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Combinatorial genomics

Edward M Barbieri, Paul Muir, Benjamin O Akhuetie-Oni, Christopher M Yellman, Farren J Isaacs
We describe a multiplex genome engineering technology in Saccharomyces cerevisiae based on annealing synthetic oligonucleotides at the lagging strand of DNA replication. The mechanism is independent of Rad51-directed homologous recombination and avoids the creation of double-strand DNA breaks, enabling precise chromosome modifications at single base-pair resolution with an efficiency of >40%, without unintended mutagenic changes at the targeted genetic loci. We observed the simultaneous incorporation of up to 12 oligonucleotides with as many as 60 targeted mutations in one transformation...
November 15, 2017: Cell
Thiemo Zambanini, Hamed Hosseinpour Tehrani, Elena Geiser, Christiane K Sonntag, Joerg M Buescher, Guido Meurer, Nick Wierckx, Lars M Blank
Ustilago trichophora RK089 has been found recently as a good natural malic acid producer from glycerol. This strain has previously undergone adaptive laboratory evolution for enhanced substrate uptake rate resulting in the strain U. trichophora TZ1. Medium optimization and investigation of process parameters enabled titers and rates that are able to compete with those of organisms overexpressing major parts of the underlying metabolic pathways. Metabolic engineering can likely further increase the efficiency of malate production by this organism, provided that basic genetic tools and methods can be established for this rarely used and relatively obscure species...
June 2017: Metabolic Engineering Communications
Mümine Şentürk, Hugo J Bellen
Drosophila melanogaster is a genetic model organism that has contributed to the discovery of numerous genes whose human homologues are associated with diseases. The development of sophisticated genetic tools to manipulate its genome accelerates the discovery of the genetic basis of undiagnosed human diseases and the elucidation of molecular pathogenic events of known and novel diseases. Here, we discuss various approaches used in flies to assess the function of the fly homologues of disease-associated genes...
November 8, 2017: Current Opinion in Neurobiology
G Aubry, H Lu
Caenorhabditis elegans is an excellent model organism for studying chemosensation as a significant part of its nervous system and genome are devoted to the detection of chemical cues. Studies of decision-making, learning, mating behaviour, and intraspecies communication require measuring the acute behavioural response to chemical stimulation. Such assays require precise and repeatable chemical delivery and are often arduous when performed manually. Microfluidic platforms have been developed for chemosensation studies in C...
November 9, 2017: Lab on a Chip
Jason Ernst, Manolis Kellis
Noncoding DNA regions have central roles in human biology, evolution, and disease. ChromHMM helps to annotate the noncoding genome using epigenomic information across one or multiple cell types. It combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer a complete annotation for each cell type. ChromHMM learns chromatin-state signatures using a multivariate hidden Markov model (HMM) that explicitly models the combinatorial presence or absence of each mark. ChromHMM uses these signatures to generate a genome-wide annotation for each cell type by calculating the most probable state for each genomic segment...
December 2017: Nature Protocols
Christina M Albanese, Suttipong Suttapitugsakul, Shruthi Perati, Linda B McGown
Limitations of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and related methods that depend upon combinatorial oligonucleotide libraries have hindered progress in this area. Our laboratory has introduced a new approach to aptamer discovery that uses oligonucleotides with sequences drawn from the human genome to capture proteins from biological samples. Specifically, we have focused on capture of proteins in nuclear extracts from human cell lines using G-quadruplex (G4) forming genomic sequences...
January 15, 2018: Talanta
Haroon Latif Khan, Shahzad Bhatti, Sana Abbas, Yousaf Latif Khan, Muhammad Aslamkhan, Rosa Maria Marquez Gonzalez, Gerardo Rodriguez Gonzalez, Hikmet Hakan Aydin, Magali Segundo Trinidad
Androgen mediating signaling is implicated in regulating the expression of reproductive related genes. Any deviation in the gene expression might be the ignitable precursor for genomic instability that inflames the genomic rearrangements and a leading cause of cancer. The main goal of this study was to determine the relationships between trinucleotide repeats of androgen receptor (AR), sex steroids, and sexual function in men presenting with reduced sperm motility. We investigated the singleton or combinatorial effects of the length of trinucleotide repeats of AR on reproductive hormones, clinical parameters, semen analyses, as well as sexual assessment function of 210 asthenospermic outpatients along with 125 normal subjects...
