scholarly journals Characterization of Long Non-Coding RNAs in the Bollworm, Helicoverpa zea, and Their Possible Role in Cry1Ac-Resistance

Insects ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 12
Author(s):  
Roger D. Lawrie ◽  
Robert D. Mitchell ◽  
Jean Marcel Deguenon ◽  
Loganathan Ponnusamy ◽  
Dominic Reisig ◽  
...  
Keyword(s):  
Gene Expression ◽  
Helicoverpa Zea ◽  
Insect Pest ◽  
Field Resistance ◽  
Pest Species ◽  
Chemical Insecticide ◽  
Significant Differential Expression ◽  
Protein Coding ◽  
Non Coding Rnas

Multiple insect pest species have developed field resistance to Bt-transgenic crops. There has been a significant amount of research on protein-coding genes that contribute to resistance, such as the up-regulation of protease activity or altered receptors. However, our understanding of the role of non-protein-coding mechanisms in Bt-resistance is minimal, as is also the case for resistance to chemical pesticides. To address this problem relative to Bt, RNA-seq was used to examine statistically significant, differential gene expression between a Cry1Ac-resistant (~100-fold resistant) and Cry1Ac-susceptible strain of Helicoverpa zea, a prevalent caterpillar pest in the USA. Significant differential expression of putative long non-coding RNAs (lncRNAs) was found in the Cry1Ac-resistant strain (58 up- and 24 down-regulated gene transcripts with an additional 10 found only in resistant and four only in susceptible caterpillars). These lncRNAs were examined as potential pseudogenes and for their genomic proximity to coding genes, both of which can be indicative of regulatory relationships between a lncRNA and coding gene expression. A possible pseudogenic lncRNA was found with similarities to a cadherin. In addition, putative lncRNAs were found significantly proximal to a serine protease, ABC transporter, and CYP coding genes, potentially involved in the mechanism of Bt and/or chemical insecticide resistance. Characterization of non-coding genetic mechanisms in Helicoverpa zea will improve the understanding of the genomic evolution of insect resistance, improve the identification of specific regulators of coding genes in general (some of which could be important in resistance), and is the first step for potentially targeting these regulators for pest control and resistance management (using molecular approaches, such as RNAi and others).

scholarly journals Identification and characterization of the gene expression profiles for protein coding and non-coding RNAs of pancreatic ductal adenocarcinomas

Oncotarget ◽  
2015 ◽  
Vol 6 (22) ◽  
pp. 19070-19086 ◽  
Author(s):  
María Laura Gutiérrez ◽  
Luis Corchete ◽  
Cristina Teodosio ◽  
María Eugenia Sarasquete ◽  
María del Mar Abad ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Protein Coding ◽  
Non Coding Rnas ◽  
Identification And Characterization

Role of MicroRNAs and Long Non-Coding RNAs in Regulating Angiogenesis in Human Breast Cancer- A Molecular Medicine Perspective

2021 ◽  
Vol 22 ◽  
Author(s):  
Vandana Golhani ◽  
Suman Kumar Ray ◽  
Sukhes Mukherjee
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Signaling Pathways ◽  
Cancer Therapeutics ◽  
Molecular Medicine ◽  
Dependent Manner ◽  
Protein Coding ◽  
Controlled Systems ◽  
Expression Of Genes ◽  
Non Coding Rnas

: MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are proficient in regulating gene expression post-transcriptionally. Considering the recent trend in exploiting non-coding RNAs (ncRNAs) as cancer therapeutics, the potential use of miRNAs and lncRNAs as biomarkers and novel therapeutic agents against angiogenesis is an important scientific aspect. An estimated 70% of the genome is actively transcribed, only 2% of which codes for known protein-coding genes. Long noncoding RNAs (lncRNAs) are a large and diverse class of RNAs > 200 nucleotides in length, and not translated into protein, and are of utmost importance and it governs the expression of genes in a temporal, spatial, and cell context-dependent manner. Angiogenesis is an essential process for organ morphogenesis and growth during development, and it is relevant during the repair of wounded tissue in adults. It is coordinated by an equilibrium of pro-and anti-angiogenic factors; nevertheless, when affected, it promotes several diseases, including breast cancer. Signaling pathways involved here are tightly controlled systems that regulate the appropriate timing of gene expression required for the differentiation of cells down a particular lineage essential for proper tissue development. Lately, scientific reports are indicating that ncRNAs, such as miRNAs, and lncRNAs, play critical roles in angiogenesis related to breast cancer. The specific roles of various miRNAs and lncRNAs in regulating angiogenesis in breast cancer, with particular focus on the downstream targets and signaling pathways regulated by these ncRNAs with molecular medicine perspective, are highlighted in this write-up.

Protein-RNA interactome analysis reveals wide association of KSHV ORF57 with host non-coding RNAs and polysomes

2021 ◽  
Author(s):  
Beatriz Alvarado-Hernandez ◽  
Yanping Ma ◽  
Nishi R. Sharma ◽  
Vladimir Majerciak ◽  
Alexei Lobanov ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Splicing ◽  
Rna Binding ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
28S Rrna ◽  
Protein Coding ◽  
Infected Cells ◽  
Non Coding Rnas ◽  
Rna Interaction

Kaposi’s sarcoma-associated herpesvirus (KSHV) ORF57 is an RNA-binding post-transcriptional regulator. We recently applied an affinity-purified anti-ORF57 antibody to conduct ORF57-CLIP (Cross-linking Immunoprecipitation) in combination with RNA-sequencing (CLIP-seq) and analyzed the genome-wide host RNA transcripts in association with ORF57 in BCBL-1 cells with lytic KSHV infection. Mapping of the CLIPed RNA reads to the human genome (GRCh37) revealed that most of the ORF57-associated RNA reads were from rRNAs. The remaining RNA reads mapped to several classes of host non-coding and protein-coding mRNAs. We found ORF57 binds and regulates expression of a subset of host lncRNAs, including LINC00324, LINC00355, and LINC00839 which are involved in cell growth. ORF57 binds snoRNAs responsible for 18S and 28S rRNA modifications, but does not interact with fibrillarin and NOP58. We validated ORF57 interactions with 67 snoRNAs by ORF57-RNA immunoprecipitation (RIP)-snoRNA-array assays. Most of the identified ORF57 rRNA binding sites (BS) overlap with the sites binding snoRNAs. We confirmed ORF57-snoRA71B RNA interaction in BCBL-1 cells by ORF57-RIP and Northern blot analyses using a 32 P-labeled oligo probe from the 18S rRNA region complementary to snoRA71B. Using RNA oligos from the rRNA regions that ORF57 binds for oligo pulldown-Western blot assays, we selectively verified ORF57 interactions with 5.8S and 18S rRNAs. Polysome profiling revealed that ORF57 associates with both monosomes and polysomes and its association with polysomes increases PABPC1 binding to, but prevent Ago2 from polysomes. Our data indicate a functional correlation with ORF57 binding and suppression of Ago2 activities for ORF57 promotion of gene expression. Significance As an RNA-binding protein, KSHV ORF57 regulates RNA splicing, stability, and translation and inhibits host innate immunity by blocking the formation of RNA granules in virus infected cells. In this report, ORF57 was found to interact many host non-coding RNAs, including lncRNAs, snoRNAs and ribosomal RNAs to carry out additional unknown functions. ORF57 binds a group of lncRNAs via the identified RNA motifs by ORF57 CLIP-seq to regulate their expression. ORF57 associates with snoRNAs independently of fibrillarin and NOP58 proteins, and with ribosomal RNA in the regions that commonly bind snoRNAs. Knockdown of fibrillarin expression decreases the expression of snoRNAs and CDK4, but not affect viral gene expression. More importantly, we found that ORF57 binds translationally active polysomes and enhances PABPC-1 but prevents Ago2 association with polysomes. Data provide a compelling evidence on how ORF57 in KSHV infected cells might regulate protein synthesis by blocking Ago2’s hostile activities on translation.

