scholarly journals The mirtron miR-1010 functions in concert with its host gene SKIP to maintain synaptic homeostasis

2018 ◽  
Author(s):  
Christopher Amourda ◽  
Timothy E. Saunders
Keyword(s):  
Feedback Loop ◽  
Host Gene ◽  
Mrna Levels ◽  
Optimal Range ◽  
Synaptic Homeostasis ◽  
Synaptic Potentials ◽  
Feedforward Loop ◽  
Intracellular Ca ◽  
Computational Analyses ◽  
Host Genes

SummaryMirtrons are non-canonical miRNAs arising by splicing and debranching from short introns. A plethora of introns have been inferred by computational analyses as potential mirtrons. Yet, few have been experimentally validated and their functions, particularly in relation to their host genes, remain poorly understood. Here, we found that larvae lacking the mirtron miR-1010 are unable to grow properly and pupariate. We show that miR-1010 downregulates nAcRβ2. Increase of cortical nAcRβ2 mediated by neural activity elevates the level of intracellular Ca2+, which in turn activates CaMKII and, further downstream, the transcription factor Adf-1. We reveal that Adf-1 initiates the expression of SKIP, the host gene of miR-1010. Preventing synaptic potentials from overshooting their optimal range requires both SKIP to temper synaptic potentials (incoherent feedforward loop) and miR-1010 to reduce nAcRβ2 mRNA levels (negative feedback loop). Our results demonstrate how a mirtron, in coordination with its host gene, contributes to maintaining homeostasis.

scholarly journals Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Étienne Fafard-Couture ◽  
Danny Bergeron ◽  
Sonia Couture ◽  
Sherif Abou-Elela ◽  
Michelle S. Scott
Keyword(s):  
Housekeeping Genes ◽  
Host Gene ◽  
Rna Modification ◽  
Human Tissues ◽  
Rna Seq ◽  
Healthy Human ◽  
Protein Coding ◽  
Conservation Level ◽  
Nucleolar Rnas ◽  
Host Genes

Abstract Background Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. Results We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver, and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level, and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. Fifty-nine percent of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs. Conclusions Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

Characterization of postsynaptic Ca2+ signals at the Drosophila larval NMJ

2011 ◽  
Vol 106 (2) ◽  
pp. 710-721 ◽  
Author(s):  
Sunil A. Desai ◽  
Gregory A. Lnenicka
Keyword(s):  
Transmitter Release ◽  
Postsynaptic Membrane ◽  
Synaptic Activity ◽  
Synaptic Efficacy ◽  
Single Action ◽  
Synaptic Homeostasis ◽  
Multiple Transcripts ◽  
Quantal Size ◽  
Intracellular Ca ◽  
Larval Neuromuscular Junction

Postsynaptic intracellular Ca2+ concentration ([Ca2+]i) has been proposed to play an important role in both synaptic plasticity and synaptic homeostasis. In particular, postsynaptic Ca2+ signals can alter synaptic efficacy by influencing transmitter release, receptor sensitivity, and protein synthesis. We examined the postsynaptic Ca2+ transients at the Drosophila larval neuromuscular junction (NMJ) by injecting the muscle fibers with Ca2+ indicators rhod-2 and Oregon Green BAPTA-1 (OGB-1) and then monitoring their increased fluorescence during synaptic activity. We observed discrete postsynaptic Ca2+ transients along the NMJ during single action potentials (APs) and quantal Ca2+ transients produced by spontaneous transmitter release. Most of the evoked Ca2+ transients resulted from the release of one or two quanta of transmitter and occurred largely at synaptic boutons. The magnitude of the Ca2+ signals was correlated with synaptic efficacy; the Is terminals, which produce larger excitatory postsynaptic potentials (EPSPs) and have a greater quantal size than Ib terminals, produced a larger Ca2+ signal per terminal length and larger quantal Ca2+ signals than the Ib terminals. During a train of APs, the postsynaptic Ca2+ signal increased but remained localized to the postsynaptic membrane. In addition, we showed that the plasma membrane Ca2+-ATPase (PMCA) played a role in extruding Ca2+ from the postsynaptic region of the muscle. Drosophila melanogaster has a single PMCA gene, predicted to give rise to various isoforms by alternative splicing. Using RT-PCR, we detected the expression of multiple transcripts in muscle and nervous tissues; the physiological significance of the same is yet to be determined.

