Biology subjects

Johannes, F.

Publications and source records attributed to Johannes, F..

3 recordsLinked to original sources

bioRxiv2017

METHimpute: Imputation-guided construction of complete methylomes from WGBS data

Whole-genome Bisulfite sequencing (WGBS) has become the standard method for interrogating plant methylomes at base resolution. However, deep WGBS measurements remain cost prohibitive for large, complex genomes and for population-level studies. As a result, most published plant methylomes are sequenced far below saturation, with a large proportion of cytosines having either missing data or insufficient coverage. Here we present METHimpute, a Hidden Markov Model (HMM) based imputation algorithm for the analysis of WGBS data. Unlike existing methods, METHimpute enables the construction of complete methylomes by inferring the methylation status and level of all cytosines in the genome regardless of coverage. Application of METHimpute to maize, rice and Arabidopsis shows that the algorithm infers cytosine-resolution methylomes with high accuracy from data as low as 6X, compared to data with 60X, thus making it a cost-effective solution for large-scale studies. Although METHimpute has been extensively tested in plants, it should be broadly applicable to other species.

bioinformatics↗

bioRxiv2017

Learning sequence patterns of AGO-sRNA affinity from high-throughput sequencing libraries to improve in silico functional small RNA detection and classification in plants

The loading of small RNA (sRNA) into Argonaute (AGO) complexes is a crucial step in all regulatory pathways identified so far in plants that depend on such non-coding sequences. Important transcriptional and post-transcriptional silencing mechanisms can be activated depending on the specific AGO protein to which sRNA bind. It is known that sRNA-AGO associations are at least partly encoded in the sRNA primary structure, but the sequence features that drive this association have not been fully explored. Here we train support vector machines (SVM) on sRNA sequencing data obtained from AGO-immunoprecipitation experiments to identify features that determine sRNA affinity to specific AGOs. Our SVM reveal that AGO affinity is strongly determined by complex k-mers in the 5 and 3 ends of sRNA, in addition to well-known features such as sRNA length and the base composition of the first nucleotide. Moreover, we find that these k-mers tend to overlap known transcription factor (TF) binding motifs, thus highlighting a close interplay between TF and sRNA-mediated transcriptional regulation. We embedded the learned SVM in a computational pipeline that can be used for de novo functional classification of sRNA sequences. This tool, called SAILS, is provided as a web portal accessible at http://sails.eu.nu.

bioinformatics↗

bioRxiv2017

Small RNAs reflect grandparental environments in apomictic dandelion

Plants can show long-term effects of environmental stresses and in some cases a stress memory has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21nt and 24nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This indicates that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent and functional changes in epigenetic gene regulation.

genetics↗