Biology subjects

Hemberg, M.

Publications and source records attributed to Hemberg, M..

5 recordsLinked to original sources

bioRxiv2018

Simulation based benchmarking of isoform quantification in single-cell RNA-seq

Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. We carried out a benchmark for five popular isoform quantification tools. Performance was generally good when run on simulated data based on SMARTer and SMART-seq2 data, but was poor for simulated Drop-seq data. Importantly, the reduction in performance for single-cell RNA-seq compared with bulk RNA-seq was small. An important biological insight comes from our analysis of real data which showed that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells.

bioinformatics↗

bioRxiv2017

scmap - A tool for unsupervised projection of single cell RNA-seq data

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues1-9 since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome8,10. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. Here, we present scmap (http://bioconductor.org/packages/scmap), a method for projecting cells from a scRNA-seq experiment onto the cell-types or individual cells identified in other experiments (the application can be run for free, without restrictions, from http://www.hemberg-lab.cloud/scmap).

bioinformatics↗

bioRxiv2017

Non-canonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

Somatic mutations show variation in density across cancer genomes. Previous studies have shown that chromatin organization and replication time domains are correlated with and thus predictive of this variation 1,2,3,4,5. Here, we analyse 1,809 whole-genome sequences from nine cancer types 6,7,8 to show that a subset of repetitive DNA sequences called non-B motifs that predict non-canonical secondary structure formation 9,10,11,12 can independently account for variation in mutation density. However, combined with epigenetic factors and replication timing, the variance explained can be improved to 43-76%. Intriguingly, ~2-fold mutation enrichment is observed directly within non-B motifs, is focused on exposed structural components, and is dependent on physical properties that are optimal for secondary structure formation. Therefore, there is mounting evidence that secondary structures arising from non-B motifs are not simply associated with increased mutation density, they are possibly causally implicated. Our results suggest that they are determinants of mutagenesis and increase the likelihood of recurrent mutations in the genome 13,6. This analysis calls for caution in the interpretation of recurrent mutations and highlights the importance of taking non-B motifs, that can simply be inferred from the reference sequence, into consideration in background models of mutability henceforth.

genomics↗

bioRxiv2017

The Human Cell Atlas

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body, by undertaking a Human Cell Atlas Project as an international collaborative effort. The aim would be to define all human cell types in terms of distinctive molecular profiles (e.g., gene expression) and connect this information with classical cellular descriptions (e.g., location and morphology). A comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, as well as provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas.

cell biology↗

bioRxiv2016

The Aquarius/EMB-4 helicase licenses co-transcriptional gene silencing

Small RNAs (sRNAs) play an ancient role in genome defence against transposable elements. In animals, plants and fungi small RNAs guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. In animals the link between small RNA pathways and the transcriptional machinery remains unclear. Here we show that the Caenorhabditis elegans germline Argonaute HRDE-1 physically interacts with the conserved RNA helicase Aquarius/EMB-4. We demonstrate that the Aquarius/EMB-4 helicase activity is required to initiate small RNA-induced co-transcriptional gene silencing. HRDE-1 and Aquarius/EMB-4 are required to silence the transcription of overlapping sets of transposable elements. Surprisingly, removal of introns from a small RNA pathway target abolishes the requirement for Aquarius/EMB-4, but not HRDE-1, for gene silencing. We conclude that the Aquarius/EMB-4 helicase activity allows HRDE-1/sRNA complexes to efficiently engage nascent RNA transcripts - in competition with the general RNA processing machinery. We postulate that Aquarius/EMB-4 facilitates the surveillance of the nascent transcriptome to detect and silence transposable elements through small RNA pathways.

molecular biology↗