scholarly journals Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1089 ◽  
Author(s):  
Rocio Enriquez-Gasca ◽  
Poppy A. Gould ◽  
Helen M. Rowe
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transposable Elements ◽  
Essential Gene ◽  
Expression Patterns ◽  
Genetic Material ◽  
Endogenous Retroviruses ◽  
Host Gene ◽  
New Genes ◽  
Host Genes

The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.

scholarly journals Cellular and molecular determinants of altered Ca2+ handling in the failing rabbit heart: primary defects in SR Ca2+ uptake and release mechanisms

2007 ◽  
Vol 292 (3) ◽  
pp. H1607-H1618 ◽  
Author(s):  
Antonis A. Armoundas ◽  
Jochen Rose ◽  
Rajesh Aggarwal ◽  
Bruno D. Stuyvers ◽  
Brian O'Rourke ◽  
...  
Keyword(s):  
Rabbit Heart ◽  
Mrna Levels ◽  
Protein Levels ◽  
Channel Current ◽  
Plasmic Reticulum ◽  
Molecular Determinants ◽  
Intracellular Ca ◽  
Rates Of Decay ◽  
Serca 2A ◽  
Uptake And Release

Myocytes from the failing myocardium exhibit depressed and prolonged intracellular Ca2+ concentration ([Ca2+]i) transients that are, in part, responsible for contractile dysfunction and unstable repolarization. To better understand the molecular basis of the aberrant Ca2+ handling in heart failure (HF), we studied the rabbit pacing tachycardia HF model. Induction of HF was associated with action potential (AP) duration prolongation that was especially pronounced at low stimulation frequencies. L-type calcium channel current ( ICa,L) density (−0.964 ± 0.172 vs. −0.745 ± 0.128 pA/pF at +10 mV) and Na+/Ca2+ exchanger (NCX) currents (2.1 ± 0.8 vs. 2.3 ± 0.8 pA/pF at +30 mV) were not different in myocytes from control and failing hearts. The amplitude of peak [Ca2+]i was depressed (at +10 mV, 0.72 ± 0.07 and 0.56 ± 0.04 μM in normal and failing hearts, respectively; P < 0.05), with slowed rates of decay and reduced Ca2+ spark amplitudes ( P < 0.0001) in myocytes isolated from failing vs. control hearts. Inhibition of sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA)2a revealed a greater reliance on NCX to remove cytosolic Ca2+ in myocytes isolated from failing vs. control hearts ( P < 0.05). mRNA levels of the α1C-subunit, ryanodine receptor (RyR), and NCX were unchanged from controls, while SERCA2a and phospholamban (PLB) were significantly downregulated in failing vs. control hearts ( P < 0.05). α1C protein levels were unchanged, RyR, SERCA2a, and PLB were significantly downregulated ( P < 0.05), while NCX protein was significantly upregulated ( P < 0.05). These results support a prominent role for the sarcoplasmic reticulum (SR) in the pathogenesis of HF, in which abnormal SR Ca2+ uptake and release synergistically contribute to the depressed [Ca2+]i and the altered AP profile phenotype.

scholarly journals Upregulation of RBM24 Exacerbates Bladder Cancer Progression by Formatting Runx1t1/TCF4/miR-625-5p Feedback Loop

2020 ◽  
Author(s):  
Yue-Wei Yin ◽  
Kai-Long Liu ◽  
Bao-Sai Lu ◽  
Wei Li ◽  
Ya-Lin Niu ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Transcription Factor ◽  
Cancer Progression ◽  
Mrna Stability ◽  
Feedback Loop ◽  
Rna Binding ◽  
Luciferase Assay ◽  
Proximity Ligation Assay ◽  
Binding Motif ◽  
Mrna Levels

