scholarly journals The tweety Gene Family: From Embryo to Disease

2021 ◽  
Vol 14 ◽  
Author(s):  
Rithvik R. Nalamalapu ◽  
Michelle Yue ◽  
Aaron R. Stone ◽  
Samantha Murphy ◽  
Margaret S. Saha
Keyword(s):  
Gene Family ◽  
Neural Development ◽  
Chloride Channels ◽  
Expression Patterns ◽  
Pediatric Brain Tumors ◽  
Structure Evolution ◽  
Cellular Functions ◽  
Stem Cell Maintenance ◽  
Embryonic And Fetal Development ◽  
Wide Range

The tweety genes encode gated chloride channels that are found in animals, plants, and even simple eukaryotes, signifying their deep evolutionary origin. In vertebrates, the tweety gene family is highly conserved and consists of three members—ttyh1, ttyh2, and ttyh3—that are important for the regulation of cell volume. While research has elucidated potential physiological functions of ttyh1 in neural stem cell maintenance, proliferation, and filopodia formation during neural development, the roles of ttyh2 and ttyh3 are less characterized, though their expression patterns during embryonic and fetal development suggest potential roles in the development of a wide range of tissues including a role in the immune system in response to pathogen-associated molecules. Additionally, members of the tweety gene family have been implicated in various pathologies including cancers, particularly pediatric brain tumors, and neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease. Here, we review the current state of research using information from published articles and open-source databases on the tweety gene family with regard to its structure, evolution, expression during development and adulthood, biochemical and cellular functions, and role in human disease. We also identify promising areas for further research to advance our understanding of this important, yet still understudied, family of genes.

scholarly journals Planarian CREB-binding protein (CBP) gene family regulates stem cell maintenance and differentiation

2020 ◽  
Author(s):  
Susanna Fraguas ◽  
Sheila Cárcel ◽  
Coral Vivancos ◽  
Ma Dolores Molina ◽  
Jordi Ginés ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Family ◽  
Binding Protein ◽  
Expression Patterns ◽  
Stem Cell Differentiation ◽  
Transferase Activity ◽  
Creb Binding Protein ◽  
Stem Cell Maintenance ◽  
Wide Range ◽  
Cell Maintenance

ABSTRACTThe regulation of stem cells plasticity and differentiation is still an open question in developmental biology. CBP (CREB-binding protein)/p300 is a conserved gene family which functions as a transcriptional co-activator and shows an important role in a wide range of cellular processes, such as cell death, DNA damage response and tumorigenesis. Moreover, CBPs have an acetyl transferase activity that is relevant as histone and non-histone acetylation results in changes in chromatin architecture and protein activity that affects gene expression. Many studies have shown the conserved functions of CBP/p300 on stem cell proliferation and differentiation. The planarian Schmidtea mediterranea is an excellent model to study in vivo the molecular mechanism underlying stem cell differentiation during regeneration. We have identified five different Smed-cbp genes in S. mediterranea that show different expression patterns. Functional analyses indicate that Smed-cbp-2 seems to be essential for stem cell maintenance and cell survival. On the other hand, the silencing of Smed-cbp-3 results in the growth of apparently normal blastemas; however, these remain largely depigmented and undifferentiated. Smed-cbp-3 silencing affects the differentiation of several cell lineages including neural, epidermal, digestive and excretory cell types. Finally, we have analyzed the predicted interactomes of CBP-2 and CBP-3 as an initial step to better understand their function on planarian stem cell biology.

Clustering of the human CLCA gene family on the short arm of chromosome 1 (1p22-31)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 1030-1032 ◽  
Author(s):  
Achim D Gruber ◽  
Bendicht U Pauli
Keyword(s):  
Gene Family ◽  
Radiation Hybrid ◽  
Chloride Channels ◽  
Mammalian Species ◽  
Expression Patterns ◽  
Family Members ◽  
Radiation Hybrid Mapping ◽  
Chromosome 1 ◽  
Hybrid Mapping ◽  
Specific Expression

