Research progress in the estimation of postmortem interval (PMI) using non-coding RNA (ncRNA) markers

Postmortem interval (PMI) estimation has always been a crucial focus and challenging issue in forensic pathology. In recent years, specific RNA molecules and their variation have been used worldwide to estimate PMI. In this review, we summarize the methods used to detect non-coding RNAs (ncRNAs) for PMI estimation based on the literature, show the existing problems and development trends, and provide technical references for relevant studies and estimation practices.

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Bioinformatics Analysis of Long Non-coding RNA and Related Diseases: An Overview

Frontiers in Genetics ◽

10.3389/fgene.2021.813873 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuxin Gong ◽

Wen Zhu ◽

Meili Sun ◽

Lei Shi

Keyword(s):

Small Rnas ◽

Bioinformatics Analysis ◽

Regulation Of Gene Expression ◽

Research Progress ◽

Biological Processes ◽

Existing Problems ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Cancer Côlon ◽

Long Non Coding Rna

Long non-coding RNAs (lncRNAs) are usually located in the nucleus and cytoplasm of cells. The transcripts of lncRNAs are >200 nucleotides in length and do not encode proteins. Compared with small RNAs, lncRNAs have longer sequences, more complex spatial structures, and more diverse and complex mechanisms involved in the regulation of gene expression. LncRNAs are widely involved in the biological processes of cells, and in the occurrence and development of many human diseases. Many studies have shown that lncRNAs can induce the occurrence of diseases, and some lncRNAs undergo specific changes in tumor cells. Research into the roles of lncRNAs has covered the diagnosis of, for example, cardiovascular, cerebrovascular, and central nervous system diseases. The bioinformatics of lncRNAs has gradually become a research hotspot and has led to the discovery of a large number of lncRNAs and associated biological functions, and lncRNA databases and recognition models have been developed. In this review, the research progress of lncRNAs is discussed, and lncRNA-related databases and the mechanisms and modes of action of lncRNAs are described. In addition, disease-related lncRNA methods and the relationships between lncRNAs and human lung adenocarcinoma, rectal cancer, colon cancer, heart disease, and diabetes are discussed. Finally, the significance and existing problems of lncRNA research are considered.

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MiR-29a: a potential therapeutic target and promising biomarker in tumors

Bioscience Reports ◽

10.1042/bsr20171265 ◽

2018 ◽

Vol 38 (1) ◽

Cited By ~ 10

Author(s):

Jin-yan Wang ◽

Qian Zhang ◽

Dan-dan Wang ◽

Wei Yan ◽

Huan-huan Sha ◽

...

Keyword(s):

Cell Proliferation ◽

Therapeutic Target ◽

Therapeutic Strategy ◽

Transcriptional Level ◽

Additional Insight ◽

Potential Therapeutic Target ◽

Rna Molecules ◽

Non Coding Rna ◽

Non Coding Rnas ◽

Novel Therapeutic

MiRNAs, small non-coding RNA molecules, were recognized to be associated with the incidence and development of diverse neoplasms. MiRNAs were small non-coding RNAs that could regulate post-transcriptional level by binding to 3′-UTR of target mRNAs. Amongst which, miR-29a was demonstrated that it had significant impact on oncogenicity in various neoplasms through binding to critical genes which enhanced or inhibited the progression of cancers. MiR-29a participated in kinds of physiological and pathological processes, including virus replication, cell proliferation, differentiation, apoptosis, fibrosis, angiogenesis, tumorigenicity, metastasis, drug-resistance, and so on. According to its sufficient sensitivity and specificity, many studies showed that miR-29a might serve as a potential therapeutic target and promising biomarker in various tumors. In this review, we discussed the functions of miR-29a and its potential application in the diagnosis, treatment and stages of carcinoma, which could provide additional insight to develop a novel therapeutic strategy.

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Long-non Coding RNAs Related to Fat Deposition in Pigs Included lncRNA Corresponding to Human MALAT1

10.20944/preprints202103.0356.v1 ◽

2021 ◽

Author(s):

Katarzyna Piórkowska ◽

Kacper Żukowski ◽

Katarzyna Ropka-Molik ◽

Mirosław Tyra

Keyword(s):

Regulatory Elements ◽

Fat Deposition ◽

Differentially Expressed ◽

Rna Molecules ◽

Non Coding Rna ◽

Sequencing Method ◽

Non Coding Rnas ◽

Potential Interactions ◽

Long Non Coding Rna ◽

Generation Sequencing

Obesity is a problem in the last decades since the development of different technologies forced the submission of a faster pace of life, resulting in nutrition style changes. In turn, domestic pigs are an excellent animal model in recognition of adiposity-related processes, corresponding to the size of individual organs, the distribution of body fat in the organism, and similar metabolism. The present study applied the next-generation sequencing method to identify adipose tissue (AT) transcriptomic signals related to increased fat content by identifying differentially expressed genes (DEGs), included long-non coding RNA molecules. The Freiburg RNA tool was applied to recognise predicting hybridisation energy of RNA-RNA interactions. The results indicated several long non-coding RNAs (lncRNAs) whose expression was significantly positively or negatively associated with fat deposition. lncRNAs play an essential role in regulating gene expression by sponging miRNA, binding transcripts, facilitating translation, or coding other smaller RNA regulatory elements. In the pig fat tissue of obese group, increased expression of lncRNAs corresponding to human MALAT1 was observed that previously recognised in the obesity-related context. Moreover, hybridisation energy analyses pinpointed numerous potential interactions between identified differentially expressed lncRNAs, and obesity-related genes and miRNAs expressed in AT.

