Organization and function of paraspeckles

2020 ◽  
Vol 64 (6) ◽  
pp. 875-882 ◽  
Author(s):  
Yang Wang ◽  
Ling-Ling Chen
Keyword(s):  
Cancer Progression ◽  
Stress Responses ◽  
Noncoding Rna ◽  
Rna Stability ◽  
Structure And Function ◽  
Physiological Processes ◽  
Cellular Stress Responses ◽  
Isoform Switching ◽  
And Function ◽  
Liquid Liquid Phase Separation

Abstract Paraspeckles are a type of subnuclear bodies built on the long noncoding RNA NEAT1 (nuclear paraspeckle assembly transcript 1, also known as MEN-ε/β or VINC-1). Paraspeckles are involved in many physiological processes including cellular stress responses, cell differentiation, corpus luteum formation and cancer progression. Recently, ultra-resolution microscopy coupled with multicolor-labeling of paraspeckle components (the NEAT1 RNA and paraspeckle proteins) revealed the exquisite details of paraspeckle structure and function. NEAT1 transcripts are radially arranged to form a core–shell spheroidal structure, while paraspeckle proteins (PSPs) localize within different layers. Functional dissection of NEAT1 shows that the subdomains of NEAT1_2 are important for RNA stability, isoform switching and paraspeckle assembly via a liquid–liquid phase separation (LLPS) mechanism. We review recent progress on structure and organization of paraspeckles as well as how paraspeckles spatiotemporally control gene regulation through sequestration of diverse proteins and RNAs in cells.

Matrix Metalloproteinases in Invertebrates

2020 ◽  
Vol 27 (11) ◽  
pp. 1068-1081
Author(s):  
Xi Liu ◽  
Dongwu Liu ◽  
Yangyang Shen ◽  
Mujie Huang ◽  
Lili Gao ◽  
...  
Keyword(s):  
Matrix Metalloproteinases ◽  
Immune Responses ◽  
Theoretical Basis ◽  
Regulatory Mechanism ◽  
Structure And Function ◽  
Catalytic Domains ◽  
Physiological Processes ◽  
Disease Occurrence ◽  
Complex Functions ◽  
And Function

Matrix Metalloproteinases (MMPs) belong to a family of metal-dependent endopeptidases which contain a series of conserved pro-peptide domains and catalytic domains. MMPs have been widely found in plants, animals, and microorganisms. MMPs are involved in regulating numerous physiological processes, pathological processes, and immune responses. In addition, MMPs play a key role in disease occurrence, including tumors, cardiovascular diseases, and other diseases. Compared with invertebrate MMPs, vertebrate MMPs have diverse subtypes and complex functions. Therefore, it is difficult to study the function of MMPs in vertebrates. However, it is relatively easy to study invertebrate MMPs because there are fewer subtypes of MMPs in invertebrates. In the present review, the structure and function of MMPs in invertebrates were summarized, which will provide a theoretical basis for investigating the regulatory mechanism of MMPs in invertebrates.

scholarly journals Expression and Function of C1orf132 Long-Noncoding RNA in Breast Cancer Cell Lines and Tissues

2021 ◽  
Vol 22 (13) ◽  
pp. 6768
Author(s):  
Afsaneh Malekzadeh Shafaroudi ◽  
Ali Sharifi-Zarchi ◽  
Saeid Rahmani ◽  
Nahid Nafissi ◽  
Seyed Javad Mowla ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Progression ◽  
Noncoding Rna ◽  
Breast Cancer Cell Lines ◽  
Mcf7 Cells ◽  
Migration Ability ◽  
Mesenchymal Transition ◽  
Migration Assay ◽  
And Function ◽  
Distal Promoter

miR-29b2 and miR-29c play a suppressive role in breast cancer progression. C1orf132 (also named MIR29B2CHG) is the host gene for generating both microRNAs. However, the region also expresses longer transcripts with unknown functions. We employed bioinformatics and experimental approaches to decipher C1orf132 expression and function in breast cancer tissues. We also used the CRISPR/Cas9 technique to excise a predicted C1orf132 distal promoter and followed the behavior of the edited cells by real-time PCR, flow cytometry, migration assay, and RNA-seq techniques. We observed that C1orf132 long transcript is significantly downregulated in triple-negative breast cancer. We also identified a promoter for the longer transcripts of C1orf132 whose functionality was demonstrated by transfecting MCF7 cells with a C1orf132 promoter-GFP construct. Knocking-out the promoter by means of CRISPR/Cas9 revealed no alterations in the expression of the neighboring genes CD46 and CD34, while the expression of miR-29c was reduced by half. Furthermore, the promoter knockout elevated the migration ability of the edited cells. RNA sequencing revealed many up- and downregulated genes involved in various cellular pathways, including epithelial to mesenchymal transition and mammary gland development pathways. Altogether, we are reporting here the existence of an additional/distal promoter with an enhancer effect on miR-29 generation and an inhibitory effect on cell migration.

