Identification of Thyroid Hormone Receptor Binding Sites and Target Genes Using ChIP-on-Chip in Developing Mouse Cerebellum

Abstract

Thyroid hormone (TH) is critical to normal brain development, but the mechanisms operating in this process are poorly understood. We used chromatin immunoprecipitation to enrich regions of DNA bound to thyroid receptor beta (TRβ) of mouse cerebellum sampled on post natal day 15. Enriched target was hybridized to promoter microarrays (ChIP-on-chip) spanning −8 kb to +2 kb of the transcription start site (TSS) of 5000 genes. We identified 91 genes with TR binding sites. Roughly half of the sites were located in introns, while 30% were located within 1 kb upstream (5′) of the TSS. Of these genes, 83 with known function included genes involved in apoptosis, neurodevelopment, metabolism and signal transduction. Two genes, MBP and CD44, are known to contain TREs, providing validation of the system. This is the first report of TR binding for 81 of these genes. ChIP-on-chip results were confirmed for 10 of the 13 binding fragments using ChIP-PCR. The expression of 4 novel TH target genes was found to be correlated with TH levels in hyper/hypothyroid animals providing further support for TR binding. A TRβ binding site upstream of the coding region of myelin associated glycoprotein was demonstrated to be TH-responsive using a luciferase expression system. Motif searches did not identify any classic binding elements, indicating that not all TR binding sites conform to variations of the classic form. These findings provide mechanistic insight into impaired neurodevelopment resulting from TH deficiency and a rich bioinformatics resource for developing a better understanding of TR binding.

Aiolos collaborates with Blimp-1 to regulate the survival of multiple myeloma cells

“…15 pXbar plots revealed that Blimp-1 and Aiolos both occupied near the promoter regions of target genes including class II, major histocompatibility complex, transactivator (CIITA), ASK1, IFIT3 and REL (Figures 2c-f). We also found some genes that were bound by either Blimp-1 (e.g., PRMT6) or Aiolos (e.g., HDAC7) (Figure 2g and h).…”

Thyroid hormone action during brain development: More questions than answers

“…Moreover, TRE´s that have been well characterized in functional studies are often far away from the transcriptional start site and may even be localized in intronic M a n u s c r i p t 11 sequences. In a recent study on thyroid hormone receptor beta binding sites and target genes using a ChIP-on-Chip approach in the developing mouse cerebellum (Dong et al, 2009) almost 50 % of the identified TR bindings sites do not even represent any of the classical TRE forms. Finally, even genes that contain a well-characterized TRE, may be regulated by thyroid hormone only in a temporally and spatially very restricted manner.…”

Thyroid hormones and the control of cell proliferation or cell differentiation: Paradox or duality?

“…Only in a few examples has it been possible to assign the control of gene expression to a specific receptor subtype (Calza et al, 2000;Abel et al, 2001;Quignodon et al, 2007;Diez et al, 2008). Finally, a recent study identified the TR 1 binding sites and target genes in the developing mouse cerebellum through the use of the ChIP-onChIP technology (Dong et al, 2009). This is the first report of a large-scale approach to identify direct THs gene targets in the developing mouse brain, and provides a first glimpse at the specific gene targets in the cerebellum.…”