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https://www.readbyqxmd.com/read/28538188/identification-and-characterization-of-a-class-of-malat1-like-genomic-loci
#1
Bin Zhang, Yuntao S Mao, Sarah D Diermeier, Irina V Novikova, Eric P Nawrocki, Tom A Jones, Zsolt Lazar, Chang-Shung Tung, Weijun Luo, Sean R Eddy, Karissa Y Sanbonmatsu, David L Spector
The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3' end module...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28537914/epigenomic-study-identifies-a-novel-mesenchyme-homeobox2-gli1-transcription-axis-involved-in-cancer-drug-resistance-overall-survival-and-therapy-prognosis-in-lung-cancer-patients
#2
Leonel Armas-López, Patricia Piña-Sánchez, Oscar Arrieta, Enrique Guzman de Alba, Blanca Ortiz-Quintero, Patricio Santillán-Doherty, David C Christiani, Joaquín Zúñiga, Federico Ávila-Moreno
Several homeobox-related gene (HOX) transcription factors such as mesenchyme HOX-2 (MEOX2) have previously been associated with cancer drug resistance, malignant progression and/or clinical prognostic responses in lung cancer patients; however, the mechanisms involved in these responses have yet to be elucidated. Here, an epigenomic strategy was implemented to identify novel MEOX2 gene promoter transcription targets and propose a new molecular mechanism underlying lung cancer drug resistance and poor clinical prognosis...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28535386/sex-differences-satellite-dna-directs-male-specific-gene-expression
#3
Patrick M Ferree
Dosage compensation in some animals involves up-regulation of genes on the male's X chromosome. A study in the fruit fly Drosophila melanogaster shows that satellite DNA, and corresponding small non-coding RNA, helps the dosage compensation machinery preferentially find X sequences.
May 22, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28535155/elevated-apobec3b-expression-drives-a-kataegic-like-mutation-signature-and-replication-stress-related-therapeutic-vulnerabilities-in-p53-defective-cells
#4
Jenni Nikkilä, Rahul Kumar, James Campbell, Inger Brandsma, Helen N Pemberton, Fredrik Wallberg, Kinga Nagy, Ildikó Scheer, Beata G Vertessy, Artur A Serebrenik, Valentina Monni, Reuben S Harris, Stephen J Pettitt, Alan Ashworth, Christopher J Lord
BACKGROUND: Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system. METHODS: We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing...
May 23, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28534229/production-of-a-gonadotropin-releasing-hormone-2-receptor-knockdown-gnrhr2-kd-swine-line
#5
A T Desaulniers, R A Cederberg, G A Mills, C A Lents, B R White
Swine are the only livestock species that produce both the second mammalian isoform of gonadotropin-releasing hormone (GNRH2) and its receptor (GNRHR2). Previously, we reported that GNRH2 and GNRHR2 mediate LH-independent testosterone secretion from porcine testes. To further explore this ligand-receptor complex, a pig model with reduced GNRHR2 expression was developed. Small hairpin RNA sequences targeting porcine GNRHR2 were subcloned into a lentiviral-based vector, lentiviral particles were generated and microinjected into the perivitelline space of zygotes, and embryos were transferred into a recipient...
May 22, 2017: Transgenic Research
https://www.readbyqxmd.com/read/28534195/identification-of-a-small-molecule-that-facilitates-the-differentiation-of-human-ipscs-escs-and-mouse-embryonic-pancreatic-explants-into-pancreatic-endocrine-cells
#6
Yasushi Kondo, Taro Toyoda, Ryo Ito, Michinori Funato, Yoshiya Hosokawa, Satoshi Matsui, Tomomi Sudo, Masahiro Nakamura, Chihiro Okada, Xiaotong Zhuang, Akira Watanabe, Akira Ohta, Nobuya Inagaki, Kenji Osafune
AIMS/HYPOTHESIS: Pancreatic beta-like cells generated from human induced pluripotent stem cells (hiPSCs) or human embryonic stem cells (hESCs) offer an appealing donor tissue source. However, differentiation protocols that mainly use growth factors are costly. Therefore, in this study, we aimed to establish efficient differentiation protocols to change hiPSCs/hESCs to insulin (INS)(+) cells using novel small-molecule inducers. METHODS: We screened small molecules that increased the induction rate of INS(+) cells from hESC-derived pancreatic and duodenal homeobox 1 (PDX1)(+) pancreatic progenitor cells...
