Thyroid Hormone Modulation of DNA Methylation in the Developing Brain.

Postembryonic brain development is dependent on thyroid hormone (T3). The actions of T3 are mediated by T3 receptors (TRs) that bind T3 response elements (T3REs) in the genome and regulate gene transcription through recruitment of histone-modifying enzymes. Methylation of DNA is another critical epigenetic modification that controls gene transcription. Using mouse and frog (T3 controls tadpole metamorphosis), I investigated T3-dependent modulation of DNA methylation, regulation of genes that control this epigenetic modification, and roles of DNA methylation in regulation of gene expression programs in the brain. I discovered that TRs directly activate the transcription of the de novo DNA methyltransferase 3a (Dnmt3a) gene that encodes a key enzyme that establishes genome-wide patterns of DNA methylation in the developing brains of mouse and frog. I identified two functional T3REs that support T3-dependent transactivation of the Dnmt3a genes. I found strong sequence conservation of the mouse T3REs among eutherian mammals. I found that the tadpole brain genome became demethylated during metamorphosis, which correlated with activation of genes that are involved in active DNA demethylation (tet2, tet3, apobec2, gadd45β, gadd45γ and tdg). Treating premetamorphic tadpoles with exogenous T3 induced tet3, gadd45γ and tdg mRNAs. I found that T3REs for known T3-regulated genes (klf9 and dnmt3a) became demethylated during metamorphosis and in response to T3. In vitro methylation of DNA fragments containing these T3REs subcloned into reporter plasmids abrogated T3-dependent transactivity, suggesting that DNA demethylation of T3REs activates T3-regulated genes. To identify gene expression programs that are regulated by DNA methylation, I conducted methylated DNA capture sequencing and RNA-sequencing in tadpole brain. I identified ~142,000 genomic regions enriched for methylated DNA and 855 regions that showed changes during metamorphosis. More than 5,000 genes showed changes in expression, and I identified thirteen patterns of expression dynamics and enriched biological pathways among these genes. I found an inverse correlation between changes in expression of genes found within 50 kb neighborhood of regions that became differentially methylated.. My findings support that T3 modulates DNA methylation in the developing brain, and that these changes may be important for the coordination of gene expression programs during postembryonic neurological development.PhDNeuroscienceUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/113640/1/ykyono_3.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/113640/2/ykyono_2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/113640/3/ykyono_1.pd

Consensus standards for acquisition, measurement, and reporting of intravascular optical coherence tomography studies

Objectives: The purpose of this document is to make the output of the International Working Group for Intravascular Optical Coherence Tomography (IWG-IVOCT) Standardization and Validation available to medical and scientific communities, through a peer-reviewed publication, in the interest of improving the diagnosis and treatment of patients with atherosclerosis, including coronary artery disease. Background: Intravascular optical coherence tomography (IVOCT) is a catheter-based modality that acquires images at a resolution of ∼10 μm, enabling visualization of blood vessel wall microstructure in vivo at an unprecedented level of detail. IVOCT devices are now commercially available worldwide, there is an active user base, and the interest in using this technology is growing. Incorporation of IVOCT in research and daily clinical practice can be facilitated by the development of uniform terminology and consensus-based standards on use of the technology, interpretation of the images, and reporting of IVOCT results. Methods: The IWG-IVOCT, comprising more than 260 academic and industry members from Asia, Europe, and the United States, formed in 2008 and convened on the topic of IVOCT standardization through a series of 9 national and international meetings. Results: Knowledge and recommendations from this group on key areas within the IVOCT field were assembled to generate this consensus document, authored by the Writing Committee, composed of academicians who have participated in meetings and/or writing of the text. Conclusions: This document may be broadly used as a standard reference regarding the current state of the IVOCT imaging modality, intended for researchers and clinicians who use IVOCT and analyze IVOCT data

A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

http://deepblue.lib.umich.edu/bitstream/2027.42/177134/2/db201087.pdfPublished versionDescription of db201087.pdf : Published versio

Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module.

Cooperative, synergistic gene regulation by nuclear hormone receptors can increase sensitivity and amplify cellular responses to hormones. We investigated thyroid hormone (TH) and glucocorticoid (GC) synergy on the Krüppel-like factor 9 (Klf9) gene, which codes for a zinc finger transcription factor involved in development and homeostasis of diverse tissues. We identified regions of the Xenopus and mouse Klf9 genes 5-6 kb upstream of the transcription start sites that supported synergistic transactivation by TH plus GC. Within these regions, we found an orthologous sequence of approximately 180 bp that is highly conserved among tetrapods, but absent in other chordates, and possesses chromatin marks characteristic of an enhancer element. The Xenopus and mouse approximately 180-bp DNA element conferred synergistic transactivation by hormones in transient transfection assays, so we designate this the Klf9 synergy module (KSM). We identified binding sites within the mouse KSM for TH receptor, GC receptor, and nuclear factor κB. TH strongly increased recruitment of liganded GC receptor and serine 5 phosphorylated (initiating) RNA polymerase II to chromatin at the KSM, suggesting a mechanism for transcriptional synergy. The KSM is transcribed to generate long noncoding RNAs, which are also synergistically induced by combined hormone treatment, and the KSM interacts with the Klf9 promoter and a far upstream region through chromosomal looping. Our findings support that the KSM plays a central role in hormone regulation of vertebrate Klf9 genes, it evolved in the tetrapod lineage, and has been maintained by strong stabilizing selection. Mol Endocrinol 2015 Jun; 29(6):856-72

A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures.

Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ∼20% of which are islet specific and occur mostly distal to known gene TSS. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validated the transcriptional enhancer activity for 2,279 of 3,378 (∼68%) tested islet CAGE elements (5% false discovery rate). TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting active enhancers at GWAS loci

Consensus standards for acquisition, measurement, and reporting of intravascular optical coherence tomography studies: a report from the International Working Group for Intravascular Optical Coherence Tomography Standardization and Validation

The purpose of this document is to make the output of the International Working Group for Intravascular Optical Coherence Tomography (IWG-IVOCT) Standardization and Validation available to medical and scientific communities, through a peer-reviewed publication, in the interest of improving the diagnosis and treatment of patients with atherosclerosis, including coronary artery disease