From DNA to Proteins: Investigating Gene Expression at The Biochemical Level

Section A-Research paper

ISSN 2063-5346 From DNA to Proteins: Investigating Gene Expression at

The Biochemical Level

Dr Sangeeta Bhimrao Dongrea, Dr.R.R.Kumarb, Dr. Gaviraj.E.Nc,

Dr. Khushal N. Pathade d

Article History: Received: 10.05.2023 Revised: 29.05.2023 Accepted: 09.06.2023

Abstract
In all living things, gene expression converts DNA into functional proteins. Understanding gene
expression pathways is essential to understanding life and has major consequences for medicine,
biotechnology, and evolutionary biology. This review discusses gene expression biochemical
processes and important molecular actors. We study RNA transcription, post-transcriptional
changes, and protein translation. We also address gene expression regulation and biological
methods. Understanding gene expression pathways will progress molecular biology and enable
targeted medicines and biotechnological uses.

Keywords: Gene expression, Transcription, Post-transcriptional Modifications, Translation,

Protein Modifications,

a
Assistant Professor, Department of Zoology,Government College Of Arts and
Science,Aurangabad. Maharashtra India. 431001
b
Dr.R.R.Kumar, Assistant Professor, Department of Biochemistry, Aarupadai Veedu Medical
College and Hospital, Vinayaka Missions Research Foundation, Puducherry
c
Dr Gaviraj.E.N, Professor & HoD, Department of Pharmacognosy, BLDEAs SSM College of
Pharmacy and Research Center, Vijayapur, Karnataka state
d
Dr. Khushal N. Pathade ,Assistant Professor and Head,P.G. Department of Botany
Dr. R. G. Bhoyar Arts, Commerce and Science College, Seloo Dist. Wardha, Maharashtra

Corresponding Author:[email protected]
Coauthor: [email protected], [email protected], [email protected]

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From DNA to Proteins: Investigating Gene Expression at The Biochemical Level
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Introduction gene expression pattern research, revealing

All living things depend on gene gene expression regulation and dynamics in
expression, which converts DNA into many biological situations. Single-cell
functional proteins. Gene expression genomics and transcriptomics have shown
converts genetic instructions into proteins cellular heterogeneity and gene expression
for metabolism, growth, differentiation, changes throughout development, disease
and environmental response. Molecular progression, and therapy response.
biology, genetics, medicine,
biotechnology, and evolutionary biology As we continue to unravel the complexities of
all need to understand gene expression. gene expression, there is a growing
Researchers can understand life's basic realization of its clinical significance. Gene
processes, the molecular foundation of expression profiling has become a valuable
illnesses, innovative therapies, and tool in diagnosing diseases, predicting patient
organism engineering by deciphering gene outcomes, and guiding personalized medicine
expression. approaches. Additionally, gene expression
The field of gene expression research has a studies have contributed to the development
rich historical context, marked by several of biotechnological applications, such as the
key discoveries that have shaped our production of recombinant proteins, genetic
understanding of this intricate process. engineering of crops, and the development of
One of the ground-breaking achievements gene therapies. In this review article, we will
was the elucidation of the structure of delve into the biochemical processes
DNA by James Watson and Francis Crick underlying gene expression, including
in 1953, which laid the foundation for transcription, post-transcriptional
understanding how genetic information is modifications, translation, and the regulatory
stored and transmitted. This discovery mechanisms that control gene expression. We
paved the way for subsequent will also explore the techniques and
investigations into gene expression. technologies used to investigate gene
expression at the biochemical level. By
The genetic code revealed the relationship comprehensively understanding the
between DNA nucleotides and amino acids intricacies of gene expression, we can unlock
in the 1960s. This discovery, together with new avenues for research, innovation, and the
Sydney Brenner, Francois Jacob, and improvement of human health [1].
Matthew Meselson's discovery of transfer
RNA (tRNA), proved RNA's importance Transcription: DNA TO RNA
in protein synthesis and illuminated
translation. In the 1960s, Severo Ochoa Transcription overview
and Marianne Grunberg-Manago Gene expression requires transcription of DNA
discovered RNA polymerase, which was into RNA molecules. Eukaryotic and
crucial to understanding transcription. This prokaryotic cells undergo this procedure.
created the groundwork for transcriptional Transcription produces mRNA, tRNA, and
regulation and gene expression rRNA, which serve diverse cell roles.
transcription factor research.
RNA polymerase/transcription factors
RNA capping, splicing, and RNA polymerase synthesises RNA from DNA.
polyadenylation, which affect RNA In prokaryotes, a single RNA polymerase
stability and protein production, have been complex synthesises all RNA, whereas in
better understood in recent decades. PCR eukaryotes, various RNA polymerases (I, II, and
and DNA sequencing quantified and III) transcribe distinct classes of genes.
profiled RNA molecules, revolutionising Transcription factors influence RNA
gene expression studies. High-throughput polymerase to regulate gene expression.
methods like microarrays and RNA Promoter regions upstream of a gene bind
sequencing have enabled genome-wide transcription factors. RNA polymerase and the
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transcription start complex may promote or Transcription factors