May 22, 2017: Diabetologia
https://www.readbyqxmd.com/read/28531310/nascent-rna-sequencing-reveals-mechanisms-of-gene-regulation-in-the-human-malaria-parasite-plasmodium-falciparum
#7
Xueqing Maggie Lu, Gayani Batugedara, Michael Lee, Jacques Prudhomme, Evelien M Bunnik, Karine G Le Roch
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#8
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28530238/micrornas-146a-b-5-and-425-3p-and-24-3p-are-markers-of-antidepressant-response-and-regulate-mapk-wnt-system-genes
#9
Juan Pablo Lopez, Laura M Fiori, Cristiana Cruceanu, Rixing Lin, Benoit Labonte, Hannah M Cates, Elizabeth A Heller, Vincent Vialou, Stacy M Ku, Christophe Gerald, Ming-Hu Han, Jane Foster, Benicio N Frey, Claudio N Soares, Daniel J Müller, Faranak Farzan, Francesco Leri, Glenda M MacQueen, Harriet Feilotter, Kathrin Tyryshkin, Kenneth R Evans, Peter Giacobbe, Pierre Blier, Raymond W Lam, Roumen Milev, Sagar V Parikh, Susan Rotzinger, Steven C Strother, Cathryn M Lewis, Katherine J Aitchison, Gayle M Wittenberg, Naguib Mechawar, Eric J Nestler, Rudolf Uher, Sidney H Kennedy, Gustavo Turecki
Antidepressants (ADs) are the most common treatment for major depressive disorder (MDD). However, only ∼30% of patients experience adequate response after a single AD trial, and this variability remains poorly understood. Here, we investigated microRNAs (miRNAs) as biomarkers of AD response using small RNA-sequencing in paired samples from MDD patients enrolled in a large, randomized placebo-controlled trial of duloxetine collected before and 8 weeks after treatment. Our results revealed differential expression of miR-146a-5p, miR-146b-5p, miR-425-3p and miR-24-3p according to treatment response...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28528706/long-noncoding-rnas-in-the-pathogenesis-of-barrett-s-esophagus-and-esophageal-carcinoma
#10
REVIEW
John M Abraham, Stephen J Meltzer
For many years, only a small fraction of the human genome was believed to regulate cell function and development. This protein-coding portion composed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk DNA. Subsequent research has revealed that most of the genome is transcribed into a broad array of noncoding RNAs, ranging in size from microRNA (20-23 nucleotides) to long noncoding RNA (lncRNA, more than 200 nucleotides). These noncoding RNA classes have been shown to use diverse molecular mechanisms to control gene expression and organ system development...
May 18, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28525966/gene-expression-of-vibrio-parahaemolyticus-growing-in-laboratory-isolation-conditions-compared-to-those-common-in-its-natural-ocean-environment
#11
Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor, Romilio T Espejo
BACKGROUND: Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. However, this condition is used for isolation in the laboratory because it is considered a necessary property for pathogenesis. In this context, revealing how gene expression enables V. parahaemolyticus to adapt to this particular condition -common to almost all V. parahaemolyticus isolates- will improve our understanding of the biology of this important pathogen...
May 19, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28525645/molecular-characterization-of-prototheca-strains-isolated-in-china-revealed-the-first-cases-of-protothecosis-associated-with-prototheca-zopfii-genotype-1
#12
Noriyuki Hirose, Zhensheng Hua, Yuichi Kato, Qiangqiang Zhang, Ruoyu Li, Kazuko Nishimura, Michiaki Masuda
In this study, six strains of Prototheca isolated in China from human patients diagnosed as protothecosis and cows with mastitis were characterized by polymerase chain reaction (PCR) and nucleotide sequencing of the ribosomal RNA gene (rDNA) and by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). The results indicated that three strains isolated from the human patients were P. zopfii genotype 1, revealing the first cases of human protothecosis associated with P. zopfii genotype 1...
May 19, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/28524354/an-aggregating-amphiphilic-squaraine-a-light-up-probe-that-discriminates-parallel-g-quadruplexes
#13
Vincenzo Grande, Filippo Doria, Mauro Freccero, Frank Würthner
G-quadruplexes (G4s) are peculiar DNA or RNA tertiary structures that are involved in the regulation of many biological events within mammalian cells, bacteria, and viruses. Although their role as versatile therapeutic targets has been emphasized for 35 years, G4 selectivity over ubiquitous double-stranded DNA/RNA, as well as G4 differentiation by small molecules, still remains challenging. Here, a new amphiphilic dicyanovinyl-substituted squaraine, SQgl, is reported to act as an NIR fluorescent light-up probe discriminating an extensive panel of parallel G4s while it is non-fluorescent in the aggregated state...
