Honorable Mention Excerpts
Bergen County Academies
Teaher: Judith Pinto
Richard Robert’s and Phil Sharp’s discovery of
introns in 1977 entirely changed the 1969 definition of a
gene by disproving the earlier notion that a gene was a
continuous segment of protein coding genetic material, as
introns do not play a direct role in protein coding. . . . .
. . . On the TPH1 gene there is a single nucleotide polymorphism,
A218C, located on intron 7, and studies have shown that this polymorphism is
associated with manic-depressive illness, as it is located in a potential
transcription-factor binding site and therefore could affect TPH1 gene
expression (1). Given that the TPH1 gene aids in the synthesis of serotonin and
a polymorphism on one of its introns could potentially lessen the gene
expression due to its location, there is a strong correlation between serotonin
dependent mental disorders and the regulatory effects of an intron. This shows
the extent to which the intron and its functions change the 1969 definition of a
gene, given that non-coding sections of DNA not only exist, but also play a
large role in gene regulation. . . . .
. . . The existence of introns as a whole as
well as their regulatory effects extends the original
definition of a gene far beyond its bounds. The discovery of
introns as well as subsequent discoveries about their
function and purpose has added to the wealth of knowledge
regarding the human genome, and additionally, offers
explanation in respect to different diseases, the ability of
transcription factors to reach a gene, and how the cell
cycle is regulated.
Winston Churchill High School
Teacher: Anat Schwartz
The plasticity of splicing allows for various mature transcripts and
disparate protein isoforms to be produced from just one gene; this phenomenon is
referred to as AS (Keren et al., 2010). General modes of alternative splicing
(AS) include exon
skipping, alternative 5’ splice site and 3’ splice site selection, intron
retention, and mutually exclusive exons. AS enhances the traditional definition
of ‘gene’ by clarifying that one gene has the ability to code for multiple
Around 94% of human genes contain alternative splicing, suggesting the
comprehensive and crucial nature of the phenomenon (Oltean and Bates, 2014). . .
. . . a recent breakthrough discovery of a novel,
naturally occurring, p53 splice isoform (p53Ψ) enforces the
importance of alternative splice site AS (Senturk et al.,
2014). Encoded by TP53, full-length p53 is a
well-characterized tumor-suppressor that promotes cell cycle
arrest and apoptosis. However, an alternative 3’ splice site
in TP53 intron 6 generates p53Ψ, which lacks features such
as DNA binding and transcription activity that exist in the
full-length p53. Even with these missing features, p53Ψ can
reprogram cells to acquire metastatic features through the
regulation of cyclophilin D activity, thus promoting –
rather than suppressing – tumorigenesis. . .
. . . AS is an elementary, essential, and
extraordinary mechanism present in the majority of human
multi-exon genes. The impact of AS on human physiological
and pathological processes is slowly gaining recognition,
but many aspects of AS remain unexplored. With the recent
advances in high-throughput sequencing technologies and
improved splicing sensitive microarrays, I am confident that
splice variants, AS’s crucial functions and splicing
regulatory networks will continue to be unveiled.
Bergen County Academies
Teacher: Judith Pinto
In 1977, two scientists independently made a
discovery that would overturn several leading notions in the
field of gene expression: RNA splicing. American molecular
biologist Philip Sharp and English molecular chemist Richard
Roberts simultaneously observed a single mRNA molecule
hybridizing into more than one stretch of DNA, contradicting
Crick’s notion of colinearity (1; 2). Roberts and Sharp
further noted that during protein synthesis the supposed
continuous genetic material sometimes breaks apart and
re-attaches itself to other pieces (1; 2). This process, now
labeled RNA splicing, is predicated on the existence of
exons and introns, both directly contradicting the now
clearly falsifiable belief that genes are discrete,
contiguous segments of DNA.
. . . some introns possess the ability to self-splice (3). One such
example, Group II introns, are found in mitochondrial genes and exhibit an
intron excision process not unlike that found in pre-messenger RNA splicing (3).
Over two decades later, a group of scientists identified the U6 catalytic metal
ligand snRNP as the catalyst for the splicing, which corresponds with the
catalytic metal structures on group II introns. Their findings suggest that
group II introns and spliceosomes share catalytic mechanisms and perhaps
evolutionary backgrounds (4). . .
