scholarly journals Cellular abundance shapes function in piRNA-guided genome defense

2021 ◽  
Author(s):  
Pavol Genzor ◽  
Parthena Konstantinidou ◽  
Daniel Stoyko ◽  
Amirhossein Manzourolajdad ◽  
Celine Marlin Andrews ◽  
...  
Keyword(s):  
Rna Interference ◽  
Sequence Space ◽  
Arms Race ◽  
Skewed Distribution ◽  
Guide Rnas ◽  
Genome Defense ◽  
Individual Sequences ◽  
Cell Diversity ◽  
Reporter Assays ◽  
And Function

Defense against genome invaders universally relies on RNA-guided immunity. Prokaryotic CRISPR-Cas and eukaryotic RNA interference pathways recognize targets by complementary base-pairing, which places the sequences of their guide RNAs at the center of self/nonself discrimination. Here, we explore the sequence space of PIWI-interacting RNAs (piRNAs), the genome defense of animals, and establish functional priority among individual sequences. Our results reveal that only the topmost abundant piRNAs are commonly present in every cell, whereas rare sequences generate cell-to-cell diversity in flies and mice. We identify a skewed distribution of sequence abundance as a hallmark of piRNA populations and show that quantitative differences of more than a 1000-fold are established by conserved mechanisms of biogenesis. Finally, our genomics analyses and direct reporter assays reveal that abundance determines function in piRNA-guided genome defense. Taken together, we identify an effective sequence space and untangle two classes of piRNAs that differ in complexity and function. The first class represents the topmost abundant sequences and drives silencing of genomic parasites. The second class sparsely covers an enormous sequence space. These rare piRNAs cannot function in every cell, every individual, or every generation but create diversity with potential for adaptation in the ongoing arms race with genome invaders.

scholarly journals Cellular abundance shapes function in piRNA-guided genome defense

2021 ◽  
Author(s):  
Pavol Genzor ◽  
Parthena Konstantinidou ◽  
Daniel Stoyko ◽  
Amirhossein Manzourolajdad ◽  
Celine Marlin Andrews ◽  
...  
Keyword(s):  
Sequence Space ◽  
Arms Race ◽  
Skewed Distribution ◽  
Guide Rnas ◽  
Genome Defense ◽  
Individual Sequences ◽  
Cell Diversity ◽  
Reporter Assays ◽  
And Function ◽  
First Time

Defense against genome invaders universally relies on RNA-guided immunity. Prokaryotic CRISPR/Cas and eukaryotic RNA interference pathways recognize targets by complementary base-pairing, which places the sequences of their guide RNAs at the center of self/nonself discrimination. Here, we explore the sequence space of PIWI-interacting RNAs (piRNAs), the genome defense of animals, and establish functional priority among individual sequences for the first time. Our results reveal that only the topmost abundant piRNAs are commonly present in every cell, while rare sequences generate cell-to-cell diversity in flies and mice. We identify a skewed distribution of sequence abundance as a hallmark of piRNA populations and show that quantitative differences of more than a thousand-fold are established by conserved mechanisms of biogenesis. Finally, our genomics analyses and direct reporter assays reveal that abundance determines function in piRNA-guided genome defense. Taken together, we identify an effective sequence space and untangle two classes of piRNAs that differ in complexity and function. The first class represents the topmost abundant sequences and drives silencing of genomic parasites. The second class sparsely covers an enormous sequence space. These rare piRNAs cannot function in every cell, every individual or every generation but create diversity with potential for adaptation in the ongoing arms race with genome invaders.

scholarly journals MSA Transformer

2021 ◽  
Author(s):  
Roshan Rao ◽  
Jason Liu ◽  
Robert Verkuil ◽  
Joshua Meier ◽  
John F. Canny ◽  
...  
Keyword(s):  
Structure Learning ◽  
State Of The Art ◽  
Language Model ◽  
Language Modeling ◽  
Language Models ◽  
Multiple Sequence ◽  
Wide Margin ◽  
Current State ◽  
Individual Sequences ◽  
And Function

