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BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences

Christian Rohde, Yingying Zhang, Richard Reinhardt, Albert Jeltsch
2010 BMC Bioinformatics  
The BISMA software is freely available as an online tool for academic purposes for the analysis of bisulfite sequencing data from both unique and repetitive sequences  ...  Results: The BISMA (Bisulfite Sequencing DNA Methylation Analysis) software for analysis of primary bisulfite sequencing data implements sequencing data extraction and enhanced data processing, quality  ...  Jurkowski for discussions about implementation of sequencing data extraction and alignment tools in web applications.  ... 
doi:10.1186/1471-2105-11-230 pmid:20459626 pmcid:PMC2877691 fatcat:5rv3ru3hpzdptng2wusbqxeubu

The Relevance of Methylation Profiles of Equine ITGAL Gene

Tomasz Ząbek, Ewelina Semik, Agnieszka Fornal, Artur Gurgul, Monika Bugno-Poniewierska
2016 Annals of Animal Science  
Comparison between qualitative RT-PCR results and DNA bisulfite sequencing of investigated set of tissues pointed to potential correlations between tissue specific methylation and tissue specific transcription  ...  These findings might be important for studies on genetic and epigenetic background of autoimmune disorders in the horse.  ...  Emerging concept in DNA methylation: role of transcription factors (2010). BISMA -fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences.  ... 
doi:10.1515/aoas-2015-0080 fatcat:sapgeokagfesdekjw2ty5ma2bi

Integrating Epigenomics into the Understanding of Biomedical Insight

Yixing Han, Ximiao He
2016 Bioinformatics and Biology Insights  
Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence.  ...  Abstr Act: Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of  ...  clones from unique and repetitive sequences http://biochem.jacobs-university.de/BdPc/Bisma/ 326 Brat-BW A fast, accurate and memory-efficient Bs aligner using the fm-index (Burrows-Wheeler transform  ... 
doi:10.4137/bbi.s38427 pmid:27980397 pmcid:PMC5138066 fatcat:ne6mu3bdhzhzno5hqjvgmxp3nu

Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases

Lin Lin, Yong Liu, Fengping Xu, Jinrong Huang, Tina Fuglsang Daugaard, Trine Skov Petersen, Bettina Hansen, Lingfei Ye, Qing Zhou, Fang Fang, Ling Yang, Shengting Li (+11 others)
2018 GigaScience  
Acknowledgements 741 This work was partially supported by grants from Danish Research Council for Independent 742 Research DFF-1337-00128 (Y.L.), the Sapere Aude Young Research Talent Prize DFF-1335  ...  Rohde C, Zhang Y, Reinhardt R, Jeltsch A: BISMA--fast and accurate 878 bisulfite sequencing data analysis of individual clones from unique and 879 repetitive sequences.  ...  analysis by bisulfite Sanger sequencing 191 193 194 8 196 sequencing and analyzed by BISMA [36]. 197 198 Fluorescence reporter cell assay 199 Five stable fluorescence reporter cell  ... 
doi:10.1093/gigascience/giy011 pmid:29635374 pmcid:PMC5888497 fatcat:4eyxpitdl5cmta2vbwyu4nprrm

Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse

Ghislain Auclair, Sylvain Guibert, Ambre Bender, Michael Weber
2014 Genome Biology  
DNMT3A and DNMT3B act redundantly to methylate the bulk genome and repetitive elements, whereas DNMT3B has a prominent role in the methylation of CpG islands on autosomes and the X chromosome.  ...  Results: We generated single-base maps of DNA methylation from the blastocyst to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity.  ...  Acknowledgements We thank Jesus del Mazo and Florence Cammas for contributing samples.  ... 
doi:10.1186/s13059-014-0545-5 pmid:25476147 pmcid:PMC4295324 fatcat:yxm4gyz3nngnvbgdw5bkgdmhk4

Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse

Ghislain Auclair, Sylvain Guibert, Ambre Bender, Michael Weber
2014 Genome Biology  
DNMT3A and DNMT3B act redundantly to methylate the bulk genome and repetitive elements, whereas DNMT3B has a prominent role in the methylation of CpG islands on autosomes and the X chromosome.  ...  Results: We generated single-base maps of DNA methylation from the blastocyst to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity.  ...  Acknowledgements We thank Jesus del Mazo and Florence Cammas for contributing samples.  ... 
doi:10.1186/preaccept-1058837845136423 pmid:25476147 pmcid:PMC4295324 fatcat:nq727obka5ggvktuxe2qbmrdhi

High throughput screening identifies SOX2 as a Super Pioneer Factor that inhibits DNA methylation maintenance at its binding sites [article]

Ludovica Vanzan, Hadrien Soldati, Victor Ythier, Santosh Anand, Nicole J Francis, Rabih Murr
2020 bioRxiv   pre-print
most PFs do not induce changes in DNA methylation at their binding sites, we identified PFs that can protect DNA from methylation and PFs that can induce DNA demethylation at methylated binding sites.  ...  Remarkably, a special class of TFs called pioneer transcription factors (PFs) can access nucleosomal DNA, leading to nucleosome remodelling and chromatin opening.  ...  BISMA -Fast and accurate 895 bisulfite sequencing data analysis of individual clones from unique and 896 repetitive sequences. BMC Bioinformatics 11, (2010). 897 70.  ... 
doi:10.1101/2020.02.10.941682 fatcat:tdo75hldtff6fhwjx4eiip3gzq

On the Analysis of DNA Methylation

Michael Stevens
2014
However, trimming reduces the length of reads which may induce more multimapped reads and thus reduce coverage. It has not yet been examined whether the first point  ...  Individual bacterial colonies were subjected to PCR using vector-specific primers and sequenced (Quintara biosciences). The data were analyzed with online software BISMA [70] .  ...  We used conventional bisulfite conversion, PCR, cloning and sequencing to validate loci where our predictions do not agree with whole genome bisulfite data, and in 11 out of 12 cases methylCRF predictions  ... 
doi:10.7936/k70c4sv8 fatcat:pjifppzmrbcbfgr444gx2japtm

Bioinformatic tools and computational methods for mapping DNA methylation variability [article]

Pavlo Lutsik, Universität Des Saarlandes, Universität Des Saarlandes
2017
The R-package RnBeads supports analysis of genome-scale pro les from In nium microarrays and bisul te sequencing, while BiQ Analyzer HT and HiMod enable complete and interactive analysis of deep locus-speci  ...  First, comprehensive and user-friendly tools were developed for processing and primary analysis of bisul te-based DNA methylation data.  ...  , and Karl Noerdstrom for valuable discussion on preprocessing of sequencing data.  ... 
doi:10.22028/d291-23222 fatcat:3tlzzolpjbdxld5mkjyikurlxq