEx), ARCHS4, and mRNA expression of drug effects on cardiomyocytes show that structural GES (sGES) are useful for identifying robust signatures of biological phenomena. sGES also enables the characterization of signatures across experimental platforms, facilitates the interoperability of expression datasets, and can describe drug action on cells.

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Alternative Splicing of Transcription Factors' Genes: Beyond the Increase of Proteome Diversity

Comparative and Functional Genomics ◽

10.1155/2009/905894 ◽

2009 ◽

Vol 2009 ◽

pp. 1-6 ◽

Cited By ~ 11

Author(s):

David Talavera ◽

Modesto Orozco ◽

Xavier de la Cruz

Keyword(s):

Transcription Factors ◽

Alternative Splicing ◽

Expression Patterns ◽

Developmental Changes ◽

Functional Families ◽

Transcription Regulators ◽

Alternatively Spliced ◽

The Impact ◽

Human And Mouse

Functional modification of transcription regulators may lead to developmental changes and phenotypical differences between species. In this work, we study the influence of alternative splicing on transcription factors in human and mouse. Our results show that the impact of alternative splicing on transcription factors is similar in both species, meaning that the ways to increase variability should also be similar. However, when looking at the expression patterns of transcription factors, we observe that they tend to diverge regardless of the role of alternative splicing. Finally, we hypothesise that transcription regulation of alternatively spliced transcription factors could play an important role in the phenotypical differences between species, without discarding other phenomena or functional families.

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