BEST1 expression in the retinal pigment epithelium is modulated by OTX family members (2009)
Esumi, Noriko, Kachi, Shu, Hackler, Laszlo, Masuda, Tomohiro, Yang, Zhiyong, Campochiaro, Peter A., ...
A number of genes preferentially expressed in the retinal pigment epithelium (RPE) are associated with retinal degenerative disease. One of these, BEST1, encodes bestrophin-1, a protein that when...
Relating periodicity of nucleosome organization and gene regulation (2009)
Wan, Jun, Lin, Jimmy, Zack, Donald J., Qian, Jiang
Motivation: The relationship between nucleosome positioning and gene regulation is fundamental yet complex. Previous studies on genomic nucleosome positions have revealed a correlation between...
TiGER: A database for tissue-specific gene expression and regulation (2008)
Liu, Xiong, Yu, Xueping, Zack, Donald J, Zhu, Heng, Qian, Jiang
Abstract Background Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do...
NEW DEVELOPMENTS Seeing the Unseen: Microarray-Based Gene Expression Profiling in Vision (2008)
Sepideh Zareparsi, Alfred Hero, Donald J. Zack, Robert W. Williams, Anand Swaroop
Completion of genome sequencing efforts of humans and model organisms 1–3 have provided exciting opportunities for vision research. Questions that were hard to envisage, let alone resolve, suddenly...
Analysis of regulatory network topology reveals functionally distinct classes of microRNAs (2008)
Yu, Xueping, Lin, Jimmy, Zack, Donald J., Mendell, Joshua T., Qian, Jiang
MicroRNAs (miRNAs) negatively regulate the expression of target genes at the post-transcriptional level. Little is known about the crosstalk between miRNAs and transcription factors (TFs). Here we...
Yu, Xueping, Lin, Jimmy, Zack, Donald J, Qian, Jiang
Abstract Background Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by...
Yu, Xueping, Lin, Jimmy, Zack, Donald J., Qian, Jiang
Tissue-specific gene expression is generally regulated by more than a single transcription factor (TF). Multiple TFs work in concert to achieve tissue specificity. In order to explore these complex...
Yu, Xueping, Lin, Jimmy, Masuda, Tomohiro, Esumi, Noriko, Zack, Donald J., Qian, Jiang
Combinatorial regulation by transcription factor complexes is an important feature of eukaryotic gene regulation. Here, we propose a new method for identification of interactions between...
Yu, Xueping, Lin, Jimmy, Zack, Donald J., Qian, Jiang
Tissue-specific gene expression is generally regulated by more than a single transcription factor (TF). Multiple TFs work in concert to achieve tissue specificity. In order to explore these complex...
Yu, Xueping, Lin, Jimmy, Zack, Donald J., Qian, Jiang
Tissue-specific gene expression is generally regulated by more than a single transcription factor (TF). Multiple TFs work in concert to achieve tissue specificity. In order to explore these complex...
Otteson, Deborah C, Lai, Hong, Liu, Yuhui, Zack, Donald J
Abstract Background In the retina, many of the genes that encode components of the visual transduction cascade and retinoid recycling are exclusively expressed in photoreceptor cells and show highly...
Qian, Jiang, Esumi, Noriko, Chen, Yangjian, Wang, Qingliang, Chowers, Itay, Zack, Donald J.
Identification of tissue-specific gene regulatory networks can yield insights into the molecular basis of a tissue's development, function and pathology. Here, we present a computational approach...
QRX, a Novel Homeobox Gene, Modulates Photoreceptor Gene Expression (2004)
Wang, Qing-liang, Chen, Shiming, Esumi, Noriko, Swain, Prabodh K., Haines, Heidi S., Peng, Guanghua, ...
A novel paired-like homeobox gene, designated as Qrx, was identified by a yeast one-hybrid screen using the bovine Rhodopsin promoter Ret-1 DNA regulatory element as bait. Qrx is preferentially...
QRX, a novel homeobox gene, modulates photoreceptor gene expression (2004)
Wang, Qing-liang, Chen, Shiming, Esumi, Noriko, Swain, Prabodh K., Haines, Heidi S., Peng, Guanghua, ...
A novel paired-like homeobox gene, designated as Qrx, was identified by a yeast one-hybrid screen using the bovine Rhodopsin promoter Ret-1 DNA regulatory element as bait. Qrx is preferentially...
QRX, a Novel Homeobox Gene, Modulates Photoreceptor Gene Expression (2004)
Wang, Qing-liang, Chen, Shiming, Esumi, Noriko, Swain, Prabodh K., Haines, Heidi S., Peng, Guanghua, ...
A novel paired-like homeobox gene, designated as Qrx, was identified by a yeast one-hybrid screen using the bovine Rhodopsin promoter Ret-1 DNA regulatory element as bait. Qrx is preferentially...
