Tissue-enriched Transcription Research Articles

TEnGExA: an R package based tool for tissue enrichment and gene expression analysis.

RNA-seq data analysis with rapidly advancing high-throughput sequencing technology, nowadays provides large number of transcripts or genes to perform downstream analysis including functional annotation and pathway analysis. However for the data from multiple tissues, downstream analysis with tissue-specific or tissue-enriched transcripts is highly preferable. However, there is still a need of tool for quickly performing tissue-enrichment and gene expression analysis irrespective of number of input genes or tissues at various fragments per kilobase of transcript per million fragments mapped (FPKM) thresholds. To fulfill this need, we presented a freely available R package and web-interface tool, TEnGExA, which allows tissue-enrichment analysis (TEA) for any number of genes or transcripts for any species provided only a read-count or FPKM-value matrix as input. Based on the different FPKM value and fold thresholds, TEnGExA classifies the user provided gene lists into tissue-enriched or tissue-specific transcripts along with other standard classes. By analyzing the published sample data from human, plant and microorganism, we signifies that TEnGExA can easily handle complex or large data from any species to provided tissue-enriched gene list for downstream analysis in quick time. In summary, TEnGExA is quick, easy to use and an efficient tool for TEA. The R package is freely available at https://github.com/ubagithub/TEnGExA/ and the GUI web interface is accessible at http://webtom.cabgrid.res.in/tissue_enrich/.

Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

BackgroundAgropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies.ResultsSingle-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035.ConclusionsFull-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.

Integrated Epigenetic Mapping of Human and Mouse Salivary Gene Regulation

Significant effort has been applied to identify the genome-wide gene expression profiles associated with salivary gland development and pathophysiology. However, relatively little is known about the regulators that control salivary gland gene expression. We integrated data from DNase1 digital genomic footprinting, RNA-seq, and gene expression microarrays to comprehensively characterize the cis- and trans-regulatory components controlling gene expression of the healthy submandibular salivary gland. Analysis of 32 human tissues and 87 mouse tissues was performed to identify the highly expressed and tissue-enriched transcription factors driving salivary gland gene expression. Following RNA analysis, protein expression levels and subcellular localization of 39 salivary transcription factors were confirmed by immunohistochemistry. These expression analyses revealed that the salivary gland highly expresses transcription factors associated with endoplasmic reticulum stress, human T-cell lymphotrophic virus 1 expression, and Epstein-Barr virus reactivation. DNase1 digital genomic footprinting to a depth of 333,426,353 reads was performed and utilized to generate a salivary gland gene regulatory network describing the genome-wide chromatin accessibility and transcription factor binding of the salivary gland at a single-nucleotide resolution. Analysis of the DNase1 gene regulatory network identified dense interconnectivity among PLAG1, MYB, and 13 other transcription factors associated with balanced chromosomal translocations and salivary gland tumors. Collectively, these analyses provide a comprehensive atlas of the cis- and trans-regulators of the salivary gland and highlight known aberrantly regulated pathways of diseases affecting the salivary glands.

Deep Sequencing Analysis of the Ixodes ricinus Haemocytome

Background Ixodes ricinus is the main tick vector of the microbes that cause Lyme disease and tick-borne encephalitis in Europe. Pathogens transmitted by ticks have to overcome innate immunity barriers present in tick tissues, including midgut, salivary glands epithelia and the hemocoel. Molecularly, invertebrate immunity is initiated when pathogen recognition molecules trigger serum or cellular signalling cascades leading to the production of antimicrobials, pathogen opsonization and phagocytosis. We presently aimed at identifying hemocyte transcripts from semi-engorged female I. ricinus ticks by mass sequencing a hemocyte cDNA library and annotating immune-related transcripts based on their hemocyte abundance as well as their ubiquitous distribution.Methodology/principal findings De novo assembly of 926,596 pyrosequence reads plus 49,328,982 Illumina reads (148 nt length) from a hemocyte library, together with over 189 million Illumina reads from salivary gland and midgut libraries, generated 15,716 extracted coding sequences (CDS); these are displayed in an annotated hyperlinked spreadsheet format. Read mapping allowed the identification and annotation of tissue-enriched transcripts. A total of 327 transcripts were found significantly over expressed in the hemocyte libraries, including those coding for scavenger receptors, antimicrobial peptides, pathogen recognition proteins, proteases and protease inhibitors. Vitellogenin and lipid metabolism transcription enrichment suggests fat body components. We additionally annotated ubiquitously distributed transcripts associated with immune function, including immune-associated signal transduction proteins and transcription factors, including the STAT transcription factor.Conclusions/significanceThis is the first systems biology approach to describe the genes expressed in the haemocytes of this neglected disease vector. A total of 2,860 coding sequences were deposited to GenBank, increasing to 27,547 the number so far deposited by our previous transcriptome studies that serves as a discovery platform for studies with I. ricinus biochemistry and physiology.

