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He, L., Dooner HK.  2009.  Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions. Proc. Natl. Acad. Sci. U.S.A.. 106:8410–8416. Abstract
We have asked here how the remarkable variation in maize haplotype structure affects recombination. We compared recombination across a genetic interval of 9S in 2 highly dissimilar heterozygotes that shared 1 parent. The genetic interval in the common haplotype is approximately 100 kb long and contains 6 genes interspersed with gene-fragment-bearing Helitrons and retrotransposons that, together, comprise 70% of its length. In one heterozygote, most intergenic insertions are homozygous, although polymorphic, enabling us to determine whether any recombination junctions fall within them. In the other, most intergenic insertions are hemizygous and, thus, incapable of homologous recombination. Our analysis of the frequency and distribution of recombination in the interval revealed that: (i) Most junctions were circumscribed to the gene space, where they showed a highly nonuniform distribution. In both heterozygotes, more than half of the junctions fell in the stc1 gene, making it a clear recombination hotspot in the region. However, the genetic size of stc1 was 2-fold lower when flanked by a hemizygous 25-kb retrotransposon cluster. (ii) No junctions fell in the hypro1 gene in either heterozygote, making it a genic recombination coldspot. (iii) No recombination occurred within the gene fragments borne on Helitrons nor within retrotransposons, so neither insertion class contributes to the interval's genetic length. (iv) Unexpectedly, several junctions fell in an intergenic region not shared by all 3 haplotypes. (v) In general, the ability of a sequence to recombine correlated inversely with its methylation status. Our results show that haplotypic structural variability strongly affects the frequency and distribution of recombination events in maize.
Li, Y., Dooner HK.  2012.  Helitron Proliferation and Gene-Fragment Capture. Topics in Current Genetics, 24: Plant Transposable Elements- Impact on Genome Structure and Function. :193-227.
Xiong, W, He L, Lai J, Dooner HK, Du C.  2014.  HelitronScanner uncovers a large overlooked cache of Helitron transposons in many genomes.. Proc. Natl. Acad. Sci. USA. DOI 10.1073/pnas.1410068111 AbstractWebsite
Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner’s predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5’ and 3’ termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by polymerase chain reaction (PCR) assays or by in-silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.
Lagrange, T, Kim TK, Orphanides G, Ebright YW, Ebright RH, Reinberg D.  1996.  High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex.. Proceedings of the National Academy of Sciences of the United States of America. 93(20):10620-5. Abstract
We have used a novel site-specific protein-DNA photocrosslinking procedure to define the positions of polypeptide chains relative to promoter DNA in binary, ternary, and quaternary complexes containing human TATA-binding protein, human or yeast transcription factor IIA (TFIIA), human transcription factor IIB (TFIIB), and promoter DNA. The results indicate that TFIIA and TFIIB make more extensive interactions with promoter DNA than previously anticipated. TATA-binding protein, TFIIA, and TFIIB surround promoter DNA for two turns of DNA helix and thus may form a "cylindrical clamp" effectively topologically linked to promoter DNA. Our results have implications for the energetics, DNA-sequence-specificity, and pathway of assembly of eukaryotic transcription complexes.
Pendergrast, PS, Ebright YW, Ebright RH.  1994.  High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates.. Science (New York, N.Y.). 265(5174):959-62. Abstract
Strategies to cleave double-stranded DNA at specific DNA sites longer than those of restriction endonucleases (longer than 8 base pairs) have applications in chromosome mapping, chromosome cloning, and chromosome sequencing--provided that the strategies yield high DNA-cleavage efficiency and high DNA-cleavage specificity. In this report, the DNA-cleaving moiety copper:o-phenanthroline was attached to the sequence-specific DNA binding protein catabolite activator protein (CAP) at an amino acid that, because of a difference in DNA bending, is close to DNA in the specific CAP-DNA complex but is not close to DNA in the nonspecific CAP-DNA complex. The resulting CAP derivative, OP26CAP, cleaved kilobase and megabase DNA substrates at a 22-base pair consensus DNA site with high efficiency and exhibited no detectable nonspecific DNA-cleavage activity.
