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

Thyroid hormone receptor alpha (THRa) is a nuclear hormone receptor that binds triiodothyronine (T3) and acts as an important transcription factor in development, metabolism and reproduction. THRa has in mammals two major splicing isoforms, THRa1 and THRa2. The better characterized isoform, THRa1, is a transcriptional stimulator of genes involved in cell metabolism and growth. The less well characterized isoform, THRa2, lacks the Ligand Binding Domain (LBD) and is thought to act as an inhibitor of THRa1 action. The ratio of THRa1 to THRa2 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 discovered a strong predominance of THRA2 transcripts at all stages of brain development and in central nervous system from healthy human adults. Overall design: bulk RNA-Seq of 24 different healthy adult human tissues (10 neuronal and 14 non-neuronal). Each sample was pooled from an average of 6 healthy individuals