. . . current research attesting to RNA splicing’s
role in abnormal mRNA transcription provide vital
information to cellular cancer development, and further
research on group II intron’s structure aid in suggesting
the evolutionary purpose of introns (10). Forty years ago,
RNA splicing contradicted existing theories and forced the
scientific community to re-examine their assumptions; now,
it lies at the backbone of describing the human genome and
its processes and forces the scientific community to further
examine and fully understand it.
James Madison Memorial High School
Teacher: Cindy Kellor
Through alternative splicing (AS), genes are now understood to be more versatile than
previously thought. However, the versatile nature that AS lends to genes also
comes with a price; one mutation in DNA can disrupt the function of multiple
gene products. Unsurprisingly, AS has been linked to many human diseases. Many
of these diseases are neurological in nature because of the prevalence of
alternatively spliced products within the nervous system. . .
. . . In 1969, one would have predicted the the genome and proteome
would be closely aligned. However, the discovery of alternative splicing
demonstrated that this is not the case. Today, we better understand and continue
to research the intricacies of translating the genome into the proteome, which
could lead to greater understanding of the mechanisms of certain diseases.
Bergen County Academies
Teacher: Judith Pinto
DNA. RNA. Protein. For years these three words served as an infallible
explanation of gene expression. The concept was so vital to the understanding of
DNA present at the time that it was called the central dogma of molecular
biology. But as with many theories, exceptions were soon discovered. . .
. . . The discovery of microRNA (miRNA) revealed a
process that forever changed the definition of a gene,
revealing the existence of DNA that coded for a new type of
RNA that was never meant to become a protein, and even
prevented the translation of other RNA. miRNA expands the
definition of a gene by redefining the final product of gene
expression and demonstrating a unique method of
post-transcriptional gene regulation. . .
. . . Since the first miRNA was discovered in 1993
in C. elegans, thousands of miRNAs have been identified in
the human genome (5). Many miRNAs are not yet understood,
but their significance has already been demonstrated. miRNAs
have important roles in cardiovascular disease,
neurodevelopmental diseases, and even cancer (3). . .
. . . miRNA extends the definition of a gene by
showing that not all genes code for proteins, and that the
final product of gene expression can be RNA. Even more
amazing is that genes that do not code for proteins can be
used to regulate the expression of other genes. Sequences
once thought to be “junk DNA” may have pivotal roles in
East Chapel Hill High School
Teacher: Patricia Berge
Modern genetics is based upon the idea of the
“central dogma” described by Francis Crick in 1956: the flow
of genetic information goes from DNA to RNA to protein. By
this traditional view, genes exist solely to code for
protein, and RNA is simply an intermediate between genes and
proteins. Recent research, however, tells us that this
picture is far from complete. For example, in the past
twenty years scientists have discovered regulatory noncoding
RNAs (ncRNAs) such as piwi-interacting RNAs, microRNAs, and
long-noncoding RNAs that do not participate as intermediates
between genes and proteins, yet, through various mechanisms,
have great effects on gene expression. . .
. . . Another small noncoding RNAi species, microRNA (miRNA), is around
22 nucleotides long and regulates expression of endogenous genetic information.
miRNA-encoding genes lie in the introns and intergenic regions of DNA,
encompassing an estimated 1.5% of the human genome (MacFarlane & Murphy, 2010). . .
. . . Genetics does not exist as a simple pathway;
it is more than the central dogma of gene to RNA to protein.
Genes do not have to code for protein, and understanding
their other products such as regulatory noncoding RNA gives
us new insight into fundamental biology—what allows our
bodies to function properly, and with that, what causes our
bodies to malfunction.
Naperville Central High School
Teacher: Nicholas DiGiovanni
In 1983, Barbra McClintock won the Nobel
Prize for discovering that segments of DNA, called
transposons, are able to move to different parts of the
chromosome. Furthermore, they do not directly make protein
products, but instead regulate other genes. The existence of
these movable cards in a shuffling genetic deck paints genes
as more fluid, complex structures than they were once
perceived to be.
The transposon defies the prevailing
view of the gene. These snippets of code are shorter than
protein-coding genes. They are repetitive, not distinct,
living in abundance along the chromosome. Unlike traditional
genes, transposable elements do not code for one specific
protein product. Instead, facilitated by RNA and DNA, they
sever themselves from their natural locations and inject
themselves into new regions, leaving both damaging mutations
and important improvements in their wake. . . .
