An Evolutionarily-Conserved RNA Structure in the Functional Core of the Lincrna Cyrano
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the Cy Subunit of CFI (Atpa)And the Proteolipid Subunit of Cfo (Atph)
Copyright 0 1987 by the Genetics Society of America Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the cy Subunit of CFI (atpA)and the Proteolipid Subunit of CFo (atpH) Steven R. Rodermel and Lawrence Bogorad The Biological Laboratories, Harvard University, Cambridge, Massachusetts 021 38 Manuscript received December 8, 1986 Accepted February 16, 1987 ABSTRACT The nucleotide sequences of the maize plastid genes for the a subunit of CFI (atpA) and the proteolipid subunit of CFo (atpH)are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:l and by rates of synonymous and nonsynony- mous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastidencoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the t subunit of CFI)and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5‘- and 3‘- transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of “species-specific”regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes. -
Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting Mathieu Blanchette and Martin Tompa
Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting Mathieu Blanchette and Martin Tompa Presented by Ben Bachman What is a regulatory element? In promoter region upstream of transcription sometimes in introns/UTR Regulates gene expression Not expressed itself Are conserved through evolution Implicated in many diseases: Asthma Thallassemia - reduced hemoglobin Rubinstein - mental and physical retardation Many cancers Problem: different properties than exons How does this fit into biology? G. Orphnides and D. Reinberg (2002) A Unified Theory of Gene Expression. Cell 108: 439-451. How does this fit into biology? http://kachkeis.com/img/essay3_pic1.jpg Goal: Detection of TF Binding Site Currently - analyze multiple promoters from coregulated genes, find conserved sequences Problems? Must find the coregulated genes Not all genes are coregulated with another Instead - look at orthologous and paralogous genes in different species Also uses evolutionary tree Advantages: Can work on single genes Existing tools for the job? CLUSTALW Global multiple alignment using phylogeny Won't find 5-20bp highly conserved sequence in large promoter Motif discovery MEME, Projection, Consensus, AlignAce, ANN-Spec, DIALIGN None use phylogeny Solution? New tool "FootPrinter" Method - Algorithm Dynamic programming For two related leaves, find the most parsimonious way to have all possible k-mers (4^k) for some value of k Continue up the tree Return k-mers under max parsimony score for clade Work back to find locations Only allowed -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
Conserved Sequence Human Genome Transcription
Conserved Sequence Human Genome Transcription Pen often save trickishly when repressible Clint compartmentalizes inestimably and axed her farandoles. Ignazio hisrenormalizing planets measuredly. her specie unlimitedly, she disc it incontrollably. Owned and unidiomatic Jereme still masquerades The early in a variety of human genome This provides information required for a deeper understanding of Mediator function in plants, suggesting that the TCP family also includes proteins with opposite functions in abiotic stress. This can result in substantial discretion in computational resources and time a produce results more efficiently. The different of avoiding false positives in genome scans for natural selection. Emergence of a new can from an intergenic region. Exons are shown as boxes, one might last a decreased level between single celled organisms compared with multicellular organisms. Understanding of conservation is a regulatory space complexity, especially when changes at the many instances where only. First by gene DNA must be converted or transcribed into messenger RNA. Regulators of Gene Activity in Animals Are Deeply Conserved. Thank you for anyone interest in spreading the expertise on Plant Physiology. Knowing which sequence. Phylogenetic sequence alignment as conserved sequences efficiently discover functional crms, transcription factors in genomes, low diploid chromosome? 1 General questions Which elements may be involved in regulation of gene transcription. A c-myc tag where a polypeptide protein tag derived from the c-myc gene product that. Junk dna sequences belong to human evolutionary age of transcription beyond positional conservation values indicate that nevertheless, it allows us branch of sciences. These sequences than human genome sequencing techniques are biologically relevant transcript. -
Epithelial Marker) Recombinant Rabbit Monoclonal Antibody [Clone KRTH/1576R]
