scholarly journals Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sandhya Chandrasekaran ◽  
Sergio Espeso-Gil ◽  
Yong-Hwee Eddie Loh ◽  
Behnam Javidfar ◽  
Bibi Kassim ◽  
...  
Keyword(s):  
Single Molecule ◽  
Mus Musculus ◽  
Endogenous Retrovirus ◽  
Cellular Stress Response ◽  
Chromatin Domain ◽  
Open Chromatin ◽  
Mus Spretus ◽  
Contact Mapping ◽  
Long Read ◽  
Mature Neurons

AbstractRegulatory mechanisms associated with repeat-rich sequences and chromosomal conformations in mature neurons remain unexplored. Here, we map cell-type specific chromatin domain organization in adult mouse cerebral cortex and report strong enrichment of Endogenous Retrovirus 2 (ERV2) repeat sequences in the neuron-specific heterochromatic B2NeuN+ megabase-scaling subcompartment. Single molecule long-read sequencing and comparative Hi-C chromosomal contact mapping in wild-derived SPRET/EiJ (Mus spretus) and laboratory inbred C57BL/6J (Mus musculus) reveal neuronal reconfigurations tracking recent ERV2 expansions in the murine germline, with significantly higher B2NeuN+ contact frequencies at sites with ongoing insertions in Mus musculus. Neuronal ablation of the retrotransposon silencer Kmt1e/Setdb1 triggers B2NeuN+ disintegration and rewiring with open chromatin domains enriched for cellular stress response genes, along with severe neuroinflammation and proviral assembly with infiltration of dendrites . We conclude that neuronal megabase-scale chromosomal architectures include an evolutionarily adaptive heterochromatic organization which, upon perturbation, results in transcriptional dysregulation and unleashes ERV2 proviruses with strong neuronal tropism.

scholarly journals NEURON-SPECIFIC CHROMOSOMAL MEGADOMAIN ORGANIZATION IS ADAPTIVE TO RECENT RETROTRANSPOSON EXPANSIONS

2021 ◽  
Author(s):  
Sandhya Chandrasekaran ◽  
Sergio Espeso-Gil ◽  
Yong-Hwee Eddie Loh ◽  
Behnam Javidfar ◽  
Bibi Kassim ◽  
...  
Keyword(s):  
Mus Musculus ◽  
Endogenous Retrovirus ◽  
Cellular Stress Response ◽  
Chromatin Domain ◽  
Open Chromatin ◽  
Mus Spretus ◽  
Stress Response Genes ◽  
Mouse Cerebral Cortex ◽  
Mature Neurons ◽  
Cell Type Specific

ABSTRACTHere, we mapped cell-type specific chromatin domain organization in adult mouse cerebral cortex and report strong enrichment of Endogenous Retrovirus 2 (ERV2) repeat sequences in the neuron-specific heterochromatic ‘B2NeuN+’ megabase-scaling subcompartment. Comparative chromosomal conformation mapping in Mus spretus and Mus musculus revealed neuron-specific reconfigurations tracking recent ERV2 retrotransposon expansions in the murine germline, with significantly higher B2 megadomain contact frequencies at sites with ongoing ERV2 insertions in Mus musculus. Ablation of the retrotransposon silencer Kmt1e/Setdb1 triggered B2 megadomain disintegration and rewiring with open chromatin domains enriched for cellular stress response genes, along with severe neuroinflammation and proviral assembly of ERV2/Intracisternal-A-Particles (IAPs) infiltrating dendrites and spines. We conclude that neuronal megadomain architectures include evolutionarily adaptive heterochromatic organization which, upon perturbation, unleashes ERV proviruses with strong tropism within mature neurons.

scholarly journals Long-range single-molecule mapping of chromatin accessibility in eukaryotes

2018 ◽  
Author(s):  
Zohar Shipony ◽  
Georgi K. Marinov ◽  
Matthew P. Swaffer ◽  
Nasa A. Sinott-Armstrong ◽  
Jan M. Skotheim ◽  
...  
Keyword(s):  
Single Molecule ◽  
Regulatory Elements ◽  
Dna Methyltransferases ◽  
Chromatin Accessibility ◽  
Chromatin State ◽  
Open Chromatin ◽  
Structure Mapping ◽  
Long Read ◽  
Distal Regulatory Elements ◽  
Resolution Single

