Identification, functional prediction, and key lncRNA verification of cold stress-related lncRNAs in rats liver

The Role of lncRNAs in Pig Muscle in Response to Cold Exposure

Cold exposure is an essential factor affecting breeding efforts in cold regions. Muscle, as an important tissue for homeothermic animals, can produce heat through shivering thermogenesis (ST) and non-shivering thermogenesis (NST) under cold exposure. Long non-coding RNAs (lncRNAs) play important roles in regulating gene expression. However, the regulatory mechanisms of lncRNAs and their role in the thermogenesis of pigs are unclear. We examined lncRNAs in the skeletal muscle of an indigenous pig breed, the Enshi black pig, when the pigs were exposed to acute or chronic cold. Three pigs were maintained inside a pig house (control group), three pigs were maintained outside the pig house for 55 d (chronic cold group), and three pigs were suddenly exposed to the conditions outside the pig house for 3 days (acute cold group). After the experiment, the longissimus dorsi of each pig were collected, and their lncRNA profiles were sequenced and analyzed. Each sample obtained nearly 12.56 Gb of clean data. A total of 11,605 non-coding RNAs were obtained, including 10,802 novel lncRNAs. The number of differentially expressed lncRNAs (DElncRNAs) was identified under acute cold (427) and cold acclimation (376), with 215 and 192 upregulated lncRNAs, respectively. However, only 113 lncRNAs were commonly upregulated by acute cold and cold acclimation. In addition, 65% of the target genes were trans-regulated by DElncRNAs. The target genes were enriched in signal transduction, immune system, cell growth and death pathways, and amino acid and carbohydrate metabolism. Compared to cold acclimation, acute cold stress-induced more DElncRNAs and response pathways. In conclusion, low temperatures altered the expression levels of lncRNAs and their target genes in muscle tissue. Some potential mechanisms were revealed, including ion migration and the metabolism of amino acids and carbohydrates.

LncRNAs elevate plant adaptation under low temperature by maintaining local chromatin landscape

Epigenetic regulation is one of the most precise and subtle ways of gene regulation, including DNA modification, histone modification, RNA modification, histone variants, chromatin remodeling, and long non-coding RNAs (lncRNAs). Chromatin modification is the most basic type of epigenetic regulation, which plays a key role in a myriad of developmental and physiological processes that have been thoroughly studied. These modifications are usually completed by a series of conserved chromatin modification complexes in eukaryotes. In recent years, a series of lncRNAs in organisms also have been described as having irreplaceable functions in biological environment adaptation, especially in biotic and abiotic stresses. Moreover, these molecules form a sophisticated regulatory network through mutual cross-regulation to achieve quantitative expression of key environmental response genes to external signals. For instance, the function of lncRNAs will directly or indirectly depend on the function of the chromatin modification complex. In this review, we mainly focus on chromatin modification, lncRNA, and their coordination mechanism to achieve the high adaptability of plants in low-temperature environments. We highlight recent findings and insights into lncRNA-mediated local chromatin environment changes during plant growth under low temperature via chromatin modification complexes, including target gene specificity for different lncRNA.

RBM3 is an outstanding cold shock protein with multiple physiological functions beyond hypothermia

RNA-binding motif protein 3 (RBM3), an outstanding cold shock protein, is rapidly upregulated to ensure homeostasis and survival in a cold environment, which is an important physiological mechanism in response to cold stress. Meanwhile, RBM3 has multiple physiological functions and participates in the regulation of various cellular physiological processes, such as antiapoptosis, circadian rhythm, cell cycle, reproduction, and tumogenesis. The structure, conservation, and tissue distribution of RBM3 in human are demonstrated in this review. Herein, the multiple physiological functions of RBM3 were summarized based on recent research advances. Meanwhile, the cytoprotective mechanism of RBM3 during stress under various adverse conditions and its regulation of transcription were discussed. In addition, the neuroprotection of RBM3 and its oncogenic role and controversy in various cancers were investigated in our review.