AbstractUnsupervised protein language models trained across millions of diverse sequences learn structure and function of proteins. Protein language models studied to date have been trained to perform inference from individual sequences. The longstanding approach in computational biology has been to make inferences from a family of evolutionarily related sequences by fitting a model to each family independently. In this work we combine the two paradigms. We introduce a protein language model which takes as input a set of sequences in the form of a multiple sequence alignment. The model interleaves row and column attention across the input sequences and is trained with a variant of the masked language modeling objective across many protein families. The performance of the model surpasses current state-of-the-art unsupervised structure learning methods by a wide margin, with far greater parameter efficiency than prior state-of-the-art protein language models.

scholarly journals The effect of hairpin loop on the structure and gene expression activity of the long-loop G-quadruplex

2021 ◽  
Author(s):  
Subramaniyam Ravichandran ◽  
Maria Razzaq ◽  
Nazia Parveen ◽  
Ambarnil Ghosh ◽  
Kyeong Kyu Kim
Keyword(s):  
Gene Expression ◽  
Rna Structure ◽  
Biological Significance ◽  
Cellular Functions ◽  
Hairpin Loops ◽  
G Quadruplex ◽  
Reporter Assays ◽  
Expression Activity ◽  
The Stability ◽  
And Function

Abstract G-quadruplex (G4), a four-stranded DNA or RNA structure containing stacks of guanine tetrads, plays regulatory roles in many cellular functions. So far, conventional G4s containing loops of 1–7 nucleotides have been widely studied. Increasing experimental evidence suggests that unconventional G4s, such as G4s containing long loops (long-loop G4s), play a regulatory role in the genome by forming a stable structure. Other secondary structures such as hairpins in the loop might thus contribute to the stability of long-loop G4s. Therefore, investigation of the effect of the hairpin-loops on the structure and function of G4s is required. In this study, we performed a systematic biochemical investigation of model G4s containing long loops with various sizes and structures. We found that the long-loop G4s are less stable than conventional G4s, but their stability increased when the loop forms a hairpin (hairpin-G4). We also verified the biological significance of hairpin-G4s by showing that hairpin-G4s present in the genome also form stable G4s and regulate gene expression as confirmed by in cellulo reporter assays. This study contributes to expanding the scope and diversity of G4s, thus facilitating future studies on the role of G4s in the human genome.

scholarly journals Mechanism and Function of Antiviral RNA Interference in Mice

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Qingxia Han ◽  
Gang Chen ◽  
Jinyan Wang ◽  
David Jee ◽  
Wan-Xiang Li ◽  
...  
Keyword(s):  
Rna Interference ◽  
Rna Replication ◽  
Interferon Response ◽  
Type I ◽  
Small Interfering Rnas ◽  
Guide Rna ◽  
Argonaute 2 ◽  
Adult Mice ◽  
And Function ◽  
Nodamura Virus

ABSTRACT Distinct mammalian RNA viruses trigger Dicer-mediated production of virus-derived small-interfering RNAs (vsiRNA) and encode unrelated proteins to suppress vsiRNA biogenesis. However, the mechanism and function of the mammalian RNA interference (RNAi) response are poorly understood. Here, we characterized antiviral RNAi in a mouse model of infection with Nodamura virus (NoV), a mosquito-transmissible positive-strand RNA virus encoding a known double-stranded RNA (dsRNA)-binding viral suppressor of RNAi (VSR), the B2 protein. We show that inhibition of NoV RNA replication by antiviral RNAi in mouse embryonic fibroblasts (MEFs) requires Dicer-dependent vsiRNA biogenesis and Argonaute-2 slicer activity. We found that VSR-B2 of NoV enhances viral RNA replication in wild-type but not RNAi-defective MEFs such as Argonaute-2 catalytic-dead MEFs and Dicer or Argonaute-2 knockout MEFs, indicating that VSR-B2 acts mainly by suppressing antiviral RNAi in the differentiated murine cells. Consistently, VSR-B2 expression in MEFs has no detectable effect on the induction of interferon-stimulated genes or the activation of global RNA cleavages by RNase L. Moreover, we demonstrate that NoV infection of adult mice induces production of abundant vsiRNA active to guide RNA slicing by Argonaute-2. Notably, VSR-B2 suppresses the biogenesis of both vsiRNA and the slicing-competent vsiRNA-Argonaute-2 complex without detectable inhibition of Argonaute-2 slicing guided by endogenous microRNA, which dramatically enhances viral load and promotes lethal NoV infection in adult mice either intact or defective in the signaling by type I, II, and III interferons. Together, our findings suggest that the mouse RNAi response confers essential protective antiviral immunity in both the presence and absence of the interferon response. IMPORTANCE Innate immune sensing of viral nucleic acids in mammals triggers potent antiviral responses regulated by interferons known to antagonize the induction of RNA interference (RNAi) by synthetic long double-stranded RNA (dsRNA). Here, we show that Nodamura virus (NoV) infection in adult mice activates processing of the viral dsRNA replicative intermediates into small interfering RNAs (siRNAs) active to guide RNA slicing by Argonaute-2. Genetic studies demonstrate that NoV RNA replication in mouse embryonic fibroblasts is inhibited by the RNAi pathway and enhanced by the B2 viral RNAi suppressor only in RNAi-competent cells. When B2 is rendered nonexpressing or nonfunctional, the resulting mutant viruses become nonpathogenic and are cleared in adult mice either intact or defective in the signaling by type I, II, and III interferons. Our findings suggest that mouse antiviral RNAi is active and necessary for the in vivo defense against viral infection in both the presence and absence of the interferon response.