Abstract Background: RNA-binding motif protein 24 (RBM24) acts as a multifunctional determinant of cell fate, proliferation, apoptosis, and differentiation during development through regulation of pre-mRNA splicing and mRNA stability. It is also implicated in carcinogenesis, but the functions of RBM24 in bladder cancer (BC) remains unclear.Methods: Cell viability was examined by colony forming and MTT assays. Real-time quantitative PCR (RT-qPCR) and western blot analysis were used to detect the protein and mRNA levels. Co-immunoprecipitation (CoIP) and proximity ligation assay (PLA) were used to determine the protein-protein interaction. Chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP), and oligo pull-down assays were used to verify DNA/RNA–protein interactions. Luciferase assay analysis was used to detect effects on transcription factor activity.Results: In the present study, we revealed that RBM24 was upregulated in BC tissues. Importantly, we found that higher level of RBM24 was correlated with poor prognosis in BC patients. Overexpression of RBM24 promoted while depletion of RBM24 inhibited BC cell proliferation in vivo and in vitro. Mechanically, RBM24 positively regulated Runx1t1 expression in BC cells by binding to and enhancing Runx1t1 mRNA stability. Runx1t1 in turn promoted RBM24 expression by interacting with TCF4. Furthermore, Runx1t1 in turn promoted RBM24 expression by interacting with the transcription factor TCF4 and depressing transcription of miR-625-5p, which directly targets and normally suppresses RBM24 expression. RBM24-regulated BC cells proliferation was moderated via the Runx1t1/TCF4/miR-625-5p feedback loop.Conclusions: In summary, these results indicate that a RBM24/Runx1t1/TCF4/miR-625-5p positive feedback loop plays a key role in BC oncogenesis. Disruption of this pathway may be a potential therapeutic strategy for BC treatment.

scholarly journals IP3/Ca2+ signals regulate larval to pupal transition under nutrient stress through the H3K36 methyltransferase dSET2

2020 ◽  
Author(s):  
Rishav Mitra ◽  
Shlesha Richhariya ◽  
Siddharth Jayakumar ◽  
Dimple Notani ◽  
Gaiti Hasan
Keyword(s):  
Dietary Protein ◽  
Feedback Loop ◽  
Deficient Diet ◽  
Release Channel ◽  
Regulate Gene Expression ◽  
Critical Weight ◽  
Histone 3 ◽  
Intracellular Ca ◽  
Protein Deficient Diet ◽  
Neuronal Genes

AbstractPersistent loss of dietary protein usually signals a shutdown of key metabolic pathways. In Drosophila larvae, that have crossed “critical weight” and can pupariate to form viable adults, such a metabolic shut-down would needlessly lead to death. IP3/Ca2+ signals in certain interneurons (vGlutVGN6341) allow Drosophila larvae to pupariate on a protein-deficient diet by partially circumventing this shutdown through upregulation of neuropeptide signaling and the expression of ecdysone synthesis genes. Here we show that IP3/Ca2+ signals in vGlutVGN6341 neurons drive expression of dSET2, a Drosophila Histone 3 Lysine 36 methyltransferase. Further, dSET2 expression is required for larvae to pupariate in the absence of dietary protein. IP3/Ca2+ signal-driven dSET2 expression upregulates key Ca2+ signaling genes through a novel positive feedback loop. Transcriptomic studies coupled with analysis of existing ChIP-seq datasets identified genes from larval and pupal stages, that normally exhibit robust H3K36 trimethyl marks on their gene bodies and concomitantly undergo stronger downregulation by knockdown of either an intracellular Ca2+ release channel the IP3R or dSET2. IP3/Ca2+ signals thus regulate gene expression through dSET2 mediated H3K36 marks on select neuronal genes for the larval to pupal transition.

scholarly journals Shared and disease-specific host gene-microbiome interactions across human diseases

