Your genome is a vast array of genes that each have different functions. In previous articles, you may have learned that gene expression occurs when DNA is transcribed into RNA which is then translated into proteins. We know that gene expression is strictly controlled and regulated by different mechanisms such as DNA methylation and histone modification, but what if there are other mechanisms?
If you have trouble differentiating between transcription and translation, think of the meaning of these words in relation to language. In transcription, you would take spoken words and put them on paper: the language is the same but the medium is different. Same with DNA and RNA: they are composed of the same elements (bases), but ultimately carry out different functions. On the other hand, translation is transforming some words from one language to another. Same with RNA and proteins: they both say the same things, but with different components ("languages").
Researchers have detected small and long RNA sequences that play a part in the regulation of gene expression. These RNA sequences are called non-coding RNA meaning that they do not code for a specific protein.
Long non-coding RNA
Long non-coding RNAs are RNA sequences that are longer than 200 nucleotides and are not translated into functional proteins.1
Non-coding RNAs have key roles in the regulation of gene expression. Long non-coding RNAs can:
- modulate chromatin function,
- regulate the assembly and function of nuclear bodies,
- alter the translation of coding mRNAs, and
- interfere with intracellular signalling pathways.1
The function of a long non-coding RNA depends on its specific interactions with affected DNA, RNA, and proteins.1 These interactions ultimately lead to the alteration of gene expression and can lead to certain disorders such as neurological disorders and cancer. 1 Statistical analysis reveals that the human genome contains more than 16,000 non-coding RNA genes however the true number is still debated.1 Most non-coding RNAs are transcribed by RNA polymerase II and have 5' end M7G caps and 3' end poly A tails that are transcribed and processed similarly to mRNAs.1
RNA stands for ribonucleic acid and is converted from DNA during transcription. Transcription is the first step in gene expression. There are many different types of RNA in the cell and only mRNA codes for proteins. Other RNAs like tRNA and non-coding RNAs regulate gene expression by influencing how a gene is transcribed and translated. tRNAs are important during translation as they help the ribosomes assemble amino acids.
Non-coding RNA gene expression
A large portion of noncoding RNAs is located inside the nucleus.1 This is different from coding mRNAs that are largely located in the cytoplasm. As previously mentioned, gene expression can be regulated via the presence of long non-coding RNAs.1 This regulation takes place at multiple levels of gene expression. Through their interactions with DNA, RNA, and proteins, long non-coding RNAs can:
- modulate chromatin structure,
- alter the transcription of genes,
- affect RNA splicing and translocation, and
- mediate the regulation of organelles.1
Can you recall the spicing process?
Non-coding RNA and chromatin regulation
We know from previous articles that RNA and DNA have negative charges. The negative charge of non-coding RNAs can neutralize the positively charged histone tails surrounding DNA, which leads to the loosening of the chromatin structure.1 This ultimately affects which genes are exposed to the RNA polymerase transcription machinery. Also, many non-coding RNAs near chromatins can interact with transcription factor proteins to inhibit or encourage their binding activity at certain DNA regions.1
Why is it important to loosen chromatin during transcription?
Long non-coding RNAs can actually interact with chromatin modifiers like histones and recruit them to the promoter of the target gene in order to activate or repress their transcription.1 The expression levels of a given non-coding RNA and the factors that it interacts with can determine the effects it has on the targeted chromatin. For example, it has been suggested that non-coding RNA sequences mediate the binding of polycomb repressive complex 2 (PRC2) to a given chromatin. 1
Polycomb repressive complex 2: A complex that represses DNA transcription.
This type of interaction occurs both in cis and trans for example the non-coding RNA sequence ANRIL can mediate PRC1 and PRC2 binding to promoters to both nearby and distant genes in order to silence their transcription.1
In addition to silencing genes, non-coding RNAs can also promote and activate the transcription of genes.1
The non-coding RNA HOTTIP can regulate the HOXA gene cluster by binding to these genes through chromatin looping.1 Once HOTTIP bind to the chromatin, it facilitates gene expression by recruiting MLL and WDR51.
Non-coding RNAs and gene silencing
Long non-coding RNAs can also directly silence genes. This can be seen in the long non-coding RNA XIST which is responsible for silencing one of the X chromosomes in female organisms.1 During development, XIST travel to one of the X chromosomes in order to silence a large section of its genes.1
Why is gene silencing important?
Long non-coding RNAs can also suppress gene expression by altering the transcription machinery directly. 1 Which alters the recruitment of transcription factors to the promoter which prevents RNA polymerase 2 from being recruited to the site of transcription.1 Altering the promoter can also alter histone modification patterns leading to tighter coils within the DNA and a reduction in chromosome accessibility.1 An example of this can be seen in mice where the Airn long non-coding RNA causes displacement of RNA polymerase 2 from the Igf2r promoter which leads to silencing of the gene1 .
There are many more ways that non-coding RNAs regulate gene expression however many of them are still under debate and are beyond the scope of your class.
Non-coding RNAs interact directly with the DNA strand by generating hybrid structures with DNA to influence chromatin accessibility to the RNA polymerase transcription machinery. These hybrid structures can be triple helices known as R-loops.1
R-Loop: A three-stranded nucleic acid structure made of DNA and RNA.