May 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28523997/differences-in-relative-levels-of-88-micrornas-in-various-regions-of-the-normal-adult-human-brain
#14
Elena Vladislavovna Filatova, Anelya Khanlarovna Alieva, Maria Igorevna Shadrina, Petr Andreevich Slominsky
AIM OF STUDY: Since the discovery of microRNAs (miRNAs) in the 1990s, our knowledge about their biology has grown considerably. The increasing number of studies addressing the role of miRNAs in development and in various diseases emphasizes the need for a comprehensive catalogue of accurate sequence, expression and conservation information regarding the large number of miRNAs proposed recently in all organs and tissues. The objective of this study was to provide data on the levels of miRNA expression in 15 tissues of the normal human brain...
May 19, 2017: MicroRNA
https://www.readbyqxmd.com/read/28522719/genome-sequence-of-a-novel-positive-sense-single-stranded-rna-virus-isolated-from-western-corn-rootworm-diabrotica-virgifera%C3%A2-virgifera-leconte
#15
Sijun Liu, Yuting Chen, Thomas W Sappington, Bryony C Bonning
The genome sequence of a novel small RNA virus was assembled from the transcriptome of the western corn rootworm, Diabrotica virgifera virgifera The assembled genome has 13,182 nucleotides with a 3' polyadenylated tail. Two open reading frames are predicted to encode polyproteins of 2,838 and 1,073 amino acids.
May 18, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28522718/genome-sequence-of-diabrotica-virgifera-virgifera-virus2-a-novel-small-rna-virus-of-the-western-corn-rootworm-diabrotica-virgifera-virgifera-leconte
#16
Sijun Liu, Yuting Chen, Thomas W Sappington, Bryony C Bonning
The genome of a novel small RNA virus, tentatively named Diabrotica virgifera virgifera virus 2 (DvvV2), was identified in the western corn rootworm, Diabrotica virgifera virgifera LeConte, through transcriptome sequencing and confirmed by reverse transcription-PCR. Here, we report the near-complete nucleotide sequence and the genome organization of DvvV2.
May 18, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#17
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28522157/antiviral-goes-viral-harnessing-crispr-cas9-to-combat-viruses-in-humans
#18
REVIEW
Jasper Adriaan Soppe, Robert Jan Lebbink
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are RNA-guided sequence-specific prokaryotic antiviral immune systems. In prokaryotes, small RNA molecules guide Cas effector endonucleases to invading foreign genetic elements in a sequence-dependent manner, resulting in DNA cleavage by the endonuclease upon target binding. A rewired CRISPR/Cas9 system can be used for targeted and precise genome editing in eukaryotic cells. CRISPR/Cas has also been harnessed to target human pathogenic viruses as a potential new antiviral strategy...
May 15, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28521398/effect-of-satb1-silencing-on-the-proliferation-invasion-and-apoptosis-of-te-1-esophageal-cancer-cells
#19
Bo Huang, Fei Xiong, Siwang Wang, Xianping Lang, Xiaodong Wang, Hongli Zhou
The aim of the present study was to investigate the effect of special AT-rich sequence-binding protein-1 (SATB1)-targeted small interfering RNA (siRNA) on the proliferation, invasion and apoptosis of TE-1 human esophageal cancer cells. SATB1 has been correlated with the metastasis and poor prognosis of colon and breast cancer, but the role of SATB1 in esophageal cancer remains unknown. Therefore, the present study constructed and transfected SATB1-siRNA into TE-1 cells in order to knockdown the expression of the SATB1 gene...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28520720/identification-of-human-short-introns
#20
Emmanuel L Abebrese, Syed H Ali, Zachary R Arnold, Victoria M Andrews, Katharine Armstrong, Lindsay Burns, Hannah R Crowder, R Thomas Day, Daniel G Hsu, Katherine Jarrell, Grace Lee, Yi Luo, Daphine Mugayo, Zain Raza, Kyle Friend
Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing. Non-canonical splicing-intron excision without the spliceosome-has been documented; most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions...
2017: PloS One
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