suppress transcription. The availability and activity of transcription
factors play a critical role in regulating
Initiation, elongation, and termination of transcription. Activator proteins enhance
transcription transcription by promoting the assembly of the
Transcription can be divided into three main transcription initiation complex, while repressor
stages: initiation, elongation, and termination. proteins inhibit transcription by interfering with
the binding of RNA polymerase [3].
Initiation Chromatin structure
At gene promoters, RNA polymerase and The accessibility of the DNA template is
transcription factors assemble during influenced by the organization of chromatin.
initiation. Transcription initiation complex. Tighter packaging of DNA in nucleosomes can
The initiation complex in prokaryotes is the hinder transcription, while more open chromatin
RNA polymerase holoenzyme, whereas in allows for easier access to the DNA template.
eukaryotes it is RNA polymerase II and Epigenetic modifications
general transcription factors [2]. Chemical modifications of DNA and histone
proteins, such as DNA methylation and histone
Elongation acetylation, can impact transcriptional activity.
After initiation, RNA polymerase unwinds Methylation of DNA at specific sites is often
the DNA helix, revealing the template strand. Post-transcriptional Modifications
By adding DNA-complementary nucleotides, RNA processing: capping, splicing, and
it synthesises RNA from 5' to 3'. RNA polyadenylation
polymerase continuously elongates the RNA Following transcription, newly synthesized
transcript by unwinding and rewinding the RNA undergoes several post-transcriptional
DNA template. modifications, collectively known as RNA
processing. These modifications are essential for
Termination maturation, stability, and functionality of the
Intrinsic and Rho-dependent transcription RNA molecules.
termination occur in prokaryotes. Intrinsic
termination occurs when the freshly Capping
synthesised RNA forms a hairpin loop and 7-methylguanosine caps mRNA's 5' end in
uracil (U) residues, dissociating RNA eukaryotes. This cap structure helps transfer
polymerase from the DNA template. Rho- mRNA from the nucleus to the cytoplasm and
dependent transcription termination needs prevents degradation. The cap helps ribosomes
Rho protein interaction to the RNA transcript. recognise mRNA during translation.
Termination in eukaryotes is more
complicated and requires termination factors Splicing
and DNA termination sequences. Most eukaryotic protein-coding genes have
introns. Splicing removes introns from pre-
FACTORS INFLUENCING TRANSCRIPTION
mRNA and joins coding areas. The
EFFICIENCY spliceosome—a combination of snRNPs and
Several factors influence the efficiency of other proteins—performs this activity.
transcription Alternative splicing generates several mRNA
Promoter strength isoforms from a gene, boosting protein
The strength of the promoter sequence diversity.
determines how often transcription is
initiated. Strong promoters result in more Polyadenylation
frequent transcription, while weak promoters mRNA has a poly(A) tail at its 3' end. During
lead to less frequent transcription. polyadenylation, poly(A) polymerase cleaves
the mRNA and adds a tail. The poly(A) tail
improves mRNA stability, nucleus export, and
translation efficiency.
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Significance of post-transcriptional coding capacity of the genome, enabling cells to

