Long non-coding RNAs (lncRNAs) play a significant role in maintaining tissue morphology and functions, and their precise regulatory effectiveness is closely related to expression patterns. However, the spatial expression patterns of lncRNAs in humans are poorly characterized. Here, we constructed five comprehensive transcriptomic atlases of human lncRNAs covering thousands of major tissue samples in normal and disease states. The lncRNA transcriptomes exhibited high consistency within the same tissues across resources, and even higher complexity in specialized tissues. Tissue-elevated (TE) lncRNAs were identified in each resource and robust TE lncRNAs were refined by integrative analysis. We detected 1 to 4684 robust TE lncRNAs across tissues; the highest number was in testis tissue, followed by brain tissue. Functional analyses of TE lncRNAs indicated important roles in corresponding tissue-related pathways. Moreover, we found that the expression features of robust TE lncRNAs made them be effective biomarkers to distinguish tissues; TE lncRNAs also tended to be associated with cancer, and exhibited differential expression or were correlated with patient survival. In summary, spatial classification of lncRNAs is the starting point for elucidating the function of lncRNAs in both maintenance of tissue morphology and progress of tissue-constricted diseases.
Humans ; Gene Expression Profiling ; Neoplasms/genetics* ; Organ Specificity ; RNA, Long Noncoding/genetics* ; Transcriptome

OBJECTIVETo examine the expression patterns of short palate, lung and nasal epithelium clone 1 (SPLUNC1) gene in human tissues.

METHODSIn situ hybridization was used to detect the expression of SPLUNC1 gene in 37 different human tissues.

RESULTSWe found that SPLUNC1 gene was not expressed in squamous epithelial cells of the palate, epidermis, esophagus, or the esophagus-cardia junction, metaplastic squamous cells in the nasopharynx, trachea, or uterus cervix, or tumor cells of esophageal squamous cell carcinoma or lung squamous cell carcinoma. SPLUNC1 gene was not expressed in the single layer columnar epithelia cells in the stomach, gallbladder, jejunum, colon, endometrium, or uterus cervix. SPLUNC1 expression was detected mainly in pseudostratified columnar epithelial cells in the nasopharynx, trachea and bronchi, and was gradually down-regulated from the upper to lower end of the respiratory tract, but was not detected in the lung tissues. SPLUNC1 expression was detected not only in the duct and serous gland cells in the parotid and submandibular glands, but also in cells of submucosal serous glands in the nasopharynx and lung, but not in the cells of the mucosal glands. The parietal cells of the gastric submucosa and epithelial cells of the lobula and ducts of the mammary glands expressed SPLUNC1. The adenocarcinoma cells in the lung, stomach, colon, mammary gland, uterus endometrium and cervix showed strong expressions of SPLUNC1 gene.

CONCLUSIONSPLUNC1 expression is highly cell-specific in association with the cell functions.

Epithelial Cells ; metabolism ; Gene Expression ; Glycoproteins ; genetics ; metabolism ; Humans ; Organ Specificity ; Phosphoproteins ; genetics ; metabolism

Sex differences are widely observed under various circumstances ranging from physiological processes to therapeutic responses, and a myriad of sex-biased genes have been identified. In recent years, transcriptomic datasets of microRNAs (miRNAs), an important class of non-coding RNAs, become increasingly accessible. However, comprehensive analysis of sex difference in miRNA expression has not been performed. Here, we identified the differentially-expressed miRNAs between males and females by examining the transcriptomic datasets available in public databases and conducted a systemic analysis of their biological characteristics. Consequently, we identified 73 female-biased miRNAs (FmiRs) and 163 male-biased miRNAs (MmiRs) across four tissues including brain, colorectal mucosa, peripheral blood, and cord blood. Our results suggest that compared to FmiRs, MmiRs tend to be clustered in the human genome and exhibit higher evolutionary rate, higher expression tissue specificity, and lower disease spectrum width. In addition, functional enrichment analysis of miRNAs show that FmiR genes are significantly associated with metabolism process and cell cycle process, whereas MmiR genes tend to be enriched for functions like histone modification and circadian rhythm. In all, the identification and analysis of sex-biased miRNAs together could provide new insights into the biological differences between females and males and facilitate the exploration of sex-biased disease susceptibility and therapy.
Biological Evolution ; Female ; Genome, Human ; Humans ; Male ; MicroRNAs ; blood ; genetics ; Organ Specificity ; Sex Characteristics ; Transcriptome