MiR-125b, a Target of CDX2, Regulates Cell Differentiation through Repression of the Core Binding Factor in Hematopoietic Malignancies

MicroRNA-125b (miR-125b), a small noncoding RNA molecule, has been found to be deregulated and functions as an oncogene in many cancers including hematopoietic malignancies. However, the mechanisms accounting for miR-125b dysregulation remain to be elucidated. The present study aims to identify the factors that might contribute to up-regulation of miR-125b in human hematopoietic malignancies and its downstream targets for lineage-specific differentiation. We at first reported that CDX2, a homeobox transcription factor, binds to promoter regions of the miR-125b gene and activates transcriptional regulation of miR-125b in malignant myeloid cells. We further revealed that increasing levels of CDX2 in malignant myeloid cells activate miR-125b expression, which in turn inhibits core binding factor β (CBFβ) translation, thereby counteracting myeloid cell differentiation, at least for granulocytic lineage, and promoting leukemogenesis. Interestingly, we found that this novel pathway including CDX2, miR-125b, and CBFβ was mediated by undergoing all-trans-retinoic acid induction. Once differentiation ensues with all-trans-retinoic acid treatment, CDX2 activity decreases, leading to a reduction in miR-125b transcription and up-regulation of CBFβ in myeloid cells and in patients. The study provides a new mechanism that contributes to hematopoietic malignancies, which could involve deregulation of miR-125b and its up- and downstream factors. As altered expression of miRNAs has been reported in a wide range of malignancies, delineating the underlying molecular mechanisms of aberrant miRNA expression and characterizing the upstream and downstream factors will help to understand important steps in the pathogenesis of these afflictions.

Positive Role of CCAAT/Enhancer-Binding Protein Homologous Protein, a Transcription Factor Involved in the Endoplasmic Reticulum Stress Response in the Development of Colitis

Although recent reports suggest that the endoplasmic reticulum (ER) stress response is induced in association with the development of inflammatory bowel disease, its role in the pathogenesis of inflammatory bowel disease remains unclear. The CCAAT/enhancer-binding protein (C/EBP) homologous protein (CHOP) is a transcription factor that is involved in the ER stress response, especially ER stress-induced apoptosis. In this study, we found that experimental colitis was ameliorated in CHOP-null mice, suggesting that CHOP exacerbates the development of colitis. The mRNA expression of Mac-1 (CD11b, a positive regulator of macrophage infiltration), Ero-1alpha, and Caspase-11 (a positive regulator of interleukin-1beta production) in the intestine was induced with the development of colitis, and this induction was suppressed in CHOP-null mice. ERO-1alpha is involved in the production of reactive oxygen species (ROS); an increase in ROS production, which is associated with the development of colitis in the intestine, was suppressed in CHOP-null mice. A greater number of apoptotic cells in the intestinal mucosa of wild-type mice were observed to accompany the development of colitis compared with CHOP-null mice, suggesting that up-regulation of CHOP expression exacerbates the development of colitis. Furthermore, this CHOP activity appears to involve various stimulatory mechanisms, such as macrophage infiltration via the induction of Mac-1, ROS production via the induction of ERO-1alpha, interleukin-1beta production via the induction of Caspase-11, and intestinal mucosal cell apoptosis.

