Spatio-Temporal Transcriptional Dynamics of Maize Long Non-Coding RNAs Responsive to Drought Stress

Long non-coding RNAs (lncRNAs) have emerged as important regulators in plant stress response. Here, we report a genome-wide lncRNA transcriptional analysis in response to drought stress using an expanded series of maize samples collected from three distinct tissues spanning four developmental stages. In total, 3488 high-confidence lncRNAs were identified, among which 1535 were characterized as drought responsive. By characterizing the genomic structure and expression pattern, we found that lncRNA structures were less complex than protein-coding genes, showing shorter transcripts and fewer exons. Moreover, drought-responsive lncRNAs exhibited higher tissue- and development-specificity than protein-coding genes. By exploring the temporal expression patterns of drought-responsive lncRNAs at different developmental stages, we discovered that the reproductive stage R1 was the most sensitive growth stage with more lncRNAs showing altered expression upon drought stress. Furthermore, lncRNA target prediction revealed 653 potential lncRNA-messenger RNA (mRNA) pairs, among which 124 pairs function in cis-acting mode and 529 in trans. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to oxidoreductase activity, water binding, and electron carrier activity. Multiple promising targets of drought-responsive lncRNAs were discovered, including the V-ATPase encoding gene, vpp4. These findings extend our knowledge of lncRNAs as important regulators in maize drought response.

Download Full-text

Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes

Briefings in Bioinformatics ◽

10.1093/bib/bby129 ◽

2019 ◽

Vol 21 (2) ◽

pp. 637-648 ◽

Cited By ~ 1

Author(s):

Aritro Nath ◽

Paul Geeleher ◽

R Stephanie Huang

Keyword(s):

Expression Patterns ◽

Imputation Accuracy ◽

High Quality ◽

Protein Coding ◽

Protein Coding Genes ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Cancer Tissues ◽

Long Non Coding Rna

Abstract Long non-coding RNAs (lncRNAs) play an important role in gene regulation and are increasingly being recognized as crucial mediators of disease pathogenesis. However, the vast majority of published transcriptome datasets lack high-quality lncRNA profiles compared to protein-coding genes (PCGs). Here we propose a framework to harnesses the correlative expression patterns between lncRNA and PCGs to impute unknown lncRNA profiles. The lncRNA expression imputation (LEXI) framework enables characterization of lncRNA transcriptome of samples lacking any lncRNA data using only their PCG profiles. We compare various machine learning and missing value imputation algorithms to implement LEXI and demonstrate the feasibility of this approach to impute lncRNA transcriptome of normal and cancer tissues. Additionally, we determine the factors that influence imputation accuracy and provide guidelines for implementing this approach.

Download Full-text

Identification of sheep lncRNAs related to the immune response to vaccines and aluminium adjuvants

BMC Genomics ◽

10.1186/s12864-021-08086-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Martin Bilbao-Arribas ◽

Endika Varela-Martínez ◽

Naiara Abendaño ◽

Damián de Andrés ◽

Lluís Luján ◽

...

Keyword(s):

Immune Response ◽

Expression Analysis ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Rna Seq ◽

Protein Coding ◽

Protein Coding Genes ◽

Livestock Species ◽

Non Coding Rnas ◽

Aluminium Adjuvant

Abstract Background Long non-coding RNAs (lncRNAs) are involved in several immune processes, including the immune response to vaccination, but most of them remain uncharacterised in livestock species. The mechanism of action of aluminium adjuvants as vaccine components is neither not fully understood. Results We built a transcriptome from sheep PBMCs RNA-seq data in order to identify unannotated lncRNAs and analysed their expression patterns along protein coding genes. We found 2284 novel lncRNAs and assessed their conservation in terms of sequence and synteny. Differential expression analysis performed between animals inoculated with commercial vaccines or aluminium adjuvant alone and the co-expression analysis revealed lncRNAs related to the immune response to vaccines and adjuvants. A group of co-expressed genes enriched in cytokine signalling and production highlighted the differences between different treatments. A number of differentially expressed lncRNAs were correlated with a divergently located protein-coding gene, such as the OSM cytokine. Other lncRNAs were predicted to act as sponges of miRNAs involved in immune response regulation. Conclusions This work enlarges the lncRNA catalogue in sheep and puts an accent on their involvement in the immune response to repetitive vaccination, providing a basis for further characterisation of the non-coding sheep transcriptome within different immune cells.