Altered genome-wide hippocampal gene expression profiles following early life lead exposure and their potential for reversal by environmental enrichment

Early life lead (Pb) exposure is detrimental to neurobehavioral development. The quality of the environment can modify negative influences from Pb exposure, impacting the developmental trajectory following Pb exposure. Little is known about the molecular underpinnings in the brain of the interaction between Pb and the quality of the environment. We examined relationships between early life Pb exposure and living in an enriched versus a non-enriched postnatal environment on genome-wide transcription profiles in hippocampus CA1. RNA-seq identified differences in the transcriptome of enriched vs. non-enriched Pb-exposed animals. Most of the gene expression changes associated with Pb exposure were reversed by enrichment. This was also true for changes in upstream regulators, splicing events and long noncoding RNAs. Non-enriched rats also had memory impairments; enriched rats had no deficits. The results demonstrate that an enriched environment has a profound impact on behavior and the Pb-modified CA1 transcriptome. These findings show the potential for interactions between Pb exposure and the environment to result in significant transcriptional changes in the brain and, to the extent that this may occur in Pb-exposed children, could influence neuropsychological/educational outcomes, underscoring the importance for early intervention and environmental enrichment for Pb-exposed children.

Transcriptomic Analysis Reveals Potential Gene Regulatory Networks Under Cold Stress of Loquat (Eriobotrya japonica Lindl.)

Loquat (Eriobotrya japonica Lindl. ) is one of the most economically important evergreen fruit crops in China, while it often suffered the injury of cold stress in winter and earlier spring, and the annual yield loss of loquat fruits caused by cold or freezing stress was immeasurable. However, knowledge about the physiological response and molecular mechanism under cold stress is still limited. To investigate the potential regulation mechanism pre- and post-cold stress in loquat and the changes in physiological indicators, a comparative transcriptome analysis was performed against a cold-resistant cv. "Huoju" and a cold-sensitive cv. "Ninghaibai". The results of physiological indicators related to cold resistance indicated that rachis was most sensitive to cold stress and was considered as the representative organ to directly evaluate cold resistance of loquat based on subordinate function analysis. Here, we compared the transcriptome profiles of rachis pre- and under cold stress in "Huoju" and "Ninghaibai". A total of 4,347 and 3,513 differentially expressed genes (DEGs) were detected in "Ninghaibai" and "Huoju", among which 223 and 166 were newly identified genes, respectively, most of them were functionally enriched in plant hormone signal transduction (Huoju: 142; Ninghaibai: 200), and there were higher plant hormone content and related DEG expression levels in "Huoju" than that of "Ninghaibai". Moreover, a total of 3,309 differentially expressed transcription factors (DETFs) were identified, and some DEGs and DETFs were screened to be subjected to co-expression network analysis based on the gene expression profile data. Some candidate DEGs, including UDP-glycosyltransferase (UGT), glycosyltransferase (GT), sugar phosphate/phosphate translocator (SPT), sugar transport protein (STP), proline-rich receptor-like protein kinase (PERK), and peroxidise (POD), were significantly affected by cold stress, and the expression level of these genes obtained from real-time quantitative RT-PCR was consistent with the pattern of transcriptome profile, which suggested that these genes might play the vital roles in cold resistance of loquat. Our results provide an invaluable resource for the identification of specific genes and TFs and help to clarify gene transcription during the cold stress response of loquat.

Transcriptome sequencing reveals the differentially expressed lncRNAs and mRNAs in response to cold acclimation and cold stress in Pomacea canaliculata

Background

Tolerance of low temperature has a significant impact on survival and expansion of invasive snail Pomacea canalicuata. Cold acclimation can enhance cold tolerance of Pomacea canalicuata. To elucidate the molecular mechanism of P. canaliculata’s responses to cold acclimation and cold stress, a high-throughput transcriptome analysis of P. canaliculata was performed, and gene expression following artificial cold acclimation and then cold stress at 0 °C for 24 h was compared using RNA sequencing.

Results

Using the Illumina platform, we obtained 151.59 G subreads. A total of 5,416 novel lncRNAs were identified, and 3166 differentially expressed mRNAs and 211 differentially expressed lncRNAs were screened with stringent thresholds. The potential antisense, cis and trans targets of lncRNAs were predicted. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that many target genes were involved in proteasome, linoleic acid metabolism and retinol metabolism under cold acclimation. The lncRNA of P. canaliculata could participate in cold acclimation by regulating the expression of E3 ubiquitin protein ligase, 26S proteasome non-ATPase dependent regulation subunit, glutathione S-transferase, sodium/glucose cotransporter and cytochrome P450.

