Day 91 MCAT Practice Question

Passage 7: Nucleic Acids

A recent study has identified a novel long non-coding RNA (lncRNA) that plays

a crucial role in the regulation of gene expression during embryonic development.

This lncRNA, named EMBRYONIC REGULATOR 1 (ER1), is highly conserved across

vertebrate species and is expressed specifically in the developing nervous system.



ER1 is a 2.5 kb transcript that is polyadenylated but does not contain any open

reading frames (ORFs) longer than 100 codons. Structural analysis of ER1 using

chemical probing methods has revealed a complex secondary structure with

multiple stem-loops and pseudoknots. These structural elements are critical for

ER1’s function, as mutations that disrupt the secondary structure result in a loss of

regulatory activity.



Functional studies have shown that ER1 acts as a scaffold for chromatin modifying

complexes, specifically the Polycomb Repressive Complex 2 (PRC2). ER1 binds to

PRC2 through a conserved 150 nt region located at its 3’ end, which folds into a

distinct stem-loop structure. This interaction recruits PRC2 to specific genomic

loci, resulting in the trimethylation of histone H3 lysine 27 (H3K27me3) and the

repression of target gene expression.

Notably, ER1 appears to regulate the expression of genes involved in neuronal

differentiation and patterning. Knockdown of ER1 in zebrafish embryos using

morpholino antisense oligonucleotides results in severe defects in brain

development, including a reduction in the size of the forebrain and midbrain

regions. RNA-seq analysis of ER1-depleted embryos has identified several key

neuronal transcription factors as potential targets of ER1-mediated repression.

To further investigate the mechanism of ER1 function, researchers have employed

CRISPR-Cas9 technology to generate a series of deletion mutants in mouse

embryonic stem cells (mESCs). By removing specific regions of the ER1 locus

and assessing the effects on PRC2 recruitment and target gene expression, they

have been able to map functional domains within the lncRNA. These studies have

revealed that, in addition to the PRC2-binding region, ER1 contains a 5’ domain that

is required for its localization to chromatin.

The CRISPR-Cas9 system used to generate deletion mutants in the ER1 locus

operates by:

A) Inducing double-stranded breaks at specific genomic locations

B) Promoting homologous recombination between the ER1 locus and a donor

template

C) Inhibiting transcription of the ER1 gene

D) Altering the epigenetic marks at the ER1 locus