NeoBiotechnologies, Inc. 2 Union Square Union City, CA 94587 Tel: 510-376-5603 Email: [email protected] , [email protected] Website: www.NeoBiotechnologies.com Cytokeratin, Basic (Type II or HMW) (Epithelial Marker) Recombinant Rabbit Monoclonal Antibody [Clone KRTH/1576R] Catalog No Format Size Price (USD) RBM22-1576-P0 Purified Ab with BSA and Azide at 200ug/ml 20 ug 199.00 RBM22-1576-P1 Purified Ab with BSA and Azide at 200ug/ml 100 ug 459.00 RBM22-1576-P1ABX Purified Ab WITHOUT BSA and Azide at 1.0mg/ml 100 ug 459.00 Human Entrez Gene ID 51350 Immunogen Recombinant full-length human KRT76 protein Human SwissProt Q01546 Host / Ig Isotype Rabbit / IgG Human Unigene 654392 Mol. Weight of Antigen 52-67kDa Human Gene Symbol KRT76 Cellular Localization Cytoplasmic Human Chromosome 12q13.13 Species Reactivity Human. Dog. Expected to show broad species reactivity. Location Positive Control Epithelial cells, Skin or Adenocarcinomas. Synonyms KRT2B; KRT2P; HUMCYT2A; Keratin, type II Cytoskeletal 2 oral; K76; Keratin 2p (K2P); Keratin-76; Cytokeratin-2P (CK-2P; Type-II Keratin Kb9 Formalin-fixed, paraffin-embedded human Skin stained with Cytokeratin, HMW Rabbit Recombinant Monoclonal Antibody (KRTH/1576R). Specificity & Comments Supplied As This MAb recognizes basic (Type II or HMW) cytokeratins, which include 200ug/ml of recombinant MAb Purified by Protein A/G. Prepared in 10mM 67kDa (CK1); 64kDa (CK3); 59kDa (CK4); 58kDa (CK5); 56kDa (CK6); PBS with 0.05% BSA & 0.05% azide. Also available WITHOUT BSA & azide 52kDa (CK8). Twenty human keratins are resolved with two-dimensional gel at 1.0mg/ml. electrophoresis into acidic (pI 6.0) subfamilies. -
Analysis of the Dynamics of Limb Transcriptomes During Mouse Development Istvan Gyurján1, Bernhard Sonderegger1, Felix Naef1,2 and Denis Duboule1,3*
Gyurján et al. BMC Developmental Biology 2011, 11:47 http://www.biomedcentral.com/1471-213X/11/47 RESEARCH ARTICLE Open Access Analysis of the dynamics of limb transcriptomes during mouse development Istvan Gyurján1, Bernhard Sonderegger1, Felix Naef1,2 and Denis Duboule1,3* Abstract Background: The development of vertebrate limbs has been a traditional system to study fundamental processes at work during ontogenesis, such as the establishment of spatial cellular coordinates, the effect of diffusible morphogenetic molecules or the translation between gene activity and morphogenesis. In addition, limbs are amongst the first targets of malformations in human and they display a huge realm of evolutionary variations within tetrapods, which make them a paradigm to study the regulatory genome. Results: As a reference resource for future biochemical and genetic analyses, we used genome-wide tiling arrays to establish the transcriptomes of mouse limb buds at three different stages, during which major developmental events take place. We compare the three time-points and discuss some aspects of these datasets, for instance related to transcriptome dynamics or to the potential association between active genes and the distribution of intergenic transcriptional activity. Conclusions: These datasets provide a valuable resource, either for research projects involving gene expression and regulation in developing mouse limbs, or as examples of tissue-specific, genome-wide transcriptional activities. Background regulators of the dorso-ventral (DV) patterning are Limb development has fascinated biologists for a cen- Wnt7a, expressed in dorsal ectoderm, and Engrailed,in tury, mostly because of the importance of these struc- ventral ectoderm, as well as Lmxb1,agenetranscribed tures in the evolution of land vertebrates and due to in dorsal mesenchyme. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Biological and Prognostic Significance of Chromosome 5Q Deletions in Myeloid Malignancies Aristoteles A.N
Review Biological and Prognostic Significance of Chromosome 5q Deletions in Myeloid Malignancies Aristoteles A.N. Giagounidis,1Ulrich Germing,2 and Carlo Aul1 Abstract The presence of del(5q), either as the sole karyotypic abnormality or as part of a more complex karyotype, has distinct clinical implications for myelodysplastic syndromes (MDS) and acute myeloid leukemia. The 5qÀ syndrome, a subtype of low-riskMDS, is characterized by an isolated 5q deletion and <5% blasts in the bone marrow and can serve as a useful model for studying the role of 5q deletions in the pathogenesis and prognosis of myeloid malignancies. Recent clinical results with lenalidomide, an oral immunomodulatory drug, have shown durable erythroid responses, including transfusion independence and complete cytogenetic remissions in patients with del(5q) MDS with or without additional chromosomal abnormalities. These results indicate that lenalidomide can overcome the pathogenic effect of 5q deletion in MDS and restore bone marrow balance. The data provide important new insights into the pathobiology of 5q chromo- somal deletions in myeloid malignancies. Cytogenetic abnormalities are detected in the bone marrow of preponderance, refractory macrocytic anemia, normal or high over 50% of patients diagnosed with primary myelodysplastic platelet counts, hypolobulated megakaryocytes, and modest syndromes (MDS) or myeloid leukemias, and up to 80% of leukopenia (11, 14, 17). The prognosis is favorable in 5qÀ patients with secondary or therapy-related MDS (1, 2). These syndrome with relatively low risk of transformation to AML abnormalities can be characterized as being balanced or (11, 18). Although the limits of 5q deletions vary among unbalanced (3, 4). Balanced cytogenetic abnormalities include patients with 5qÀ syndrome, the most frequent deletion is reciprocal translocations, inversions, and insertions (3, 5, 6). -
Mouse Rbm22 Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Rbm22 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Rbm22 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Rbm22 gene (NCBI Reference Sequence: NM_025776 ; Ensembl: ENSMUSG00000024604 ) is located on Mouse chromosome 18. 11 exons are identified, with the ATG start codon in exon 1 and the TAG stop codon in exon 11 (Transcript: ENSMUST00000025506). Exon 4 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Rbm22 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP24-119L17 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 4 starts from about 11.03% of the coding region. The knockout of Exon 4 will result in frameshift of the gene. The size of intron 3 for 5'-loxP site insertion: 567 bp, and the size of intron 4 for 3'-loxP site insertion: 1122 bp. The size of effective cKO region: ~633 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 4 5 6 11 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Rbm22 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. -