October 30, 2017: Systems Biology in Reproductive Medicine
Tayaza Fadason, Cameron Ekblad, John R Ingram, William S Schierding, Justin M O'Sullivan
The mechanisms that underlie the association between obesity and type 2 diabetes are not fully understood. Here, we investigated the role of the 3D genome organization in the pathogeneses of obesity and type-2 diabetes. We interpreted the combined and differential impacts of 196 diabetes and 390 obesity associated single nucleotide polymorphisms (SNPs) by integrating data on the genes with which they physically interact (as captured by Hi-C) and the functional [i.e., expression quantitative trait loci (eQTL)] outcomes associated with these interactions...
2017: Frontiers in Genetics
Leyla Y Bustamante, Gareth T Powell, Yen-Chun Lin, Michael D Macklin, Nadia Cross, Alison Kemp, Paula Cawkill, Theo Sanderson, Cecile Crosnier, Nicole Muller-Sienerth, Ogobara K Doumbo, Boubacar Traore, Peter D Crompton, Pietro Cicuta, Tuan M Tran, Gavin J Wright, Julian C Rayner
A highly effective vaccine would be a valuable weapon in the drive toward malaria elimination. No such vaccine currently exists, and only a handful of the hundreds of potential candidates in the parasite genome have been evaluated. In this study, we systematically evaluated 29 antigens likely to be involved in erythrocyte invasion, an essential developmental stage during which the malaria parasite is vulnerable to antibody-mediated inhibition. Testing antigens alone and in combination identified several strain-transcending targets that had synergistic combinatorial effects in vitro, while studies in an endemic population revealed that combinations of the same antigens were associated with protection from febrile malaria...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
Derek J Mattern, Vito Valiante, Fabian Horn, Lutz Petzke, Axel A Brakhage
Filamentous fungi produce numerous high-value natural products (NPs). The biosynthetic genes for NPs are normally clustered in the genome. A valuable NP class is represented by the insecticidal austinoids. We previously determined their biosynthesis in the fungus Aspergillus calidoustus. After further computational analysis looking into the austinoid gene clusters in two additional distantly related fungi, Aspergillus nidulans and Penicillium brasilianum, a rearrangement of the genes was observed that corresponded to the diverse austinoid derivatives produced by each strain...
November 2, 2017: ACS Chemical Biology
Aurélie Auguste, Alexandra Leary
The demonstration of frequent defects in the DNA damage response in high grade ovarian cancer has paved the way for a new therapeutic approach aimed at exploiting this unique vulnerability. The efficacy of poly (ADP) ribose polymerase inhibitors (PARPi) in patients with homologous recombination (HR) DNA repair deficient ovarian cancer (OC) resulting from a BRCA1/2 mutation has provided the proof of concept for synthetic lethality. Thus, olaparib is now approved by the EMA as maintenance therapy after response to a platinum regimen for patients with recurrent, platinum-sensitive, high-grade serous, BRCA1/2-mutated ovarian cancer...
October 17, 2017: Bulletin du Cancer
Kathryn G Roberts
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a recently described subtype of B-cell precursor ALL with a gene expression profile similar to Ph-positive ALL and a high frequency of IKZF1 alterations. The prevalence of Ph-like ALL increases with age, ranging from 10-15% of children to over 25% of young adults with ALL. It occurs more frequently in males and is associated with adverse clinical features including elevated minimal residual disease levels and poor survival in both children and adults...
September 2017: Best Practice & Research. Clinical Haematology
Akhileshwar Namani, Qin Qin Cui, Yihe Wu, Hongyan Wang, Xiu Jun Wang, Xiuwen Tang
Mutations in Kelch-like ECH-associated protein 1 (KEAP1) cause the aberrant activation of nuclear factor erythroid-derived 2-like 2 (NRF2), which leads to oncogenesis and drug resistance in lung cancer cells. Our study was designed to identify the genes involved in lung cancer progression targeted by NRF2. A series of microarray experiments in normal and cancer cells, as well as in animal models, have revealed regulatory genes downstream of NRF2 that are involved in wide variety of pathways. Specifically, we carried out individual and combinatorial microarray analysis of KEAP1 overexpression and NRF2 siRNA-knockdown in a KEAP1 mutant-A549 non-small cell lung cancer (NSCLC) cell line...