An example of how triplexes mediate gene expression can be seen in the activation of the proto-oncogene sphingosine kinase 1 (SPHK1).1 When proliferation signals are released, the long non-coding RNA forms a triple helix with the SPHK1 gene upstream of the genes enhancer.1 This helps to recruit chromatin modifiers that activate the transcription of SPHK1.
An oncogene is a specific genetic sequence associated with an increased risk of cancer development. When oncogenes are transcribed, the cell constantly divides resulting in tumor growth.
Several long non-coding RNAs regulate gene expression through R-loops with the help of proteins. In mesenchymal stem cells (mESCs) the long non-coding RNA TARID creates an R loop at the CpG rich promoter of the TCF21 gene.1 A special protein called GADD45A recognizes and binds to the R- loop at the TCF21 promoter. This binding recruits the DNA demethylating factor TET1 which removes the silencing methylation from the TCF21 gene and causes it to be transcriptionally active1 (see Fig. 2).
Non-coding RNA classification
There are multiple types of non-coding RNAs that each play different roles in the regulation of gene expression. Lets see some of them:
MicroRNA
MicroRNA's (miRNA) function in transcriptional and post-transcriptional modification during gene expression by base pairing with complementary sequences on the messenger RNA (mRNA) transcript.2 This binding usually results in gene silencing via the repression of translation or the degradation of the transcript.2 The mechanisms by which this occurs are still under investigation however they play an essential role in controlling which genes are expressed.
miRNAs are used in biological research to test a protein's function
Ribosomal and transfer RNAs
Another important noncoding RNA is ribosomal RNA (rRNA). This form of non-coding RNA functions to regulate gene expression at the level of translation. Together with the transfer RNA (tRNA), another non-coding RNA, they take part in the translation process. rRNA is part of the ribosomes, while tRNA is an adapter molecule that links the codons in an mRNA transcript to the corresponding amino acids that they code for.2
Similarly, another type of non-coding RNA that works during translation is small nucleolar RNA (snowRNA). SnowRNA's are a class of small RNA molecules that function to guide covalent modifications of ribosomal RNA transfer RNA and small nuclear RNAs. These covalent modifications are usually methylation (addition of methyl groups) or pseudouridylation (addition of an isomer of uridine).2
Translation is the processing of converting mRNA into a protein amino acid sequence. mRNA base pairs are organized in groups of three called codons. Each codon codes for an amino acid which dictates the protein function and structure. Mutations that shift base pairs out of their rightful place can seriously affect the structure and function of a protein leading to diseases.
Small nuclear RNA
Small nuclear RNAs (snRNAs) get their name from the fact that these RNAs are 150 nucleotides and their primary function is involved in the pre-mRNA in the nucleus.2 SnRNA's also aid in the regulation of transcription factors and make up a part of the spliceosome complex that is responsible for removing introns during splicing.2 Do not confuse these snRNAs with the previously mentioned snowRNAs.2
The exact mechanisms by which non-coding RNAs regulate translation and splicing are beyond the scope of your course but it is good to understand the roles that non-coding RNAs play in regulating gene expression.
Non-coding RNA prediction
Bioinformatics now has powerful tools to support biological experiments in understanding non-coding RNAs. Through experimentations, researchers have been able to sequence a vast amount of non-coding RNAs, and test their function. Bioinformaticians, however, can boost the reach of experimental findings by analysing extra interactions from the RNA with other molecules in the cell4. Doing this experimentally would take much too long, but a computer can cross-reference the RNA sequence with other molecules extremely fast, aiding researchers in finding possible high-interest interactions and focusing on them.
Non-coding RNA impact factor
Apart from designating a type of RNA, Non-coding RNA is also a scientific journal concerned with non-coding RNA research. Scientific journals all have an "impact factor", which determines how influential that journal is.
The impact factor (IF) of a journal, or journal impact factor (JIF), is a calculation of how many times on average an article in that journal is cited in a given year.
While the measure is not perfect (for example, journals that publish more review articles will get higher IFs because more people cite reviews), it is widely used in the scientific community. An impact factor of more than 10 is considered outstanding, and more than 3 is considered good. Usually, journals fall within the 0-2 IF range.
As of January 2023, the Non-coding RNA journal has an impact factor of 7.353, but this can change from year to year.
Non-Coding RNA - Key takeaways
- Long non-coding RNAs are RNA sequences that are longer than 200 nucleotides that are not translated into functional proteins.
- Non-coding RNAs have key roles in the regulation of gene expression.
- Non-coding RNAs near chromatins can interact with transcription factor proteins to inhibit or encourage their binding activity at certain DNA regions.
- MicroRNA's (miRNA) function in transcriptional and post-transcriptional modification during gene expression by base pairing with complementary sequences on the messenger RNA (mRNA) transcript.
References
- Statello, L., Guo, CJ., Chen, LL. et al. Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol 22, 96–118 (2021). https://doi.org/10.1038/s41580-020-00315-9
- Henrik's Lab. All types of non-coding RNA. 2021
- https://academic-accelerator.com/Impact-of-Journal/Non-coding-RNA
- Rincón-Riveros, A., Morales, D., Rodríguez, J. A., Villegas, V., and López-Kleine, L. Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions. Int J Mol Sci. 2021 Nov; 22(21): 11397. https//doi.org/10.3390/ijms222111397
Explanations 
Exams 
Magazine 