2021 ◽  
Author(s):  
Sambhawa Priya ◽  
Michael B. Burns ◽  
Tonya Ward ◽  
Ruben A. T. Mars ◽  
Beth Adamowicz ◽  
...  
Keyword(s):  
Host Gene ◽  
Gastrointestinal Disorders ◽  
Gut Microbes ◽  
Specific Host ◽  
Specific Manner ◽  
Inflammatory Bowel ◽  
Irritable Bowel ◽  
Potential Interactions ◽  
Host Genes ◽  
Disease Specific

While the gut microbiome and host gene regulation separately contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here, we developed a machine learning-based framework to jointly analyze host transcriptomic and microbiome profiles from 416 colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease, and irritable bowel syndrome. We identified potential interactions between gut microbes and host genes that are disease-specific, as well as interactions that are shared across the three diseases, involving host genes and gut microbes previously implicated in gastrointestinal inflammation, gut barrier protection, energy metabolism, and tumorigenesis. In addition, we found that mucosal gut microbes that have been associated with all three diseases, such as Streptococcus, interact with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes.

Intragenic tRNA-promoted R-loops orchestrate transcription interference for plant oxidative stress responses

2021 ◽  
Author(s):  
Kunpeng Liu ◽  
Qianwen Sun
Keyword(s):  
Oxidative Stress ◽  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Rna Polymerases ◽  
Host Gene ◽  
Trna Genes ◽  
Nudix Hydrolase ◽  
C Subunit ◽  
Host Genes ◽  
Transcription Interference

Abstract Eukaryotic genomes are transcribed by at least three RNA polymerases, RNAPI, II, and III. Co-transcriptional R-loops play diverse roles in genome regulation and maintenance. However, little is known about how R-loops regulate transcription interference, the transcriptional event that is caused by different RNA polymerases transcribing the same genomic templates. Here, we established that the intragenic tRNA genes can promote sense R-loop enrichment (named intra-tR-loops) in Arabidopsis thaliana, and found that intra-tR-loops are decreased in an RNAPIII mutant, nrpc7-1 (NUCLEAR RNA POLYMERASE C, SUBUNIT 7). NRPC7 is co-localized with RNAPIIS2P at intragenic tRNA genes and interferes with RNAPIIS2P elongation. Conversely, the binding of NRPC7 at intragenic tRNA genes is increased following inhibition of RNAPII elongation. The transcription of specific tRNA host genes is inhibited by RNAPIII, and the inhibition of tRNA host genes is intra-tR-loop dependent. Moreover, alleviating the inhibition of tRNAPro-induced intra-tR-loops on its host gene AtNUDX1 (Arabidopsis Nudix hydrolase 1) promotes oxidative stress tolerance in Arabidopsis thaliana. Our work suggests intra-tR-loops regulate host gene expression by modulating RNA polymerases interference.

Aberrant Co-Expression of Micrornas and Host Genes in Leukemia: Evidence for a Common Transcript from Meta-Analysis and Microarray Data.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2232-2232
Author(s):  
Serban San-Marina ◽  
Fernando Suarez Saiz ◽  
Haytham Khoury ◽  
Mark D. Minden
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Gene Expression Data ◽  
Microarray Data ◽  
Meta Analysis ◽  
Host Gene ◽  
Expression Data ◽  
Host Gene Expression ◽  
Intronic Mirnas ◽  
Host Genes