Download Full-text

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens

BMC Genomics ◽

10.1186/s12864-021-07679-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Junxiao Ren ◽

Weihua Tian ◽

Keren Jiang ◽

Zhang Wang ◽

Dandan Wang ◽

...

Keyword(s):

Lipid Metabolism ◽

Chicken Liver ◽

Functional Enrichment ◽

Integrated Analysis ◽

Rna Seq ◽

Protein Coding ◽

Chip Sequencing ◽

Functional Sites ◽

Protein Coding Genes ◽

A Genome

Abstract Background Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken liver is poorly understood. To identify estrogen-responsive genes and estrogen functional sites on a genome-wide scale, we determined expression profiles of mRNAs, lncRNAs, and miRNAs in estrogen-treated ((17β-estradiol)) and control chicken livers using RNA-Sequencing (RNA-Seq) and studied the estrogen receptor α binding sites by ChIP-Sequencing (ChIP-Seq). Results We identified a total of 990 estrogen-responsive genes, including 962 protein-coding genes, 11 miRNAs, and 17 lncRNAs. Functional enrichment analyses showed that the estrogen-responsive genes were highly enriched in lipid metabolism and biological processes. Integrated analysis of the data of RNA-Seq and ChIP-Seq, identified 191 genes directly targeted by estrogen, including 185 protein-coding genes, 4 miRNAs, and 2 lncRNAs. In vivo and in vitro experiments showed that estrogen decreased the mRNA expression of PPARGC1B, which had been reported to be linked with lipid metabolism, by directly increasing the expression of miR-144-3p. Conclusions These results increase our understanding of the functional network of estrogen in chicken liver and also reveal aspects of the molecular mechanism of estrogen-related lipid metabolism.

Download Full-text

Non-coding RNAs in the pathogenesis of COPD

Thorax ◽

10.1136/thoraxjnl-2014-206560 ◽

2015 ◽

Vol 70 (8) ◽

pp. 782-791 ◽

Cited By ~ 39

Author(s):

Elise G De Smet ◽

Pieter Mestdagh ◽

Jo Vandesompele ◽

Guy G Brusselle ◽

Ken R Bracke

Keyword(s):

Pulmonary Inflammation ◽

Expression Patterns ◽

Premature Death ◽

Cigarette Smoke Exposure ◽

Transcriptional Level ◽

Protein Coding ◽

Altered Expression ◽

Progressive Decline ◽

Rna Molecules ◽

Non Coding Rnas

A large part of the human genome is transcribed in non-coding RNAs, transcripts that do not code for protein, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). MiRNAs are short single-stranded RNA molecules that negatively regulate gene expression at the post-transcriptional level. They play an important regulatory role in many biological processes. Consequently, altered expression of these non-coding RNAs has been shown to lead to inflammation and disease. In contrast, lncRNAs, can both enhance or repress the expression of protein-coding genes. COPD is typically caused by tobacco smoking and leads to a progressive decline in lung function and a premature death. Exaggerated pulmonary inflammation is a hallmark feature in this disease, leading to obstructive bronchiolitis and emphysema. In this review, we discuss the miRNA expression patterns in lungs of patients with COPD and in mouse models and we highlight various miRNAs involved in COPD pathogenesis. In addition, we briefly discuss a specific lncRNA that is upregulated upon cigarette smoke exposure, providing a short introduction to this more recently discovered group of non-coding RNAs.

Download Full-text

Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops

BMC Genomics ◽

10.1186/s12864-021-07602-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Sadhana Singh ◽

Himabindu Kudapa ◽

Vanika Garg ◽

Rajeev K. Varshney

Keyword(s):

Drought Stress ◽

Candidate Genes ◽

Developmental Stages ◽

Biological Activities ◽

Expression Patterns ◽

Genome Wide ◽

Legume Crops ◽

Root Tissues ◽

Semi Arid ◽

Comprehensive Study

Abstract Background Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops. Results In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes. Conclusion As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.