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Host Non-Coding RNA Regulates Influenza A Virus Replication

Viruses ◽

10.3390/v14010051 ◽

2021 ◽

Vol 14 (1) ◽

pp. 51

Author(s):

Yuejiao Liao ◽

Shouqing Guo ◽

Geng Liu ◽

Zhenyu Qiu ◽

Jiamin Wang ◽

...

Keyword(s):

Signaling Pathway ◽

Influenza A Virus ◽

Influenza A ◽

Janus Kinase ◽

Research Progress ◽

Receptor Signaling ◽

Non Coding Rna ◽

Receptor Signaling Pathway ◽

Non Coding Rnas ◽

Virus Interactions

Outbreaks of influenza, caused by the influenza A virus (IAV), occur almost every year in various regions worldwide, seriously endangering human health. Studies have shown that host non-coding RNA is an important regulator of host–virus interactions in the process of IAV infection. In this paper, we comprehensively analyzed the research progress on host non-coding RNAs with regard to the regulation of IAV replication. According to the regulation mode of host non-coding RNAs, the signal pathways involved, and the specific target genes, we found that a large number of host non-coding RNAs directly targeted the PB1 and PB2 proteins of IAV. Nonstructural protein 1 and other key genes regulate the replication of IAV and indirectly participate in the regulation of the retinoic acid-induced gene I-like receptor signaling pathway, toll-like receptor signaling pathway, Janus kinase signal transducer and activator of transcription signaling pathway, and other major intracellular viral response signaling pathways to regulate the replication of IAV. Based on the above findings, we mapped the regulatory network of host non-coding RNAs in the innate immune response to the influenza virus. These findings will provide a more comprehensive understanding of the function and mechanism of host non-coding RNAs in the cellular anti-virus response as well as clues to the mechanism of cell–virus interactions and the discovery of antiviral drug targets.

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Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

International Journal of Molecular Sciences ◽

10.3390/ijms21103711 ◽

2020 ◽

Vol 21 (10) ◽

pp. 3711

Author(s):

Melina J. Sedano ◽

Alana L. Harrison ◽

Mina Zilaie ◽

Chandrima Das ◽

Ramesh Choudhari ◽

...

Keyword(s):

Rna Sequencing ◽

Expression Patterns ◽

Biological Significance ◽

Rna Seq ◽

Biological Functions ◽

Protein Coding ◽

Rna Molecules ◽

Non Coding Rna ◽

Genome Wide ◽

Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

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Long Non-Coding RNAs in Multiple Myeloma

Non-Coding RNA ◽

10.3390/ncrna5010013 ◽

2019 ◽

Vol 5 (1) ◽

pp. 13 ◽

Cited By ~ 8

Author(s):

Romana Butova ◽

Petra Vychytilova-Faltejskova ◽

Adela Souckova ◽

Sabina Sevcikova ◽

Roman Hajek

Keyword(s):

Multiple Myeloma ◽

Plasma Cells ◽

Current Knowledge ◽

Biological Processes ◽

Cell Distribution ◽

Rna Molecules ◽

Non Coding Rna ◽

Non Coding Rnas ◽

New Treatment ◽

Long Non Coding Rna

Multiple myeloma (MM) is the second most common hematooncological disease of malignant plasma cells in the bone marrow. While new treatment brought unprecedented increase of survival of patients, MM pathogenesis is yet to be clarified. Increasing evidence of expression of long non-coding RNA molecules (lncRNA) linked to development and progression of many tumors suggested their important role in tumorigenesis. To date, over 15,000 lncRNA molecules characterized by diversity of function and specificity of cell distribution were identified in the human genome. Due to their involvement in proliferation, apoptosis, metabolism, and differentiation, they have a key role in the biological processes and pathogenesis of many diseases, including MM. This review summarizes current knowledge of non-coding RNAs (ncRNA), especially lncRNAs, and their role in MM pathogenesis. Undeniable involvement of lncRNAs in MM development suggests their potential as biomarkers.