scholarly journals Genome-wide identification and analysis of class III peroxidases in Betula pendula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kewei Cai ◽  
Huixin Liu ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Plant Life ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
And Function

Abstract Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. Results We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

scholarly journals The Importance of GLWamide Neuropeptides in Cnidarian Development and Physiology

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Toshio Takahashi ◽  
Masayuki Hatta
Keyword(s):  
Basic Structure ◽  
Signaling Molecules ◽  
Structure And Function ◽  
Amino Acid Residues ◽  
Peptide Signaling ◽  
Physiological Processes ◽  
History Of ◽  
Species Specific ◽  
And Function ◽  
Potential Use

The peptide-signaling molecules (<50 amino acid residues) occur in a wide variety of invertebrate and vertebrate organisms, playing pivotal roles in physiological, endocrine, and developmental processes. While some of these peptides display similar structures in mammals and invertebrates, others differ with respect to their structure and function in a species-specific manner. Such a conservation of basic structure and function implies that many peptide-signaling molecules arose very early in the evolutionary history of some taxa, while species-specific characteristics led us to suggest that they also acquire the ability to evolve in response to specific environmental conditions. In this paper, we describe GLWamide-family peptides that function as signaling molecules in the process of muscle contraction, metamorphosis, and settlement in cnidarians. The peptides are produced by neurons and are therefore referred to as neuropeptides. We discuss the importance of the neuropeptides in both developmental and physiological processes in a subset of hydrozoans, as well as the potential use as a seed compound in drug development and aspects related to the protection of corals.

Structure and function of channel-forming peptaibols

1993 ◽  
Vol 26 (4) ◽  
pp. 365-421 ◽  
Author(s):  
M. S. P. Sansom
Keyword(s):  
Electrical Properties ◽  
Molecular Level ◽  
Structure And Function ◽  
Atomic Resolution ◽  
Excitable Cells ◽  
Channel Proteins ◽  
Physiological Processes ◽  
Transport Of Ions ◽  
And Function

Transport of ions through channels is fundamental to a number of physiological processes, especially the electrical properties of excitable cells (Hille, 1992). To understand this process at a molecular level requires atomic resolution structures of channel proteins.

scholarly journals Environmental cues induce a long noncoding RNA–dependent remodeling of the nucleolus

2013 ◽  
Vol 24 (18) ◽  
pp. 2943-2953 ◽  
Author(s):  
Mathieu D. Jacob ◽  
Timothy E. Audas ◽  
James Uniacke ◽  
Laura Trinkle-Mulcahy ◽  
Stephen Lee
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
De Novo ◽  
Intergenic Spacer ◽  
Structure And Function ◽  
Functional Adaptation ◽  
Distinct Region ◽  
Environmental Signals ◽  
Mammalian Cell Lines ◽  
And Function

The nucleolus is a plurifunctional organelle in which structure and function are intimately linked. Its structural plasticity has long been appreciated, particularly in response to transcriptional inhibition and other cellular stresses, although the mechanism and physiological relevance of these phenomena are unclear. Using MCF-7 and other mammalian cell lines, we describe a structural and functional adaptation of the nucleolus, triggered by heat shock or physiological acidosis, that depends on the expression of ribosomal intergenic spacer long noncoding RNA (IGS lncRNA). At the heart of this process is the de novo formation of a large subnucleolar structure, termed the detention center (DC). The DC is a spatially and dynamically distinct region, characterized by an 8-anilino-1-naphthalenesulfonate–positive hydrophobic signature. Its formation is accompanied by redistribution of nucleolar factors and arrest in ribosomal biogenesis. Silencing of regulatory IGS lncRNA prevents the creation of this structure and allows the nucleolus to retain its tripartite organization and transcriptional activity. Signal termination causes a decrease in IGS transcript levels and a return to the active nucleolar conformation. We propose that the induction of IGS lncRNA by environmental signals operates as a molecular switch that regulates the structure and function of the nucleolus.

scholarly journals SRPassing Co-translational Targeting: The Role of the Signal Recognition Particle in Protein Targeting and mRNA Protection