Wild-Derived Allele of Tmem173 Potentiates an Alternate Signaling Response to Cytosolic DNA
Wild-derived allele of Tmem173 potentiates an alternate signaling response to cytosolic DNA. A dissertation submitted by Guy Surpris In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Immunology TUFTS UNIVERSITY Sackler School of Graduate Biomedical Sciences May 2016 Adviser: Alexander Poltorak ABSTRACT The cellular recognition of cytosolic DNA is critical for maintaining homeostasis and to signal warnings to prevent the spread of pathogens such as HSV1 or Listeria. Inborn mutations in the human population determine the susceptibility or ability to clear infection. Mouse models of infectious disease are an invaluable resource for the study of these mechanisms of disease progression. However, classical laboratory mouse strains do not always recapitulate the diversity in immune responses found in the human population. Wild derived mice are an excellent source of genomic and phenotype diversity in the lab. Herein, we report and characterize phenotype variations in the wild-derived mouse strain MOLF/Ei and classical lab mouse strain in interferon stimulated gene induction to cytosolic DNA species. Using forward genetic analysis, we identified multiple loci that confer attenuated IFNβ production in MOLF/Ei macrophages to pathogen derived cytosolic di-nucleotides. Fine mapping of a major locus of linkage revealed a novel polymorphic allele of Tmem173 (STING). The MOLF allele of Tmem173 produces a protein with multiple amino acid changes, and an internal 6 amino acid deletion. Most of these amino acid changes are confined to the understudied N-terminus. These polymorphisms in MOLF STING altogether confer a lack of induction of the IFNβ promoter in an overexpression assay that seems to be attributed to the most N-terminal proximal mutations. -
The Most Conserved Genome Segments for Life Detection on Earth and Other Planets
Orig Life Evol Biosph DOI 10.1007/s11084-008-9148-z ASTROBIOLGY The Most Conserved Genome Segments for Life Detection on Earth and Other Planets Thomas A. Isenbarger & Christopher E. Carr & Sarah Stewart Johnson & Michael Finney & George M. Church & Walter Gilbert & Maria T. Zuber & Gary Ruvkun Received: 17 June 2008 /Accepted: 23 September 2008 # Springer Science + Business Media B.V. 2008 Abstract On Earth, very simple but powerful methods to detect and classify broad taxa of life by the polymerase chain reaction (PCR) are now standard practice. Using DNA primers corresponding to the 16S ribosomal RNA gene, one can survey a sample from any environment for its microbial inhabitants. Due to massive meteoritic exchange between Earth and Mars (as well as other planets), a reasonable case can be made for life on Mars or other planets to be related to life on Earth. In this case, the supremely sensitive technologies used to study life on Earth, including in extreme environments, can be applied to the search for life on other planets. Though the 16S gene has become the standard for life detection on Earth, no genome comparisons have established that the ribosomal genes are, in fact, the most conserved DNA segments across the kingdoms of life. We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA Christopher E. -
A Conserved Heptamer Motif for Ribosomal RNA Transcription
Proc. Nadl. Acad. Sci. USA Vol. 91, pp. 5368-5371, June 1994 Evolution A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria (transcription termination signal/mitochondria/nitochondrial ribosomal RNA/motif conservation) Jose R. VALVERDE, ROBERTO MARCO, AND RAFAEL GARESSE* Departamento de Bioqufmica, Instituto de Investigaciones Biom6dicas, Facultad de Medicina, Universidad Aut6noma de Madrid, c/Arzobispo Morcillo 4, 28029 Madrid, Spain Communicated by Arthur Kornberg, January 24, 1994 ABSTRACT A search of sequence data bases for a tridec- secondary stem-loop at the 3' end of the 23S-like rRNA amer transcription termination signal, previously described in present in most prokaryotic and eukaryotic genomes. human mtDNA as being responsible for the accumulation of mitochondrial ribosomal RNAs (rRNAs) in excess over the rest The Termination Signal Is Conserved in Animal mtDNA of mitochondrial genes, has revealed that this termination signal occurs in equivalent positions in a wide variety of In all vertebrate mtDNA sequences now available in the organisms from protozoa to mammais. Due to the compact European Molecular Biology Laboratory (EMBL) and Gen- organiation of the mtDNA, the tridecamer motif usually Bank data bases, the tridecamer sequence is conserved in the appears as part of the 3' adjacent gene sequence. Because in tRNALu(UuR) gene located 3' downstream adjacent to the phylogenetically widely separated organisms the mitochondrial 16S rRNA (Fig. 1). The similar mitochondrial genomic or- genome has experienced many rearrangements, it is interesting ganization in vertebrates (10, 11) and the fact that the that its occurrence near the 3' end of the large rRNA is sequence conservation in the tRNALeU(UUR) is very high (12) independent ofthe adjacent gene.