Gene Expression Variation in the Adult Human Retina (2003)
Chowers, Itay, Liu, Dongmei, Farkas, Ronald H., Gunatilaka, Tushara L., Hackam, Abigail S., Bernstein, Steven, ...
Despite evidence that differences in gene expression levels contribute significantly to phenotypic variation across individuals, there has been only limited effort to study gene expression variation...
Gene expression variation in the adult human retina (2003)
Chowers, Itay, Liu, Dongmei, Farkas, Ronald H., Gunatilaka, Tushara L., Hackam, Abigail S., Bernstein, Steven L., ...
Despite evidence that differences in gene expression levels contribute significantly to phenotypic variation across individuals, there has been only limited effort to study gene expression variation...
Gene Expression Variation in the Adult Human Retina (2003)
Chowers, Itay, Liu, Dongmei, Farkas, Ronald H., Gunatilaka, Tushara L., Hackam, Abigail S., Bernstein, Steven, ...
Despite evidence that differences in gene expression levels contribute significantly to phenotypic variation across individuals, there has been only limited effort to study gene expression variation...
Transcriptome analysis of the retina (2002)
Swaroop, Anand, Zack, Donald J
Abstract The retina offers unique opportunities to define the molecular and cellular pathways mediating neuronal function and disease because of its morphological complexity, well-defined role in...
Functional analysis of cone-rod homeobox (CRX) mutations associated with retinal dystrophy (2002)
Chen, Shiming, Wang, Qing-Liang, Xu, Siqun, Liu, Ivy, Li, Lili Y., Wang, Yufang, ...
Mutations in the photoreceptor transcription factor cone–rod homeobox (CRX) have been identified in patients with several forms of retinal degenerative disease. To investigate the mechanisms by...
Isolation and Characterization of a Zebrafish Homologue of the Cone Rod Homeobox Gene (2001)
Yuhui Liu, Yu-chi Shen, Joshua S. Rest, Pamela A. Raymond, Donald J. Zack
this article, we describe the identification and characterization of a zebrafish ortholog of Crx. The only Crx genes identified to date are mammalian (human, bovine, mouse, and rat.) Phylogenetic...
Fei, Yijian, Matragoon, Suraporn, Smith, Sylvia B., Overbeek, Paul A., Chen, Shiming, Zack, Donald J., ...
The essential control elements in the interphotoreceptor retinoid-binding protein gene (IRBP) promoter are located between −156 and +19. The −156/−109 sequence contains a...
Typescript.
Li, Xiaodong, Chen, Shiming, Wang, Qingliang, Zack, Donald J., Snyder, Solomon H., Borjigin, Jimo
The circadian hormone melatonin is synthesized predominantly in the pineal gland by the actions of two pineal-specific enzymes: serotonin N-acetyltransferase (NAT) and...
Transcriptome analysis of the retina
Swaroop, Anand, Zack, Donald J
The retina offers unique opportunities to define the molecular and cellular pathways mediating neuronal function and disease because of its morphological complexity, well-defined role in visual...
Qian, Jiang, Esumi, Noriko, Chen, Yangjian, Wang, Qingliang, Chowers, Itay, Zack, Donald J.
Identification of tissue-specific gene regulatory networks can yield insights into the molecular basis of a tissue's development, function and pathology. Here, we present a computational approach...
Wilkie, Susan E., Li, Yang, Deery, Evelyne C., Newbold, Richard J., Garibaldi, Daniel, Bateman, J. Bronwyn, ...
Mutations in the gene for guanylate cyclase–activating protein-1 (GCAP1) (GUCA1A) have been associated with autosomal dominant cone dystrophy (COD3). In the present study, a severe disease...
ROLES OF CELL-INTRINSIC AND MICROENVIRONMENTAL FACTORS IN PHOTORECEPTOR CELL DIFFERENTIATION
Bradford, Rebecca L., Wang, Chenwei, Zack, Donald J., Adler, Ruben
Photoreceptor differentiation requires the coordinated expression of numerous genes. It is unknown whether those genes share common regulatory mechanisms or are independently regulated by distinct...
Yu, Xueping, Lin, Jimmy, Masuda, Tomohiro, Esumi, Noriko, Zack, Donald J., Qian, Jiang
Combinatorial regulation by transcription factor complexes is an important feature of eukaryotic gene regulation. Here, we propose a new method for identification of interactions between...
Yu, Xueping, Lin, Jimmy, Zack, Donald J., Qian, Jiang
Tissue-specific gene expression is generally regulated by more than a single transcription factor (TF). Multiple TFs work in concert to achieve tissue specificity. In order to explore these complex...
