Non-coding RNA: It’s Not Junk

Boland, C. Richard

doi:10.1007/s10620-017-4506-1

Cited by 55 publications

(24 citation statements)

References 14 publications

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“…In general, lncRNAs refer to nonprotein coding RNAs that are longer than 200 nucleotides [ 11 , 13 ]. Considering the distinctive structure of lncRNAs, which is different from other regulatory ncRNAs with quite short sequences similar to microRNAs (miRNAs) and short-interfering RNAs (siRNAs), lncRNAs have specific biological functions and, therefore, may be quite irreplaceable for the physical regulation [ 14 , 15 , 16 ]. Gene transcription regulation, post transcriptional regulation, and epigenetic regulation are the three main biological functions of lncRNAs according to existing literature [ 17 , 18 , 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

Tissue Expression Difference between mRNAs and lncRNAs

Lei

Zhang

Pan

et al. 2018

IJMS

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Messenger RNA (mRNA) and long noncoding RNA (lncRNA) are two main subgroups of RNAs participating in transcription regulation. With the development of next generation sequencing, increasing lncRNAs are identified. Many hidden functions of lncRNAs are also revealed. However, the differences in lncRNAs and mRNAs are still unclear. For example, we need to determine whether lncRNAs have stronger tissue specificity than mRNAs and which tissues have more lncRNAs expressed. To investigate such tissue expression difference between mRNAs and lncRNAs, we encoded 9339 lncRNAs and 14,294 mRNAs with 71 expression features, including 69 maximum expression features for 69 types of cells, one feature for the maximum expression in all cells, and one expression specificity feature that was measured as Chao-Shen-corrected Shannon’s entropy. With advanced feature selection methods, such as maximum relevance minimum redundancy, incremental feature selection methods, and random forest algorithm, 13 features presented the dissimilarity of lncRNAs and mRNAs. The 11 cell subtype features indicated which cell types of the lncRNAs and mRNAs had the largest expression difference. Such cell subtypes may be the potential cell models for lncRNA identification and function investigation. The expression specificity feature suggested that the cell types to express mRNAs and lncRNAs were different. The maximum expression feature suggested that the maximum expression levels of mRNAs and lncRNAs were different. In addition, the rule learning algorithm, repeated incremental pruning to produce error reduction algorithm, was also employed to produce effective classification rules for classifying lncRNAs and mRNAs, which gave competitive results compared with random forest and could give a clearer picture of different expression patterns between lncRNAs and mRNAs. Results not only revealed the heterogeneous expression pattern of lncRNA and mRNA, but also gave rise to the development of a new tool to identify the potential biological functions of such RNA subgroups.

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Section: Introductionmentioning

confidence: 99%

Tissue Expression Difference between mRNAs and lncRNAs

Lei

Zhang

Pan

et al. 2018

IJMS

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“…We should be reminded that the human genetic content that codes for proteins is 1.5% only, whereas the non-coding but regulation-relevant genetic content is about 98.5% (Boland, 2017). Additionally, we must not forget that viruses represent the most abundant genetic elements on this planet, outnumbering cellular genetic content by 10 times.…”

Section: Virus Communicationmentioning

confidence: 99%

What is Life?

Witzany¹

2020

Front. Astron. Space Sci.

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In searching for life in extraterrestrial space, it is essential to act based on an unequivocal definition of life. In the twentieth century, life was defined as cells that self-replicate, metabolize, and are open for mutations, without which genetic information would remain unchangeable, and evolution would be impossible. Current definitions of life derive from statistical mechanics, physics, and chemistry of the twentieth century in which life is considered to function machine like, ignoring a central role of communication. Recent observations show that context-dependent meaningful communication and network formation (and control) are central to all life forms. Evolutionary relevant new nucleotide sequences now appear to have originated from social agents such as viruses, their parasitic relatives, and related RNA networks, not from errors. By applying the known features of natural languages and communication, a new twenty-first century definition of life can be reached in which communicative interactions are central to all processes of life. A new definition of life must integrate the current empirical knowledge about interactions between cells, viruses, and RNA networks to provide a better explanatory power than the twentieth century narrative.

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“…28 A large portion of the human genome is transcribed into RNA at low levels. 30 Noncoding RNA (ncRNA) genes are abundant in the human genome. According to a recent annotation, the human genome contains 9078 small ncRNA and 13 333 long ncRNA genes.…”

Section: Revelations From the Hgpmentioning

confidence: 99%

“… 6 Nearly, all repeat sequences in humans are derived from transposable elements (interspersed repetitive elements). 32 (7) About 45% 30 of the human genome contains 4 main categories of interspersed repetitive elements: short interspersed elements, long interspersed elements, DNA transposons, and elements with long terminal repeats (LTR elements). 33 Another 25% is composed of shorter tandem repeats such as satellites, microsatellites, and minisatellites.…”

Section: Revelations From the Hgpmentioning

confidence: 99%

“… 33 Another 25% is composed of shorter tandem repeats such as satellites, microsatellites, and minisatellites. 30 (8) In general, recombination occurs at a much faster rate in the distal parts (~20 Mb) and on shorter arms of chromosomes, such that at the minimum, 1 crossover event takes place in each chromosome arm during meiosis. 6 (9) Men have twice as high mutation rate than women during meiosis.…”

Section: Revelations From the Hgpmentioning

confidence: 99%

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Genomic Interventions in Medicine

Aworunse

Adeniji

Oyesola

et al. 2018

Bioinform Biol Insights

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Lately, the term “genomics” has become ubiquitous in many scientific articles. It is a rapidly growing aspect of the biomedical sciences that studies the genome. The human genome contains a torrent of information that gives clues about human origin, evolution, biological function, and diseases. In a bid to demystify the workings of the genome, the Human Genome Project (HGP) was initiated in 1990, with the chief goal of sequencing the approximately 3 billion nucleotide base pairs of the human DNA. Since its completion in 2003, the HGP has opened new avenues for the application of genomics in clinical practice. This review attempts to overview some milestone discoveries that paved way for the initiation of the HGP, remarkable revelations from the HGP, and how genomics is influencing a paradigm shift in routine clinical practice. It further highlights the challenges facing the implementation of genomic medicine, particularly in Africa. Possible solutions are also discussed.

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Non-coding RNA: It’s Not Junk

Cited by 55 publications

References 14 publications

Tissue Expression Difference between mRNAs and lncRNAs

Tissue Expression Difference between mRNAs and lncRNAs

What is Life?

Genomic Interventions in Medicine

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