scholarly journals DICER1 and PRKRA in Colon Adenocarcinoma

2008 ◽  
Vol 3 ◽  
pp. BMI.S600 ◽  
Author(s):  
S. Chiosea ◽  
M. Acquafondata ◽  
J. Luo ◽  
SF. Kuan ◽  
RR. Seethala
Keyword(s):  
Rna Interference ◽  
Gene Array ◽  
Colon Adenocarcinoma ◽  
Clinicopathologic Features ◽  
Array Analysis ◽  
Gene Array Analysis ◽  
Microrna Profile ◽  
The Status ◽  
And Function ◽  
Dicer1 Expression

Differential microRNA expression in colon adenocarcinoma (CA) was previously reported. MicroRNA biogenesis and function requires a set of proteins designated as the microRNA machinery, which includes DICER1 and PRKRA. Loss of heterozygosity at 14q32.13 DICER1 locus was detected in up to 60% of CA cases. The in silico gene array analysis of CA showed down-regulation of DICER1 and an up-regulation of PRKRA. Immunohistochemically, DICER1 expression was abnormal in 65% of CA (95 of 147 cases). PRKRA was deregulated in 70% of CA (32 of 46 cases). Expression of DICER1 and PRKRA was correlated with clinicopathologic features of CA. DICER1 up-regulation was seen more commonly in women. Only 10 of 46 cases immunostained for both DICER1 and PRKRA showed normal levels of both DICER1 and PRKRA. Microsatellite status of 32 cases was determined. Microsatellite instable cases showed DICER1 up-regulation more commonly when compared to microsatellite stable cases; however, this trend was not statistically significant. Abnormal DICER1 and/or PRKRA expression might explain the observed changes in microRNA profile. The status of the endogenous DICER1 and PRKRA in CA may help to predict the response to future RNA interference-based therapy.

Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency

2005 ◽  
Vol 23 (11) ◽  
pp. 1440-1444 ◽  
Author(s):  
Volker Patzel ◽  
Sascha Rutz ◽  
Isabell Dietrich ◽  
Christian Köberle ◽  
Alexander Scheffold ◽  
...  
Keyword(s):  
Rna Interference ◽  
Guide Rnas

RNA Interference Decreases PAR-2 Expression and Function in Human Airway Smooth Muscle Cells

2006 ◽  
Vol 34 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Thomas Trian ◽  
Pierre-Olivier Girodet ◽  
Olga Ousova ◽  
Roger Marthan ◽  
J. Manuel Tunon-de-Lara ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Rna Interference ◽  
Smooth Muscle Cells ◽  
Airway Smooth Muscle ◽  
Muscle Cells ◽  
Airway Smooth Muscle Cells ◽  
Human Airway Smooth Muscle ◽  
Human Airway ◽  
And Function
Sign in / Sign up

Export Citation Format

Share Document