scholarly journals Multiple Known Mechanisms and a Possible Role of an Enhanced Immune System in Bt-Resistance in a Field Population of the Bollworm, Helicoverpa zea: Differences in Gene Expression with RNAseq

2020 ◽  
Vol 21 (18) ◽  
pp. 6528
Author(s):  
Roger D. Lawrie ◽  
Robert D. Mitchell III ◽  
Jean Marcel Deguenon ◽  
Loganathan Ponnusamy ◽  
Dominic Reisig ◽  
...  
Keyword(s):  
Gene Expression ◽  
Serine Proteases ◽  
Helicoverpa Zea ◽  
Insect Pests ◽  
Global Gene Expression ◽  
Field Resistance ◽  
Bt Resistance ◽  
Imd Pathway ◽  
Immune Pathway

Several different agricultural insect pests have developed field resistance to Bt (Bacillus thuringiensis) proteins (ex. Cry1Ac, Cry1F, etc.) expressed in crops, including corn and cotton. In the bollworm, Helicoverpa zea, resistance levels are increasing; recent reports in 2019 show up to 1000-fold levels of resistance to Cry1Ac, a major insecticidal protein in Bt-crops. A common method to analyze global differences in gene expression is RNA-seq. This technique was used to measure differences in global gene expression between a Bt-susceptible and Bt-resistant strain of the bollworm, where the differences in susceptibility to Cry1Ac insecticidal proteins were 100-fold. We found expected gene expression differences based on our current understanding of the Bt mode of action, including increased expression of proteases (trypsins and serine proteases) and reduced expression of Bt-interacting receptors (aminopeptidases and cadherins) in resistant bollworms. We also found additional expression differences for transcripts that were not previously investigated, i.e., transcripts from three immune pathways-Jak/STAT, Toll, and IMD. Immune pathway receptors (ex. PGRPs) and the IMD pathway demonstrated the highest differences in expression. Our analysis suggested that multiple mechanisms are involved in the development of Bt-resistance, including potentially unrecognized pathways.

scholarly journals Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome

2019 ◽  
Author(s):  
Jason Talkish ◽  
Haller Igel ◽  
Rhonda J. Perriman ◽  
Lily Shiue ◽  
Sol Katzman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Isoforms ◽  
Yeast Genome ◽  
Protein Coding ◽  
Coding Sequences ◽  
New Genes ◽  
Eukaryotic Genes ◽  
Non Coding Rnas ◽  
The Creation ◽  
New Protein

