scholarly journals Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C

2017 ◽  
Author(s):  
Caiti Smukowski Heil ◽  
Joshua N. Burton ◽  
Ivan Liachko ◽  
Anne Friedrich ◽  
Noah A. Hanson ◽  
...  
Keyword(s):  
Common Mechanism ◽  
Chromosome Conformation ◽  
Hybrid Species ◽  
Pichia Membranifaciens ◽  
Assembly Method ◽  
Capture Method ◽  
Yeast Genomes ◽  
Yeast Hybrid ◽  
Environmental Microbes ◽  
Mixed Communities

AbstractInterspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the method’s application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample. Our assembly method has enabled us to de-convolute 4 bacterial and 4 yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes.

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma

Gut ◽  
2019 ◽  
Vol 69 (6) ◽  
pp. 1039-1052 ◽  
Author(s):  
Wen Fong Ooi ◽  
Amrita M Nargund ◽  
Kevin Junliang Lim ◽  
Shenli Zhang ◽  
Manjie Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Therapy Resistance ◽  
Regulatory Elements ◽  
Genomic Rearrangements ◽  
Common Mechanism ◽  
Whole Genome ◽  
Structural Variations ◽  
Chromosome Conformation ◽  
Chip Sequencing

ObjectiveGenomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS).DesignWe applied PeNChIP-seq to 11 primary GCs and matched normal tissues combined with WGS profiles of >200 GCs. Epigenome profiles were analysed alongside matched RNA-seq data to identify tumour-associated enhancer-based SVs with altered cancer transcription. Functional validation of candidate enhancer-based SVs was performed using CRISPR/Cas9 genome editing, chromosome conformation capture assays (4C-seq, Capture-C) and Hi-C analysis of primary GCs.ResultsPeNChIP-seq/WGS revealed ~150 enhancer-based SVs in GC. The majority (63%) of SVs linked to target gene deregulation were associated with increased tumour expression. Enhancer-based SVs targeting CCNE1, a key driver of therapy resistance, occurred in 8% of patients frequently juxtaposing diverse distal enhancers to CCNE1 proximal regions. CCNE1-rearranged GCs were associated with high CCNE1 expression, disrupted CCNE1 topologically associating domain (TAD) boundaries, and novel TAD interactions in CCNE1-rearranged primary tumours. We also observed IGF2 enhancer-based SVs, previously noted in colorectal cancer, highlighting a common non-coding genetic driver alteration in gastric and colorectal malignancies.ConclusionIntegrated paired-end NanoChIP-seq and WGS of gastric tumours reveals tumour-associated regulatory SV in regions associated with both simple and complex genomic rearrangements. Genomic rearrangements may thus exploit enhancer-hijacking as a common mechanism to drive oncogene expression in GC.

A statistical model of intra-chromosome contact maps

Soft Matter ◽  
2015 ◽  
Vol 11 (5) ◽  
pp. 1019-1025 ◽  
Author(s):  
Leonid I. Nazarov ◽  
Mikhail V. Tamm ◽  
Vladik A. Avetisov ◽  
Sergei K. Nechaev
Keyword(s):  
Fine Structure ◽  
Statistical Model ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Contact Maps ◽  
Genome Wide ◽  
A Genome ◽  
Capture Method ◽  
Chromosome Maps

A statistical model describing a fine structure of the intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi–C) is proposed.

scholarly journals capC-MAP : A Software Package for Analysis of Capture-C data

2018 ◽  
Author(s):  
Adam Buckle ◽  
Nick Gilbert ◽  
Davide Marenduzzo ◽  
Chris A. Brackley
Keyword(s):  
Data Processing ◽  
Software Package ◽  
Ease Of Use ◽  
Data Capture ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Capture Method

AbstractWe present capC-MAP, a software package for the analysis of Capture-C data. Capture-C is a “many-to-all” chromosome-conformation-capture method. We summarise the method, then detail capC-MAP, the first software specifically designed and optimised for Capture-C data. capC-MAP has been developed with ease-of-use and flexibility in mind: the entire pipe-ine can be run with a single command, or the component programs can be run individually for custom data processing, in a strategy that will suit computational as well as experimental researchers. Finally, we compare and benchmark capC-MAP against another package which can perform (though is not optimised for) analysis of Capture-C data.

scholarly journals Dynamic 3D Locus Organization and Its Drivers Underpin Immunoglobulin Recombination

2021 ◽  
Vol 11 ◽  
Author(s):  
Carolyn H. Rogers ◽  
Olga Mielczarek ◽  
Anne E. Corcoran
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Adaptive Immune System ◽  
Regulatory Elements ◽  
Common Mechanism ◽  
Chromosome Conformation ◽  
Igh Locus ◽  
Horizon Scanning ◽  
V Genes ◽  
Repertoire Sequencing