Robert H. Costa: In Memoriam (1957-2006)

Robert Henry (Rob) Costa, an authority on liver biology and cancer, died on September 1, 2006 at his home in Oak Park, IL. Rob was born in Galesburg, IL and grew up in Bethesda, MD. He attended the University of California at Irvine, where he received his doctorate in Molecular Virology in 1985 under the guidance of Dr. Edward K. Wagner. Rob characterized several genes encoded by the type I herpes simplex virus at a time when many techniques of molecular biology were still in their infancy. Rob was instrumental in identifying the viral transcripts, including the late genes, which are important in the viral life cycle.In 1985, Rob joined the laboratory of Dr. James E. Darnell, Jr. at the Rockefeller University for postdoctoral training. At that time, the Darnell laboratory was testing the hypothesis that tissue-enriched transcription factors were responsible for tissue-specific gene expression and tissue development. Rob, along with two other colleagues, Drs. Eseng Lai and Dennis R. Grayson, characterized the promoter region of the mouse prealbumin gene, which is mainly expressed in the liver. More importantly, Rob and colleagues discovered and characterized several liver-enriched transcription factors, including HNF3s or FoxAs, some of which were later shown to be also critical for mammalian development. These studies provided insights into mechanisms for liver-specific gene expression and laid the foundation of our current understanding of liver development.Rob joined the Northwestern University Medical School as an Assistant Professor in 1988. In 1989, he moved to the University of Illinois at Chicago where he rose to the rank of professor of biochemistry and molecular genetics. Throughout his career, Rob believed in digging deep for new information with cutting edge technologies. He was an imaginative thinker and was passionate about the process of discovery. He would leave the comfort zone and apply novel approaches much more easily than many of us. He was always generous with his time, reagents, and thoughtful advice. He exuded energy and enthusiasm, making his presence felt in a very positive way.Rob directed a vigorous research program. His laboratory identified a number of the fork-head family of genes that play key roles in liver-specific gene expression. Among his many contributions is the discovery of FoxM1b, a critical gene that is essential for liver development and liver cell proliferation. He showed that increasing the expression of FoxM1b in liver cells of aged mice make them behave as though they were cells in young mice, thereby restoring the proliferation potential of juveniles in aged animals. This work was published in the Proceedings of the National Academy of Science in 2002 and featured in ASBMB Today in the February, 2003 issue. His laboratory showed that FoxM1b plays a crucial role in mammalian cell division by stimulating expression of genes necessary for cell cycle progression. Several genes that regulate G2-M progression are critically dependent on FoxM1b, and cells lacking FoxM1b fail to enter M phase.More recently, Rob's laboratory showed that expression of FoxM1b is essential for the development of liver cancer. Conditional deletion of FoxM1b in the liver rendered mice refractory to hepatocellular carcinoma (HCC) development following treatment with DEN/Phenobarbital, which causes HCC in littermates expressing normal level of FoxM1b. His laboratory also discovered that FoxM1b is a target of the tumor suppressor ARF. This work was published in Genes & Development in 2004. Based on these studies, he pioneered a new approach to treat liver cancer by using small molecules derived from ARF to disrupt the function of FoxM1b. This new approach is currently under development.Widely regarded as a star in the liver field, Rob was a leading authority in the molecular analysis of liver biology and cell proliferation. He organized several prestigious national conferences on liver gene expression and development and chaired scientific sessions at major international conferences in the United States and Europe. He served as an editorial board member and peer reviewer for several prestigious journals, including Hepatology, The Journal Biological Chemistry and several of the AACR journals. In addition, Rob sat on numerous review panels for the NIH.A respected innovator and beloved colleague, Rob trained numerous graduate students and postdocs and helped mentor many junior faculty members. In February, 2006, he was diagnosed with stage IV pancreatic cancer with liver and bone metastases. Rob battled his illness heroically with uncommon courage, grace, and fortitude. He never gave up hope or his sense of humor, and he continued to work assiduously while undergoing chemotherapy. His wife Jane and son Sam, the anchors of his life, made it possible for him to stay optimistic. His death at the height of his career is a tragic loss to science and the scientific community. In him, we will remember an outstanding scientist, a loyal friend, an exemplary mentor, and a fine human being. We will miss him greatly.

