scholarly journals Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

2018 ◽  
Author(s):  
Peter Kindgren ◽  
Ryan Ard ◽  
Maxim Ivanov ◽  
Sebastian Marquardt
Keyword(s):  
Rna Polymerase Ii ◽  
Freezing Tolerance ◽  
Biological Significance ◽  
Antisense Strand ◽  
Fitness Costs ◽  
Profound Impact ◽  
Non Coding Rna ◽  
Cold Sensitive ◽  
Long Non Coding Rna ◽  
Transcriptional Direction

SummaryMost DNA in the genomes of higher organisms does not encode proteins, but is transcribed by RNA polymerase II (RNAPII) into long non-coding RNA (lncRNA). The biological significance of most lncRNA is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect the timing of maximal CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. asCBF1 transcription is anti-correlated with CBF1 expression. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVK-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Inversion of the transcriptional direction of a lncRNA cascade relative to the genes in a co-regulated cluster provides an elegant inbuilt negative feedback for cluster expression. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to suboptimal environmental conditions.

scholarly journals DNA Processing in The Context of Non-Coding Transcription

2020 ◽  
Author(s):  
Uthra Gowthaman ◽  
Desiré García-Pichardo ◽  
Yu Jin ◽  
Isabel Schwarz ◽  
Sebastian Marquardt
Keyword(s):  
Rna Polymerase Ii ◽  
Dna Sequences ◽  
Molecular Mechanisms ◽  
Environmental Changes ◽  
Biological Significance ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Functional Dna ◽  
The Impact ◽  
Dna Processing

RNA polymerase II (RNAPII) frequently transcribes non-protein coding DNA sequences in eukaryotic genomes into long non-coding RNA (lncRNA). Here, we focus on the impact of the act of lncRNA transcription on nearby functional DNA units. Distinct molecular mechanisms linked to the position of lncRNA relative to the coding gene illustrate how non-coding transcription controls gene expression. We review the biological significance of the act of lncRNA transcription on DNA processing, highlighting common themes, such as mediating cellular responses to environmental changes. This review presents the background in chromatin signaling to appreciate examples in different organisms where we can interpret functions of non-coding DNA through the act of RNAPII transcription.

scholarly journals Natural Antisense Transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock

2020 ◽  
Author(s):  
Rebecca A. Mosig ◽  
Allison N. Castaneda ◽  
Jacob C. Deslauriers ◽  
Landon P. Frazier ◽  
Kevin L. He ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Negative Feedback ◽  
Feedback Loop ◽  
Antisense Strand ◽  
Negative Feedback Loop ◽  
Novel Transcript ◽  
Non Coding Rna ◽  
In Trans ◽  
In Cis ◽  
Long Non Coding Rna

AbstractCircadian transcriptome studies identified a novel transcript at the Period2 (Per2) locus, which we named Per2AS. Per2AS is a long non-coding RNA transcribed from the antisense strand of Per2, and is expressed rhythmically and anti-phasic to Per2 mRNA. Previously, we mathematically tested the hypothesis that Per2AS and Per2 mutually inhibit each other’s expression by forming a double negative feedback loop, and found that Per2AS expands the oscillatory domain. In this study, we have experimentally tested this prediction by perturbing the expression of Per2AS in mouse fibroblasts. We found that Per2AS represses Per2 pre-transcriptionally in cis and regulates the amplitude of the circadian clock, but not period or phase. Unexpectedly, we also found that Per2 positively regulates Per2AS post-transcriptionally, indicating that Per2AS and Per2 form a single negative feedback loop. Because knock-down of Per2 does not recapitulate the phenotypes of Per2AS perturbation and Per2AS also activates Bmal1 in trans, we propose that Per2AS regulates the amplitude of the circadian clock without producing a protein by rewiring the molecular clock circuit.

scholarly journals A long non-coding RNA is required for targeting centromeric protein A to the human centromere

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Delphine Quénet ◽  
Yamini Dalal
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Biochemical Characterization ◽  
Protein A ◽  
Human Centromere ◽  
Non Coding Rna ◽  
Histone H3 Variant ◽  
Centromeric Protein ◽  
Long Non Coding Rna

The centromere is a specialized chromatin region marked by the histone H3 variant CENP-A. Although active centromeric transcription has been documented for over a decade, the role of centromeric transcription or transcripts has been elusive. Here, we report that centromeric α-satellite transcription is dependent on RNA Polymerase II and occurs at late mitosis into early G1, concurrent with the timing of new CENP-A assembly. Inhibition of RNA Polymerase II-dependent transcription abrogates the recruitment of CENP-A and its chaperone HJURP to native human centromeres. Biochemical characterization of CENP-A associated RNAs reveals a 1.3 kb molecule that originates from centromeres, which physically interacts with the soluble pre-assembly HJURP/CENP-A complex in vivo, and whose down-regulation leads to the loss of CENP-A and HJURP at centromeres. This study describes a novel function for human centromeric long non-coding RNAs in the recruitment of HJURP and CENP-A, implicating RNA-based chaperone targeting in histone variant assembly.

