title: Genome-wide analysis of Pax8 binding provides new insights into thyroid functions.
abstract: BACKGROUND
  The transcription factor Pax8 is essential for the differentiation of thyroid cells. However, there are few data on genes transcriptionally regulated by Pax8 other than thyroid-related genes. To better understand the role of Pax8 in the biology of thyroid cells, we obtained transcriptional profiles of Pax8-silenced PCCl3 thyroid cells using whole genome expression arrays and integrated these signals with global cis-regulatory sequencing studies performed by ChIP-Seq analysis
  
  
  RESULTS
  Exhaustive analysis of Pax8 immunoprecipitated peaks demonstrated preferential binding to intragenic regions and CpG-enriched islands, which suggests a role of Pax8 in transcriptional regulation of orphan CpG regions. In addition, ChIP-Seq allowed us to identify Pax8 partners, including proteins involved in tertiary DNA structure (CTCF) and chromatin remodeling (Sp1), and these direct transcriptional interactions were confirmed in vivo. Moreover, both factors modulate Pax8-dependent transcriptional activation of the sodium iodide symporter (Nis) gene promoter. We ultimately combined putative and novel Pax8 binding sites with actual target gene expression regulation to define Pax8-dependent genes. Functional classification suggests that Pax8-regulated genes may be directly involved in important processes of thyroid cell function such as cell proliferation and differentiation, apoptosis, cell polarity, motion and adhesion, and a plethora of DNA/protein-related processes.
  
  
  CONCLUSIONS
  Our study provides novel insights into the role of Pax8 in thyroid biology, exerted through transcriptional regulation of important genes involved in critical thyrocyte processes. In addition, we found new transcriptional partners of Pax8, which functionally cooperate with Pax8 in the regulation of thyroid gene transcription. Besides, our data demonstrate preferential location of Pax8 in non-promoter CpG regions. These data point to an orphan CpG island-mediated mechanism that represents a novel role of Pax8 in the transcriptional output of the thyrocyte.
authors.affiliation: Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas-CSIC y Universidad Autónoma de Madrid-UAM, C/Arturo Duperier 4, Madrid 28029, Spain.
authors.forename: Sergio
authors.initials: S
authors.lastname: Ruiz-Llorente
authors.forename: Enrique
authors.initials: E
authors.lastname: Carrillo Santa de Pau
authors.forename: Ana
authors.initials: A
authors.lastname: Sastre-Perona
authors.forename: Cristina
authors.initials: C
authors.lastname: Montero-Conde
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Gómez-López
authors.forename: James A
authors.initials: JA
authors.lastname: Fagin
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.forename: David G
authors.initials: DG
authors.lastname: Pisano
authors.forename: Pilar
authors.initials: P
authors.lastname: Santisteban
mesh_terms: D000818:Animals; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D002454:Cell Differentiation; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands; D005786:Gene Expression Regulation; D020868:Gene Silencing; D016678:Genome; D055106:Genome-Wide Association Study; D006367:HeLa Cells; D006801:Humans; D046228:Microarray Analysis; D000072636:PAX8 Transcription Factor; D051761:Paired Box Transcription Factors / Q000037:antagonists & inhibitors / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism; D051381:Rats; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D016329:Sp1 Transcription Factor / Q000235:genetics / Q000378:metabolism; D027981:Symporters / Q000235:genetics / Q000378:metabolism; D013961:Thyroid Gland / Q000166:cytology / Q000378:metabolism*; D014162:Transfection; D000099209:Sodium-Iodide Symporters
chemical_list: D000076246:CCCTC-Binding Factor; D000072636:PAX8 Transcription Factor; D051761:Paired Box Transcription Factors; D034741:RNA, Small Interfering; D012097:Repressor Proteins; D016329:Sp1 Transcription Factor; D027981:Symporters; D000099209:Sodium-Iodide Symporters; C000619697:CTCF protein, human; C499497:Pax8 protein, rat