AbstractIntrons are a prevalent feature of eukaryotic genomes, yet their origins and contributions to genome function and evolution remain mysterious. In budding yeast, repression of the highly transcribed intron-containing ribosomal protein genes (RPGs) globally increases splicing of non-RPG transcripts through reduced competition for the spliceosome. We show that under these “hungry spliceosome” conditions, splicing occurs at more than 150 previously unannotated locations we call protointrons that do not overlap known introns. Protointrons use a less constrained set of splice sites and branchpoints than standard introns, including in one case AT-AC in place of GT-AG. Protointrons are not conserved in all closely related species, suggesting that most are not under selection. Some are found in non-coding RNAs (e. g. CUTs and SUTs), where they may contribute to the creation of new genes. Others are found across boundaries between noncoding and coding sequences, or within coding sequences, where they offer pathways to the creation of new protein variants, or new regulatory controls for existing genes. We define protointrons as (1) nonconserved intron-like sequences that are (2) infrequently spliced, and importantly (3) are not currently understood to contribute to gene expression or regulation in the way that standard introns function. A very few protointrons in S. cerevisiae challenge this classification by their increased splicing frequency and potential function, consistent with the proposed evolutionary process of “intronization”, whereby new standard introns are created. This snapshot of intron evolution highlights the important role of the spliceosome in the expansion of transcribed genomic sequence space, providing a pathway for the rare events that may lead to the birth of new eukaryotic genes and the refinement of existing gene function.Author SummaryThe protein coding information in eukaryotic genes is broken by intervening sequences called introns that are removed from RNA during transcription by a large protein-RNA complex called the spliceosome. Where introns come from and how the spliceosome contributes to genome evolution are open questions. In this study, we find more than 150 new places in the yeast genome that are recognized by the spliceosome and spliced out as introns. Since they appear to have arisen very recently in evolution by sequence drift and do not appear to contribute to gene expression or its regulation, we call these protointrons. Protointrons are found in both protein-coding and non-coding RNAs and are not efficiently removed by the splicing machinery. Although most protointrons are not conserved, a few are spliced more efficiently, and are located where they might begin to play functional roles in gene expression, as predicted by the proposed process of intronization. The challenge now is to understand how spontaneously appearing splicing events like protointrons might contribute to the creation of new genes, new genetic controls, and new protein isoforms as genomes evolve.

scholarly journals Highly Divergent Neuropeptide - non-coding RNA regulatory networks underpin variant host-finding behaviours in Steinernema species infective juveniles

2020 ◽  
Author(s):  
Neil D. Warnock ◽  
Erwan Atcheson ◽  
Ciaran McCoy ◽  
Johnathan J. Dalzell
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Regulatory Networks ◽  
Host Finding ◽  
Protein Coding ◽  
Rna Analysis ◽  
New Family ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Shared Gene

AbstractWe conducted a transcriptomic and small RNA analysis of infective juveniles (IJs) from three behaviourally distinct Steinernema species. Substantial variation was found in the expression of shared gene orthologues, revealing gene expression signatures that correlate with behavioural states. 97% of predicted microRNAs are novel to each species. Surprisingly, our data provide evidence that isoform variation can effectively convert protein-coding neuropeptide genes into non-coding transcripts, which may represent a new family of long non-coding RNAs. These data suggest that differences in neuropeptide gene expression, isoform variation, and small RNA interactions could contribute to behavioural differences within the Steinernema genus.

scholarly journals Common Features in lncRNA Annotation and Classification: A Survey

2021 ◽  
Vol 7 (4) ◽  
pp. 77
Author(s):  
Christopher Klapproth ◽  
Rituparno Sen ◽  
Peter F. Stadler ◽  
Sven Findeiß ◽  
Jörg Fallmann
Keyword(s):  
Gene Expression ◽  
Disease Progression ◽  
In Silico ◽  
Therapeutic Targets ◽  
Untranslated Regions ◽  
Protein Coding ◽  
Coding Sequence ◽  
Common Features ◽  
Research Gap ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. Their molecular functions range from miRNA sponging to chromatin-associated mechanisms, leading to effects in disease progression and establishing them as diagnostic and therapeutic targets. Still, only a few representatives of this diverse class of RNAs are well studied, while the vast majority is poorly described beyond the existence of their transcripts. In this review we survey common in silico approaches for lncRNA annotation. We focus on the well-established sets of features used for classification and discuss their specific advantages and weaknesses. While the available tools perform very well for the task of distinguishing coding sequence from other RNAs, we find that current methods are not well suited to distinguish lncRNAs or parts thereof from other non-protein-coding input sequences. We conclude that the distinction of lncRNAs from intronic sequences and untranslated regions of coding mRNAs remains a pressing research gap.

scholarly journals Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and widespread in trans effects on the protein regulatory network

2020 ◽  
Author(s):  
Laura Natalia Balarezo-Cisneros ◽  
Steven Parker ◽  
Marcin G Fraczek ◽  
Soukaina Timouma ◽  
Ping Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Environmental Conditions ◽  
Mode Of Action ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Genome Wide ◽  
In Trans ◽  
Non Coding Rnas ◽  
The Impact