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Research Progress on the Bamboo Timber Preservation

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.159.216 ◽

2010 ◽

Vol 159 ◽

pp. 216-221 ◽

Cited By ~ 1

Author(s):

Ya Di Liu ◽

Wen Jin Liu

Keyword(s):

Physiological Characteristics ◽

Research Progress ◽

General Situation ◽

Development Trends ◽

Composite Board ◽

Existing Problems ◽

Furniture Manufacturing ◽

Systematic Understanding ◽

At Home

With the extensive utilization of the bamboo industrialization, especially in developmental fields of bamboo-based panel, bamboo composite board, bamboo decoration, furniture manufacturing, which makes the application of bamboo have a broader prospect. However, the bamboo and its products in process of processing, transport and implementation often appear mildew, decay, moth-eaten, especially the mildew, it not only affects the appearance of bamboo and its products, but also creates damage conditions for other bacteria and insects. Therefore, bamboo timber preservation processing is the essential link for using bamboo industrialization. From the kinds of bamboo mould and its physiological characteristics, anti-mould technology and the types of mould inhibitor, this paper introduces the general situation at home and abroad and the existing problems and development trends of bamboo timber preservation, aiming to have a more comprehensive and systematic understanding of people for the bamboo mould and timber preservation, and to provide references for further study on the comprehensive anti-mould technology and preparation.

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Research Progress on Plant Long Non-Coding RNA

Plants ◽

10.3390/plants9040408 ◽

2020 ◽

Vol 9 (4) ◽

pp. 408

Author(s):

Ling Wu ◽

Sian Liu ◽

Haoran Qi ◽

Heng Cai ◽

Meng Xu

Keyword(s):

Growth And Development ◽

Protein Modification ◽

Plant Molecular Biology ◽

Research Progress ◽

Current Status ◽

Sequence Length ◽

Small Molecular Weight ◽

Rna Molecules ◽

Non Coding Rnas

Non-coding RNAs (ncRNAs) that were once considered “dark matter” or “transcriptional noise” in genomes are research hotspots in the field of epigenetics. The most well-known microRNAs (miRNAs) are a class of short non-coding, small molecular weight RNAs with lengths of 20–24 nucleotides that are highly conserved throughout evolution. Through complementary pairing with the bases of target sites, target gene transcripts are cleaved and degraded, or translation is inhibited, thus regulating the growth and development of organisms. Unlike miRNAs, which have been studied thoroughly, long non-coding RNAs (lncRNAs) are a group of poorly conserved RNA molecules with a sequence length of more than 200 nucleotides and no protein encoding capability; they interact with large molecules, such as DNA, RNA, and proteins, and regulate protein modification, chromatin remodeling, protein functional activity, and RNA metabolism in vivo through cis- or trans-activation at the transcriptional, post-transcriptional, and epigenetic levels. Research on plant lncRNAs is just beginning and has gradually emerged in the field of plant molecular biology. Currently, some studies have revealed that lncRNAs are extensively involved in plant growth and development and stress response processes by mediating the transmission and expression of genetic information. This paper systematically introduces lncRNA and its regulatory mechanisms, reviews the current status and progress of lncRNA research in plants, summarizes the main techniques and strategies of lncRNA research in recent years, and discusses existing problems and prospects, in order to provide ideas for further exploration and verification of the specific evolution of plant lncRNAs and their biological functions.

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Non-coding RNA in cystic fibrosis

Biochemical Society Transactions ◽

10.1042/bst20170469 ◽

2018 ◽

Vol 46 (3) ◽

pp. 619-630 ◽

Cited By ~ 13

Author(s):

Arlene M.A. Glasgow ◽

Chiara De Santi ◽

Catherine M. Greene

Keyword(s):

Cystic Fibrosis ◽

Chloride Ion ◽

Altered Expression ◽

Rna Molecules ◽

Non Coding Rna ◽

Small Ncrnas ◽

Non Coding Rnas ◽

Regulatory Rnas ◽

And Function ◽

Near Future

Non-coding RNAs (ncRNAs) are an abundant class of RNAs that include small ncRNAs, long non-coding RNAs (lncRNA) and pseudogenes. The human ncRNA atlas includes thousands of these specialised RNA molecules that are further subcategorised based on their size or function. Two of the more well-known and widely studied ncRNA species are microRNAs (miRNAs) and lncRNAs. These are regulatory RNAs and their altered expression has been implicated in the pathogenesis of a variety of human diseases. Failure to express a functional cystic fibrosis (CF) transmembrane receptor (CFTR) chloride ion channel in epithelial cells underpins CF. Secondary to the CFTR defect, it is known that other pathways can be altered and these may contribute to the pathophysiology of CF lung disease in particular. For example, quantitative alterations in expression of some ncRNAs are associated with CF. In recent years, there has been a series of published studies exploring ncRNA expression and function in CF. The majority have focussed principally on miRNAs, with just a handful of reports to date on lncRNAs. The present study reviews what is currently known about ncRNA expression and function in CF, and discusses the possibility of applying this knowledge to the clinical management of CF in the near future.

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How to find small non-coding RNAs in bacteria

Biological Chemistry ◽

10.1515/bc.2005.140 ◽

2005 ◽

Vol 386 (12) ◽

pp. 1219-1238 ◽

Cited By ~ 120

Author(s):

Jörg Vogel ◽

Cynthia Mira Sharma

Keyword(s):

Small Rnas ◽

Rna Binding ◽

Rna Binding Proteins ◽

Critical Role ◽

Rna Molecules ◽

Regulatory Circuit ◽

Non Coding Rna ◽

Genome Wide ◽

Response To Stress ◽

Non Coding Rnas

AbstractSmall non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacteriumEscherichia coli. Orthologs of theseE. colisRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.

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