Wang, W, Messing J.  2011.  High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS One. 6:e24670. AbstractWebsite
BACKGROUND: Chloroplast genomes provide a wealth of information for evolutionary and population genetic studies. Chloroplasts play a particularly important role in the adaption for aquatic plants because they float on water and their major surface is exposed continuously to sunlight. The subfamily of Lemnoideae represents such a collection of aquatic species that because of photosynthesis represents one of the fastest growing plant species on earth. METHODS: We sequenced the chloroplast genomes from three different genera of Lemnoideae, Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana by high-throughput DNA sequencing of genomic DNA using the SOLiD platform. Unfractionated total DNA contains high copies of plastid DNA so that sequences from the nucleus and mitochondria can easily be filtered computationally. Remaining sequence reads were assembled into contiguous sequences (contigs) using SOLiD software tools. Contigs were mapped to a reference genome of Lemna minor and gaps, selected by PCR, were sequenced on the ABI3730xl platform. CONCLUSIONS: This combinatorial approach yielded whole genomic contiguous sequences in a cost-effective manner. Over 1,000-time coverage of chloroplast from total DNA were reached by the SOLiD platform in a single spot on a quadrant slide without purification. Comparative analysis indicated that the chloroplast genome was conserved in gene number and organization with respect to the reference genome of L. minor. However, higher nucleotide substitution, abundant deletions and insertions occurred in non-coding regions of these genomes, indicating a greater genomic dynamics than expected from the comparison of other related species in the Pooideae. Noticeably, there was no transition bias over transversion in Lemnoideae. The data should have immediate applications in evolutionary biology and plant taxonomy with increased resolution and statistical power.
Heidecker, G, Chaudhuri S, Messing J.  1991.  Highly clustered zein gene sequences reveal evolutionary history of the multigene family. Genomics. 10:719-32. AbstractWebsite
We have determined the nucleotide sequences of zein cDNA clones ZG14, ZG15, and ZG35. The three clones have 95 to 98% homology to the previously published sequence of clone A20, and 84% homology to sequences of the zein subfamily A30. Comparison of all sequences of the A30 and A20 subfamilies highlights the following features: the 5' nontranslated regions are 68 and 57 nucleotides in length for the A20- and A30-like mRNAs, respectively, and contain at least three repeats of the consensus sequence ACGAACAAta/gG; the majority of these genes are highly clustered as judged from pulsed-field gel electrophoresis of high molecular weight maize DNA. Furthermore, we discuss a model for the evolution of the multigene family which stresses the special importance of unequal crossingover and gene conversion in this system.
Codelia, VA, Irvine KD.  2012.  Hippo Signaling Goes Long Range. Cell. 150:669-670.Website
Staley, B K, Irvine KD.  2012.  Hippo signaling in Drosophila: Recent advances and insights. Developmental Dynamics. 241:3-15.
Justice, MC, Hogan BP, Vershon AK.  1997.  Homeodomain-DNa Interactions of the Pho2 Protein are Promoter-dependent. Nucleic Acids Res. 25:4730-4739. Abstract
The homeodomain (HD) is a conserved sequence-specific DNA-binding motif found in many eukaryotic transcriptional regulatory proteins. Despite the wealth of in vitro data on the mechanism HD proteins use to bind DNA, comparatively little is known about the roles of individual residues in these domains in vivo . The Saccharomyces cerevisiae Pho2 protein contains a HD that shares significant sequence identity with the Drosophila Engrailed protein. We have used the co-crystal structure of Engrailed as a model to predict how Pho2 might contact DNA and have examined how individual residues of the Pho2 HD contribute to transcriptional activation in vivo and to DNA binding in vitro. Our results demonstrate that Pho2 and Engrailed share many similar DNA-binding characteristics. However, our results also show that some highly conserved residues, which contact the DNA in many HD structures, make relatively small contributions to the DNA-binding affinity and in vivo activity of the Pho2 protein. We also show that the N-terminal arm of the Pho2 HD is a critical component in determining the DNA-binding specificity of the protein and that the requirements for residues in the N-terminal arm are promoter-dependent for Pho2 transcriptional activation and DNA binding.
