miRNAs and neural alternative polyadenylation specify the virgin behavioral state

SummaryHow are diverse regulatory strategies integrated to impose appropriately patterned gene expression that underlie in vivo phenotypes? Here, we reveal how coordinated miRNA regulation and neural-specific alternative polyadenylation (APA) of a single locus controls complex behaviors. Our entry was the unexpected observation that deletion of Bithorax-Complex (BX-C) miRNAs converts virgin female flies into a subjective post-mated behavioral state, normally induced by seminal proteins following copulation. Strikingly, this behavioral switch is directly attributable to misregulation of homothorax (hth). We localize specific CNS abdominal neurons where de-repressed Hth compromises virgin behavior in BX-C miRNA mutants. Moreover, we use genome engineering to demonstrate that precise mutation of hth 3’UTR sites for BX-C miRNAs, or deletion of its neural 3’ UTR extension containing most of these sites, both induce post-mated behaviors in virgins. Thus, facilitation of miRNA-mediated repression by neural APA is required for virgin females to execute behaviors appropriate to their internal state.

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Calcium functional imaging with high-resolution CT in the inner ear

Scientific Reports ◽

10.1038/s41598-021-94857-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hisaya Tanioka ◽

Sayaka Tanioka

Keyword(s):

Internal State ◽

Texture Synthesis ◽

Biological Information ◽

Endolymphatic Sac ◽

Otolith Organs ◽

Synthesis Algorithm ◽

Utricular Macula ◽

Positional Vertigo ◽

Paroxysmal Positional Vertigo

AbstractAlthough the otolith and otolith organs correlate with vertigo and instability, there is no method to investigate them without harmful procedures. We will create the technique for 3D microanatomical images of them, and investigate the in vivo internal state and metabolisms. The otolith and otolith organs images were reconstructed from a texture synthesis algorithm under the skull volume rendering algorithm using a cutting-plane method. The utricular macula was elongated pea-shaped. The saccular macula was almost bud-shaped. The changes in the amount of CaCO3 in the maculae and the endolymphatic sac showed various morphologies, reflecting the balance status of each subject. Both shapes and volumes were not always constant depending on time. In Meniere’s disease (MD), the saccular macula was larger and the utricular macula was smaller. In benign paroxysmal positional vertigo (BPPV), the otolith increased in the utricular macula but did not change much in the saccular macula. The saccule, utricle, and endolymphatic sac were not constantly shaped according to their conditions. These created 3D microanatomical images can allow detailed observations of changes in physiological and biological information. This imaging technique will contribute to our understanding of pathology and calcium metabolism in the in vivo vestibulum.

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Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence

Nature Communications ◽

10.1038/s41467-021-21894-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ryan Lusk ◽

Evan Stene ◽

Farnoush Banaei-Kashani ◽

Boris Tabakoff ◽

Katerina Kechris ◽

...

Keyword(s):

Rna Sequencing ◽

Dna Sequence ◽

Mammalian Species ◽

Alternative Polyadenylation ◽

Sequence Information ◽

Rna Seq ◽

Average Precision ◽

Polyadenylation Sites ◽

Dna Nucleotide Sequence

AbstractAnnotation of polyadenylation sites from short-read RNA sequencing alone is a challenging computational task. Other algorithms rooted in DNA sequence predict potential polyadenylation sites; however, in vivo expression of a particular site varies based on a myriad of conditions. Here, we introduce aptardi (alternative polyadenylation transcriptome analysis from RNA-Seq data and DNA sequence information), which leverages both DNA sequence and RNA sequencing in a machine learning paradigm to predict expressed polyadenylation sites. Specifically, as input aptardi takes DNA nucleotide sequence, genome-aligned RNA-Seq data, and an initial transcriptome. The program evaluates these initial transcripts to identify expressed polyadenylation sites in the biological sample and refines transcript 3′-ends accordingly. The average precision of the aptardi model is twice that of a standard transcriptome assembler. In particular, the recall of the aptardi model (the proportion of true polyadenylation sites detected by the algorithm) is improved by over three-fold. Also, the model—trained using the Human Brain Reference RNA commercial standard—performs well when applied to RNA-sequencing samples from different tissues and different mammalian species. Finally, aptardi’s input is simple to compile and its output is easily amenable to downstream analyses such as quantitation and differential expression.