This study is aimed at gaining insights into the brain site-specific proteomic senescence signature while comparing physiologically aged brains with aging-related dementia brains (for example, Alzheimer's disease (AD)). Our study of proteomic differences within the hippocampus (Hp), parietal cortex (pCx) and cerebellum (Cb) could provide conceptual insights into the molecular mechanisms involved in aging-related neurodegeneration. Using an isobaric tag for relative and absolute quantitation (iTRAQ)-based two-dimensional liquid chromatography coupled with tandem mass spectrometry (2D-LC-MS/MS) brain site-specific proteomic strategy, we identified 950 proteins in the Hp, pCx and Cb of AD brains. Of these proteins, 31 were significantly altered. Most of the differentially regulated proteins are involved in molecular transport, nervous system development, synaptic plasticity and apoptosis. Particularly, proteins such as Gelsolin (GSN), Tenascin-R (TNR) and AHNAK could potentially act as novel biomarkers of aging-related neurodegeneration. Importantly, our Ingenuity Pathway Analysis (IPA)-based network analysis further revealed ubiquitin C (UBC) as a pivotal protein to interact with diverse AD-associated pathophysiological molecular factors and suggests the reduced ubiquitin proteasome degradation system (UPS) as one of the causative factors of AD.
Aged, 80 and over ; Alzheimer Disease/*metabolism ; Brain/*metabolism ; Female ; Gelsolin/genetics/metabolism ; Humans ; Male ; Membrane Proteins/genetics/metabolism ; Neoplasm Proteins/genetics/metabolism ; Organ Specificity ; Proteome/genetics/*metabolism ; Tenascin/genetics/metabolism ; Ubiquitin C/genetics/metabolism

To examine whether or not the regulatory sequence of chicken ovalbumin gene can drive transgene expression specifically in hen oviduct, the authors constructed an oviduct-specific expression vector (pOV), containing 3.0 kilobases (kb) of the 5'-flanking sequence and 3.0 kb of the 3'-flanking sequence of the chicken ovalbumin gene. Jellyfish green fluorescence protein (EGFP) reporter gene and bacterial LacZ reporter gene were respectively inserted into the downstream of the 5'-regulatory region. The recombinants were named as pOVEGFP and pOVLacZ. Two transfer systems, in vitro and in vivo, were used to verify the function of the vector. In vitro, the plasmid DNA pOVEGFP and pEGFP-N1 were transfected respectively by the polyethyleneimine procedure into the primary chicken oviduct epithelium (PCOE) and fibroblasts cells isolated from laying hens. In vivo, the recombinant vector pOVLacZ was injected into egg-laying hens via wing vein and the tissues were collected for RT-PCR analysis. The results showed that expression of pEGFP-N1 was achieved at low level in oviduct epithelial cells and at high level in fibroblasts, but that the recombinant vector was not expressed in both cells. RT-PCR analysis showed that the LacZ gene was transcribed in the oviduct, but not in the heart, liver, kidney and spleen of the injected hens. Accordingly, the beta-galactosidase activity was only detected in the oviduct magnum (116.7 mU/ml) and eggs (16.47 mU/ml). These results indicated that the cloned regulation regions of chicken ovalbumin gene could drive exogenous gene expression specifically in the oviducts of hens. In vivo gene injection via wing vein may serve as a rapid production system of recombinant proteins in chicken eggs. In addition, the cultured primary oviduct cells from laying hens were not efficient temporary expression systems for analyzing the function of regulating elements of ovalbumin gene.
Animals ; Cells, Cultured ; Chickens ; Cloning, Molecular ; methods ; Fallopian Tubes ; metabolism ; Female ; Organ Specificity ; Ovalbumin ; biosynthesis ; genetics ; Protein Engineering ; methods ; Recombinant Proteins ; biosynthesis ; Transfection ; methods ; Women

OBJECTIVETo study the characteristics of a novel human testis-specific gene, HSD-9, and its encoding protein.