Swiegers, G F, Huang J, Brimblecombe R, Chen J, Dismukes CG, Mueller-Westerhoff U T, Spiccia L, Wallace G G.  2009.  Homogeneous Catalysts with a Mechanical (“Machine-like”) Action. Chemistry – A European Journal. 15:4746-4759.Website
Klimuk, E, Akulenko N, Makarova KS, Ceyssens P-J, Lavigne R, Severinov K.  2013.  Host RNA polymerase inhibitors encoded by φKMV-like phages of Pseudomonas. Virology. 436:67-74.
Ananyev, GM, Dismukes GC.  2005.  How fast can Photosystem II split water? Kinetic performance at high and low frequencies Photosynthesis Research. 84:355-365.Website
Padgett, RW, Wozney JM, Gelbart WM.  1993.  Human BMP sequences can confer normal dorsal-ventral patterning in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America. 90:2905-9. AbstractWebsite
The type beta transforming growth factor family is composed of a series of processed, secreted growth factors, several of which have been implicated in important regulatory roles in cell determination, inductive interactions, and tissue differentiation. Among these factors, the sequence of the DPP protein from Drosophila is most similar to two of the vertebrate bone morphogenetic proteins, BMP2 and BMP4. Here we report that the human BMP4 ligand sequences can function in lieu of DPP in Drosophila embryos. We introduced the ligand region from human BMP4 into a genomic fragment of the dpp gene in place of the Drosophila ligand sequences and recovered transgenic flies by P-element transformation. We find that this chimeric dpp-BMP4 transgene can completely rescue the embryonic dorsal-ventral patterning defect of null dpp mutant genotypes. We infer that the chimeric DPP-BMP4 protein can be processed properly and, by analogy with the action of other family members, can activate the endogenous DPP receptor to carry out the events necessary for dorsal-ventral patterning. Our evidence suggests that the DPP-BMP4 signal transduction pathway has been functionally conserved for at least 600 million years.
Park, EC, Ghose P, Shao Z, Ye Q, Kang L, Xu XZ, Powell-Coffman JA, Rongo C.  2012.  Hypoxia regulates glutamate receptor trafficking through an HIF-independent mechanism.. EMBO Journal. Epub ahead of print AbstractWebsite
Oxygen influences behaviour in many organisms, with low levels (hypoxia) having devastating consequences for neuron survival. How neurons respond physiologically to counter the effects of hypoxia is not fully understood. Here, we show that hypoxia regulates the trafficking of the glutamate receptor GLR-1 in C. elegans neurons. Either hypoxia or mutations in egl-9, a prolyl hydroxylase cellular oxygen sensor, result in the internalization of GLR-1, the reduction of glutamate-activated currents, and the depression of GLR-1-mediated behaviours. Surprisingly, hypoxia-inducible factor (HIF)-1, the canonical substrate of EGL-9, is not required for this effect. Instead, EGL-9 interacts with the Mint orthologue LIN-10, a mediator of GLR-1 membrane recycling, to promote LIN-10 subcellular localization in an oxygen-dependent manner. The observed effects of hypoxia and egl-9 mutations require the activity of the proline-directed CDK-5 kinase and the CDK-5 phosphorylation sites on LIN-10, suggesting that EGL-9 and CDK-5 compete in an oxygen-dependent manner to regulate LIN-10 activity and thus GLR-1 trafficking. Our findings demonstrate a novel mechanism by which neurons sense and respond to hypoxia.