Project description:In zebrafish, there are interactions between black pigment cells (melanophores) and yellow pigment cells (xanthophores) for pigment-pattern formation. However, the detailed molecular mechanism of these interactions remains largely unknown. We used microarray for identifying the molecular basis of these interactions by comparing gene expression between melanophores and xanthophores. Zebrafish pigment cells were collected from adult-fish fins by centrifugal separation or using cell sorter. melanophores vs. xanthophores
Project description:In zebrafish, there are interactions between black pigment cells (melanophores) and yellow pigment cells (xanthophores) for pigment-pattern formation. However, the detailed molecular mechanism of these interactions remains largely unknown. We used microarray for identifying the molecular basis of these interactions by comparing gene expression between melanophores and xanthophores.
2013-05-30 | GSE42129 | GEO
Project description:Study on the Pigment Formation Mechanism of Macrobrachium rosenbergii
Project description:To understand molecular mechanism of stripe patterning in the embryonic skin of Japanese quail, we compared gene expression profile between black stripe and yelllow stripe by using RNA seq method. Most of differential expression genes were known pigmentation-related genes, but some are unknown role in pigment pattern formation.
Project description:Comprehensive utilization of cottonseeds is limited by the presence of pigment gland and its inclusion gossypol. The ideal cotton is glandless-seeds and glanded-plant, a trait found in only few Australian wild cotton species, including Gossypium bickii. Introgressing the trait to cultivated species is proved to be difficult. Understanding the biological processes towards pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding cultivated cotton varieties with the trait of glandless-seeds and glanded-plant. Single-cell RNA sequencing (scRNA-seq) was performed on 12,222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48-hours after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others, and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. In this study, integrating pigment gland cells developmental trajectory, transcription factors regulatory networks, and core transcription factors functional validation, a relatively complete model was proposed for pigment gland formation. Light and gibberellin were verified to promote the formation of pigment glands. Besides, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11) and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. These findings shed new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.
Project description:Comprehensive utilization of cottonseeds is limited by the presence of pigment gland and its inclusion gossypol. The ideal cotton is glandless-seeds and glanded-plant, a trait found in only few Australian wild cotton species, including Gossypium bickii. Introgressing the trait to cultivated species is proved to be difficult. Understanding the biological processes towards pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding cultivated cotton varieties with the trait of glandless-seeds and glanded-plant. Single-cell RNA sequencing (scRNA-seq) was performed on 12,222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48-hours after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others, and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. In this study, integrating pigment gland cells developmental trajectory, transcription factors regulatory networks, and core transcription factors functional validation, a relatively complete model was proposed for pigment gland formation. Light and gibberellin were verified to promote the formation of pigment glands. Besides, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11) and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. These findings shed new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.
Project description:<p>DNA Inverted Repeats as an At-risk Motif for Palindromic Gene Amplificatio defines oncogene amplification that is configured as a series of inverted duplications (palindromic gene amplification). There are several, recurrently amplified oncogenes throughout the human genome. However, it remains unclear whether this recurrent amplification is solely a manifestation of increased fitness resulting from random amplification mechanisms, or if genomic locus-specific amplification mechanism plays a role. </p> <p>In this study, we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification in HER2-positive breast tumors. We investigated eight tumors in this study, of which five tumors were HER2-positive, and three tumors were HER2-negative. HER2-status was determined by clinical FISH tests. We applied three genomic approaches to investigate the amplification mechanism: (1) copy number analysis by array-CGH on the Affymetrix SNP6.0 platform (8 files), (2) sequencing of DNA libraries enriched with tumor-derived palindromic DNA (Genome-wide Analysis of Palindrome Formation, GAPF-seq) (8 files) and (3) unbiased whole genome sequencing (WGS) (1 file). These molecular data is made available in the dbGaP. </p> <p>Genomic studies using tumor DNA was approved under the Internal Institutional Review Board at the Cleveland Clinic (IRB07-136: EXEMPT: Chromosome Breakage and DNA Palindrome Formation). Specimens were obtained and methods were carried out under the auspices of IRB 7881 (Evaluation of Genetic and Molecular Markers in Patients with Breast Cancer). All patients consented to allow their cancer specimens to be used by researchers in an anonymized fashion. The consent form indicates that publication will take place without identifiers to protect the identity of any specific individual.</p> <p>We observed significant and enrichment of palindromic DNA within amplified ERBB2 genomic segments in four out of five HER2-positive tumors. None of three HER2-negative tumors showed such enrichment. Palindromic DNA was particularly enriched at amplification peaks and boundaries between amplified and normal copy-number regions. Thus, palindromic gene amplification shaped the amplified ERBB2 locus. The moderate enrichment of palindromic DNA throughout the amplified segments leads us to propose that the ERBB2 locus is amplified through a mechanism that repeatedly generates palindromic DNA, such as Breakage-Fusion-Bridge cycles. Our results reveal a potential interaction between local genomic environments and gene amplification mechanisms. </p> <p>This study is published under the title "Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors" <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=28211519" target="_blank">(PMID:28211519)</a>. </p>
Project description:Fish are richly and diversely coloured and have a complex palette of pigment cells. We first investigated the diversity of skin cells in Kohaku koi by single-cell sequencing.
Project description:As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.
Project description:We report that decreased expression and activity of AhR exacerbates murine neovascular age-related macular degeneration, and increases cell migration and tube formation. The mechanism involves increased expression of pro-angiogenic mediators and altered matrix degradation. The results of our study suggest that the AhR signaling pathway may be important in multiple AMD related pathways. Gene expression analysis in the retinal pigment epithelium (RPE)-choroid tissue from AhR knockout mice contrasted against wild-type age-matched controls.