Non-coding RNAs and Dosage Compensation: Mechanisms and Implications last

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Non-coding RNA Regulation of Gene Expression

Overview of Non-coding RNAs

Non-coding RNAs (ncRNAs) are RNA molecules that are not translated into proteins but play crucial roles in regulating gene expression. They include small RNAs such as siRNAs and microRNAs, as well as long non-coding RNAs (lncRNAs). These molecules are involved in diverse cellular processes, including gene silencing, dosage compensation, and defense against genomic parasites.

siRNA (small interfering RNA): Short double-stranded RNAs that guide the RNA-induced silencing complex (RISC) to complementary mRNA targets, leading to their degradation.
microRNA (miRNA): Endogenously encoded small RNAs that regulate gene expression post-transcriptionally, typically by binding to the 3' UTR of target mRNAs and inhibiting translation or promoting degradation.
lncRNA (long non-coding RNA): Transcripts longer than 200 nucleotides that do not code for proteins but can regulate gene expression at multiple levels, including chromatin modification, transcription, and post-transcriptional processing.

Functions of RNA Interference (RNAi)

RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation by neutralizing targeted mRNA molecules. The main functions of RNAi include:

Transposon silencing: Suppression of mobile genetic elements to maintain genome stability.
Viral defense: Degradation of viral RNA to protect the cell from infection.
Gene regulation: Fine-tuning of gene expression during development and in response to environmental cues.

Long Non-coding RNAs (lncRNAs)

Characteristics of lncRNAs

Transcripts longer than 200 nucleotides.
Not translated into proteins.
Often poly-adenylated.
Show weak sequence homology across species.
Not dependent on Dicer for their function.

lncRNAs are involved in a variety of cellular processes, many of which are still being elucidated. They are especially important in epigenetic regulation and dosage compensation.

Dosage Compensation and X-inactivation

Dosage Compensation: The Problem

In species with sex chromosomes, such as mammals, females (XX) have two X chromosomes while males (XY) have only one. This difference could lead to an imbalance in the expression of X-linked genes. Dosage compensation mechanisms have evolved to equalize gene expression between the sexes.

Females (XX): Two copies of each X-linked gene.
Males (XY): One copy of each X-linked gene.

This difference necessitates mechanisms to ensure similar levels of X-linked gene products in both sexes.

X-inactivation in Mammals

X-inactivation is the process by which one of the two X chromosomes in female mammals is transcriptionally silenced to achieve dosage compensation. Key features include:

Random: Either the maternal or paternal X chromosome is inactivated in each cell.
Occurs in somatic cells during embryonic development and is passed to daughter cells during mitosis.
Does not occur in males (who have only one X chromosome).
Barr body: The inactivated X chromosome forms a condensed structure visible in the nucleus.
Stable within cell lineage but resets in the germline for the next generation.

Example: Calico cats display black and yellow-orange patches of fur color due to random X-inactivation of different alleles controlling pigment.

Molecular Mechanism: Xist and Tsix

The X-inactivation center (XIC) contains several lncRNAs, most notably Xist and Tsix:

Xist: Expressed from the inactive X chromosome; coats the chromosome and triggers its silencing via chromatin modification and DNA condensation.
Tsix: Expressed from the active X chromosome (temporarily); acts as an antisense regulator of Xist, preventing its expression on the active X.
Both Xist and Tsix are expressed at low levels on both X chromosomes before inactivation.
Neither Xist nor Tsix encodes a protein; both function as lncRNAs.

Experimental Evidence

Dicer mutants: X-inactivation is not affected, indicating that Xist function is not Dicer-dependent.
Xist deletion: Removing Xist prevents X-inactivation.
Tsix mutants: Xist coats the chromosome lacking Tsix, leading to its inactivation.
Xist autosomal transgene: Ectopic expression of Xist on an autosome can silence that autosome, demonstrating Xist's sufficiency for chromosome inactivation and its action in cis.

Dosage Compensation Mechanisms in Other Organisms

Organism	Sex Chromosome System	Dosage Compensation Mechanism
Eutherian mammals	XX (female), XY (male)	Random X-inactivation in females
Drosophila (Fly)	XX (female), XY/XO (male)	Increased transcription of X in males (2-fold upregulation)
Worms (C. elegans)	XX (hermaphrodite), XO (male)	Repression of X transcription by half in hermaphrodites

Dosage Compensation in Drosophila: Role of roX lncRNA

In Drosophila, the lncRNA roX (RNA on the X) is essential for dosage compensation:

roX is expressed from the X chromosome and recruits the male-specific lethal (msl) complex to upregulate gene expression.
Without roX, the msl complex localizes to autosomes instead of the X chromosome.
roX-autosomal transgenes can recruit the msl complex to autosomes, demonstrating the targeting function of roX.

Implications of X-inactivation for X-linked Traits

Color Blindness Example

Color blindness is an X-linked recessive trait, more common in males. In heterozygous females, X-inactivation leads to mosaic expression:

Some retinal cells express the normal allele, while others express the mutant allele, depending on which X chromosome is inactivated.
This mosaicism can result in patches of cells with and without color photoreceptors.

What are lncRNAs?

Transcripts longer than 200 nucleotides.
Not translated into proteins.
Not dependent on Dicer for function.
Often poly-adenylated.
Show weak sequence homology.

Do lncRNAs and miRNAs Break Crick's Central Dogma?

The central dogma of molecular biology describes the flow of genetic information: DNA → RNA → Protein. Non-coding RNAs such as lncRNAs and miRNAs regulate gene expression at the RNA level, introducing additional layers of control not originally described in the central dogma.

Summary Table: Key Features of Non-coding RNAs

Type	Size	Function	Dependency	Example
siRNA	~21-23 nt	mRNA degradation, gene silencing	Dicer-dependent	RNAi pathway
miRNA	~21-25 nt	Translational repression, mRNA degradation	Dicer-dependent	let-7, lin-4
lncRNA	>200 nt	Chromatin modification, transcriptional regulation, dosage compensation	Not Dicer-dependent	Xist, Tsix, roX

Key Equations and Concepts

Central Dogma:

Dosage Compensation: Ensures equal expression of X-linked genes in males and females despite differences in X chromosome number.

Additional info:

Calico cats are a classic example of X-inactivation in action, as their fur color patterns result from random inactivation of X chromosomes carrying different pigment alleles.
lncRNAs are increasingly recognized as key regulators in many biological processes, but the full extent of their functions remains an active area of research.