Download Full-text

Coordinate regulation of long non-coding RNAs and protein-coding genes in germ-free mice

BMC Genomics ◽

10.1186/s12864-018-5235-3 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 15

Author(s):

Joseph Dempsey ◽

Angela Zhang ◽

Julia Yue Cui

Keyword(s):

Protein Coding ◽

Coordinate Regulation ◽

Germ Free ◽

Protein Coding Genes ◽

Non Coding Rnas

Download Full-text

Effect of Drought on Storage Root Development and Gene Expression Profile of Sweetpotato under Greenhouse and Field Conditions

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.139.3.317 ◽

2014 ◽

Vol 139 (3) ◽

pp. 317-324 ◽

Cited By ~ 12

Author(s):

Julio Solis ◽

Arthur Villordon ◽

Niranjan Baisakh ◽

Don LaBonte ◽

Nurit Firon

Keyword(s):

Drought Stress ◽

Differential Expression ◽

Root Development ◽

Water Deprivation ◽

Expression Patterns ◽

Storage Root ◽

Altered Expression ◽

Sand Control ◽

Binding Factor ◽

Drought Conditions

Greenhouse and field culture systems were used to study the effect of drought conditions on the storage root (SR) formation in ‘Beauregard’ sweetpotato (Ipomoea batatas). In the greenhouse culture system, drought was simulated by withholding water for 5 and 10 days after transplanting (DAT) cuttings in dry sand. Control plants received water at planting and every 3 days thereafter. In the field studies, natural drought conditions and selective irrigation were used to impose water deprivation during the critical SR formation period. Greenhouse drought for 5 and 10 DAT reduced the number of SRs by 42% and 66%, respectively, compared with the controls. Field drought resulted in a 49% reduction in U.S. #1 SR yield compared with the irrigated condition. Quantitative real-time polymerase chain reaction (PCR) analysis showed differential expression of a set of sweetpotato transcription factors and protein kinases among greenhouse-grown plants subjected to well-watered conditions and water deficit during 5 DAT. A significant enhancement of expression was observed for known drought stress-associated genes such as an abscisic acid-responsive elements-binding factor, dehydration-responsive element-binding factor, and homeo-domain-zip proteins. Members of calcium-binding proteins showed differential expression under drought stress. For the first time it is reported that knotted1-like homeobox and BEL1-like genes showed altered expression in response to drought stress under a greenhouse condition. In summary, the results suggest that water deprivation during the SR formation period influences root development and expression patterns of stress-responsive genes and those previously found associated with SR formation in sweetpotato.

Download Full-text

The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

Wellcome Open Research ◽

10.12688/wellcomeopenres.17204.1 ◽

2021 ◽

Vol 6 ◽

pp. 258

Author(s):

Konrad Lohse ◽

Alexander Mackintosh ◽

Roger Vila ◽

◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Sex Chromosome ◽

Gene Annotation ◽

Protein Coding ◽

Individual Male ◽

Protein Coding Genes ◽

A Genome ◽

Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

Download Full-text

The Absence of Universally-Conserved Protein-coding Genes

10.1101/842633 ◽

2019 ◽

Author(s):

Change Laura Tan

Keyword(s):

Public Access ◽

Orphan Genes ◽

Protein Coding ◽

Great Opportunity ◽

Protein Coding Genes ◽

Phylogenetic Profiles ◽

Gene Count ◽

A Genome ◽

Wide Scale ◽

Specific Species

AbstractPublic access to thousands of completely sequenced and annotated genomes provides a great opportunity to address the relationships of different organisms, at the molecular level and on a genome-wide scale. Via comparing the phylogenetic profiles of all protein-coding genes in 317 model species described in the OrthoInspector3.0 database, we found that approximately 29.8% of the total protein-coding genes were orphan genes (genes unique to a specific species) while < 0.01% were universal genes (genes with homologs in each of the 317 species analyzed). When weighted by potential birth event, the orphan genes comprised 82% of the total, while the universal genes accounted for less than 0.00008%. Strikingly, as the analyzed genomes increased, the sum total of universal and nearly-universal genes plateaued while that of orphan and nearly-orphan genes grew continuously. When the compared species increased to the inclusion of 3863 bacteria, 711 eukaryotes, and 179 archaea, not one of the universal genes remained. The results speak to a previously unappreciated degree of genetic biodiversity, which we propose to quantify using the birth-event-weighted gene count method.

Download Full-text