Li, Xiaodong, Chen, Shiming, Wang, Qingliang, Zack, Donald J., Snyder, Solomon H., Borjigin, Jimo
The circadian hormone melatonin is synthesized predominantly in the pineal gland by the actions of two pineal-specific enzymes: serotonin N-acetyltransferase (NAT) and...
Transcriptome analysis of the retina
Swaroop, Anand, Zack, Donald J
The retina offers unique opportunities to define the molecular and cellular pathways mediating neuronal function and disease because of its morphological complexity, well-defined role in visual...
Qian, Jiang, Esumi, Noriko, Chen, Yangjian, Wang, Qingliang, Chowers, Itay, Zack, Donald J.
Identification of tissue-specific gene regulatory networks can yield insights into the molecular basis of a tissue's development, function and pathology. Here, we present a computational approach...
Wilkie, Susan E., Li, Yang, Deery, Evelyne C., Newbold, Richard J., Garibaldi, Daniel, Bateman, J. Bronwyn, ...
Mutations in the gene for guanylate cyclase–activating protein-1 (GCAP1) (GUCA1A) have been associated with autosomal dominant cone dystrophy (COD3). In the present study, a severe disease...
Yu, Xueping, Lin, Jimmy, Masuda, Tomohiro, Esumi, Noriko, Zack, Donald J., Qian, Jiang
Combinatorial regulation by transcription factor complexes is an important feature of eukaryotic gene regulation. Here, we propose a new method for identification of interactions between...
Yu, Xueping, Lin, Jimmy, Zack, Donald J., Qian, Jiang
Tissue-specific gene expression is generally regulated by more than a single transcription factor (TF). Multiple TFs work in concert to achieve tissue specificity. In order to explore these complex...
Campochiaro, Peter A., Okamoto, Naoyuki, Tobe, Takao, Hackett, Sean F., Ozaki, Hiroaki, Zack, Donald J.
Ozaki, Hiroaki, Okamoto, Naoyuki, Ortega, Sagrario, Chang, Michelle, Ozaki, Keiko, Sadda, Srinivas, ...
Basic fibroblast growth factor (FGF2) is constitutively expressed in the retina and its expression is increased by a number of insults, but its role in the retina is still uncertain. This study was...
Platelet-Derived Growth Factor-A-Induced Retinal Gliosis Protects against Ischemic Retinopathy
Yamada, Haruhiko, Yamada, Eri, Ando, Akira, Seo, Man-Seong, Esumi, Noriko, Okamoto, Naoyuki, ...
Retinal astrocytes are located in the nerve fiber layer and along retinal blood vessels and have been hypothesized to participate in the induction and maintenance of the blood-retinal barrier....
Seo, Man Seong, Okamoto, Naoyuki, Vinores, Melissa A., Vinores, Stanley A., Hackett, Sean F., Yamada, Haruhiko, ...
Expression of platelet-derived growth factor (PDGF)-A and PDGF-B is increased in patients with proliferative retinopathies in which traction retinal detachments occur. Previous studies have...
Fibroblast Growth Factor-2 Decreases Hyperoxia-Induced Photoreceptor Cell Death in Mice
Yamada, Haruhiko, Yamada, Eri, Ando, Akira, Esumi, Noriko, Bora, Naba, Saikia, Jina, ...
Fibroblast growth factor-2 (FGF2) has neurotrophic effects in vitro and in vivo. It has been demonstrated to decrease photoreceptor cell death in rats exposed to constant light and in rats with an...
Ohno-Matsui, Kyoko, Hirose, Akira, Yamamoto, Satoru, Saikia, Jina, Okamoto, Naoyuki, Gehlbach, Peter, ...
Transgenic mice with vascular endothelial growth factor (VEGF) driven by the rhodopsin promoter (rho/VEGF mice) develop neovascularization that originates from the deep capillary bed of the retina...
Expression and permeation properties of the K+ channel Kir7.1 in the retinal pigment epithelium
Shimura, Masahiko, Yuan, Yukun, Chang, Jinghua T, Zhang, Suiyuan, Campochiaro, Peter A, Zack, Donald J, ...
Bovine Kir7.1 clones were obtained from a retinal pigment epithelium (RPE)-subtracted cDNA library. Human RPE cDNA library screening resulted in clones encoding full-length human Kir7.1.Northern blot...
TiGER: A database for tissue-specific gene expression and regulation
Liu, Xiong, Yu, Xueping, Zack, Donald J, Zhu, Heng, Qian, Jiang
Analysis of regulatory network topology reveals functionally distinct classes of microRNAs
Yu, Xueping, Lin, Jimmy, Zack, Donald J., Mendell, Joshua T., Qian, Jiang
MicroRNAs (miRNAs) negatively regulate the expression of target genes at the post-transcriptional level. Little is known about the crosstalk between miRNAs and transcription factors (TFs). Here we...