The CLCA gene family is a novel family of calcium-activated chloride channels. Several family members have recently been cloned from different mammalian species with distinct, highly tissue-specific expression patterns. Here, we describe radiation hybrid mapping of the human CLCA2 and CLCA3 genes using the Genebridge 4 panel. Both genes were mapped to adjacent loci on the short arm of chromosome 1 (1p22-31), a region to which the human CLCA1 had been assigned earlier. The results show clustering of all human CLCA family members known so far despite their moderately low levels of sequence homology and their heterogeneous expression patterns.Key words: radiation hybrid mapping, human chromosome 1p22-31, calcium-activated chloride channels.

scholarly journals Genome-Wide Analysis of MYB Gene Family in Chinese Bayberry (Morella rubra) and Identification of Members Regulating Flavonoid Biosynthesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yunlin Cao ◽  
Huimin Jia ◽  
Mengyun Xing ◽  
Rong Jin ◽  
Donald Grierson ◽  
...  
Keyword(s):  
Gene Family ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Flavonoid Biosynthesis ◽  
Structure Evolution ◽  
Chinese Bayberry ◽  
Genome Wide Analysis ◽  
Myb Gene ◽  
Genome Wide ◽  
Family Analysis

Chinese bayberry (Morella rubra), the most economically important fruit tree in the Myricaceae family, is a rich source of natural flavonoids. Recently the Chinese bayberry genome has been sequenced, and this provides an opportunity to investigate the organization and evolutionary characteristics of MrMYB genes from a whole genome view. In the present study, we performed the genome-wide analysis of MYB genes in Chinese bayberry and identified 174 MrMYB transcription factors (TFs), including 122 R2R3-MYBs, 43 1R-MYBs, two 3R-MYBs, one 4R-MYB, and six atypical MYBs. Collinearity analysis indicated that both syntenic and tandem duplications contributed to expansion of the MrMYB gene family. Analysis of transcript levels revealed the distinct expression patterns of different MrMYB genes, and those which may play important roles in leaf and flower development. Through phylogenetic analysis and correlation analyses, nine MrMYB TFs were selected as candidates regulating flavonoid biosynthesis. By using dual-luciferase assays, MrMYB12 was shown to trans-activate the MrFLS1 promoter, and MrMYB39 and MrMYB58a trans-activated the MrLAR1 promoter. In addition, overexpression of 35S:MrMYB12 caused a significant increase in flavonol contents and induced the expression of NtCHS, NtF3H, and NtFLS in transgenic tobacco leaves and flowers and significantly reduced anthocyanin accumulation, resulting in pale-pink or pure white flowers. This indicates that MrMYB12 redirected the flux away from anthocyanin biosynthesis resulting in higher flavonol content. The present study provides valuable information for understanding the classification, gene and motif structure, evolution and predicted functions of the MrMYB gene family and identifies MYBs regulating different aspects of flavonoid biosynthesis in Chinese bayberry.

Differential expression of the ras gene family in mice

1987 ◽  
Vol 7 (4) ◽  
pp. 1535-1540 ◽  
Author(s):  
J Leon ◽  
I Guerrero ◽  
A Pellicer
Keyword(s):  
Gene Family ◽  
Differential Expression ◽  
Adult Mouse ◽  
Expression Patterns ◽  
Cellular Functions ◽  
Ras Gene ◽  
Ras Genes ◽  
Mouse Tissues

We compared the expression of the ras gene family (H-ras, K-ras, and N-ras) in adult mouse tissues and during development. We found substantial variations in expression among different organs and in the amounts of the different transcripts originating from each gene, especially for the N-ras gene. The expression patterns were consistent with the reported preferential tissue activation of ras genes and suggested different cellular functions for each of the ras genes.

scholarly journals Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11938
Author(s):  
Shilin Sun ◽  
Bo Wang ◽  
Qi Jiang ◽  
Zhuoran Li ◽  
Site Jia ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gene Family ◽  
Expression Patterns ◽  
Structure Evolution ◽  
Gene Gain ◽  
Betula Platyphylla ◽  
Ros Scavenging ◽  
Promoter Regions ◽  
Chromosomal Distribution ◽  
Qrt Pcr