scholarly journals The Intriguing Conundrum of a Nonconserved Multifunctional Protein of Citrus Tristeza Virus That Interacts with a Viral Long Non-Coding RNA

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2129
Author(s):  
Sung-Hwan Kang ◽  
Vicken Aknadibossian ◽  
Laxmi Kharel ◽  
Shachinthaka D. Dissanayaka Mudiyanselage ◽  
Ying Wang ◽  
...  
Keyword(s):  
Virus Infection ◽  
Citrus Tristeza Virus ◽  
Biological Significance ◽  
Wild Type Virus ◽  
Virus Protein ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Tristeza Virus ◽  
Citrus Tristeza

Citrus tristeza virus (CTV), the largest non-segmented plant RNA virus, has several peculiar features, among which is the production of a 5′-terminal long non-coding RNA (lncRNA) termed low-molecular-weight tristeza 1 (LMT1). In this study, we found that p33, a unique viral protein that performs multiple functions in the virus infection cycle, specifically binds LMT1, both in vivo and in vitro. These results were obtained through the expression of p33 under the context of the wild type virus infection or along with a mutant CTV variant that does not produce LMT1 as well as via ectopic co-expression of p33 with LMT1 in Nicotiana benthamiana leaves followed by RNA immunoprecipitation and rapid amplification of cDNA ends assays. Further experiments in which a recombinant p33 protein and an in vitro transcribed full-length LMT1 RNA or its truncated fragments were subjected to an electrophoretic mobility shift assay demonstrated that p33 binds to at least two distinct regions within LMT1. To the best of our knowledge, this is the first report of a plant virus protein binding to a lncRNA produced by the same virus. The biological significance of the interaction between these two viral factors is discussed.

Innate immune responses and type 1 diabetes: A role for a long non-coding RNA?

2014 ◽  
Vol 9 (S 01) ◽  
Author(s):  
MP Ashton ◽  
I Tan ◽  
L Mackin ◽  
C Elso ◽  
E Chu ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Immune Responses ◽  
Innate Immune ◽  
Innate Immune Responses ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Long non-coding RNA expression profiles in human parathyroid tumors

2017 ◽  
Author(s):  
Annamaria Morotti ◽  
Irene Forno ◽  
Valentina Andre ◽  
Andrea Terrasi ◽  
Chiara Verdelli ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Rna Expression ◽  
Parathyroid Tumors ◽  
Non Coding Rna ◽  
Long Non Coding Rna

The Variant rs145204276 of GAS5 is Associated with the Development and Prognosis of Gastric Cancer

2018 ◽  
Vol 27 (1) ◽  
pp. 19-24 ◽  
Author(s):  
Qianjun Li ◽  
Gang Ma ◽  
Huimin Guo ◽  
Suhua Sun ◽  
Ying Xu ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Survival Rate ◽  
Cancer Progression ◽  
Regulatory Mechanism ◽  
Tumor Stage ◽  
Kaplan Meier ◽  
Non Coding Rna ◽  
Early Tumor ◽  
Long Non Coding Rna ◽  
Clinicopathological Variables

Background & Aims: Down-regulation of the growth arrest specific transcript 5 (GAS5) (long non-coding RNA) is associated with cell proliferation of gastric cancer (GC) and a poor prognosis. We aimed to investigate whether the variant rs145204276 of GAS5 is associated with the prognosis of GC in the Chinese population, and to unveil the regulatory mechanism underlying the GAS5 expression in GC tissues.Method: 1,253 GC patients and 1,354 healthy controls were included. The frequency of the genotype del/del and the allele del of rs145204276 were compared between the patients and the controls and between different subgroups of patients classified by clinicopathological variables. The overall survival rate was analyzed according to the Kaplan-Meier method using the log-rank test.Results: The frequency of genotype del/del was significantly lower in patients than in the controls (7.0% vs. 9.1%, p = 0.001). Kaplan-Meier analysis showed that genotype del/del was significantly associated with a higher survival rate (p = 0.01). Patients with late tumor stage were found to have a significantly lower rate of genotype del/del than those with an early tumor stage (4.9% vs. 8.8%, p = 0.01). Patients with UICC III and IV were found to have a significantly lower rate of genotype del/del than those with UICC I and II (5.3% vs. 8.1%, p = 0.02).Conclusion: The variant rs145204276 of GAS5 is associated with the development and prognosis of GC. The allele del of rs145204276 is associated with a remarkably lower incidence of cancer progression and metastasis.

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