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CRISPR/Cas9-mediated genome engineering of CXCR4 decreases the malignancy of hepatocellular carcinoma cells in vitro and in vivo

Oncology Reports ◽

10.3892/or.2017.5601 ◽

2017 ◽

Vol 37 (6) ◽

pp. 3565-3571 ◽

Cited By ~ 7

Author(s):

Xiaoli Wang ◽

Wenmei Zhang ◽

Yan Ding ◽

Xingrong Guo ◽

Yahong Yuan ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Genome Engineering ◽

Carcinoma Cells ◽

Hepatocellular Carcinoma Cells

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Tissue-specific alternative splicing of hybrid Shaker/lacZ genes correlates with kinetic differences in Shaker K+ currents in vivo

Neuron ◽

10.1016/0896-6273(95)90318-6 ◽

1995 ◽

Vol 14 (3) ◽

pp. 613-623 ◽

Cited By ~ 14

Author(s):

John R Mottes ◽

Linda E Iverson

Keyword(s):

Alternative Splicing ◽

Tissue Specific ◽

Specific Alternative ◽

K Currents

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Design of a biochemical circuit motif for learning linear functions

Journal of The Royal Society Interface ◽

10.1098/rsif.2014.0902 ◽

2014 ◽

Vol 11 (101) ◽

pp. 20140902 ◽

Cited By ~ 6

Author(s):

Matthew R. Lakin ◽

Amanda Minnich ◽

Terran Lane ◽

Darko Stefanovic

Keyword(s):

Internal State ◽

Linear Functions ◽

Learning Performance ◽

Adaptive Behaviour ◽

Biological Processes ◽

Biochemical System ◽

Biochemical Systems ◽

Robustness To Noise ◽

Novel Design

Learning and adaptive behaviour are fundamental biological processes. A key goal in the field of bioengineering is to develop biochemical circuit architectures with the ability to adapt to dynamic chemical environments. Here, we present a novel design for a biomolecular circuit capable of supervised learning of linear functions, using a model based on chemical reactions catalysed by DNAzymes. To achieve this, we propose a novel mechanism of maintaining and modifying internal state in biochemical systems, thereby advancing the state of the art in biomolecular circuit architecture. We use simulations to demonstrate that the circuit is capable of learning behaviour and assess its asymptotic learning performance, scalability and robustness to noise. Such circuits show great potential for building autonomous in vivo nanomedical devices. While such a biochemical system can tell us a great deal about the fundamentals of learning in living systems and may have broad applications in biomedicine (e.g. autonomous and adaptive drugs), it also offers some intriguing challenges and surprising behaviours from a machine learning perspective.

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Characterization, modelling and mitigation of gene expression burden in mammalian cells

10.1101/867549 ◽

2019 ◽

Cited By ~ 2

Author(s):

T Frei ◽

F Cella ◽

F Tedeschi ◽

J Gutierrez ◽

GB Stan ◽

...

Keyword(s):

Gene Expression ◽

Mammalian Cells ◽

Genome Engineering ◽

Host Cells ◽

Genetic Circuits ◽

Circuit Performance ◽

Resource Requirements ◽

Synthetic Circuit ◽

Resource Aware

AbstractDespite recent advances in genome engineering, the design of genetic circuits in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here we demonstrate that competition for limited transcriptional and translational resources dynamically couples otherwise independent co-expressed exogenous genes, leading to diminished performance and contributing to the divergence between intended and actual function. We also show that the expression of endogenous genes is likewise impacted when genetic payloads are expressed in the host cells. Guided by a resource-aware mathematical model and our experimental finding that post-transcriptional regulators have a large capacity for resource redistribution, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the novel use of endogenous miRNAs as integral components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement of in vivo synthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells.

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Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy

10.1101/637199 ◽

2019 ◽

Cited By ~ 1

Author(s):

Annie Lee ◽

Chandana Kondapalli ◽

Daniel M. Virga ◽

Tommy L. Lewis ◽

So Yeon Koo ◽

...