Background DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear. Methods The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results. Results A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17­ were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17­-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

scholarly journals Slc4 Gene Family in Spotted Sea Bass (Lateolabrax maculatus): Structure, Evolution, and Expression Profiling in Response to Alkalinity Stress and Salinity Changes

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1271
Author(s):  
Ling-Yu Wang ◽  
Yuan Tian ◽  
Hai-Shen Wen ◽  
Peng Yu ◽  
Yang Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Sea Bass ◽  
Duplication Event ◽  
Structure Evolution ◽  
Genome Duplication Event ◽  
Physiological Processes ◽  
Lateolabrax Maculatus ◽  
Solute Carrier

The solute carrier 4 (SLC4) family is a class of cell membranes transporters involved in base transport that plays crucial roles in diverse physiological processes. In our study, 15 slc4 genes were identified and annotated in spotted sea bass, including five members of Cl−/HCO3− exchangers, eight genes coding Na+-dependent HCO3− transporters, and two copies of Na+-coupled borate transporters. The gene sequence and structure, chromosomal and syntenic arrangement, phylogenetic and evolution profiles were analyzed. Results showed that the slc4 gene in teleosts obviously expanded compared with higher vertebrates, arising from teleost-specific whole genome duplication event. Most gene sites of slc4 in spotted sea bass were under strong purifying selection during evolution, while positive selection sites were only detected in slc4a1b, slc4a8, and slc4a10b. Additionally, qRT-PCR results showed that different slc4 genes exhibited distinct branchial expression patterns after alkalinity and salinity stresses, of which the strongly responsive members may play essential roles during these physiological processes. Our study provides the systemic overview of the slc4 gene family in spotted sea bass and enables a better understanding for the evolution of this family and further deciphering the biological roles in maintaining ion and acid–base homeostasis in teleosts.

scholarly journals Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses

2021 ◽  
Vol 22 (23) ◽  
pp. 13048
Author(s):  
Aili Liu ◽  
Mengyuan Wei ◽  
Yong Zhou ◽  
Donghua Li ◽  
Rong Zhou ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Sesamum Indicum ◽  
Specific Gene ◽  
Transgenic Yeast ◽  
Group I ◽  
Wide Range

SIMILAR TO RCD-ONEs (SROs) comprise a small plant-specific gene family which play important roles in regulating numerous growth and developmental processes and responses to environmental stresses. However, knowledge of SROs in sesame (Sesamum indicum L.) is limited. In this study, four SRO genes were identified in the sesame genome. Phylogenetic analysis showed that 64 SROs from 10 plant species were divided into two groups (Group I and II). Transcriptome data revealed different expression patterns of SiSROs over various tissues. Expression analysis showed that Group II SROs, especially SiSRO2b, exhibited a stronger response to various abiotic stresses and phytohormones than those in Group I, implying their crucial roles in response to environmental stimulus and hormone signals. In addition, the co-expression network and protein-protein interaction network indicated that SiSROs are associated with a wide range of stress responses. Moreover, transgenic yeast harboring SiSRO2b showed improved tolerance to salt, osmotic and oxidative stress, indicating SiSRO2b could confer multiple tolerances to transgenic yeast. Taken together, this study not only lays a foundation for further functional dissection of the SiSRO gene family, but also provides valuable gene candidates for genetic improvement of abiotic stress tolerance in sesame.

scholarly journals Differential expression of the ras gene family in mice.

1987 ◽  
Vol 7 (4) ◽  
pp. 1535-1540 ◽  
Author(s):  
J Leon ◽  
I Guerrero ◽  
A Pellicer
Keyword(s):  
Gene Family ◽  
Differential Expression ◽  
Adult Mouse ◽  
Expression Patterns ◽  
Cellular Functions ◽  
Ras Gene ◽  
Ras Genes ◽  
Mouse Tissues

We compared the expression of the ras gene family (H-ras, K-ras, and N-ras) in adult mouse tissues and during development. We found substantial variations in expression among different organs and in the amounts of the different transcripts originating from each gene, especially for the N-ras gene. The expression patterns were consistent with the reported preferential tissue activation of ras genes and suggested different cellular functions for each of the ras genes.