Conclusions

These results broaden our understanding of cold acclimation and cold stress associated lncRNAs and mRNAs, and provide new insights into lncRNA mediated regulation of P. canaliculata cold acclimation and cold stress response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08622-5.

Long non-coding RNAs and their potential impact on diagnosis, prognosis, and therapy in prostate cancer: racial, ethnic, and geographical considerations

INTRODUCTION

Advances in high-throughput sequencing have greatly advanced our understanding of long non-coding RNAs (lncRNAs) in a relatively short period of time. This has expanded our knowledge of cancer, particularly how lncRNAs drive many important cancer phenotypes via their regulation of gene expression.

AREAS COVERED

Men of African descent are disproportionately affected by PC in terms of incidence, morbidity, and mortality. LncRNAs could serve as biomarkers to differentiate low-risk from high-risk diseases. Additionally, they may represent therapeutic targets for advanced and castrate-resistant cancer. We review current research surrounding lncRNAs and their association with PC. We discuss how lncRNAs can provide new insights and diagnostic biomarkers for African American men. Finally, we review advances in computational approaches that predict the regulatory effects of lncRNAs in cancer.

EXPERT OPINION

PC diagnostic biomarkers that offer high specificity and sensitivity are urgently needed. PC specific lncRNAs are compelling as diagnostic biomarkers owing to their high tissue and tumor specificity and presence in bodily fluids. Recent studies indicate that PCA3 clinical utility might be restricted to men of European descent. Further work is required to develop lncRNA biomarkers tailored for men of African descent.

The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways

The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments. These ncRNAs have the ability to regulate gene expression and modify metabolic pathways. Thus, they may have important roles as diagnostic biomarkers or therapeutic targets in various diseases, including neurodegenerative disorders, especially Parkinson's disease. Recently, through diverse sequencing technologies and a wide variety of bioinformatic analytical tools, such as reverse transcriptase quantitative PCR, microarrays, next-generation sequencing and long-read sequencing, numerous ncRNAs have been shown to be associated with neurodegenerative disorders, including Parkinson's disease. In this review article, we will first introduce the biogenesis of different ncRNAs, including microRNAs, PIWI-interacting RNAs, circular RNAs, long noncoding RNAs, and tRNA-derived fragments. The pros and cons of the detection platforms of ncRNAs and the reproducibility of bioinformatic analytical tools will be discussed in the second part. Finally, the recent discovery of numerous PD-associated ncRNAs and their association with the diagnosis and pathophysiology of PD are reviewed, and microRNAs and long ncRNAs that are transported by exosomes in biofluids are particularly emphasized.

Integrated study of circRNA, lncRNA, miRNA, and mRNA networks in mediating the effects of testicular heat exposure

The World Health Organization has recognized that testicular function is temperature dependent. Testicular heat exposure caused by occupational factors, lifestyle, and clinical diseases can lead to different degrees of reproductive problems. The aim of this study was to reveal the transcriptional regulatory network and its potential crucial roles in mediating the effects of testicular heat exposure. Testicular tissue was collected from a group of mice subjected to scrotal heat exposure as well as a control group. RNA was isolated from both groups and used for high-throughput sequencing. Using differential transcriptome expression analysis, 172 circRNAs, 279 miRNAs, 465 lncRNAs, and 2721 mRNAs were identified as significantly differentially expressed in mouse testicular tissue after heat exposure compared with the control group. Through Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, differentially expressed lncRNAs and mRNAs were found to have potentially important functions in meiotic cell cycle (GO:0051321), cytoplasm (GO:0005737), membrane raft (GO:0045121), MAPK signaling (mmu04010), purine metabolism (mmu00230), and homologous recombination (mmu03440). Some of the most upregulated and downregulated lncRNAs and circRNAs were predicted to be associated with numerous miRNAs and mRNAs through competing endogenous RNA regulatory network analysis, which were validated with molecular biology experiments. This research provides high-throughput sequencing data of a testicular heat exposure model and lays the foundation for further study on circRNAs, miRNAs, and lncRNAs that are involved in male reproductive diseases related to elevated testicular temperature.

