Overview of Non-Coding RNAs

Overview of Non-Coding RNAs

• Definition and Importance of ncRNAs:
  • Non-coding RNAs (ncRNAs) are RNA molecules that do not encode proteins yet play critical roles in cellular functions.
  • Approximately 80% of transcription in human cells produces ncRNAs, while only 20% results in mRNAs.
  • ncRNAs can adopt complex structures, such as stem-loops, enhancing their interactions with proteins, DNA, RNA, and other small molecules.

Types of Non-Coding RNAs and Their Functions

1. Alternation of Protein Function and Stability:
   • ncRNAs bind to proteins, altering their structures and functions, potentially affecting catalytic activities and stability.
2. Blocking:
   • Prevents cellular processes by binding to DNA (e.g., the Shine-Dalgarno sequence) and blocking ribosome attachment, regulating translation.
3. Scaffold:
   • ncRNAs can form complexes with multiple proteins, facilitating various cellular processes.
4. Guide:
   • Directs proteins to specific cellular locations. For instance, the telomerase RNA component (TERC) guides telomerase to telomeres, acting as a DNA replication template.
5. Decoy:
   • Recognizes and sequesters other ncRNAs.
6. Ribozyme:
   • Certain ncRNAs possess catalytic abilities, facilitating various biochemical reactions.

Mechanisms of Action of Non-Coding RNAs

HOTAIR and Chromatin Regulation

• HOTAIR:
  • A 2.2-kb-long ncRNA that impacts chromatin structure and RNA polymerase binding, hence influencing transcriptional repression.
  • Located on chromosome 12, acts as a scaffold for two histone-modifying complexes: PRC2 (which trimethylates lysine 27 on histone H3) and LSD1 (which demethylates lysines), resulting in inhibition of transcription.

RNA Interference (RNAi)

• RNAi Process:
  • Involves silencing mRNA through double-stranded RNA (dsRNA). Includes key players: microRNAs (miRNAs) and small interfering RNAs (siRNAs).
  • miRNAs: Derived from endogenous genes, can inhibit multiple mRNAs.
  • siRNAs: Typically derive from exogenous sources, targeting specific mRNAs.
• Steps of RNA Interference:
  1. Processing by Drosha/DGCR8: In the nucleus, a precursor miRNA is cleaved into a smaller hairpin RNA by the Drosha/DGCR8 complex.
  2. Transport to Cytoplasm: Processed pre-miRNA is transported to the cytoplasm via Exportin 5.
  3. Processing by Dicer: Dicer further cleaves pre-miRNA into mature miRNA (approx. 22 nucleotides) and processes pre-siRNA into dsRNA.
  4. Binding to RISC: Mature miRNA combines with the RNA-induced silencing complex (RISC) to target specific mRNA.

RNA-Induced Silencing Complex (RISC)

• RISC binds to single-stranded RNA that interacts with proteins.
• It can inhibit translation or degrade mRNA, with different outcomes for miRNA (often inhibits translation) and siRNA (typically cleaves mRNA).

Non-Coding RNAs in Protein Targeting

• Role of ncRNAs in Protein Localization:
  • ncRNAs are crucial for directing proteins to specific cellular locales, such as the plasma membrane or endoplasmic reticulum.
• Signal Recognition Particle (SRP):
  • An RNA-protein complex that aids in targeting.
  • Recognizes ER signal sequences (6-12 hydrophobic amino acids) and facilitates GTP hydrolysis for targeting.

CRISPR-Cas System: An Adaptive Defense Mechanism

Phases of the CRISPR-Cas System

1. Adaptation:
   • Acquiring spacers from bacteriophage DNA integrated into the CRISPR locus.
2. Expression:
   • Transcription of CRISPR locus to produce pre-crRNA and tracrRNA necessary for interference.
3. Interference:
   • crRNA guides the tracrRNA-Cas9 complex to complementary bacteriophage DNA where Cas9 induces double-strand breaks, inhibiting bacteriophage proliferation.

PIWI-Interacting RNAs (piRNAs) and Transposable Elements

• Function of piRNAs:
  • Interact with PIWI proteins to silence transposable elements (TEs) in animal genomes, protecting gene integrity.
• Mechanism of piRNA Action:
  • Processed from pre-piRNA transcripts, typically 24-31 nucleotides long, they form complexes known as piRISCs and piRITS, degrading TE RNA in the cytosol or silencing transcription in the nucleus.

Non-Coding RNAs and Human Diseases

• Association with Genetic Disorders:
  • First link identified in 2001 related to cartilage-hair hypoplasia (CHH).
  • Mutations in the RNaseMRP complex ncRNA cause defects in rRNA and mRNA processing.
  • DROSHA gene mutations linked to ALS (amyotrophic lateral sclerosis).
• ncRNAs in Cancer:
  • miRNAs can act as oncogenes or tumor suppressors; the miR-200 family inhibits epithelial-mesenchymal transition (EMT).
  • HOTAIR overexpression in cancers correlates with poor prognosis.
• ncRNAs in Neurological Disorders:
  • 70% of miRNAs expressed in the brain are crucial for neuronal function; abnormal miRNA expression ties to Alzheimer's disease.
• ncRNAs in Cardiovascular Diseases:
  • miR-1 regulates ion channels critical for cardiac signaling; altered miRNA expression in heart failure patients correlates with disease progression.

Examples of Non-Coding RNAs Associated with Human Diseases

• ncRNA(s) and Disease(s):
  • miR-200 family: Several cancers (bladder, melanoma, stomach, colorectal).
  • HOTAIR: Breast, lung, colorectal cancers.
  • piRNAs/PIWI proteins: Testicular cancer.
  • Drosha: ALS, Alzheimer's disease, multiple sclerosis.
  • miR-1: Heart arrhythmias; changes indicate heart failure.
  • Other miRNAs linked to various malignancies, illustrating their important roles in disease pathology.