Analysis of the genomic DNA of the harmful dinoflagellate Prorocentrum minimum: a brief survey focused on the noncoding RNA gene sequences

2015 ◽  
Vol 28 (1) ◽  
pp. 335-344 ◽  
Author(s):  
Thangaraj Ponmani ◽  
Ruoyu Guo ◽  
Jang-Seu Ki
Keyword(s):  
Genomic Dna ◽  
Noncoding Rna ◽  
Prorocentrum Minimum ◽  
Gene Sequences ◽  
Harmful Dinoflagellate

Hottip-Mediated R-Loops Regulate CTCF TAD Boundary to Control WNT/b-Catenin Pathway in AML Genome

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 44-45
Author(s):  
Huacheng Luo ◽  
Ganqian Zhu ◽  
Xiaoyan Ma ◽  
David F. Claxton ◽  
Yi Qiu ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Research Funding ◽  
Noncoding Rna ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Integrated Analysis ◽  
Specific Gene ◽  
Loop Structure ◽  
Range Interaction ◽  
Transcription Program

lncRNA, transcribed from genomic DNA, can form a DNA: RNA hybridization structure to access regulatory elements. HOX loci associated long noncoding RNA (lncRNA), HOTTIP, acts as an epigenetic regulator to define oncogenic HOXA topologically associated domain (TAD) and drive HOXA associated leukemic transcription program. Activation of HOTTIP promoted AML pathogenesis by perturbing leukemic transcription program and hematopoietic/progenitor stem cells (HS/PCs) function. However, the mechanism by which HOTTIP accesses and regulates genomic DNA transcriptional output remains unknown. Here, Combined RNA-seq, ChIP-seq, NG-Capture-C and Hi-C integrated analysis demonstrated that HOTTIP dependent stratification/formation of TADs at WNT/b-catenin loci is critical for b-catenin (CTNNB1) target gene transcription in AML cells. We further showed that HOTTIP specifically interacts with CTCF-occupied TAD boundary CTCF binding sites (CBSs) at b-catenin and its target loci (e.g. MYC and MECOM) by formation of R-loops. To test whether HOTTIP-mediated R-loops contribute to boundary maintanence and TAD stablization, we created CRISPR/dCas9-RNaseH-mediated disruption of R-loop structure In MOLM13 cells by which the Ribonuclease H (RNase H) was targeted to the HOTTIP/CTCF co-occupied CTNNB1 or MYC boundary CBSs to specifically target RNA: DNA hybridization region. Our DNA-RNA immunoprecipitation (DRIP)-qPCR data indicated that CRISPR/dCas9-RNaseH-mediated sgRNAs disrupted the R-loop structure in MYC and CTNNB1 defined TAD boundary regions. Furthermore, HOTTIP CHIRP-qPCR and CTCF CHIP-qPCR suggested that loss of R-loop structure in MYC or CTNNB1 TAD boundary CBSs decreased both CTCF and HOTTIP binding in these CBSs. Disruption of R-loops also affects the long-range interaction within CTNNB1 or MYC TADs that are important for WNT/b-catenin signaling network and AML leukemogenesis. In conclusion, our finding demonstrated that HOTTIP forming DNA∙RNA hybridized R-loops mediate AML genome organization at specific gene loci and control leukemic transcription program. Thus, HOTTIP lncRNA mediated R-loop structure will be considered as a novel molecular mechanism in AML leukemogensis. Disclosures Claxton: Daiichi Sankyo Co: Research Funding; Astellas Pharma: Research Funding; Incyte Corporation: Research Funding; Cyclacel Pharmaceuticals, Inc.: Research Funding.

scholarly journals Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983

2006 ◽  
Vol 56 (8) ◽  
pp. 1721-1724 ◽  
Author(s):  
Franco Dellaglio ◽  
Marc Vancanneyt ◽  
Akihito Endo ◽  
Peter Vandamme ◽  
Giovanna E. Felis ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Dna ◽  
Taxonomic Status ◽  
Single Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Biochemical Characteristics ◽  
Binding Level

The taxonomic status of the species Lactobacillus durianis and Lactobacillus vaccinostercus is briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1523 bp), partial recA gene sequences (99.5 % similarity over 600 bp) and partial hsp60 gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA–DNA binding level (87 %) and similar genomic DNA G+C contents (41–44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of the Bacteriological Code, the name Lactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the name Lactobacillus durianis should be considered a later heterotypic synonym.

scholarly journals Pathology and immune response of the blue mussel (Mytilus edulis L.) after an exposure to the harmful dinoflagellate Prorocentrum minimum

Harmful Algae ◽  
2008 ◽  
Vol 7 (5) ◽  
pp. 630-638 ◽  
Author(s):  
Eve Galimany ◽  
Inke Sunila ◽  
Hélene Hégaret ◽  
Montserrat Ramón ◽  
Gary H. Wikfors
Keyword(s):  
Immune Response ◽  
Mytilus Edulis ◽  
Blue Mussel ◽  
Prorocentrum Minimum ◽  
Harmful Dinoflagellate

Hox-type and non-Hox homeobox gene sequences in genomic DNA of the sea urchin Holopneustes purpurescens

Gene ◽  
1997 ◽  
Vol 201 (1-2) ◽  
pp. 107-110 ◽  
Author(s):  
Valerie B. Morris ◽  
Jennifer Brammall ◽  
Maria Byrne ◽  
Marianne Frommer
Keyword(s):  
Sea Urchin ◽  
Genomic Dna ◽  
Homeobox Gene ◽  
Gene Sequences

scholarly journals Characterization of Rhodobacter sphaeroides Gene RSP1977

2012 ◽  
Vol 1 (1) ◽  
pp. 33-38
Author(s):  
Arlie Joe Green ◽  
Aaron Setterdahl
Keyword(s):  
Molecular Biology ◽  
Rhodobacter Sphaeroides ◽  
Genomic Dna ◽  
Expression Vector ◽  
Photosynthetic Bacterium ◽  
Cloning Vector ◽  
Gene Sequences ◽  
Competent Cells

Rhodobacter sphaeroides is a purple, non-sulfur, photosynthetic bacterium whose entire genomic DNA has been sequenced, however, many of the genes in its genome have not been characterized in order to determine their function in the bacterium.  Furthermore, many of the genes in R. sphaeroides are very similar to gene sequences in other organisms.  Therefore, upon determining the functions of R. sphaeroides genes, it will help lead to a better understanding of the functions of genes in other organisms.  This research is an attempt to isolate, purify and characterize proteins from R. sphaeroides using techniques in biochemistry, molecular biology, informatics, and genetics.  To date, the gene RSP1977 has been successfully isolate, cloned, and analyzed.  It has been attempted to insert the gene into the pSC-B-amp/kan cloning vector, to transform the vector into competent cells, then re-isolate the vector and confirm the insertion of RSP1977.  However, confirmation has not yet been obtained of successful insertion and re-purification.  The next steps, after confirmation would be to insert the gene into the pET-21b(+) expression vector and express the protein.  Once the protein is expressed, its functions will be studied and determined.

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