September 19, 2017: Oncotarget
Martin Kampmann
Next-generation DNA sequencing technologies have led to a massive accumulation of genomic and transcriptomic data from patients and healthy individuals. The major challenge ahead is to understand the functional significance of the elements of the human genome and transcriptome, and implications for diagnosis and treatment. Genetic screens in mammalian cells are a powerful approach to systematically elucidating gene function in health and disease states. In particular, recently developed CRISPR/Cas9-based screening approaches have enormous potential to uncover mechanisms and therapeutic strategies for human diseases...
October 24, 2017: ACS Chemical Biology
Monica Soldi, Tommaso Mari, Luciano Nicosia, Daniele Musiani, Gianluca Sigismondo, Alessandro Cuomo, Giulio Pavesi, Tiziana Bonaldi
The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type-specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking...
September 13, 2017: Nucleic Acids Research
Yuta Adachi, Kazuyoshi Watanabe, Kenji Kita, Hidenori Kitai, Hiroshi Kotani, Yuki Sato, Naohiko Inase, Seiji Yano, Hiromichi Ebi
Fibroblast growth factor receptor 1 (FGFR1) amplification has been identified in 10-20% of patients with squamous non-small-cell lung cancer. Preclinical models showed promising activity of specific FGFR inhibitors, but early clinical trials showed that only a small fraction of patients with FGFR1-amplified lung cancer responded to FGFR inhibitors. These unsatisfactory results were partly explained by heterogeneous amplicons around the 8p11 genomic region, leading to false-positive amplification results. Furthermore, discrepancies in the gene amplification and protein expression of FGFR1 were also reported...
October 26, 2017: Carcinogenesis
Yulan Deng, Shangyi Luo, Chunyu Deng, Tao Luo, Wenkang Yin, Hongyi Zhang, Yong Zhang, Xinxin Zhang, Yujia Lan, Yanyan Ping, Yun Xiao, Xia Li
Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial cancer pathways. Recently, there is considerable evidence showing that, mutual exclusivity reflects alternative functions in tumor initiation and progression, or suggests adverse effects of their concurrence...
August 31, 2017: Briefings in Bioinformatics
Trisevgeni Rapakoulia, Xin Gao, Yi Huang, Michiel de Hoon, Mariko Okada-Hatakeyama, Harukazu Suzuki, Erik Arner
Motivation: Drug combination therapy for treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect, while reducing the likelihood of drug resistance. In order to reduce time and cost spent in comprehensive screens, methods are needed which can model additive effects of possible drug combinations. Results: We here show that the transcriptional response to combinatorial drug treatment at promoters, as measured by single molecule CAGE technology, is accurately described by a linear combination of the responses of the individual drugs at a genome wide scale...
August 14, 2017: Bioinformatics
Tomohiro Kohmoto, Kiyoshi Masuda, Takuya Naruto, Shoichiro Tange, Katsutoshi Shoda, Junichi Hamada, Masako Saito, Daisuke Ichikawa, Atsushi Tajima, Eigo Otsuji, Issei Imoto
High-throughput next-generation sequencing is a powerful tool to identify the genotypic landscapes of somatic variants and therapeutic targets in various cancers including gastric cancer, forming the basis for personalized medicine in the clinical setting. Although the advent of many computational algorithms leads to higher accuracy in somatic variant calling, no standard method exists due to the limitations of each method. Here, we constructed a new pipeline. We combined two different somatic variant callers with different algorithms, Strelka and VarScan 2, and evaluated performance using whole exome sequencing data obtained from 19 Japanese cases with gastric cancer (GC); then, we characterized these tumors based on identified driver molecular alterations...
2017: Journal of Medical Investigation: JMI
Rebekka Mauser, Goran Kungulovski, Corinna Keup, Richard Reinhardt, Albert Jeltsch
BACKGROUND: Histone post-translational modifications (PTMs) play central roles in chromatin-templated processes. Combinations of two or more histone PTMs form unique interfaces for readout and recruitment of chromatin interacting complexes, but the genome-wide mapping of coexisting histone PTMs remains an experimentally difficult task. RESULTS: We introduce here a novel type of affinity reagents consisting of two fused recombinant histone modification interacting domains (HiMIDs) for direct detection of doubly modified chromatin...
September 25, 2017: Epigenetics & Chromatin
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