Junk DNA or Loops of Hope

priyankamathur35
May 20
5 min read

Humans are organized into organ systems, such as the nervous system, which includes the brain and spinal cord, and the circulatory system, comprising the heart and blood vessels, among others. Organs make up organ systems, while each organ is made up of tissues, which are groups of cells considered the basic unit of life. A single cell contains the nucleus, in which resides the genetic information for the organisms to function, develop, and reproduce called DNA.

Each cell contains about 2 meters of DNA, tightly packed with histone proteins to form a chromosome. Can you imagine something of that length fitting inside an approximately 6 micrometer wide cell? The DNA helix made up of four chemical bases, adenine, thymine, cytosine and guanine, creates genes that can form RNA and proteins. Surprisingly, complex organism like humans have only about 20,000 protein -forming genes, that is almost same as in case of a simple roundworm and strikingly identical with chimpanzee. That accounts for just 1.5% of the genome, the remaining 98% of the genome was previously considered as “Junk”. The ENCyclopedia Of DNA Elements ( ENCODE) Project has identified that the so -called Junk DNA are actually the loops of hope, they do not make proteins instead form non-coding RNAs regulating the expression of protein-forming genes. In agreement with proteins, the non-coding RNAs govern embryonic development, maintain physiological homeostasis and are also associated with hereditary and non-hereditary diseases, including diabetes and cancer.

Based on their function, the non-coding RNAs are divided into House-keeping ncRNAs and Regulatory ncRNAs.

Housekeeping ncRNAs are essential molecules and form core components in the mechanism of protein translation and splicing. These include ribosomal RNAs, which are structural and enzymatic component of ribosomes, by combining with ribosomal protein, it allows attachment of messenger RNA and initiate translation.

Transfer RNAs, are the next essential component for protein translation, as it recognize the sequence of codons on the messenger RNA and attach the corresponding amino acid to form a polypeptide chain.
Small Nuclear RNAs are the key components of the spliceosome and remove the intron sequences, so that the exons join to form protein-coding messenger RNA.
Small Nucleolar RNAs as the name suggests, are found in the nucleolus to perform activation of RNAs by methylation.

Regulatory ncRNAs are capable of interacting with DNA, RNA and proteins and play an important role in gene silencing, activation or repression of gene expression, embryonic development and cell differentiation. Based on the length, they are divided into Long non-coding RNAs and Short non-coding RNAs.

The Long ncRNAs group are more than 200 nucleotides in length and includes lnc RNAs, lincRNA or long intergenic RNAs, long intronic RNAs enhancer RNA and circular RNAs. The can regulate gene expression by, the negative charge of lncRNAs can neutralize the positive charge on histone tails of chromatin, allowing exposure to initiate or repress promoter molecules, acting as a switch for gene expression. The most evident and critical example is XIST, a long ncRNA responsible for X chromosome inactivation in cells of female mammals, as XIST spread over one of the X chromosomes and silences its genes.
Circular RNAs are highly stable, covalently closed-loop structures that can bind microRNAs and proteins and regulate gene expression. These are also associated with cell proliferation and cell-death, also regulate immune response by modulating immunogenic receptors.
The other category is the Small non-coding RNAs such as microRNAs (21-23nts in length), small interfering RNA, piwi-interacting RNAs.

Among them microRNAs have gained wide attention of scientist because of their small size, bioavailability and functional ability to inhibit gene expression at post-transcriptional level. Several research outputs consistently associate miRNAs with rare genetic diseases as well as onset and progression of complex diseases such as cancers, inflammatory diseases, progression of heart disease, vascular disorders and developmental disorders.

MicroRNAs bind to complementary sequences on messenger RNAs to induce degradation or repression translation into proteins.
Small Interfering RNAs are components of defense against virus, as well guide degradation of complementary messenger RNAs.
PIWI-interacting RNAs can associate with PIWI proteins to silence transposable elements and are critical for embryonic development.

Non-coding RNAs in Diagnosis and Treatment

The existence of so many species of non-coding RNA validates that they are essential in regulation of cellular functions and their disbalance may be associated with onset and progression of various diseases, including cancer.

A variety of miRNAs are present in the body fluids including blood, serum, plasma, cerebrospinal fluid, amniotic fluid and even saliva and colostrum. Their abundance and expression vary in case of diseases like cancers, cardiovascular and metabolic diseases.

MicroRNAs are packed in exosomes and released from tissues or tumor cells into circulation. Therefore, specific pattern of microRNA expressions are being studied to exploit their role as biomarkers in diseases like diabetes, fibrosis, breast, ovarian, colon cancers and many more.

However efficient these small loops of hope could be, a major setback scientist face today is the delivery into the system. RNAs are highly unstable in biological fluids as they can be degraded by ribonucleases, or attached by the immune system generating inflammation or adverse reactions . In addition to these, they might not be able to enter the target cell or might target any other gene.

Therefore, various delivery and stabilization methods are now being explored to improve the efficacy of these molecules. Earlier, AAV vector systems were used, but there was an insecurity of triggering a viral infection. For some years now, scientists have developed lipid nanoparticles that encapsulate the mRNA or microRNA and keep them stable in the biological fluids. These LNP may be chemically modified for stability and combined with specific antibodies for targeted delivery. Also, Aptamer-siRNA combinations are used to deliver siRNAs to cancer cells.

Some examples of advances in research

The Covid-19 vaccine developed by Pfizer- BioNTech and Moderna, contains messenger RNA specific for the spike protein of the SARS CoV-2 virus, that triggers an immune response, in turn preparing the body to fight if it encounters the Virus.
Astra Zeneca and Johnson & Johnson developed the Covid-19 vaccine using, viral vector adenovirus to carry mRNA forming the spike protein of SARS CoV-2 virus and trigger an immune response.
Oncogenic miRNAs combined with doxorubicin for cancer therapy and conjugate therapy of miRNA-122 inhibitor with anti-viral drugs to treat Hepatitis C virus have been formulated where these treatment strategies have reached clinical trials.
MicroRNA sponges that contains many binding sites of desired miRNAs have been used in treatment of cardiovascular diseases and breast cancer.
Liposomes, extracellular vesicles, nanoparticles and some polymers have also been utilized to accomplish miRNA-delivery into the target cells. MiR-34a and miR-125b carried through liposomes and extracellular vesicles in treatment for carcinomas.
LNA-i-miR-221 is an example of a drug that targets miR-221, involved in many types of cancers. A Phase I clinical study demonstrated its safety and potential efficacy in treating multiple myeloma.

References:

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A diagram illustrating the function of various Non-coding RNA and their importance in disease diagnosis and treatment.
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