2021 ◽  
Vol 22 (12) ◽  
pp. 6284
Author(s):  
Morgana K. Kellogg ◽  
Sarah C. Miller ◽  
Elena B. Tikhonova ◽  
Andrey L. Karamyshev
Keyword(s):  
Endoplasmic Reticulum ◽  
Noncoding Rna ◽  
Protein Targeting ◽  
Signal Recognition Particle ◽  
Structure And Function ◽  
Secretory Proteins ◽  
Signal Recognition ◽  
Domains Of Life ◽  
And Function

Signal recognition particle (SRP) is an RNA and protein complex that exists in all domains of life. It consists of one protein and one noncoding RNA in some bacteria. It is more complex in eukaryotes and consists of six proteins and one noncoding RNA in mammals. In the eukaryotic cytoplasm, SRP co-translationally targets proteins to the endoplasmic reticulum and prevents misfolding and aggregation of the secretory proteins in the cytoplasm. It was demonstrated recently that SRP also possesses an earlier unknown function, the protection of mRNAs of secretory proteins from degradation. In this review, we analyze the progress in studies of SRPs from different organisms, SRP biogenesis, its structure, and function in protein targeting and mRNA protection.

scholarly journals Does Thermal Stress Modulate the Biochemical and Physiological Responses of Ruditapes Decussatus Exposed to the Progestin Levonorgestrel?

2021 ◽  
Author(s):  
Asma Mannai ◽  
Leila HMIDA ◽  
Zied BOURAOUI ◽  
Hamadi GUERBEJ ◽  
Tahar GHARRED ◽  
...  
Keyword(s):  
Chronic Conditions ◽  
Abiotic Factors ◽  
Physiological Responses ◽  
Structure And Function ◽  
Warning Sign ◽  
Ruditapes Decussatus ◽  
Physiological Processes ◽  
Lysosomal Membrane Stability ◽  
And Function ◽  
Increasing Temperature

Abstract The combined effects of the abiotic factors such as temperature and synthetic progestins on the biochemical and physiological performances of marine clam Ruditapes decssatus under sub-chronic conditions are poorly studied. Here, we investigated the effects of levonorgestrel (1000 ng/l) alone or combined with increasing temperature of 20, 24 and 28°C on the biochemical and physiological responses and the gonad histology of the clam (Ruditapes decussatus) for 28 days. Our results revealed that, in clams treated with levonorgestrel (LNG) alone, there was an impairment of the defense against oxidative stress related to the inductions of CAT, GST and PSH, a reduction in the lysosomal membrane stability, a physiological disturbance via an increase in the level of estradiol, a decrease in the number of gonad oocytes and a reduction in vitellogenin like protein. Furthermore, exposure to heat stress of 20°C, 24°C and 28°C, alone or in combination with LNG, enhanced SOD antioxidant activity which was ineffective in preventing lipoperoxidation and altered clam’s physiological processes of reproduction via dramatic reduction of gonad oocyte numbers and of vitellogenin like protein reserves. Overall, these findings can be taken as a warning sign of temperature and levonorgestrel progestin effect that can lead to effective changes in the structure and function of target vital organs, such as the gonads of the clam Ruditapes decussatus, and this may have implications for the whole organism and populations.

scholarly journals The Regulatory Activity of Noncoding RNAs in ILCs

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2742
Author(s):  
Alessio Grimaldi ◽  
Giuseppe Pietropaolo ◽  
Helena Stabile ◽  
Andrea Kosta ◽  
Cristina Capuano ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Rna Stability ◽  
Lymphoid Cells ◽  
Circular Rnas ◽  
Transcriptional Networks ◽  
Regulatory Activity ◽  
Protein Coding ◽  
Host Protection ◽  
Microbial Infections ◽  
And Function

Innate lymphoid cells (ILCs) are innate lymphocytes playing essential functions in protection against microbial infections and participate in both homeostatic and pathological contexts, including tissue remodeling, cancer, and inflammatory disorders. A number of lineage-defining transcription factors concur to establish transcriptional networks which determine the identity and the activity of the distinct ILC subsets. However, the contribution of other regulatory molecules in controlling ILC development and function is also recently emerging. In this regard, noncoding RNA (ncRNAs) represent key elements of the complex regulatory network of ILC biology and host protection. ncRNAs mostly lack protein-coding potential, but they are endowed with a relevant regulatory activity in immune and nonimmune cells because of their ability to control chromatin structure, RNA stability, and/or protein synthesis. Herein, we summarize recent studies describing how distinct types of ncRNAs, mainly microRNAs, long ncRNAs, and circular RNAs, act in the context of ILC biology. In particular, we comment on how ncRNAs can exert key effects in ILCs by controlling gene expression in a cell- or state-specific manner and how this tunes distinct functional outputs in ILCs.

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