METHODSHSD-9 was a novel gene from a human germ cells-specific ESTs library established in our laboratory. We used an electronic cloning method to obtain HSD-9 gene, and analyzed the characteristics of this novel gene and encoding product by bioinformatics methods, detected its expressing profile using a Northern blot assay, prepared specific rabbit polyclonal antibodies against HSD-9 protein, observed the localization of this protein in the germ cells and some somatic cells with confocal microscopy.

RESULTSHSD-9 was expressed in human testes, and its rat homolog was found in the varying germ cells. HSD-9 protein could partly be colocalized with clathrin.

CONCLUSIONSHSD-9 is specific in human testes, and the expression pattern of its encoding product is similar to those of some endocytosis proteins. It is speculated that HSD-9 protein may function in the endocytosis.

Amino Acid Sequence ; Animals ; Base Sequence ; Clathrin ; metabolism ; Humans ; Male ; Membrane Proteins ; biosynthesis ; genetics ; Molecular Sequence Data ; Organ Specificity ; Rabbits ; Rats ; Testis ; metabolism

As part of our efforts to identify novel contraceptive targets in the epididymis we performed transcriptional profiling on each of the 10 and 19 segments of the mouse and rat epididymidis, respectively, using Affymetrix whole genome microarrays. A total of 17 096 and 16 360 probe sets representing transcripts were identified as being expressed in the segmented mouse and rat epididymal transcriptomes, respectively. Comparison of the expressed murine transcripts against a mouse transcriptional profiling database derived from 22 other mouse tissues identified 77 transcripts that were expressed uniquely in the epididymis. The expression of these genes was further evaluated by reverse transcription polymerase chain reaction (RT-PCR) analysis of RNA from 21 mouse tissues. RT-PCR analysis confirmed epididymis-specific expression of Defensin Beta 13 and identified two additional genes with expression restricted only to the epididymis and testis. Comparison of the 16 360 expressed transcripts in the rat epididymis with data of 21 other tissues from a rat transcriptional profiling database identified 110 transcripts specific for the epididymis. Sixty-two of these transcripts were further investigated by qPCR analysis. Only Defensin 22 (E3 epididymal protein) was shown to be completely specific for the epididymis. In addition, 14 transcripts showed more than 100-fold selective expression in the epididymis. The products of these genes might play important roles in epididymal and/or sperm function and further investigation and validation as contraceptive targets are warranted. The results of the studies described in this report are available at the Mammalian Reproductive Genetics (MRG) Database (http://mrg.genetics.washington.edu/).
Animals ; Epididymis ; physiology ; Gene Expression Profiling ; methods ; Male ; Mice ; Organ Specificity ; RNA ; genetics ; isolation & purification ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic

Calmegin is a testis-specific molecular chaperon playing a key role in spermatogenesis. However, the transcriptional regulatory mechanisms for calmegin expression are entirely unknown. Herein, we revealed that calmegin is transcriptionally regulated by histone deacetylase (HDAC) and CpG methyltransferase. The cDNA microarray analysis of the human fibrosarcoma cells treated with trichostatin A (TSA) showed an increased level of calmegin mRNA. The induction of calmegin mRNA by TSA was added by the treatment with 5-aza-2'-deoxycytidine (5'Aza- dC), implying that epigenetic alterations are involved in the transcriptional repression of the gene. Moreover, chromatin immunoprecipitation assay using an anti-acetyl-histone H3 antibody exhibited that the proximal region (-152~-31) of the calmegin promoter is responsible for HDAC-mediated transcriptional repression of the gene. These results demonstrate that calmegin expression is regulated by HDAC and CpG methyltransferase in a coordinative way.
Animals ; Calcium-Binding Proteins/*genetics ; Cell Line, Tumor ; *Gene Expression Regulation ; Histone Deacetylases/*metabolism ; Humans ; Male ; Methyltransferases/*metabolism ; Mice ; Molecular Chaperones/*genetics ; Organ Specificity ; Promoter Regions (Genetics)/genetics ; Research Support, Non-U.S. Gov't ; Testis/*metabolism ; *Transcription, Genetic

