scholarly journals Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Martial Marbouty ◽  
Axel Cournac ◽  
Jean-François Flot ◽  
Hervé Marie-Nelly ◽  
Julien Mozziconacci ◽  
...  
Keyword(s):  
Natural Environment ◽  
Yeast Species ◽  
Integrated Approach ◽  
Chromosome Conformation Capture ◽  
Microbial Populations ◽  
Individual Species ◽  
Chromosome Organization ◽  
Model Species ◽  
Chromosome Conformation ◽  
Genomic Analyses

Genomic analyses of microbial populations in their natural environment remain limited by the difficulty to assemble full genomes of individual species. Consequently, the chromosome organization of microorganisms has been investigated in a few model species, but the extent to which the features described can be generalized to other taxa remains unknown. Using controlled mixes of bacterial and yeast species, we developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual genomes and their average organization within a mix of organisms. Not only can meta3C be applied to species already sequenced, but a single meta3C library can be used for assembling, scaffolding and characterizing the tridimensional organization of unknown genomes. By applying meta3C to a semi-complex environmental sample, we confirmed its promising potential. Overall, this first meta3C study highlights the remarkable diversity of microorganisms chromosome organization, while providing an elegant and integrated approach to metagenomic analysis.

scholarly journals Author response: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

2014 ◽  
Author(s):  
Martial Marbouty ◽  
Axel Cournac ◽  
Jean-François Flot ◽  
Hervé Marie-Nelly ◽  
Julien Mozziconacci ◽  
...  
Keyword(s):  
Chromosome Conformation Capture ◽  
Author Response ◽  
Chromosome Organization ◽  
Chromosome Conformation

Cross-species meta-analysis of transcriptome changes during the morula to blastocyst transition: metabolic and physiological changes take center stage

2021 ◽  
Author(s):  
Peter Z. Schall ◽  
Keith E. Latham
Keyword(s):  
Inner Cell Mass ◽  
Cholesterol Biosynthesis ◽  
Meta Analysis ◽  
Cell Mass ◽  
Tca Cycle ◽  
Individual Species ◽  
Sequencing Data ◽  
Model Species ◽  
Ampk Signaling ◽  
Estrogen Receptor Signaling

The morula to blastocyst transition (MBT) culminates with formation of inner cell mass (ICM) and trophectoderm (TE) lineages. Recent studies identified signaling pathways driving lineage specification, but some features of these pathways display significant species divergence. To better understand evolutionary conservation of the MBT, we completed a meta-analysis of RNA sequencing data from five model species and ICM-TE differences from four species. While many genes change in expression during the MBT within any given species, the number of shared DEGs is comparatively small, and the number of shared ICM-TE DEGs is even smaller. DEGs related to known lineage determining pathways (e.g., POU5F1) are seen, but the most prominent pathways and functions associated with shared DEGs or shared across individual species DEG lists impact basic physiological and metabolic activities, such as TCA cycle, unfolded protein response, oxidative phosphorylation, sirtuin signaling, mitotic roles of polo-like kinases, NRF2-mediated oxidative stress, estrogen receptor signaling, apoptosis, necrosis, lipid and fatty acid metabolism, cholesterol biosynthesis, endocytosis, AMPK signaling, homeostasis, transcription, and cell death. We also observed prominent differences in transcriptome regulation between ungulates and non-ungulates, particularly for ICM- and TE-enhanced mRNAs. These results extend our understanding of shared mechanisms of the MBT and ICM/TE formation and should better inform the selection of model species for particular applications.

scholarly journals Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Romain Koszul ◽  
Laurent Debarbieux ◽  
Martial Marbouty
Keyword(s):  
Murine Model ◽  
Bacterial Genome ◽  
Chromosome Conformation Capture ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Chromosome Conformation

ABSTRACT The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.

scholarly journals SisterC: A novel 3C-technique to detect chromatin interactions between and along sister chromatids

2020 ◽  
Author(s):  
Marlies E. Oomen ◽  
Adam K. Hedger ◽  
Jonathan K. Watts ◽  
Job Dekker
Keyword(s):  
Cell Cycle ◽  
Single Strand ◽  
Chromosome Conformation Capture ◽  
Brdu Incorporation ◽  
Chromosome Conformation ◽  
Strand Breaks ◽  
Chromatin Interactions ◽  
Sister Chromatids ◽  
Single Strand Breaks ◽  
Capture Techniques

Abstract Current chromosome conformation capture techniques are not able to distinguish sister chromatids. Here we describe the protocol of SisterC1: a novel Hi-C technique that leverages BrdU incorporation and UV/Hoechst-induced single strand breaks to identify interactions along and between sister chromatids. By synchronizing cells, BrdU is incorporated only on the newly replicated strand, which distinguishes the two sister chromatids2,3. This is followed by Hi-C4 of cells that can be arrested in different stages of the cell cycle, e.g. in mitosis. Before final amplification of the Hi-C library, strands containing BrdU are specifically depleted by UV/Hoechst treatment. SisterC libraries are then sequenced using 50bp paired end reads, followed by mapping using standard Hi-C processing tools. Interactions can then be assigned as inter- or intra-sister interactions based on read orientation.

scholarly journals A streamlined tethered chromosome conformation capture protocol

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Idan Gabdank ◽  
Sreejith Ramakrishnan ◽  
Anne M. Villeneuve ◽  
Andrew Z. Fire
Keyword(s):  
Chromosome Conformation Capture ◽  
Chromosome Conformation
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