GATA-4 and Nkx-2.5 coactivate Nkx-2 DNA binding targets: role for regulating early cardiac gene expression.

The cardiogenic homeodomain factor Nkx-2.5 and serum response factor (SRF) provide strong transcriptional coactivation of the cardiac alpha-actin (alphaCA) promoter in fibroblasts (C. Y. Chen and R. J. Schwartz, Mol. Cell. Biol. 16:6372-6384, 1996). We demonstrate here that Nkx-2.5 also cooperates with GATA-4, a dual C-4 zinc finger transcription factor expressed in early cardiac progenitor cells, to activate the alphaCA promoter and a minimal promoter, containing only multimerized Nkx-2.5 DNA binding sites (NKEs), in heterologous CV-1 fibroblasts. Transcriptional activity requires the N-terminal activation domain of Nkx-2.5 and Nkx-2.5 binding activity through its homeodomain but does not require GATA-4's activation domain. The minimal interactive regions were mapped to the homeodomain of Nkx-2.5 and the second zinc finger of GATA-4. Removal of Nkx-2.5's C-terminal inhibitory domain stimulated robust transcriptional activity, comparable to the effects of GATA-4 on wild-type Nkx-2.5, which in part facilitated Nkx-2.5 DNA binding activity. We postulate the following simple model: GATA-4 induces a conformational change in Nkx-2.5 that displaces the C-terminal inhibitory domain, thus eliciting transcriptional activation of promoters containing Nkx-2.5 DNA binding targets. Therefore, alphaCa promoter activity appears to be regulated through the combinatorial interactions of at least three cardiac tissue-enriched transcription factors, Nkx-2.5, GATA-4, and SRF.

Determination of tissue specificity of the enhancer by combinatorial operation of tissue-enriched transcription factors. Both HNF-4 and C/EBP beta are required for liver-specific activity of the ornithine transcarbamylase enhancer.

The enhancer of the rat ornithine transcarbamylase gene is located 11 kilobases upstream from the transcription start site and has been shown to be hepatoma cell-specific. Using transgenic mice, we showed that this enhancer is capable of activating transcription in a liver-specific manner, inverting the tissue specificity of the homologous promoter that is by itself more active in the small intestine than in the liver. Transient transfection analysis with cultured hepatoma cells indicated that the enhancer activity resides in the approximately 110-base pair region containing four protein-binding sites, two for hepatocyte nuclear factor-4 (HNF-4) and two for CCAAT/enhancer binding protein (C/EBP), both of which are liver-selective transcription factors. Concatemerization of a region containing one HNF-4 and one C/EBP site led to reconstitution of the hepatoma cell-specific enhancer, and intactness of these two sites was strictly required for the enhancer activity. Furthermore, cotransfection experiments showed that both HNF-4 and C/EBP beta are necessary, and neither alone sufficient, for activation of the reconstituted enhancer in nonhepatic cells. Requirement of combinatorial operation of at least two liver-enriched transcription factors for transcriptional activation successfully explains why these liver-selective but not strictly liver-specific factors can confer more restricted liver specificity on transcription of their target genes.

Regulation of cytochrome P450 genes: molecular mechanisms.

The xenobiotic-metabolizing cytochrome P450s are found in the CYP1, CYP2, CYP3 and CYP4 subfamilies (Gonzalez, 1988). These P450s have been extensively studied in a number of organisms including bacteria, yeast, fish, chickens, rats, mice, rabbits and humans. The P450 genes are under control of diverse regulatory networks that govern their expression. These networks include foreign chemical receptors that activate gene expression through binding to inducible enhancer elements and tissue-enriched transcription factors that control constitutive expression. This review focuses on recent developments on the molecular mechanisms of P450 gene control.