Interferons play critical roles in tumor pathogenesis by controlling apoptosis and through cellular anti-proliferative and differentiation activities. Interferon inducible transmembrane protein (IFITM) family genes have been implicated in several cellular processes such as the homotypic cell adhesion functions of IFN and cellular anti-proliferative activities. Expression levels of IFITM genes have been found to be up-regulated in gastric cancer cells and colorectal tumors. IFITM3 (also known as 1-8U) is a member of the IFITM family, and has been described as a key player in specification of germ cell fate. IFITM3 was first isolated from a genetic screen aimed at identifying genes involved in acquisition of germ cell competence. It has been proposed that epiblast cells have the highest expression of IFITM3 initiated germ cell specification and that homotypic association can discriminate germ cells from their somatic neighbors. In an attempt to better understand the genetic influences of IFITM3 on ulcerative colitis, we have identified possible variation sites and single nucleotide polymorphisms (SNPs) through two exons and their boundary IFITM3 intron sequences including the ~2.1 kb promoter regions. To determine whether or not these IFITM3 SNPs are associated with susceptibility to ulcerative colitis, frequencies of the genotype and allele of IFITM3 polymorphisms were analyzed on genomic DNAs isolated from patients with ulcerative colitis and from healthy controls. We also investigated the haplotype frequencies constructed by these SNPs in both groups. In this study, we also showed that expression level of IFITM3 mRNA was significantly higher in tissues of the ileum and cecum of the digestive system. We identified a total of seven SNPs and multiple variation regions in the IFITM3 gene. The genotype frequency of the g.-204T>G polymorphism in patients with ulcerative colitis was significantly different from that of the control group. Our results strongly suggest that polymorphisms of the IFITM3 gene may be associated with susceptibility to ulcerative colitis.
Cecum/*metabolism ; Colitis, Ulcerative/epidemiology/*genetics/immunology ; Gene Expression Profiling ; Gene Frequency ; Genetic Association Studies ; Genetic Predisposition to Disease ; Haplotypes ; Ileum/*metabolism ; Korea ; Membrane Proteins/*genetics/immunology/metabolism ; Organ Specificity ; Polymorphism, Single Nucleotide ; RNA-Binding Proteins/*genetics/immunology/metabolism

To clone and analyze a member of the Auxin/indole-3-acetic acid (Aux/IAA) gene family, RgIAA1, from Rehmannia glutinosa. The transcriptional EST database of R. glutinosa was used to clone the new Aux/IAA gene by cDNA probe of AtIAA14. Bioinformatics was applied to analyze the sequence characteristics of RgIAA1 protein and construct phylogenetiC trees. Quantitative RT-PCR has been applied to detect the transcription level of RgIAA1 in seven tissues as well as in leaves under three stresses. The results showed that, the cDNA sequence of RgIAA1 contains 903 bp was obtained. The open reading frame (ORF) of RgIAA1 was 681 bp encoding 226 amino acids, which has typical structural domains and characteristic sequence of Aux/IAA family proteins. RgIAA1 showed the highest expression level in unfolded leaf, followed by the stem. And the expression of RglAA1 was quickly decreased with leaf growing up. The transcription level increased under continuous cropping conditions while it reduced both in salinity and waterlogging stresses. RgIAA1, an Aux/IAA gene from R. glutinosa has been obtained for the first time, which can lay the foundation for further studies about its molecular function in development and responses to stress.
Amino Acid Sequence ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Indoleacetic Acids ; metabolism ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Plant Proteins ; chemistry ; genetics ; Rehmannia ; classification ; genetics ; physiology ; Stress, Physiological ; genetics