Basic genetics and patterns of inheritance
Hung N. Winn, Frank A. Chervenak, Roberto Romero in Clinical Maternal-Fetal Medicine Online, 2021
Genes are composed of deoxyribonucleic acid (DNA) and are contained on the chromosomes. Each strand of DNA has a specific sequence of four nucleotides, each containing a different base, adenine, thymine, cytosine, or guanine. Adenine pairs with thymine and cytosine pairs with guanine as two complementary strands of DNA are wound together to form a double helix. Genes have a common basic structure (Fig. 20). First, there are upstream sequences that regulate transcription, known as promoters and enhancers. Then, there is a transcription initiation site, followed by a series of alternating exons and introns. The DNA sequence serves as a template from which messenger RNA (mRNA) is made; this process is known as transcription. As transcription proceeds, a primary mRNA is made from the DNA sequence of the gene, which includes the introns. The intron sequences are then spliced out and the exons are linked together to form the mature mRNA molecule. Thus, the exons are the only portions of the gene that specify the final protein product. The mature mRNA molecule is used to make the protein product by the process of translation. Groups of three nucleotides, called codons, code for specific amino acids. Transfer RNA (tRNA) and ribosomal RNA (rRNA) interact with the mRNA to assemble the amino acids into a polypeptide chain to form the final protein molecule.
Gene Expression
Danilo D. Lasic in LIPOSOMES in GENE DELIVERY, 2019
Functional introns can increase the mRNA production up to two orders of magnitude. They are placed immediately downstream from the promoter+enhancer region and can significantly increase gene expression. The mechanism of their action remains unknown although it is likely that they facilitate transcription. Their function can be sensitive to in vivo vs. in vitro conditions. cDNA, being a marker or therapeutic gene, is followed by 3’UTR which provides for mRNA stability, its efficient transport to the cytoplasm, and can increase the efficiency of mRNA translation. The stability of mRNA varies from minutes to hours and therefore rates of mRNA decay regulate gene expression. Stability is a function of structure and it is likely that the polyA tract protects RNA against rapid degradation. The polyA signal is a sequence which specifies to the cell to add about 300 A bases to the 3’ end of RNA transcript. Transcription is terminated at highly curved, AT-rich motifs.
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).
Interplay of heavy chain introns influences efficient transcript splicing and affects product quality of recombinant biotherapeutic antibodies from CHO cells
Published in mAbs, 2023
Emma Kelsall, Claire Harris, Titash Sen, Diane Hatton, Sarah Dunn, Suzanne Gibson
Interestingly, sequence optimization failed to improve the expression from two of the best-performing plasmids (gDNA∆2 and cDNA +1). This is likely due to the highly optimized arrangement of other expression elements in these plasmids. It would be interesting to investigate if sequence optimization improved the expression of a completely intron-less-HC cassette as our study has revealed that introns in the HC have minimal influence on expression and can be removed without significantly affecting antibody titers. This was surprising due to the well-documented role of introns in enhancing gene expression. A possible explanation of the benefits seen by including introns is that these are context specific and are brought about by crosstalk of splicing with transcription, mRNA decay, and transcript stability. In the context of biotherapeutic mAb expression plasmids, because a very strong heterologous promoter is driving HC expression and typically it is the HC expression that dictates mAb expression levels,37 the promoter’s activity likely supersedes everything else. It is possible that the interplay between the endogenous HC promoter and introns would be different with introns playing a more significant role in HC expression.
Strategies for targeting RNA with small molecule drugs
Published in Expert Opinion on Drug Discovery, 2023
Christopher L. Haga, Donald G. Phinney
RNA splicing is a complicated key regulatory step in the generation of the diverse repertoire of human proteins from the limited protein-coding genome. The splicing process is carried out in the spliceosome, a large complex consisting of hundreds of proteins, snRNAs, and five small nuclear ribonucleoproteins (snRNP) which act in concert to bind and remove intronic sequences [63]. The vast majority of protein-coding transcripts undergo such carefully orchestrated splicing events. However, when pre-mRNA processing and splicing deviate from the norm, splicing disorders can occur. Because every intron-containing gene requires a certain level of processing and splicing, mutations falling within a canonical splice site can lead to aberrant gene translation and potentially to disease. Two such well-explored diseases concerning small molecule RNA targeting are familial dysautonomia (FD) and spinal muscular atrophy (SMA).
Myeloid neoplasm with ETV6::ACSl6 fusion: landscape of molecular and clinical features
Published in Hematology, 2022
Zhan Su, Xin Liu, Weiyu Hu, Jie Yang, Xiangcong Yin, Fang Hou, Yaqi Wang, Jinglian Zhang
The vast majority of cases showed characteristic t(5;12)(q31;p13) chromosomal abnormalities or t(5;12)(q23-31;p13) (n = 2) and t(5;12)(q31-33;p13) (n = 1). Two cases harboring t(5;12) have been reported, but the authors supplied no detailed information about the translocation breakpoint. One case had a complex karyotype involving 5q and 12p [9]. To date, a total of six ETV6::ACSL6 variants and three reciprocal variants of ACSL6::ETV6 have been reported, which are summarized in Figure 2. The coexistence of two reciprocal chimeric genes was observed (n = 2). There were also cases in which two ETV6::ACSL6 variants coexisted (n = 2). The most commonly reported variant (n = 6) is ETV6::ACSL6, the breakpoint of which is flanked by exon 1 of ETV6 and exon 2 of ACSL6. Intron retention and truncated exons (or alternative splicing) may be found in some variants.
Related Knowledge Centers
- Adenoviridae
- Cistron
- Exon
- Rna Editing
- Untranslated Region
- Nucleic Acid Sequence
- Gene
- Transcription
- Interrupted Gene
- Protein Splicing
- Rna Editing