AbstractNon-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response of different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT530, SUT468) or rRNA processing (SUT075 and snR30). Overall, this data captures and integrates the regulatory and phenotypic network of ncRNAs and protein coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis.Author SummaryThe yeast genome contains 25% of non-coding RNA molecules (ncRNAs), which do not translate into proteins but are involved in regulation of gene expression. ncRNAs can affect nearby genes by physically interfering with their transcription (cis mode of action), or they interact with DNA, proteins or others RNAs to regulate the expression of distant genes (trans mode of action). Examples of cis-acting ncRNAs have been broadly described, however genome-wide studies to identify functional trans-acting ncRNAs involved in global gene regulation are still lacking. Here, we used the ncRNA yeast deletion collection to score their impact on cellular function in different environmental conditions. A group of 20 ncRNAs mutants with broad fitness diversity were selected to investigate their effect on the protein and ncRNA expression network. We showed a high correlation between altered phenotypes and global transcriptional changes, in an environmental dependent manner. We confirmed the widespread trans acting expressional regulation of ncRNAs in the genome and their role in affecting transcription factors. These findings support the notion of the involvement on ncRNAs in fine tuning the cellular expression via regulations of TFs, as an advantageous RNA-mediated mechanism that can be fast and cost-effective for the cells.

scholarly journals PHASIS: A computational suite for de novo discovery and characterization of phased, siRNA-generating loci and their miRNA triggers

2017 ◽  
Author(s):  
Atul Kakrana ◽  
Pingchuan Li ◽  
Parth Patel ◽  
Reza Hammond ◽  
Deepti Anand ◽  
...  
Keyword(s):  
De Novo ◽  
Sequencing Data ◽  
Protein Coding ◽  
Secondary Sirnas ◽  
Integrated Methods ◽  
Non Coding Rnas

AbstractPhased, secondary siRNAs (phasiRNAs) are found widely in plants, from protein-coding transcripts and long, non-coding RNAs; animal piRNAs are also phased. Integrated methods characterizing “PHAS” loci are unavailable, and existing methods are quite limited and inefficient in handling large volumes of sequencing data. The PHASIS suite described here provides complete tools for the computational characterization of PHAS loci, with an emphasis on plants, in which these loci are numerous. Benchmarked comparisons demonstrate that PHASIS is sensitive, highly scalable and fast. Importantly, PHASIS eliminates the requirement of a sequenced genome and PARE/degradome data for discovery of phasiRNAs and their miRNA triggers.

scholarly journals PVT1: A Rising Star among Oncogenic Long Noncoding RNAs

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Teresa Colombo ◽  
Lorenzo Farina ◽  
Giuseppe Macino ◽  
Paola Paci
Keyword(s):  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Competing Endogenous Rna ◽  
Protein Coding ◽  
Myc Oncogene ◽  
Non Coding Rnas

It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, and (mis)function. However, while the functional characterization of short non-coding RNAs has been reaching maturity, there is still a paucity of well characterized long noncoding RNAs, even though large studies in recent years are rapidly increasing the number of annotated ones. The long noncoding RNA PVT1 is encoded by a gene that has been long known since it resides in the well-known cancer risk region 8q24. However, a couple of accidental concurrent conditions have slowed down the study of this gene, that is, a preconception on the primacy of the protein-coding over noncoding RNAs and the prevalent interest in its neighbor MYC oncogene. Recent studies have brought PVT1 under the spotlight suggesting interesting models of functioning, such as competing endogenous RNA activity and regulation of protein stability of important oncogenes, primarily of the MYC oncogene. Despite some advancements in modelling the PVT1 role in cancer, there are many questions that remain unanswered concerning the precise molecular mechanisms underlying its functioning.

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