scholarly journals Genomic Analysis of Sugar Transporter Gene Family in Cultivated Peanut (Arachis Hypogaea): Evolution, Expression Profiles and Gene Variation

2020 ◽  
Author(s):  
zhijun Xu ◽  
Sheng Zhao ◽  
Xiaowen Hu ◽  
Xiaoli Wu ◽  
Yang Liu
Keyword(s):  
Gene Family ◽  
Arachis Hypogaea ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Structure Evolution ◽  
Gene Variation ◽  
A Genome ◽  
Cultivated Peanut

Abstract BackgroundSugar transporter (STP) gene family, belonging to the major facilitator superfamily, plays significant roles in monosaccharide distribution and many aspects of physiological processes. However, little information was available about the STP genes in cultivated peanut (Arachis hypogaea), an important edible and oil crop. The recent release of the whole-genome sequence of cultivated peanut allowed us to perform a genome-wide investigation into the phylogeny and expression profiling of peanut STP genes.ResultsA total of thirty-six STP genes containing the Sugar_tr conserved motifs were identified from the A. hypogaea genome and all the genes were renamed on the basis of their respective chromosome distribution. According to their phylogenetic features, the STPs were classified into four groups. The structure of the STP genes and their encoded proteins were examined. Synteny analysis and phylogenetic comparison of the STP genes provided deep insight into the evolutionary characteristics of peanut STP genes. The segmental duplication events played a major role in the expansion of the peanut STP gene family and homeologous chromosomes rearrangement may lead to the exchange of STP genes between the A and B sub-genome. Expression profiles derived from transcriptome data exhibited distinct expression patterns of AhSTP genes in various tissues. Among them, four AhSTP genes, AhSTP3, AhSTP9, AhSTP19, AhSTP28, exhibited high expression in early stage of pod formulate in subsp. hypogaea, and in developing phase of seed in subsp. fastigiate, suggesting these genes may be involved in the development of pod and seed. Gene variation analysis of the four genes utilizing the subspecies genome sequences indicated multiple variations occurred in gene sequence or promoter region, and provided valuable clues for the different expression profiles of the four genes during seed development in subsp. hypogaea and subsp. fastigiate.ConclusionThirty-six STP genes were identified in cultivated peanut and their protein character,structure,evolution characteristics, expression patterns and gene variation were analyzed.This study provided a foundation for further functional characterization of STP genes with an aim of cultivated peanut crop improvement.

scholarly journals DUBs Activating the Hedgehog Signaling Pathway: A Promising Therapeutic Target in Cancer

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1518
Author(s):  
Francesca Bufalieri ◽  
Ludovica Lospinoso Severini ◽  
Miriam Caimano ◽  
Paola Infante ◽  
Lucia Di Marcotullio
Keyword(s):  
Drug Targets ◽  
Hedgehog Signaling ◽  
Dynamic Balance ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Signaling Transduction ◽  
E3 Ligases ◽  
Stem Cell Maintenance ◽  
Wide Range ◽  
Potential Applications

The Hedgehog (HH) pathway governs cell proliferation and patterning during embryonic development and is involved in regeneration, homeostasis and stem cell maintenance in adult tissues. The activity of this signaling is finely modulated at multiple levels and its dysregulation contributes to the onset of several human cancers. Ubiquitylation is a coordinated post-translational modification that controls a wide range of cellular functions and signaling transduction pathways. It is mediated by a sequential enzymatic network, in which ubiquitin ligases (E3) and deubiquitylase (DUBs) proteins are the main actors. The dynamic balance of the activity of these enzymes dictates the abundance and the fate of cellular proteins, thus affecting both physiological and pathological processes. Several E3 ligases regulating the stability and activity of the key components of the HH pathway have been identified. Further, DUBs have emerged as novel players in HH signaling transduction, resulting as attractive and promising drug targets. Here, we review the HH-associated DUBs, discussing the consequences of deubiquitylation on the maintenance of the HH pathway activity and its implication in tumorigenesis. We also report the recent progress in the development of selective inhibitors for the DUBs here reviewed, with potential applications for the treatment of HH-related tumors.

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