A functional adaptive immune system must generate enormously diverse antigen receptor (AgR) repertoires from a limited number of AgR genes, using a common mechanism, V(D)J recombination. The AgR loci are among the largest in the genome, and individual genes must overcome huge spatial and temporal challenges to co-localize with optimum variability. Our understanding of the complex mechanisms involved has increased enormously, due in part to new technologies for high resolution mapping of AgR structure and dynamic movement, underpinning mechanisms, and resulting repertoires. This review will examine these advances using the paradigm of the mouse immunoglobulin heavy chain (Igh) locus. We will discuss the key regulatory elements implicated in Igh locus structure. Recent next generation repertoire sequencing methods have shown that local chromatin state at V genes contribute to recombination efficiency. Next on the multidimensional scale, we will describe imaging studies that provided the first picture of the large-scale dynamic looping and contraction the Igh locus undergoes during recombination. We will discuss chromosome conformation capture (3C)-based technologies that have provided higher resolution pictures of Igh locus structure, including the different models that have evolved. We will consider the key transcription factors (PAX5, YY1, E2A, Ikaros), and architectural factors, CTCF and cohesin, that regulate these processes. Lastly, we will discuss a plethora of recent exciting mechanistic findings. These include Rag recombinase scanning for convergent RSS sequences within DNA loops; identification of Igh loop extrusion, and its putative role in Rag scanning; the roles of CTCF, cohesin and cohesin loading factor, WAPL therein; a new phase separation model for Igh locus compartmentalization. We will draw these together and conclude with some horizon-scanning and unresolved questions.

Kindler's Syndrome with Recurrent Neutropenia: Report of Two Cases from Saudi Arabia

2020 ◽  
Author(s):  
Yousef Binamer ◽  
Muzamil A. Chisti
Keyword(s):  
Autosomal Recessive ◽  
Common Mechanism ◽  
Sequencing Analysis ◽  
Loss Of Function ◽  
Skin Atrophy ◽  
Whole Exome ◽  
Infancy And Childhood ◽  
Genetics And Genomics ◽  
New Feature ◽  
Generation Sequencing

AbstractKindler syndrome (KS) is a rare photosensitivity disorder with autosomal recessive mode of inheritance. It is characterized by acral blistering in infancy and childhood, progressive poikiloderma, skin atrophy, abnormal photosensitivity, and gingival fragility. Besides these major features, many minor presentations have also been reported in the literature. We are reporting two cases with atypical features of the syndrome and a new feature of recurrent neutropenia. Whole exome sequencing analysis was done using next-generation sequencing which detected a homozygous loss-of-function (LOF) variant of FERMT1 in both patients. The variant is classified as a pathogenic variant as per the American College of Medical Genetics and Genomics guidelines. Homozygous LOF variants of FERMT1 are a common mechanism of KS and as such confirm the diagnosis of KS in our patients even though the presentation was atypical.

STUDY OF PEDIATRIC INJURIES: PATTERNS AND OUTCOME

2019 ◽  
Vol 3 (8) ◽  
Author(s):  
Yasir. B. Elshambaty
Keyword(s):  
School Level ◽  
Common Mechanism ◽  
Injury Patterns ◽  
Severe Injuries ◽  
Injured Child ◽  
Cross Sectional ◽  
Pediatric Injuries ◽  
Pediatric Injury ◽  
The Common ◽  
Structured Questionnaire

Purpose this study aims to show the patterns and outcome of pediatric injury among those living in Albaha region in Saudi Arabia Methods this is a cross-sectional descriptive household-based study, included children between 0-17 years old both male and female. The data were collected with structured questionnaire between 20 Nov – 20 Dec 2018 and  analyzed with SPSS version 25 Results the total of participants was 257 injured child. 199(77.4%) are male and 58(22.6%) are female. About 44%of them were injured at pre-school level and 56% were traumatized at school age. The least incidence of injury occurred in those less than 2 yrs and higher incidence in those between 3-10 yrs old. The most common mechanism of injury was falling from height. The most affected group age by RTA accidents was 11-17 yrs old. Approximately 83% of the injured children required hospital management. Only one third of the injuries were  associated complications. The most common injured anatomic part was the upper limb and the least affected part was the spine. Only 5% of the injuries were associated with a disability and the common was loss of organ or part of it. Paralysis occurred in less than 1% and head injury resulted in disabilities more than 1%. Conclusion the vast majority of the injuries in our participants are not serious. The severe injuries were associated with RTA-related trauma. Most of injuries due to falling from height are not serious. We recommend not to allow the children to drive cars. Keywords: pediatric injuries; injury patterns; household.

A common mechanism links activities of butyrate in the colon

2017 ◽  
Author(s):  
Mohit S. Verma ◽  
Michael J. Fink ◽  
Gabriel L Salmon ◽  
Nadine Fornelos ◽  
Takahiro E. Ohara ◽  
...  
Keyword(s):  
Stem Cells ◽  
Histone Deacetylases ◽  
Biological Activities ◽  
Short Chain Fatty Acids ◽  
Common Mechanism ◽  
Epithelial Stem Cells ◽  
Degree Of Unsaturation ◽  
Structure Activity ◽  
Starting Point ◽  
New Compounds

Two biological activities of butyrate in the colon (suppression of proliferation of colonic epithelial stem cells and inflammation) correlate with inhibition of histone deacetylases. Cellular and biochemical studies of molecules similar in structure to butyrate, but different in molecular details (functional groups, chain-length, deuteration, oxidation level, fluorination, or degree of unsaturation) demonstrated that these activities were sensitive to molecular structure, and were compatible with the hypothesis that butyrate acts by binding to the Zn<sup>2+</sup> in the catalytic site of histone deacetylases. Structure-activity relationships drawn from a set of 36 compounds offer a starting point for the design of new compounds targeting the inhibition of histone deacetylases. The observation that butyrate was more potent than other short-chain fatty acids is compatible with the hypothesis that crypts evolved (at least in part), to separate stem cells at the base of crypts from butyrate produced by commensal bacteria.

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