Unveiling Gene Isoforms by RNA Sequencing

What Is Gene Isoform?

Gene isoforms are different variations or versions of a gene that can be produced by alternative splicing or alternative transcription initiation and termination. These isoforms are often present in the same organism or cell type but differ in their coding sequence or in the regulatory elements that control their expression.

Alternative splicing is a process in which different combinations of exons (coding regions) within a gene are spliced together to produce multiple mRNA transcripts. This can result in the generation of different protein isoforms with distinct functions or properties. Alternative transcription initiation and termination involve the use of different transcription start sites or polyadenylation sites, respectively, leading to the production of mRNA transcripts that may differ in their untranslated regions (UTRs) or in the inclusion of specific exons.

Alternative splicing mechanisms. (Aguiar et al., 2018)

What Causes Gene Isoforms?

Several factors contribute to the generation of gene isoforms. These include the presence of different splice sites or alternative promoters within the gene's DNA sequence, as well as the activity of splicing factors and regulatory proteins that can influence the splicing or transcriptional process. Additionally, environmental cues, cellular signaling pathways, and developmental stages can also affect the production of specific gene isoforms.

The existence of gene isoforms allows organisms to increase their protein diversity and functionality without significantly increasing the number of genes in their genomes. It provides a mechanism for fine-tuning gene expression and adapting to different cellular contexts or environmental conditions.

Why Is It Important to Know Gene Isoforms?

• Functional diversity: Gene isoforms can have distinct functions and properties. They can produce proteins with different structural features, enzymatic activities, subcellular localization, or interaction partners. By knowing the isoforms present in a particular cell or tissue, researchers can better understand the diverse functions and roles of genes in different biological processes.
• Disease mechanisms: Many diseases, including genetic disorders and cancer, are associated with alterations in gene isoforms. Dysregulation of alternative splicing or transcription processes can lead to the production of abnormal isoforms that may contribute to disease development or progression. Investigating isoform-specific changes can provide insights into disease mechanisms and potential therapeutic targets.
• Biomarkers and diagnostics: Specific isoforms can serve as biomarkers for disease diagnosis, prognosis, or therapeutic response. The detection of disease-associated isoforms in patient samples can provide valuable information for personalized medicine, allowing for targeted therapies and monitoring of treatment outcomes.
• Drug discovery and development: Gene isoforms can exhibit different sensitivities or responses to therapeutic interventions. Understanding isoform-specific functions and interactions can aid in the design of drugs that selectively target particular isoforms, potentially leading to enhanced efficacy and reduced side effects. Read our article Single-Cell RNA Sequencing in Drug Discovery and Development for more information.
• Evolutionary and comparative genomics: Studying gene isoforms across different species can provide insights into evolutionary processes and the conservation or divergence of isoform regulation. Comparative analyses of isoforms can shed light on the functional importance of specific isoforms and their evolutionary dynamics.
• Precision medicine: Knowledge of gene isoforms can contribute to precision medicine approaches by considering individual genetic variation and isoform-specific effects in disease management and treatment decisions.

What Is the Difference Between Isoform and Variant?

The terms "isoform" and "variant" are often used interchangeably, but they can have slightly different meanings depending on the context. Isoforms refer to different forms of a gene resulting from alternative splicing or transcription processes, while variants are genetic changes or mutations that can occur within a specific gene. Isoforms provide functional diversity, while variants can have implications for disease susceptibility or genetic variation.

In general, a gene isoform refers to different forms or versions of a gene that arise from processes such as alternative splicing or alternative transcription initiation and termination. Gene isoforms are mRNA molecules that arise from the same gene locus but have structural differences, including variations in transcription start sites (TSSs), protein-coding DNA sequences (CDSs), and/or untranslated regions (UTRs). These variations in isoforms can result in different functions, activities, or expression patterns.

On the other hand, a variant typically refers to a genetic variation or mutation within a specific gene. Variants can arise from single nucleotide changes (SNPs), insertions, deletions, or larger structural alterations in the DNA sequence. Variants can occur in any region of the gene, including coding regions (exons) or non-coding regions (introns, UTRs, promoters, etc.).