modifications produce a wide range of proteins with varied
Post-transcriptional modifications have functions. It plays a crucial role in
several important functions developmental processes, tissue specialization,
mRNA stability and response to environmental cues.
The addition of a 5' cap and a poly(A) tail to Dysregulation of alternative splicing can result
mRNA increases its stability by protecting it in various human diseases, including cancer and
from degradation by exonucleases. The neurological disorders. The complexity and
longer the poly(A) tail, the longer the mRNA diversity introduced by alternative splicing
molecule persists in the cytoplasm[4]. contribute significantly to the intricacies of gene
expression and provide a mechanism for cells to
mRNA export fine-tune their protein repertoire in response to
Post-transcriptional modifications, different physiological conditions.
particularly capping and polyadenylation, aid
TRANSLATION: RNA TO PROTEINS
in the transport of mRNA from the nucleus to
Translation overview
the cytoplasm. Export factors recognize these
Translation converts mRNA into proteins. It
modifications and facilitate the translocation
occurs in prokaryotic and eukaryotic cell
of mRNA through nuclear pores.
cytoplasm. Translation requires ribosomes,
tRNA, amino acids, and protein factors.
Translation efficiency
Ribosomes and tRNA
The presence of a 5' cap and a poly(A) tail
Ribosomes are protein-rRNA complexes. They
influences translation initiation and enhances
synthesise protein during translation. Ribosomes
the efficiency of protein synthesis. The cap
start protein synthesis on mRNA with their big
structure facilitates the binding of the
and small components.
ribosome to the mRNA, while the poly(A)
Translation requires tRNA molecules. Each
tail enhances ribosome recruitment and
tRNA molecule contains an anticodon sequence
stability.
that matches the mRNA codon. Ribosomes
connect tRNA and mRNA.
Regulation of gene expression
Post-transcriptional modifications play a
Translation start, elongation, and end
crucial role in the regulation of gene
Translation involves initiation, elongation,
expression. Alternative splicing allows for
and termination.
the generation of different mRNA isoforms,
Initiation
leading to the production of multiple protein
The small ribosomal subunit binding to mRNA
variants from a single gene. This process
begins. The ribosome searches mRNA until the
contributes to cellular diversity and the
start codon (typically AUG). The ribosome
regulation of developmental processes.
reads from the start codon. Initiation factors
help the initiation complex and big ribosomal
Alternative splicing and its impact on
subunit assemble. Methionine-carrying initiator
protein diversity
tRNA binds to the start codon at the ribosomal
Alternative splicing is a post-transcriptional
P-site [6].
mechanism that allows for the production of
different mRNA isoforms by selectively
Elongation
including or excluding exons during splicing.
Polypeptide chain elongation adds amino acids.
This process significantly increases protein
Elongation factors help ribosomes travel along
diversity and functionality. Alternative
mRNA, guaranteeing codon recognition and
splicing can lead to the production of protein
peptide bond production. tRNA molecules
isoforms with distinct functions, tissue-
successively transport amino acids to the
specific expression patterns, or different
ribosome as the ribosome scans mRNA codons.
subcellular localizations [5].
The expanding polypeptide chain and incoming
By generating different mRNA isoforms from
amino acid generate peptide bonds. The
a single gene, alternative splicing expands the
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uncharged tRNA leaves the E-site as the protein interactions, modulate cellular signaling
ribosome moves along the mRNA. pathways, and direct protein localization within the
cell.
Termination
Termination signals the end of translation. Examples of co- and post-translational
When the ribosome encounters a stop codon modifications include phosphorylation, where
(UAA, UAG, or UGA), release factors bind phosphate groups are added to specific amino
to the A-site of the ribosome, causing the acid residues by protein kinases, and
release of the completed polypeptide chain. acetylation, which involves the addition of
The ribosomal subunits dissociate from the acetyl groups to lysine residues. These
mRNA, and the components are recycled for modifications can alter protein conformation,
subsequent rounds of translation. enzyme activity, protein-protein interactions,
and protein stability.
Co- and post-translational modifications
After translation, proteins may undergo co- Glycosylation is another important modification
and post-translational modifications to where sugar molecules are attached to proteins.
achieve their functional conformation and This modification influences protein folding,
activity. These modifications include: stability, and recognition by other molecules.
Additionally, lipidation involves the attachment
Folding and conformational changes of lipid molecules, such as fatty acids or
Proteins often undergo complex folding isoprenoids, to proteins, which can affect their
processes to attain their functional three- membrane association and cellular
dimensional structure. Molecular chaperones localization.Proteolytic cleavage is a process
assist in correct folding and prevent protein where specific peptide bonds within a protein
aggregation. are selectively cleaved by proteases. This
modification can generate active protein
Covalent modifications fragments or regulate protein function by
Proteins can undergo various covalent removing inhibitory or regulatory regions.
modifications, including phosphorylation,
acetylation, methylation, glycosylation, and Furthermore, proteins can assemble into
lipidation. These modifications can affect complexes or higher-order structures to carry
protein activity, stability, localization, and out specialized functions. Assembly can involve
interactions with other molecules [7]. the interaction of different protein subunits,
forming functional protein complexes, such as
Proteolytic cleavage enzymes or protein channels. Overall, co- and
Some proteins undergo proteolytic cleavage, post-translational modifications are crucial for
where specific peptide bonds are cleaved to protein functionality, regulation, and
generate smaller functional protein diversification. They contribute to the
fragments. This process is important for complexity of cellular processes, signalling
activating certain proteins or generating networks, and organismal development,
bioactive peptides. enabling proteins to perform their specific roles
in a precise and regulated manner [8].
Assembly into complexes INVESTIGATING GENE EXPRESSION AT THE
Proteins may assemble into multi-subunit BIOCHEMICAL LEVEL
complexes or higher-order structures to carry Experimental techniques
out specific functions. These assemblies often RNA sequencing, microarrays, and qPCR
involve interactions between different protein Several experimental techniques are employed
subunits.Co- and post-translational to investigate gene expression at the
modifications play crucial roles in expanding biochemical level.
the functional repertoire of proteins and RNA sequencing (RNA-seq)
regulating their activities. These modifications RNA-seq is a powerful technique that allows
can fine-tune protein function, enable protein- for the comprehensive analysis of the
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transcriptome. It involves the sequencing of modifications and protein dynamics.

