This study was purposed to investigate the expression of the growth-factor independence 1 (GFI1) in patients with leukemia and its clinical significance. Bone marrow mononuclear cells were obtained from 65 newly diagnosed leukemia patients including 24 acute myeloid leukemia (AML), 18 chronic myelogenous leukemia (CML), 6 acute lymphoblastic leukemia (ALL), 17 blast crisis of chronic myelogenous leukemia and 13 patients with iron deficiency anemia (IDA) were used as controls. The relative expression of gene gfi1 was detected by reverse transcriptase-polymerase chain reaction (RT-PCR) and taqman quantitative real-time reverse transcription polymerase chain reaction (QRT-PCR). The results showed that gene expression of gene gfi1 in leukemia patients was obviously higher than that in controls and the difference was statistically significant (p < 0.01), in which the expression of gene gfi1 in newly diagnosed CML patients was higher than that in newly diagnosed AML, newly diagnosed ALL, CML-BCP patients and the difference was significant (p < 0.01). Expression of gene gfi1 in lymphocytic blast crisis of CML was higher than that in nonlymphocytic blast crisis of CML, and the difference was significant. It is concluded that gene gfi1 may play an important role in leukemia, especially in CML incidence and progression. The high level expression of gene gfi1 may be participate in the development of lymphoma.
DNA-Binding Proteins ; genetics ; Gene Expression ; Humans ; Leukemia ; genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription Factors ; genetics ; Transcription, Genetic ; genetics

OBJECTIVETo investigate the underlying tumor susceptibility mechanisms and reasons for the high risk of cancer in Fanconi anemia (FA).

METHODSGene Set Enrichment Analysis (GSEA) was performed to compare gene expression profiles between 21 FA patients' bone marrow (BM) mononuclear cell (BMNC) and 11 normal controls in cancer related gene sets from NCBI GEO database, then core enriched genes were identified by further investigation. Through enrichment analyzing biological processes of gene ontology sets and structural genomic gene sets between FA expression profiles and control, more details related with its tumor susceptibility had been revealed.

RESULTSCompared with normal control, gene expression in FA group had significant been enriched in resistance to Bcl-2 inhibitor gene set, fibroblast growth factors signalling pathways, insulin and insulin-like growth factors (IGF) signalling pathways induced cancer genesis gene sets. The high level of D4S234E, SST, FGFs, IGFs, FGFRs and IGFBP expression provided an initiate environment for tumorgenesis and drug resistance. There were significant differences in biogenesis extracellular molecules and cytomembrane structure organizations between FA and control. Genes with promoter regions around transcription start sites containing either motif RRCAGGTGNCV or CCTNTMAGA were enriched and those former genes match annotation for tumorgenic transcription factor 3 (TCF3).

CONCLUSIONSThe high tumor susceptibility of FA patients may be closely related with the dramatic changes in cancer related growth factors and hormones environment. This study provides new insights into tumor susceptibility mechanism in FA patients.

Basic Helix-Loop-Helix Transcription Factors ; genetics ; Case-Control Studies ; Fanconi Anemia ; genetics ; Female ; Gene Expression ; Genes, Neoplasm ; Genetic Predisposition to Disease ; Humans ; Insulin-Like Growth Factor Binding Proteins ; genetics ; Male ; Neoplasms ; genetics ; Promoter Regions, Genetic ; Signal Transduction ; genetics ; Somatomedins ; genetics ; Transcription Initiation Site ; Transcriptome

To understand the functions of the kidney, the transcriptome of each part of the nephron needs to be profiled using a highly sensitive and unbiased tool. RNA sequencing (RNA-seq) has revolutionized transcriptomic research, enabling researchers to define transcription activity and functions of genomic elements with unprecedented sensitivity and precision. Recently, RNA-seq for polyadenylated messenger RNAs [poly(A)'-mRNAs] and classical microdissection were successfully combined to investigate the transcriptome of glomeruli and 14 different renal tubule segments. A rat kidney is perfused with and incubated in collagenase solution, and the digested kidney was manually dissected under a stereomicroscope. Individual glomeruli and renal tubule segments are identified by their anatomical and morphological characteristics and collected in phosphate-buffered saline. Poly(A)'-tailed mRNAs are released from cell lysate, captured by oligo-dT primers, and made into complementary DNAs (cDNAs) using a highly sensitive reverse transcription method. These cDNAs are sheared by sonication and prepared into adapter-ligated cDNA libraries for Illumina sequencing. Nucleotide sequences reported from the sequencing reaction are mapped to the rat reference genome for gene expression analysis. These RNA-seq transcriptomic data were highly consistent with prior knowledge of gene expression along the nephron. The gene expression data obtained in this work are available as a public Web page (https://helixweb.nih.gov/ESBL/Database/NephronRNAseq/) and can be used to explore the transcriptomic landscape of the nephron.
Animals ; Base Sequence ; Collagenases ; DNA, Complementary ; Gene Expression ; Gene Library ; Genome ; Kidney ; Microdissection ; Nephrons* ; Rats ; Reverse Transcription ; RNA* ; RNA, Messenger ; Sequence Analysis, RNA* ; Sonication ; Transcriptome*

In this study, the 5' -flanking proximal region of stress-induced gene encoding betaine aldehyde dehydrogenase was isolated by Adaptor-PCR and TAIL-PCR from halophyte Suaeda liaotungensis. 1993 bp sequence was obtained by sequencing. The transcription start site, which localized at 62 bases upstream of the start ATG, was predicted using TSSP-TCM program. The functional elements were analysed by PLACE programm. The SlBADH gene promoter contains the basic elements: TATA-box, CAAT-box, and stress-induced elements: salt responsed element, cold, dehydration, ABA and frozen responsed elements, WUN responsed elements and HSE. Obtaining the promoter of betaine aldehyde dehydrogenase gene from Suaeda liaotungensis provides a foundation for analyzing the stress-induced promoter elements, studying the relationship between structure and founction of the promoter, and investigating the molecular mechanism of BADH gene regulation.
Base Sequence ; Betaine-Aldehyde Dehydrogenase ; genetics ; Chenopodiaceae ; enzymology ; genetics ; Cold Temperature ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genes, Plant ; Molecular Sequence Data ; Plant Proteins ; genetics ; Promoter Regions, Genetic ; Salts ; Sequence Analysis, DNA ; Transcription Initiation Site

OBJECTIVETo investigate whether α-hemoglobin stabilizing protein (AHSP), the α-globin-specific molecular chaperone, is regulated by erythroid transcription factor NF-E2.