. . . Introducing a transposon within a gene can cause vast differences
in its effect. The angiotensin-converting enzyme causes blood vessels to narrow
and is coded by the ACE gene, which comes in two different variants. When the
gene has no transposable element present, it is known as ACE-D. In this case,
blood vessels can constrict normally. Occasionally, however, an Alu element will
relocate itself into the ACE gene, transforming the ACE gene. The variant that
contains the insertion of an Alu element is known as ACE-I, and the
transposon-altered gene changes the enzyme. The new proteins dilate blood
vessels, take in oxygen, and increase muscle mass, giving the body the ability
to engage in sustained cardiovascular exercise, such as distance running
(Jamshidi et al). . .
. . . Whereas many genes produce proteins useful
for the body, transposons produce RNA designed to suppress
products. Scattered around the genome, these pockets of
genetic code have developed methods of controlling
themselves, ensuring their continued presence and success in
the genetic code.
Eureka High School
Teacher: Lindsey Mueller
In 2001, the Human Genome Project
determined that in the human genome, the 21,000 genes that
code for proteins make up only 2% of the human genome (Park
2012). The other 98% was considered “junk” DNA. In other
words, nobody really knew what its function was. Today, we
know that the majority of this “junk” DNA does serve a
purpose. However, its function is not necessarily to produce
proteins as the traditional definition of a gene suggests. . .
. . . In females, there are two copies of the X
chromosome in each cell. However, only one copy is active.
The other copy is inactive and forms a Barr body in the
cell’s nucleus. Located on the q arm of the X chromosome,
Xist does not code for a protein but rather stays in the
nucleus of the cell and coats the inactive X chromosome,
aiding in the formation of the Barr body. . .
. . . Whether they regulate genes on another
chromosome, imprint an allele, or inactivate a whole
chromosome, lncRNAS are genes that don’t code for proteins
but are still a necessary part of the genome.
James Madison Memorial High School
Teacher: Cindy Kellor
In 1977, Richard Roberts and Phillip Sharp independently determined
that eukaryotic genes were not continuous, but instead contained many
interruptions (The Nobel Foundation). They noticed that every time mRNA
transcribed a strand of DNA, the mRNA was shorter than the DNA strand it had
copied. They eventually realized that the mRNA was shorter because it did not
include stretches of DNA now known as introns. . .
. . . A promoter is a sequence of DNA that serves as an on/off switch
for genes (Leja). These types of switches control, for example, when in their
lives men can grow a beard or go bald. Promoters also are responsible for why
different kinds of cells make different kinds of proteins. . .
. . . Telomeres are yet another example of
noncoding DNA found in the human genome. They are located on
the tips of each chromosome and are especially important
during DNA replication. When this occurs, the outer ends of
the telomeres are lopped off through a process known as
nucleolytic degradation. Telomeres serve as buffers that
protect coding DNA from being lost during replication. If
any exons were shortened during replication, imperfect
copies would be created that might produce harmful proteins
or fail to make necessary ones (Shammas 28, 29). . .
. . .The bulk of our genome, in the form of
noncoding DNA, is instead involved with regulating,
decoding, and managing our genetic information in ways we
are only beginning to understand.
Stuyvesant High School
While at first scientists believed that genes only
encode proteins, the mapping of the human genome showed that
only around 2% of our DNA codes for proteins. This shocking
discovery led us to wonder what exactly the rest of our DNA
does. Recently, the Encyclopedia of DNA Elements (Encode)
project showed that around one fifth of the human genome
consists of genes that, rather than encode proteins per se,
provide ways to regulate the creation of proteins [Jha,
2012]. . .
. . . Retrotransposons make up nearly half of the
human genome, and they exploit cells in order to survive and
proliferate. They pose a constant threat to humans, as, if
they insert themselves into genes that encode functional
proteins, they can disable those genes or activate them when
they are not needed. . .
. . . The silencing of certain genes after they
have already been transcribed is an incredibly important
process in humans. Were it not for fine-tuned processes like
RNA interference, we would be no more complex than the
simplest organisms on Earth.