cDNA generated from RNA samples,
providing information about the identity and
abundance of RNA molecules. RNA-seq can Protein-protein interactions
identify known and novel transcripts, detect Understanding protein-protein interactions is
alternative splicing events, and quantify gene crucial for elucidating cellular processes and
expression levels accurately. signalling pathways. Various techniques are
used to study protein-protein interactions,
Microarrays including co-immunoprecipitation, yeast two-
Microarrays are a widely used technique for hybrid assays, and proximity-based assays such
gene expression analysis. They consist of as the proximity ligation assay (PLA) and the
small glass slides or chips with immobilized bimolecular fluorescence complementation
DNA probes representing thousands of genes. (BiFC) assay. These methods help identify
The RNA samples are labeled and hybridized interacting protein partners and map protein
to the microarray, enabling the measurement interaction networks.
of gene expression levels. Microarrays
provide a snapshot of gene expression across Genome-wide studies: chromatin
a large number of genes and allow for the immunoprecipitation and DNA methylation
identification of differentially expressed analysis Genome-wide studies allow for the
genes. investigation of gene regulation and epigenetic
modifications on a global scale.
qPCR (quantitative polymerase chain
reaction) Chromatin immunoprecipitation (ChIP)
qPCR is a highly sensitive and specific ChIP is a technique used to identify DNA
technique used to quantify gene expression regions bound by specific proteins, such as
levels. It relies on the amplification of transcription factors or histone modifications. It
specific target sequences using fluorescently involves cross-linking proteins to DNA,
labeled probes or DNA-binding dyes. qPCR followed by immunoprecipitation of the protein-
provides quantitative information about gene DNA complexes. The isolated DNA can be
expression and is particularly useful for analysed by techniques such as PCR,
studying a small number of genes in detail microarrays, or next-generation sequencing,
[9]. providing information about protein-DNA
interactions and genome-wide occupancy
Proteomics approaches patterns [10].
Mass spectrometry and protein-protein
interactions DNA methylation analysis
Proteomics is the study of the entire DNA methylation is an epigenetic modification
complement of proteins expressed in a cell or that plays a critical role in gene regulation.
tissue. Several approaches are used to Various methods, such as bisulfite sequencing
investigate protein expression and and methylation-specific PCR, are used to study
interactions. DNA methylation patterns across the genome.
These techniques provide information about the
Mass spectrometry (MS) DNA methylation status of specific CpG sites or
Mass spectrometry is a powerful technique on a genome-wide scale, aiding in the
for protein identification and quantification. understanding of epigenetic regulation of gene
It involves the ionization and fragmentation expression.
of proteins, followed by the measurement of
the mass-to-charge ratio of the resulting These experimental techniques, including RNA
peptides. This information is used to identify sequencing, microarrays, qPCR, mass
the proteins present in a sample and spectrometry, protein-protein interaction assays,
determine their relative abundance. MS can chromatin immunoprecipitation, and DNA
also provide insights into post-translational methylation analysis, are essential for
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investigating gene expression at the developmental processes. Single-cell genomics