Abstract In leukemia, the integrity of the transcriptome is altered by chromosomal translocations, deletions, duplications, as well as by epigenetic changes in chromatin structure. By targeting mRNAs for translational repression or RNase-dependent hydrolysis (AU-rich miRNAs or shRNA-like effects), the micro RNA (miRNA) component of the transcriptome is estimated to regulate expression of up to 30% of all proteins. Yet the causes and role of deregulated miRNA expression in malignancy are largely unknown, in part because promoter events are not characterized. Since more than one-third of all known mammalian miRNA genes are encoded in the introns of protein-coding genes they may be regulated by the same promoter events that regulate host-gene mRNA expression. To provide experimental validation for coordinated expression of miRNAs and their host genes we compared Affymetrix U133A gene expression data for the promyelocytic NB4 and acute myelogenous leukemia AML2 cell lines with the expression of miRNA precursors. We found similar patterns of host gene expression in the two cell lines and a good correlation with the expression of miRNA precursors in NB4 cells (r=0.464, N=30 miRNAs, p<0.016). To further demonstrate that host gene mRNAs and miRNAs are expressed from common transcripts, we activated promoter events by enforcing the expression of Lyl1 a basic helix-loop-helix transcription factor that is often over-expressed in AML. This resulted in a greater than 2-fold increase in hsa-mir-126-1, 032-2, 107-1, 026a, -023b, -103-2, and 009-3-1 intronic miRNA precursors and a corresponding increase in host gene expression. Meta-analysis of microarray data across many experiments and platforms (available through Oncomine.org) has been used to study the cancer transcriptome. To help determine if intronic miRNAs play a substantial role in malignancy, we correlated host gene expression data with the expression of predicted miRNA targets. Less than 20% of all differentially expressed genes in leukemia and lymphoma were predicted targets, compared to 68% in breast cancer. Since the Gene Ontology term “ion binding” is most commonly associated with miRNA host genes, the data suggest that this cancer module is relatively inactive in leukemia and lymphoma, compared to breast cancer. Gene cluster analysis of a leukemia data set using only miRNA host gene expression was able to classify patients into similar (but not identical) subsets as did an analysis based on over 20,000 transcripts. To further demonstrate that miRNAs and their host genes are expressed from the same transcription unit, we correlated the expression of miRNA targets with that of genes that are either hosts for miRNAs or are situated several kilobases downstream of a miRNA, and thus belong to different transcription units. We applied this analysis to a subset of 81 AML patients that presented a normal karyotype and found significant negative correlations (p<0.01) between the levels of host genes for hsa-mir-15b, -103-1, and -128 and the expression ranks of their predicted gene targets, but no statistically significant correlation between non-host genes and targets for up-stream miRNAs. These data demonstrate co-regulated expression of host genes and intronic miRNAs and the usefulness of intronic miRNAs in cancer profiling.

The physiology of ovarian oxytocin

1999 ◽  
Vol 7 (1) ◽  
pp. 11-25 ◽  
Author(s):  
Richard Ivell
Keyword(s):  
Corpus Luteum ◽  
Feedback Loop ◽  
Uterine Contraction ◽  
Venous Blood ◽  
Mrna Levels ◽  
Ruminant Species ◽  
Bovine Corpus Luteum ◽  
Prostaglandin F ◽  
Very High ◽  
Specific Mrna

The notion of an oxytocic principle residing within the ovary is not new. In as early as 1910, Ott and Scott showed that an extract of bovine corpus luteum could induce milk letdown and uterine contraction. However, it took a further 70 years before the identification of this principle with the nonapeptide hormone oxytocin (OT) was made at the peptide and mRNA levels. This was followed by the identification of the peptide in ovarian tissues and ovarian venous blood from a wide variety of species, including humans, monkeys, pigs and ruminants (reviewed in 7, 8). For the majority of non-ruminant species the levels of expression of the peptide and its specific mRNA are relatively low, implying that whatever function the ovarian hormone has in these species, it is most likely to be at the local, paracrine level. Ruminants are an exception. Cows and sheep both produce very high levels of OT and OT-mRNA – the latter attaining concentrations of approximately 1% of all transcripts – within the corpus luteum of the early oestrous cycle. In ruminants, evolution has culminated in a systemic link between ovarian OT production and OT receptors in the endometrium of the uterus, inducing there the production of prostaglandin-F2∞ (PGF2∞) which completes a positive feedback loop to the ovary by stimulating further OT release (reviewed in 10). It is important to note, however, that natural selection can only act on a preexisting system. In this case, it has developed a systemic endocrine pathway in ruminants from a local ovarian OT system present probably in all mammals. There is even evidence for OT-related peptides, such as mesotocin and vasotocin, within the ovaries of marsupials and chicken, though their function is not known.

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