Biology subjects

Benoit, G.

Publications and source records attributed to Benoit, G..

8 recordsLinked to original sources

bioRxiv2025

High-quality metagenome assembly from nanopore reads with nanoMDBG

Third-generation long-read sequencing technologies, have been shown to significantly enhance the quality of metagenome assemblies. The results obtained using the highly accurate reads generated by PacBio HiFi have been particularly notable yielding hundreds of circularized, complete genomes as metagenome-assembled genomes (MAGs) without manual intervention. Oxford Nanopore Technologies (ONT) has recently improved the accuracy of its sequencing reads, achieving a per-base error rate of approximately 1-2%. Given the high-throughput, convenience and low-cost of ONT sequencing this could accelerate the uptake of long read metagenomics. However, current metagenome assemblers are optimized for PacBio HiFi data and underperform on the latest ONT data and do not scale to the large data sets that it enables. We present nanoMDBG, an evolution of the metaMDBG HiFi assembler, designed to support newer ONT sequencing data through a novel pre-processing step that performs fast and accurate error correction in minimizer-space. Across a range of ONT datasets, including a large 400 Gbp soil sample sequenced specifically for this study, nanoMDBG reconstructs up to twice as many high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. As a result of these advances, we show that the latest ONT technology can now produce results comparable to those obtained using PacBio HiFi sequencing at the same sequencing depth.

bioinformatics↗

bioRxiv2024

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

Long-read metagenomic sequencing is a powerful approach for cataloging the microbial diversity present in complex microbiomes, including the human gut microbiome. We performed a deep-sequencing experiment using PacBio HiFi reads to obtain metagenome-assembled genomes (MAGs) from a pooled human gut microbiome. We performed long-read metagenome assembly using two methods (hifiasm-meta, metMDBG), used improved bioinformatic and proximity ligation binning strategies to cluster contigs and identify MAGs, and developed a novel framework to compare and consolidate MAGs (pb-MAG-mirror). We found proximity ligation binning yielded more MAGs than bioinformatic binning, but our novel comparison framework resulted in higher MAG yields than either binning strategy individually. In total, from 255 Gbp of total HiFi data we produced 595 total MAGs (including 175 high-quality MAGs) using hifiasm-meta, and 547 total MAGs (including 277 high-quality MAGs) with metaMDBG. Hifiasm-meta assembled almost twice as many strain-level MAGs as metaMDBG (246 vs. 156), but both assembly methods produced up to five strains for a species. Approximately 85% of the MAGs were assigned to known species, but we recovered >35 high-quality MAGs that represent uncultured diversity. Based on strict similarity scores, we found 125 MAGs were unequivocally shared across the assembly methods at the strain level, representing [~]22% of the total MAGs recovered per method. Finally, we detected more total viral sequences in the metaMDBG assembly versus the hifiasm-meta assembly ([~]6,700 vs. [~]4,500). Overall, we find the use of HiFi sequencing, improved metagenome assembly methods, and complementary binning strategies is highly effective for rapidly cataloging microbial genomes in complex microbiomes.

microbiology↗

bioRxiv2024

TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell fate acquisition

Acquisition of cell identity is associated with a remodeling of the epigenome in part through active DNA demethylation. The T:G mismatch DNA glycosylase (TDG) participates to this process by removing 5-methylcytosines that have been oxidized by Ten-Eleven-Translocation (TET) enzymes. Despite this well-defined molecular function, a comprehensive view of the biological function of TDG is still lacking, especially during cell differentiation. Here, we combined transcriptomic and epigenomic approaches in a Tdg knock-out epiblast stem-like cell model to decipher TDG function in pluripotent cells and their retinoic acid-induced progeny. We determined that TDG occupies a majority of active promoters, a large fraction of which are also engaged by the transcription factor ATF4. Consistently, neural fate commitment upon retinoic acid treatment is associated with a TDG-dependent sustained expression of ATF4-dependent genes, in relation with a TDG-associated nucleosome positioning at promoters. We further evidenced that TDG maintains ATF4 pathway activity by positively regulating the mammalian target of rapamycin complex 1 (mTORC1), favoring neural cell fate commitment. These observations highlight the central role of TDG in cell differentiation and support a model linking metabolic reprogramming to cell fate acquisition.

genomics↗

bioRxiv2023

Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs

We introduce a novel metagenomics assembler for high-accuracy long reads. Our approach, implemented as metaMDBG, combines highly efficient de Bruijn graph assembly in minimizer space, with both a multi-k' approach for dealing with variations in genome coverage depth and an abundance-based filtering strategy for simplifying strain complexity. The resulting algorithm is more efficient than the state-of-the-art but with better assembly results. metaMDBG was 1.5 to 12 times faster than competing assemblers and requires between one-tenth and one-thirtieth of the memory across a range of data sets. We obtained up to twice as many high-quality circularised prokaryotic metagenome assembled genomes (MAGs) on the most complex communities, and a better recovery of viruses and plasmids. metaMDBG performs particularly well for abundant organisms whilst being robust to the presence of strain diversity. The result is that for the first time it is possible to efficiently reconstruct the majority of complex communities by abundance as nearcomplete MAGs.