biochemical level. They enable researchers to and transcriptomics methods like scRNA-seq
explore the transcriptional and translational profile gene expression patterns in individual
landscape, protein-pro tein interactions, and cells, revealing distinct cell populations, unusual
epigenetic modifications that underlie gene cell types, and dynamic cellular states [12].
expression regulation. By utilizing these
techniques, researchers can gain valuable insights Spatial transcriptomics
into the complex mechanisms of gene expression, Spatial transcriptomics technologies enable the
identify biomarkers, and understand the
mapping of gene expression patterns within
functional implications of gene regulation in
various biological processes and disease
intact tissues, providing information about the
conditions.The integration of multiple omics
spatial organization of cells and their gene
approaches, such as transcriptomics, expression profiles. These techniques allow
proteomics, and epigenomics, can provide a researchers to study the spatial relationships
comprehensive view of gene expression between different cell types and their role in
regulation. By combining data from different tissue function and disease.
levels of gene expression control, researchers
can decipher the intricate networks and Long-read sequencing
interactions between genes, proteins, and Traditional short-read sequencing techniques
epigenetic modifications, leading to a more have limitations in accurately reconstructing
comprehensive understanding of cellular full-length transcripts and detecting complex
processes [11]. genomic rearrangements. Long-read sequencing
Furthermore, advancements in technology technologies, such as PacBio and Oxford
and bioinformatics have enabled high- Nanopore, provide the ability to sequence long
throughput and genome-wide analyses, fragments of DNA or RNA, allowing for more
allowing researchers to study gene expression accurate characterization of transcript isoforms,
on a global scale. These approaches provide a identification of structural variations, and
wealth of data that can be mined for investigation of gene expression in repetitive
identifying key regulatory elements, gene regions of the genome.
expression patterns, and potential therapeutic
targets. Overall, the combination of Computational modelling and machine
experimental techniques, proteomics learning approaches
approaches, and genome-wide studies allows Computational modelling and machine learning
for a holistic investigation of gene expression approaches have become increasingly important
at the biochemical level. These approaches in analysing and interpreting gene expression
provide valuable insights into the complex data. These approaches offer valuable insights
regulatory mechanisms governing gene into gene regulatory networks, functional
expression and contribute to our annotations, and predictions of gene function.
understanding of cellular processes, disease Computational models can integrate multi-
mechanisms, and the development of novel omics data and provide a systems-level
therapeutic strategies. understanding of gene expression regulation and
its impact on cellular processes.
ADVANCES AND FUTURE DIRECTIONS Machine learning algorithms can be trained on
Emerging technologies for studying gene large-scale gene expression datasets to identify
expression patterns, classify samples, predict disease
The field of gene expression research outcomes, and discover novel biomarkers.
continues to advance with the development of These approaches enable the identification of
new technologies. Some emerging gene expression signatures associated with
technologies that hold promise for studying specific diseases, patient subtypes, or treatment
gene expression include: responses, which can facilitate personalized
Single-cell genomics and transcriptomics medicine and the development of targeted
Single-cell gene expression research reveals therapies [13].
cellular heterogeneity, cell lineage, and
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Therapeutic implications and personalized which significantly impact gene expression and
medicine contribute to protein diversity. Next, we
