TY - JOUR T1 - Genomic variation. Impact of regulatory variation from RNA to protein. JF - Science Y1 - 2015 A1 - Battle, Alexis A1 - Khan, Zia A1 - Wang, Sidney H A1 - Mitrano, Amy A1 - Ford, Michael J A1 - Pritchard, Jonathan K A1 - Gilad, Yoav KW - 3' Flanking Region KW - 5' Flanking Region KW - Cell Line KW - Exons KW - Gene Expression Regulation KW - Genetic Variation KW - HUMANS KW - PHENOTYPE KW - Protein Biosynthesis KW - Quantitative Trait Loci KW - Ribosomes KW - RNA, Messenger KW - Transcription, Genetic AB -

The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation.

VL - 347 CP - 6222 M3 - 10.1126/science.1260793 ER - TY - JOUR T1 - Primate transcript and protein expression levels evolve under compensatory selection pressures. JF - Science Y1 - 2013 A1 - Khan, Zia A1 - Ford, Michael J A1 - Cusanovich, Darren A A1 - Mitrano, Amy A1 - Pritchard, Jonathan K A1 - Gilad, Yoav KW - Animals KW - Evolution, Molecular KW - Gene Expression Regulation KW - HUMANS KW - Macaca mulatta KW - Pan troglodytes KW - Protein Biosynthesis KW - RNA, Messenger KW - Selection, Genetic KW - Species Specificity KW - Transcription, Genetic AB -

Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.

VL - 342 CP - 6162 M3 - 10.1126/science.1242379 ER - TY - JOUR T1 - The genome and its implications. JF - Adv Parasitol Y1 - 2011 A1 - Teixeira, Santuza M A1 - El-Sayed, Najib M A1 - Araújo, Patrícia R KW - Animals KW - Antigens, Protozoan KW - Chagas Disease KW - Chromosomes KW - Comparative Genomic Hybridization KW - DNA, Protozoan KW - Gene Expression Regulation KW - Genetic Variation KW - Genome, Protozoan KW - Host-Parasite Interactions KW - HUMANS KW - Species Specificity KW - Synteny KW - Transcription, Genetic KW - Transfection KW - Trypanosoma cruzi AB -

Trypanosoma cruzi has a heterogeneous population composed of a pool of strains that circulate in the domestic and sylvatic cycles. Genome sequencing of the clone CL Brener revealed a highly repetitive genome of about 110Mb containing an estimated 22,570 genes. Because of its hybrid nature, sequences representing the two haplotypes have been generated. In addition, a repeat content close to 50% made the assembly of the estimated 41 pairs of chromosomes quite challenging. Similar to other trypanosomatids, the organization of T. cruzi chromosomes was found to be very peculiar, with protein-coding genes organized in long polycistronic transcription units encoding 20 or more proteins in one strand separated by strand switch regions. Another remarkable feature of the T. cruzi genome is the massive expansion of surface protein gene families. Because of the high genetic diversity of the T. cruzi population, sequencing of additional strains and comparative genomic and transcriptome analyses are in progress. Five years after its publication, the genome data have proven to be an essential tool for the study of T. cruzi and increasing efforts to translate this knowledge into the development of new modes of intervention to control Chagas disease are underway.

VL - 75 M3 - 10.1016/B978-0-12-385863-4.00010-1 ER - TY - JOUR T1 - Genome-wide analysis reveals novel genes essential for heme homeostasis in Caenorhabditis elegans. JF - PLoS Genet Y1 - 2010 A1 - Severance, Scott A1 - Rajagopal, Abbhirami A1 - Rao, Anita U A1 - Cerqueira, Gustavo C A1 - Mitreva, Makedonka A1 - El-Sayed, Najib M A1 - Krause, Michael A1 - Hamza, Iqbal KW - Animals KW - Caenorhabditis elegans KW - Dose-Response Relationship, Drug KW - Gene Expression Profiling KW - Gene Expression Regulation KW - genes KW - Genome-Wide Association Study KW - Heme KW - Homeostasis KW - HUMANS KW - Leishmania KW - Nematoda KW - Trypanosoma AB -