bioinformatics↗

bioRxiv2022

One model fits all: combining inferenceand simulation of gene regulatorynetworks

The rise of single-cell data highlights the need for a nondeterministic view of gene expression, while offering new opportunities regarding gene regulatory network inference. We recently introduced two strategies that specifically exploit time-course data, where single-cell profiling is performed after a stimulus: HARISSA, a mechanistic network model with a highly efficient simulation procedure, and CARDAMOM, a scalable inference method seen as model calibration. Here, we combine the two approaches and show that the same model driven by transcriptional bursting can be used simultaneously as an inference tool, to reconstruct biologically relevant networks, and as a simulation tool, to generate realistic transcriptional profiles emerging from gene interactions. We verify that CARDAMOM quantitatively reconstructs causal links when the data is simulated from HARISSA, and demonstrate its performance on experimental data collected on in vitro differentiating mouse embryonic stem cells. Overall, this integrated strategy largely overcomes the limitations of disconnected inference and simulation. Author summaryGene regulatory network (GRN) inference is an old problem, to which single-cell data has recently offered new challenges and breakthrough potential. Many GRN inference methods based on single-cell transcriptomic data have been developed over the last few years, while GRN simulation tools have also been proposed for generating synthetic datasets with realistic features. However, except for benchmarking purposes, these two fields remain largely disconnected. In this work, building on a combination of two methods we recently described, we show that a particular GRN model can be used simultaneously as an inference tool, to reconstruct a biologically relevant network from time-course single-cell gene expression data, and as a simulation tool, to generate realistic transcriptional profiles in a non-trivial way through gene interactions. This integrated strategy demonstrates the benefits of using the same executable model for both simulation and inference.

systems biology↗

bioRxiv2021

Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain.

The formation of a diploid zygote is a highly complex cellular process that is entirely controlled by maternal gene products stored in the egg cytoplasm. This highly specialized transcriptional program is tightly controlled at the chromatin level in the female germline. As an extreme case in point, the massive and specific ovarian expression of the essential thioredoxin Deadhead (DHD) is critically regulated in Drosophila by the histone demethylase Lid and its partner, the histone deacetylase complex scaffold Sin3A, via yet unknown mechanisms. Here, we identified the Brahma chromatin remodeler sub-unit Snr1 and the insulator component Mod(mdg4) as essential for dhd expression and investigated how these epigenomic effectors act with Lid and Sin3A to hyperactivate dhd. Using Cut&Run chromatin profiling with a dedicated data analysis procedure, we found that dhd is intriguingly embedded in an H3K27me3/H3K9me3-enriched mini-domain flanked by DNA regulatory elements, including a dhd promoter-proximal element essential for its expression. Surprisingly, Lid, Sin3A, Snr1 and Mod(mdg4) impact H3K27me3 and this regulatory element in distinct manners. However, we show that these effectors activate dhd independently of H3K27me3/H3K9me3, and that these marks are not required to repress dhd. Together, our study demonstrates an atypical and critical role for chromatin regulators Lid, Sin3A, Snr1 and Mod(mdg4) to trigger tissue-specific hyperactivation within a unique heterochromatin mini-domain. AUTHOR SUMMARYGene expression is tightly regulated by conserved protein complexes that act at the chromatin level to allow or restrict transcription. Such epigenetic control of gene activity defines the identity of different cell types during development, as well as their response to environmental cues. Yet, how multiple chromatin factors converge to achieve precise gene regulation remains difficult to address, partly due to the lack of biological situations where these intricate relationships can be studied. In this paper, we have addressed this issue by dissecting the regulation of deadhead, an essential gene specifically and massively expressed in the Drosophila germline. Unexpectedly, we found that its hyperactivation occurs despite deadhead being embedded in an apparently unfavorable chromatin mini-domain, notably featuring repressive histone modifications. We further demonstrate that four chromatin effectors, Lid, Sin3A, Snr1 and Mod(mdg4), have distinct, atypical and essential roles to ensure deadhead expression within this chromatin environment. Together, our findings put into perspective our understanding on these regulatory factors by illustrating how they can exert a biologically essential function via non-canonical mechanisms.

genetics↗

bioRxiv2019

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical and physical context of the ocean (the seascape) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.

ecology↗

bioRxiv2019

The Lid/KDM5 histone demethylase complex activates a critical effector of the oocyte-to-zygote transition

Following fertilization of a mature oocyte, the formation of a diploid zygote involves a series of coordinated cellular events that ends with the first embryonic mitosis. In animals, this complex developmental transition is almost entirely controlled by maternal gene products. How such a crucial transcriptional program is established during oogenesis remains poorly understood. Here, we have performed an shRNA-based genetic screen in Drosophila to identify genes required to form a diploid zygote. We found that the Lid/KDM5 histone demethylase and its partner, the Sin3A-HDAC1 deacetylase complex, are necessary for sperm nuclear decompaction and karyogamy. Surprisingly, transcriptomic analyses revealed that these histone modifiers are required for the massive transcriptional activation of deadhead (dhd), which encodes a maternal thioredoxin involved in sperm chromatin remodeling. Unexpectedly, while lid knock-down tends to slightly favor the accumulation of its target, H3K4me3, on the genome, this mark was lost at the dhd locus. We propose that Lid/KDM5 and Sin3A cooperate to establish a local chromatin environment facilitating the unusually high expression of dhd, a key effector of the oocyte-to-zygote transition.

genetics↗