The study of gene expression has significant examined the translation process from RNA to
implications for therapeutics and proteins, highlighting the involvement of
personalized medicine. Understanding the ribosomes, transfer RNA (tRNA), and the steps
gene expression profiles of normal and of initiation, elongation, and termination. We
diseased tissues can help identify novel also discussed co- and post-translational
therapeutic targets and develop more modifications that occur after protein synthesis,
effective treatments. Gene expression-based influencing protein structure, activity, and
biomarkers can aid in the diagnosis, localization [16].
prognosis, and prediction of treatment
responses in various diseases [14]. Moving forward, we explored various
experimental techniques for investigating gene
Personalized medicine aims to tailor medical expression at the biochemical level. These
treatments to individual patients based on included RNA sequencing, microarrays, qPCR,
their specific genetic makeup and gene mass spectrometry, protein-protein interaction
expression profiles. Gene expression data can assays, chromatin immunoprecipitation, and
guide treatment decisions, optimize drug DNA methylation analysis. These techniques
selection, and improve patient outcomes. provide valuable insights into gene expression
Additionally, gene expression profiling can patterns, protein interactions, and epigenetic
aid in identifying patients who are likely to regulation, contributing to our understanding of
respond to specific therapies, avoiding cellular processes and disease mechanisms. We
unnecessary treatments and minimizing side then discussed recent advances in the field, such
effects. Advancements in gene editing as single-cell genomics and transcriptomics,
technologies, such as CRISPR-Cas9, also rely spatial transcriptomics, long-read sequencing,
on a deep understanding of gene expression computational modelling, and machine learning
patterns and regulation. Precise modulation approaches. These advances enable more
of gene expression holds promise for precise and comprehensive analysis of gene
therapeutic interventions, including gene expression data, leading to the identification of
therapy and targeted gene silencing, to novel regulatory mechanisms, biomarkers, and
correct genetic disorders and treat diseases. potential therapeutic targets [17].
In the future, the integration of multi-omics
data, advanced computational approaches, Continued research in gene expression is of
and the continued development of novel utmost importance. It enhances our
technologies will further enhance our understanding of fundamental biological
understanding of gene expression, its processes, cellular development, and disease
regulation, and its impact on human health. pathogenesis. Gene expression studies provide
These advancements will pave the way for valuable insights into the underlying
more effective therapies, personalized mechanisms of diseases, enabling the
medicine approaches, and improved patient development of targeted therapies and
outcomes [15]. personalized medicine approaches. Future
prospects in the field of gene expression
CONCLUSION research are promising [18]. With emerging
In this review article, we explored the process technologies, we can expect to uncover further
of gene expression at the biochemical level. complexities and nuances in gene regulation.
We discussed the transcription of DNA to The integration of multi-omics data, advanced
RNA, including the role of RNA polymerase, computational approaches, and high-throughput
transcription factors, and the factors techniques will lead to more comprehensive and
influencing transcription efficiency. We then accurate analyses. This will facilitate the
delved into post-transcriptional discovery of novel regulatory networks,
modifications, such as capping, splicing, biomarkers, and therapeutic interventions.
polyadenylation, and alternative splicing, Finally, biochemical gene expression studies are
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essential for understanding cellular processes Biology of the Gene (7th ed., pp. 368-402).
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