RNA sequencing reveals a strong predominance of THRA splicing isoform 2 in the developing and adult human brain

Abstract

Thyroid hormone receptor alpha (THR alpha) is a nuclear hormone receptor that binds triiodothyronine (T3) and acts as an important transcription factor in development, metabolism, and reproduction. In mammals, THR alpha has two major splicing isoforms, THR alpha 1 and THR alpha 2. The better-characterized isoform, THR alpha 1, is a transcriptional stimulator of genes involved in cell metabolism and growth. The less-well-characterized isoform, THR alpha 2, lacks the ligand-binding domain (LBD) and is thought to act as an inhibitor of THR alpha 1 activity. The ratio of THR alpha 1 to THR alpha 2 splicing isoforms is therefore critical for transcriptional regulation in different tissues and during development. However, the expression patterns of both isoforms have not been studied in healthy human tissues or in the developing brain. Given the lack of commercially available isoform-specific antibodies, we addressed this question by analyzing four bulk RNA-sequencing datasets and two scRNA-sequencing datasets to determine the RNA expression levels of human THRA1 and THRA2 transcripts in healthy adult tissues and in the developing brain. We demonstrate how 10X Chromium scRNA-seq datasets can be used to perform splicing-sensitive analyses of isoforms that differ at the 3 '-end. In all datasets, we found a strong predominance of THRA2 transcripts at all examined stages of human brain development and in the central nervous system of healthy human adults.