Heme is a cofactor in proteins that function in almost all sub-cellular compartments and in many diverse biological processes. Heme is produced by a conserved biosynthetic pathway that is highly regulated to prevent the accumulation of heme--a cytotoxic, hydrophobic tetrapyrrole. Caenorhabditis elegans and related parasitic nematodes do not synthesize heme, but instead require environmental heme to grow and develop. Heme homeostasis in these auxotrophs is, therefore, regulated in accordance with available dietary heme. We have capitalized on this auxotrophy in C. elegans to study gene expression changes associated with precisely controlled dietary heme concentrations. RNA was isolated from cultures containing 4, 20, or 500 microM heme; derived cDNA probes were hybridized to Affymetrix C. elegans expression arrays. We identified 288 heme-responsive genes (hrgs) that were differentially expressed under these conditions. Of these genes, 42% had putative homologs in humans, while genomes of medically relevant heme auxotrophs revealed homologs for 12% in both Trypanosoma and Leishmania and 24% in parasitic nematodes. Depletion of each of the 288 hrgs by RNA-mediated interference (RNAi) in a transgenic heme-sensor worm strain identified six genes that regulated heme homeostasis. In addition, seven membrane-spanning transporters involved in heme uptake were identified by RNAi knockdown studies using a toxic heme analog. Comparison of genes that were positive in both of the RNAi screens resulted in the identification of three genes in common that were vital for organismal heme homeostasis in C. elegans. Collectively, our results provide a catalog of genes that are essential for metazoan heme homeostasis and demonstrate the power of C. elegans as a genetic animal model to dissect the regulatory circuits which mediate heme trafficking in both vertebrate hosts and their parasites, which depend on environmental heme for survival.

VL - 6 CP - 7 M3 - 10.1371/journal.pgen.1001044 ER - TY - JOUR T1 - Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. JF - PLoS Pathog Y1 - 2007 A1 - Bringaud, Frederic A1 - Müller, Michaela A1 - Cerqueira, Gustavo Coutinho A1 - Smith, Martin A1 - Rochette, Annie A1 - el-Sayed, Najib M A A1 - Papadopoulou, Barbara A1 - Ghedin, Elodie KW - 3' Untranslated Regions KW - Animals KW - Base Sequence KW - Biological Evolution KW - Down-Regulation KW - Gene Expression Regulation KW - Genome, Protozoan KW - Leishmania KW - Leishmania major KW - Molecular Sequence Data KW - Retroelements KW - RNA, Messenger KW - sequence alignment KW - Trypanosoma brucei brucei KW - Trypanosoma cruzi AB -

Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3'-untranslated regions (3'UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3'UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.

VL - 3 CP - 9 M3 - 10.1371/journal.ppat.0030136 ER - TY - JOUR T1 - Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics JF - Bioinformatics (Oxford, England)Bioinformatics (Oxford, England) Y1 - 2005 A1 - Haft, Daniel H. A1 - J. Selengut A1 - Brinkac, Lauren M. A1 - Zafar, Nikhat A1 - White, Owen KW - Chromosome mapping KW - database management systems KW - Databases, Genetic KW - documentation KW - Gene Expression Profiling KW - Gene Expression Regulation KW - Genomics KW - Information Storage and Retrieval KW - Microbiological Techniques KW - natural language processing KW - Prokaryotic Cells KW - Proteome KW - signal transduction KW - software KW - User-Computer Interface KW - Vocabulary, Controlled AB - MOTIVATION: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics. RESULTS: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl. VL - 21 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15347579?dopt=Abstract ER - TY - JOUR T1 - The transcription factor Eyes absent is a protein tyrosine phosphatase JF - NatureNature Y1 - 2003 A1 - Tootle, Tina L. A1 - Silver, Serena J. A1 - Davies, Erin L. A1 - Newman, Victoria A1 - Latek, Robert R. A1 - Mills, Ishara A. A1 - J. Selengut A1 - Parlikar, Beth E. W. A1 - Rebay, Ilaria KW - Amino Acid Motifs KW - Amino Acid Sequence KW - Animals KW - Antibodies, Phospho-Specific KW - Drosophila melanogaster KW - Drosophila Proteins KW - Embryonic Induction KW - eye KW - Eye Proteins KW - Gene Expression Regulation KW - Kinetics KW - Mice KW - Models, Molecular KW - Molecular Sequence Data KW - Mutation KW - Phosphorylation KW - Protein Conformation KW - Protein Tyrosine Phosphatases KW - Substrate Specificity KW - Transcription Factors AB - Post-translational modifications provide sensitive and flexible mechanisms to dynamically modulate protein function in response to specific signalling inputs. In the case of transcription factors, changes in phosphorylation state can influence protein stability, conformation, subcellular localization, cofactor interactions, transactivation potential and transcriptional output. Here we show that the evolutionarily conserved transcription factor Eyes absent (Eya) belongs to the phosphatase subgroup of the haloacid dehalogenase (HAD) superfamily, and propose a function for it as a non-thiol-based protein tyrosine phosphatase. Experiments performed in cultured Drosophila cells and in vitro indicate that Eyes absent has intrinsic protein tyrosine phosphatase activity and can autocatalytically dephosphorylate itself. Confirming the biological significance of this function, mutations that disrupt the phosphatase active site severely compromise the ability of Eyes absent to promote eye specification and development in Drosophila. Given the functional importance of phosphorylation-dependent modulation of transcription factor activity, this evidence for a nuclear transcriptional coactivator with intrinsic phosphatase activity suggests an unanticipated method of fine-tuning transcriptional regulation. VL - 426 N1 - http://www.ncbi.nlm.nih.gov/pubmed/14628053?dopt=Abstract ER - TY - JOUR T1 - Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression. JF - Exp Parasitol Y1 - 2002 A1 - Bartholomeu, Daniella C A1 - Silva, Rosiane A A1 - Galvão, Lucia M C A1 - el-Sayed, Najib M A A1 - Donelson, John E A1 - Teixeira, Santuza M R KW - Animals KW - Base Sequence KW - Blotting, Northern KW - DNA, Complementary KW - DNA, Protozoan KW - Gene Expression Regulation KW - Half-Life KW - Life Cycle Stages KW - Molecular Sequence Data KW - RNA Processing, Post-Transcriptional KW - RNA, Messenger KW - RNA, Protozoan KW - Transcription, Genetic KW - Transfection KW - Trypanosoma cruzi KW - Tubulin AB -

Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of alpha- and beta-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two beta-tubulin mRNAs of 1.9 and 2.3 kb were found to differ mainly by an additional 369 nucleotides at the end of the 3' untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, alpha- and beta-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of alpha- and beta-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3' UTR plus downstream intergenic region of the alpha-tubulin gene and that both positive and negative elements occur in the equivalent regions of the beta-tubulin gene.

VL - 102 CP - 3-4 ER - TY - JOUR T1 - Drosophila melanogaster genes for U1 snRNA variants and their expression during development. JF - Nucleic Acids Res Y1 - 1990 A1 - Lo, P C A1 - Mount, S M KW - Animals KW - Base Sequence KW - Blotting, Southern KW - Cloning, Molecular KW - Drosophila melanogaster KW - Gene Expression Regulation KW - genes KW - Genetic Variation KW - Molecular Sequence Data KW - Nucleic Acid Conformation KW - Pseudogenes KW - Restriction Mapping KW - RNA, Small Nuclear AB -

We have cloned and characterized a complete set of seven U1-related sequences from Drosophila melanogaster. These sequences are located at the three cytogenetic loci 21D, 82E, and 95C. Three of these sequences have been previously studied: one U1 gene at 21D which encodes the prototype U1 sequence (U1a), one U1 gene at 82E which encodes a U1 variant with a single nucleotide substitution (U1b), and a pseudogene at 82E. The four previously uncharacterized genes are another U1b gene at 82E, two additional U1a genes at 95C, and a U1 gene at 95C which encodes a new variant (U1c) with a distinct single nucleotide change relative to U1a. Three blocks of 5' flanking sequence similarity are common to all six full length genes. Using specific primer extension assays, we have observed that the U1b RNA is expressed in Drosophila Kc cells and is associated with snRNP proteins, suggesting that the U1b-containing snRNP particles are able to participate in the process of pre-mRNA splicing. We have also examined the expression throughout Drosophila development of the two U1 variants relative to the prototype sequence. The U1c variant is undetectable by our methods, while the U1b variant exhibits a primarily embryonic pattern reminiscent of the expression of certain U1 variants in sea urchin, Xenopus, and mouse.

VL - 18 CP - 23 ER - TY - JOUR T1 - Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. JF - Mol Cell Biol Y1 - 1985 A1 - Mount, S M A1 - Rubin, G M KW - Amino Acid Sequence KW - Animals KW - Base Sequence KW - Codon KW - DNA Helicases KW - DNA Transposable Elements KW - Drosophila melanogaster KW - Gene Expression Regulation KW - Gene Products, gag KW - Integrases KW - Repetitive Sequences, Nucleic Acid KW - Retroviridae KW - RNA-Directed DNA Polymerase KW - Viral Envelope Proteins KW - Viral Proteins AB -

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

VL - 5 CP - 7 ER -