Keyword(s):

Genome Engineering ◽

Pyramidal Neurons ◽

Es Cells ◽

Mitochondrial Fission ◽

Significant Loss ◽

Synaptic Loss ◽

Structural Remodeling ◽

Swedish Mutation ◽

Human Neurons

AbstractDuring the early stages of Alzheimer’s disease (AD) in both mouse models and human patients, soluble forms of Amyloid-β1-42 oligomers (Aβ42o) trigger loss of excitatory synapses (synaptotoxicity) in cortical and hippocampal pyramidal neurons (PNs) prior to the formation of insoluble Aβ plaques. We observed a spatially restricted structural remodeling of mitochondria in the apical tufts of CA1 PNs dendrites in the hAPPSWE,IND transgenic AD mouse model (J20), corresponding to the dendritic domain receiving presynaptic inputs from the entorhinal cortex and where the earliest synaptic loss is detected in vivo. We also observed significant loss of mitochondrial biomass in human neurons derived from a new model of human ES cells where CRISPR-Cas9-mediated genome engineering was used to introduce the ‘Swedish’ mutation bi-allelically (APPSWE/SWE). Recent work uncovered that Aβ42o mediates synaptic loss by over-activating the CAMKK2-AMPK kinase dyad, and that AMPK is a central regulator of mitochondria homeostasis in non-neuronal cells. Here, we demonstrate that Aβ42o-dependent over-activation of CAMKK2-AMPK mediates synaptic loss through coordinated MFF-dependent mitochondrial fission and ULK2-dependent mitophagy in dendrites of PNs. We also found that the ability of Aβ42o-dependent mitochondrial remodeling to trigger synaptic loss requires the ability of AMPK to phosphorylate Tau on Serine 262. Our results uncover a unifying stress-response pathway triggered by Aβo and causally linking structural remodeling of dendritic mitochondria to synaptic loss.

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TSAPA: identification of tissue-specific alternative polyadenylation sites in plants

Bioinformatics ◽

10.1093/bioinformatics/bty044 ◽

2018 ◽

Vol 34 (12) ◽

pp. 2123-2125 ◽

Cited By ~ 3

Author(s):

Guoli Ji ◽

Moliang Chen ◽

Wenbin Ye ◽

Sheng Zhu ◽

Congting Ye ◽

...

Keyword(s):

Alternative Polyadenylation ◽

Tissue Specific ◽

Specific Alternative ◽

Polyadenylation Sites

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miRNA Clusters with Down-Regulated Expression in Human Colorectal Cancer and Their Regulation

International Journal of Molecular Sciences ◽

10.3390/ijms21134633 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4633 ◽

Cited By ~ 1

Author(s):

Paulína Pidíkova ◽

Richard Reis ◽

Iveta Herichova

Keyword(s):

Colorectal Cancer ◽

Transcriptional Control ◽

In Vitro Models ◽

Mirna Regulation ◽

Regulated Expression ◽

Mirna Clusters ◽

Position Regulation ◽

Non Coding Rnas

Regulation of microRNA (miRNA) expression has been extensively studied with respect to colorectal cancer (CRC), since CRC is one of the leading causes of cancer mortality worldwide. Transcriptional control of miRNAs creating clusters can be, to some extent, estimated from cluster position on a chromosome. Levels of miRNAs are also controlled by miRNAs “sponging” by long non-coding RNAs (ncRNAs). Both types of miRNA regulation strongly influence their function. We focused on clusters of miRNAs found to be down-regulated in CRC, containing miR-1, let-7, miR-15, miR-16, miR-99, miR-100, miR-125, miR-133, miR-143, miR-145, miR-192, miR-194, miR-195, miR-206, miR-215, miR-302, miR-367 and miR-497 and analysed their genome position, regulation and functions. Only evidence provided with the use of CRC in vivo and/or in vitro models was taken into consideration. Comprehensive research revealed that down-regulated miRNA clusters in CRC are mostly located in a gene intron and, in a majority of cases, miRNA clusters possess cluster-specific transcriptional regulation. For all selected clusters, regulation mediated by long ncRNA was experimentally demonstrated in CRC, at least in one cluster member. Oncostatic functions were predominantly linked with the reviewed miRNAs, and their high expression was usually associated with better survival. These findings implicate the potential of down-regulated clusters in CRC to become promising multi-targets for therapeutic manipulation.

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