Long non-coding RNAs (lncRNAs) in spermatogenesis and male infertility

BACKGROUND

Long non-coding RNAs (lncRNAs) have a size of more than 200 bp and are known to regulate a host of crucial cellular processes like proliferation, differentiation and apoptosis by regulating gene expression. While small noncoding RNAs (ncRNAs) such as miRNAs, siRNAs, Piwi-interacting RNAs have been extensively studied in male germ cell development, the role of lncRNAs in spermatogenesis remains largely unknown.

OBJECTIVE

In this article, we have reviewed the biology and role of lncRNAs in spermatogenesis along with the tools available for data analysis.

RESULTS AND CONCLUSIONS

Till date, three microarray and four RNA-seq studies have been undertaken to identify lncRNAs in mouse testes or germ cells. These studies were done on pre-natal, post-natal, adult testis, and different germ cells to identify lncRNAs regulating spermatogenesis. In case of humans, five RNA-seq studies on different germ cell populations, including two on sperm, were undertaken. We compared three studies on human germ cells to identify common lncRNAs and found 15 lncRNAs (LINC00635, LINC00521, LINC00174, LINC00654, LINC00710, LINC00226, LINC00326, LINC00494, LINC00535, LINC00616, LINC00662, LINC00668, LINC00467, LINC00608, and LINC00658) to show consistent differential expression across these studies. Some of the targets of these lncRNAs included CENPB, FAM98B, GOLGA6 family, RPGR, TPM2, GNB5, KCNQ10T1, TAZ, LIN28A, CDKN2B, CDKN2A, CDKN1A, CDKN1B, CDKN1C, EZH2, SUZ12, VEGFA genes. A lone study on human male infertility identified 9879 differentially expressed lncRNAs with three (lnc32058, lnc09522, and lnc98497) of them showing specific and high expression in immotile sperm in comparison to normal motile sperm. A few lncRNAs (Mrhl, Drm, Spga-lncRNAs, NLC1-C, HongrES2, Tsx, LncRNA-tcam1, Tug1, Tesra, AK015322, Gm2044, and LncRNA033862) have been functionally validated for their roles in spermatogenesis. Apart from rodents and humans, studies on sheep and bull have also identified lncRNAs potentially important for spermatogenesis. A number of these non-coding RNAs are strong candidates for further research on their roles in spermatogenesis.

Knockdown of lncRNA LINC01234 Suppresses the Tumorigenesis of Liver Cancer via Sponging miR-513a-5p

Background

Liver cancer is a frequent malignancy with poor prognosis and high mortality all over the world. It has been reported many lncRNAs could modulate the tumorigenesis of liver cancer. To identify novel potential targets for liver cancer, the differential expressed lncRNAs between liver cancer and adjacent normal tissues was analyzed with bioinformatics tool.

Methods

The differential expressed lncRNAs between liver cancer and adjacent normal tissues were analyzed with bioinformatics tool. Cell viability and proliferation was tested by CCK8 and Ki67, respectively. Apoptosis of liver cancer cells was tested by flow cytometry. Gene and protein expressions in liver cancer cells were measured by qRT-PCR and western blot, respectively. In vivo model of liver cancer was established to detect the effect of LINC01234 on liver cancer in vivo.

Results

LINC01234 was found to be negatively correlated with the survival rate of patients with liver cancer. Moreover, knockdown of LINC01234 significantly suppressed the proliferation and invasion of liver cancer cells via inducing the apoptosis. Meanwhile, miR-513a-5p was sponged by LINC01234, and USP4 was found to be a direct target of miR-513a-5p. In addition, LINC01234 knockdown inhibited the tumorigenesis of liver cancer via inactivating TGF-β signaling. Furthermore, silencing of LINC01234 notably inhibited the tumor growth of liver cancer in vivo.

Conclusion

Downregulation of LINC01234 could inhibit the tumorigenesis of liver cancer via mediation of miR-513a-5p/USP4/TGF-β axis. Thus, LINC01234 might serve as a new target for the treatment of liver cancer.