METHODSWe established the stable cell line with NF-E2p45 (the larger subunit of NF-E2) short hairpin RNA to silence its expression. Western blot, real-time polymerase chain reaction, and chromatin immunoprecipitation (ChIP) analysis were performed to detect the expression of AHSP, the histone modifications at AHSP gene locus, and the binding of GATA-1 at the AHSP promoter with NF-E2p45 deficiency. ChIP was also carried out in dimethyl sulfoxide (DMSO)-induced DS19 cells and estrogen-induced G1E-ER4 cells to examine NF-E2 binding to the AHSP gene locus and its changes during cell erythroid differentiation. Finally, luciferase assay was applied in HeLa cells transfected with AHSP promoter fragments to examine AHSP promoter activity in the presence of exogenous NF-E2p45.

RESULTSWe found that AHSP expression was highly dependent on NF-E2p45. NF-E2 bound to the regions across AHSP gene locus in vivo, and the transcription of AHSP was transactivated by exogenous NF-E2p45. In addition, we observed the decrease of H3K4 trimethylation and GATA-1 occupancy at the AHSP gene locus in NF-E2p45-deficient cells. Restoration of GATA-1 in G1E-ER4 cells in turn led to increased DNA binding of NF-E2p45.

CONCLUSIONNF-E2 may play an important role in AHSP gene regulation, providing new insights into the molecular mechanisms underlying the erythroid-specific expression of AHSP as well as new possibilities for β-thalassemia treatment.

Base Sequence ; Blood Proteins ; genetics ; DNA Primers ; GATA1 Transcription Factor ; physiology ; Gene Expression Regulation ; physiology ; Gene Silencing ; HeLa Cells ; Humans ; Methylation ; Molecular Chaperones ; genetics ; NF-E2 Transcription Factor, p45 Subunit ; physiology ; Promoter Regions, Genetic ; Reverse Transcriptase Polymerase Chain Reaction

OBJECTIVE: To evaluate the effect of transduced tumor necrosis factor-a(TNF-a) gene expression on growth of human bladder tumor cell lines in vitro. MATERIALS AND METHODS: The complete cDNA of TNF-a was introduced to three human bladder tumor cell lines(F-24, J-82, HT-1197) using a retroviral vector, a recombinant form of Molony murine leukemia virus with TNF-a and Neo gene and transfected cells were selected by exposure to neomycin analog G418. Gene transfer and expression were confirmed by polymerase chain reaction(PCR) and reverse transcription polymerase chain reaction(RT-PCR)-Southern blotting. Cell growth was measured by MTT assay Result is Successful gene transfer and expression were confirmed in all three cell bladder tumor lines. Growth of transfected cells were compared with parental cell lines and no differences were found in all three cell lines(p>0.05). CONCLUSION: Expression of transduced TNF-t gene could not show any effect on growth of human bladder tumor cells in vitro.
Cell Line* ; DNA, Complementary ; Gene Expression* ; Genetic Therapy ; Humans* ; Leukemia Virus, Murine ; Necrosis ; Neomycin ; Parents ; Reverse Transcription ; Tumor Necrosis Factor-alpha* ; Urinary Bladder Neoplasms* ; Urinary Bladder* ; Zidovudine

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

No abstract available.
Gene Expression Profiling* ; RNA ; Transcriptome*

Humans ; Transcriptome ; Gene Expression Profiling

CpG-island margins and non-island-CpG sites round the transcription start sites of CpG-island-positive and -negative genes are methylated to various degrees in a tissue-specific manner. These methylation-variable CpG sites were analyzed to delineate a relationship between the methylation and transcription of the tissue-specific genes. The level of tissue-specific transcription was estimated by counting the number of the total transcripts in the SAGE (serial analysis of gene expression) database. The methylation status of 12 CpG-island margins and 21 non-island CpG sites near the key tissue-specific genes was examined in pluripotent stromal cells obtained from fat and bone marrow samples as well as in lineage-committed cells from marrow bulk, stomach, colon, breast, and thyroid samples. Of the 33 CpG sites examined, 10 non-island-CpG sites, but none of the CpG-island margins were undermethylated concurrent with tissue-specific expression of their nearby genes. The net methylation of the 33 CpG sites and the net amount of non-island-CpG gene transcripts were high in stomach tissues and low in stromal cells. The present findings suggest that the methylation of the non-island-CpG sites is inversely associated with the expression of the nearby genes, and the concert effect of transitional-CpG methylation is linearly associated with the stomach-specific genes lacking CpG-islands.
Adipose Tissue/cytology ; Adolescent ; Adult ; Adult Stem Cells/cytology/*metabolism ; Aged ; CpG Islands/*genetics ; *DNA Methylation ; Female ; Gene Expression Profiling ; Humans ; Male ; Middle Aged ; Polymerase Chain Reaction ; Stomach/cytology/*metabolism ; Stromal Cells/metabolism ; Transcription Initiation Site ; Transcription, Genetic