Toxicogenomics
Frank A. Barile in Barile’s Clinical Toxicology, 2019
The borderlines of a protein-encoding gene are assigned as the positions at which transcription initiates and terminates. The coding domain is the center of the gene, which consists of the nucleotide sequence that is translated into the sequence of amino acids in the protein. The coding domain appears with the initiation codon (ATG) and completes with one of the termination codons (TAA, TAG, or TGA). On both sides of the coding domain are DNA sequences that are transcribed but are not translated. Both the coding domain and the untranslated domains are interspersed by introns. Genes are grouped into exons and introns. The exons are the components that are present in the mature transcript (messenger RNA [mRNA]), while the introns are abolished from the primary transcript by a procedure called splicing (Figure 12.1).
Introduction to Molecular Biology
Martin G. Pomper, Juri G. Gelovani, Benjamin Tsui, Kathleen Gabrielson, Richard Wahl, S. Sam Gambhir, Jeff Bulte, Raymond Gibson, William C. Eckelman in Molecular Imaging in Oncology, 2008
RNA splicing is the process by which introns (the regions of RNA that do not code for proteins) are removed from the pre-mRNA and the remaining exons (regions that carry the code needed for protein synthesis) are connected to reform a single continuous RNA molecule. In 1989, Tom Cech won the Nobel Prize for his works on the mechanism of RNA splicing (9), prize that he shared with Sidney Altman for his work on RNA. Although the splicing occurs after the complete pre-mRNA synthesis and end-capping, some primary transcripts with many exons can be spliced during transcription. The splicing process needs to be very accurate, because an error in only one nucleotide (removal or addition) can cause a complete shift in the open reading frame of the code. This shift will, therefore, result in a new sequence of codons that will end in a completely different amino acid sequence or possibly insert a stop codon for the termination of the synthesis of the peptide. This kind of error in the splicing process accounts for about 15% of the genetic disease. The machine responsible for the RNA splicing is called spliceosome and is composed of a large enzymatic complex, which includes 145 different proteins (snRNPs or small nuclear ribonucleoproteins) and several snRNAs. This complex recognizes specific splice sites in the introns of pre-mRNA sequences. A pre-mRNA can be spliced in many different ways, thus producing different mature mRNAs that encode for different protein sequences. This process is called alternative splicing and it allows the production of a large amount of proteins from a limited amount of DNA.
Genetic and Biological Alterations in Cancer
Anthony R. Mundy, John M. Fitzpatrick, David E. Neal, Nicholas J. R. George in The Scientific Basis of Urology, 2010
The first step in transcription is the production of pre-mRNA which contains both intron and exon sequences. Splicing occurs when introns are removed and exons are joined to produce the final mRNA for protein translation. Alternative (as opposed to constitutive) splicing allows pre-mRNA to be processed into different final mRNA sequences and hence proteins which may have different functional effects. The process of splicing is performed in the nucleus by the spliceosome (a large multi-protein complex) and is regulated by enhancers and silencers, which identify the exon-intron boundary. It has become recently evident that the process of splicing can be significantly altered in the cancer cell. This may be the result of a mutation in the enhancers and repressors of splicing or due to changes in the splicing machinery itself (29). In bladder cancer, for example, different FGFR3 transcript has been observed in benign as opposed to cancer cells as a result of alternate splicing at the pre-mRNA stage (30). Alternative splicing of fibroblast growth factors (FGF) receptors has also been reported in prostate cancer cells and clinical tissue (31). High throughput techniques have now been introduced to look for global splicing changes in cancer ad other diseases. Li et al. have recently determined mRNA isoform specific signatures for prostate cancers using a large custom made splicing array (32). The significance of splicing changes and their exploitation for therapy is still at an early stage but is an area of active interest among cancer biologists.