While isoforms and variants can be related, not all gene variants lead to the generation of isoforms, and not all isoforms are a result of genetic variants. Isoforms can be produced through normal cellular processes and regulation, whereas variants often represent genetic changes or mutations that can be associated with diseases or genetic diversity within a population.

Methods of Gene Isoforms Detection

Identifying gene isoforms involves a combination of experimental and computational methods. One widely used approach is RNA sequencing (RNA-Seq), which involves sequencing RNA molecules and mapping the resulting reads to a reference genome. By analyzing the patterns of mapped reads and splice junctions, researchers can identify different isoforms and determine their expression levels. Isoform-specific microarrays provide another method, utilizing probes designed to target specific isoforms and enabling their quantification. PCR-based approaches involve selectively amplifying isoforms using specific primers and comparing the resulting products. Databases such as Ensembl and UCSC Genome Browser provide comprehensive annotations of known isoforms, while computational analysis tools like Cufflinks and StringTie can analyze RNA-Seq data to predict and reconstruct isoforms. By combining these methods, collaborating with experts, and leveraging bioinformatics resources, researchers can enhance the accuracy and efficiency of gene isoform identification.

Gene isoform detection using RNA-seq has been greatly enhanced by the advent of both short-read and long-read sequencing technologies, such as PacBio and Oxford Nanopore sequencing. Short-read sequencing provides high-throughput and accurate quantification of gene expression, while long-read sequencing enables the detection and characterization of full-length isoforms with complex structures.

Methodological approaches to single-cell isoform studies. (Arzalluz-Luque et al., 2018)

How To Identify Gene Isoforms by RNA Sequencing?

Identifying gene isoforms by RNA-seq involves several computational and bioinformatic analyses. Here is a general step-by-step approach to identify gene isoforms using RNA-seq data:

• Read Alignment: Start by aligning the RNA-seq reads to a reference genome or transcriptome. This step can be performed using alignment algorithms such as STAR, HISAT2, or TopHat, which map the reads to the reference sequences while considering potential splice junctions.
• Transcript Assembly: After alignment, assemble the aligned reads into transcripts or isoforms. There are different approaches for transcript assembly, including de novo assembly and guided assembly. De novo assembly methods, such as Trinity and Oases, reconstruct transcripts directly from the aligned reads without relying on a reference transcriptome. Guided assembly methods, such as Cufflinks or StringTie, use the alignment information to guide the assembly process.
• Transcript Quantification: Once the transcripts or isoforms are assembled, quantify their expression levels. This step estimates the abundance of each isoform in the RNA-seq sample. Tools such as featureCounts, HTSeq, or Salmon can be used for transcript quantification.
• Differential Expression Analysis: If you are interested in comparing isoform expression between different conditions, perform a differential expression analysis. This analysis identifies isoforms that are differentially expressed between experimental groups. Tools like DESeq2, edgeR, or limma can be used for this analysis.
• Isoform Annotation: To annotate the isoforms and determine their biological function, compare them against existing reference databases such as Ensembl, RefSeq, or GENCODE. This step helps in assigning functional annotations, identifying coding or non-coding isoforms, and understanding their potential protein-coding capacity.
• Visualization and Interpretation: Visualize the expression patterns of the identified isoforms using tools like IGV (Integrative Genomics Viewer) or genome browsers. This step allows you to inspect the aligned reads and verify the isoform structures. Additionally, functional enrichment analysis can help in understanding the biological processes associated with specific isoforms.

References:

1. Aguiar, Derek, et al. "Bayesian nonparametric discovery of isoforms and individual specific quantification." Nature communications 9.1 (2018): 1681.
2. Arzalluz-Luque, Ángeles, and Ana Conesa. "Single-cell RNAseq for the study of isoforms—how is that possible?." Genome biology 19.1 (2018): 1-19.