Antisense Oligonucleotide Therapy for Ophthalmic Conditions
Published in Seminars in Ophthalmology, 2021
Kevin Ferenchak, Iris Deitch, Rachel Huckfeldt
A review of the pathway from gene to protein is helpful in understanding the mechanism of AON. Genes are composed of introns and exons, and exons are the sequences of base pairs that are expressed. DNA is transcribed in the nucleus to a complementary strand of pre-mRNA. Before leaving the nucleus, non-coding intronic regions are excised from this primary transcript and exons are spliced together at a spliceosome. The mRNA is then transported to the cytoplasm where it is translated on ribosomes in sets of three bases into amino acids, which aggregate to form proteins that are critical for the health and function of a cell. Misspellings of even a single base pair can cause a pathogenic shift in the sequence of amino acids, leading to aberrant splicing and a malfunctioning protein. Studies have estimated that more than 10% of genetic disorders are caused by single base pair mutations at exon-intron junctions that alter splicing.14,15 Alterations in both exons and introns can be associated with pathogenic changes in the genetic sequence such as nonsense mutation causing a premature termination, missense mutations changing an amino acid, and frameshift mutations caused by insertion or deletion of a set of base pairs not divisible by three, thus altering every amino acid downstream.
Modeling association between multivariate correlated outcomes and high-dimensional sparse covariates: the adaptive SVS method
Published in Journal of Applied Statistics, 2019
J. Pecanka, A. W. van der Vaart, M. A. Jonker
In this section we present the results of an eQTL analysis of the expression data generated by the Geuvadis RNA sequencing project for 1000 Genomes samples [14]. The goal is to identify a SNP-driven gene expression regulation process known as alternative splicing. About 94% of our genes are so called interrupted genes [26], which means that they consist of several regions of different functional type referred to as exons and introns. The number of exons in human genes varies between 1 and 363 and the average number of exons per gene is about 10 [21]. During DNA transcription the genetic code undergoes a process called splicing, when introns are removed while exons are preserved and transcribed into RNA (i.e. expressed). Crucially, however, not all exons are always expressed, which means that the same genetic code in a gene can lead to different RNA transcripts. This occurs when, during RNA transcription, different subsets of exons are expressed. This phenomenon when a single gene produces different RNA transcripts is called alternative splicing. Interestingly, different RNA transcripts do not have to result in differential protein expression.
Investigation on glucocorticoid receptors within platelets from adult patients with immune thrombocytopenia
Published in Hematology, 2020
Kam Chau Yung, Cheng Wei Xu, Ze Wen Zhang, Wen Jun Yu, Qian Li, Xian Ru Xu, Ya Fei Han, Xin Jia Wang, Jun Yin
The glucocorticoid receptor (GR) belonging to the nuclear transcription factor, is expressed in virtually all cells of the human body, which is widely found in the cytoplasm of various cells of the body. The amount of expression varies from different tissues [2]. All GRs are encoded by the nuclear receptor subfamily 3 group C member 1 (NR3C1) gene, which is located on the short arm of chromosome 5, consisting of 9 core exons (exons 1–9). Exon 1 is variable and encodes the 5′-untranslated region of the gene, controlled by alternative promotor usage. Seven in the middle (exons 2–8) are common to all GR isoforms. But the exon 9 by alternative splicing includes two isoforms (exons 9α and 9β) which generate either a GRα- or GRβ-encoding transcript [3]. There are 777 amino acids in GRα, while 742 amino acids in GRβ. These two isoforms share identical amino acids 1–727. There are extra 50 amino acids since amino acids 728 in GRα, whereas only 15 additional amino acids in GRβ. GRα contains three major functional domains, including N-terminal domain (NTD, first 421 amino acids), DNA-binding domain (DBD, the next 65 amino acids) and hormone-binding domain (HBD, the last 251 amino acids). There is the hinge region (amino acids 486–526) between DBD and HBD, which provides flexibility for the structure of GR. Because of the sequence of amino acids, GRβ has a shortened ligand-binding domain (LBD) which cannot bind glucocorticoids [4].