AbstractActive regulatory elements in eukaryotes are typically characterized by an open, nucleosome-depleted chromatin structure; mapping areas of open chromatin has accordingly emerged as a widely used tool in the arsenal of modern functional genomics. However, existing approaches for profiling chromatin accessibility are limited by their reliance on DNA fragmentation and short read sequencing, which leaves them unable to provide information about the state of chromatin on larger scales or reveal coordination between the chromatin state of individual distal regulatory elements. To address these limitations, we have developed a method for profiling accessibility of individual chromatin fibers at multi-kilobase length scale (SMAC-seq, or Single-Molecule long-read Accessible Chromatin mapping sequencing assay), enabling the simultaneous, high-resolution, single-molecule assessment of the chromatin state of distal genomic elements. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases (CpG and GpC 5-methylcytosine (5mC) and N6-methyladenosine (m6A) enzymes) and the ability of long-read single-molecule nanopore sequencing to directly read out the methylation state of individual DNA bases. Applying SMAC-seq to the budding yeast Saccharomyces cerevisiae, we demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule protection footprints of nucleosomes and transcription factors, and quantify the correlation between the chromatin states of distal genomic elements.

scholarly journals Recent advances in the detection of base modifications using the Nanopore sequencer

2019 ◽  
Vol 65 (1) ◽  
pp. 25-33 ◽  
Author(s):  
Liu Xu ◽  
Masahide Seki
Keyword(s):  
Single Molecule ◽  
Statistical Tests ◽  
Regulation Of Gene Expression ◽  
Detection Methods ◽  
Open Chromatin ◽  
Rna Molecules ◽  
Base Modification ◽  
Dna And Rna ◽  
Long Read ◽  
Nanopore Sequencer

Abstract DNA and RNA modifications have important functions, including the regulation of gene expression. Existing methods based on short-read sequencing for the detection of modifications show difficulty in determining the modification patterns of single chromosomes or an entire transcript sequence. Furthermore, the kinds of modifications for which detection methods are available are very limited. The Nanopore sequencer is a single-molecule, long-read sequencer that can directly sequence RNA as well as DNA. Moreover, the Nanopore sequencer detects modifications on long DNA and RNA molecules. In this review, we mainly focus on base modification detection in the DNA and RNA of mammals using the Nanopore sequencer. We summarize current studies of modifications using the Nanopore sequencer, detection tools using statistical tests or machine learning, and applications of this technology, such as analyses of open chromatin, DNA replication, and RNA metabolism.

scholarly journals Sequencing of Methylase-Accessible Regions In Integral Circular Extrachromosomal DNA Reveals Differences In Chromatin Structure

2021 ◽  
Author(s):  
Weitian Chen ◽  
Zhe Weng ◽  
Zhe Xie ◽  
Yeming Xie ◽  
Chen Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Regulatory Mechanisms ◽  
Open Chromatin ◽  
Nanopore Sequencing ◽  
Extrachromosomal Dna ◽  
Circular Dna ◽  
Short Read Sequencing ◽  
Sequencing Studies ◽  
Long Read ◽  
Accessible Chromatin

Abstract Background Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In the majority of conventional sequencing studies, the high-throughput short-read sequencing largely ignores the epigenetic status of most ecDNA regions except for the junctional areas. MethodsHere, we developed the sequencing of enzyme-accessible chromatin in circular DNA (CCDA-seq) method, which uses methylase to label open chromatin without fragmentation and exonuclease to enrich the ecDNA sequencing depth, followed by long-read nanopore sequencing. ResultsUsing CCDA-seq, we observed significantly different patterns in nucleosome/regulator binding in ecDNA at a single-molecule resolution. ConclusionsThese results deepen the understanding of ecDNA regulatory mechanisms.

scholarly journals Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Weitian Chen ◽  
Zhe Weng ◽  
Zhe Xie ◽  
Yeming Xie ◽  
Chen Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Regulatory Mechanisms ◽  
Open Chromatin ◽  
Nanopore Sequencing ◽  
Extrachromosomal Dna ◽  
Circular Dna ◽  
Short Read Sequencing ◽  
Sequencing Studies ◽  
Long Read ◽  
Accessible Chromatin

Abstract Background Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In most conventional sequencing studies, the high-throughput short-read sequencing largely ignores the epigenetic status of most ecDNA regions except for the junctional areas. Methods Here, we developed a method of sequencing enzyme-accessible chromatin in circular DNA (CCDA-seq) based on the use of methylase to label open chromatin without fragmentation and exonuclease to enrich ecDNA sequencing depth, followed by long-read nanopore sequencing. Results Using CCDA-seq, we observed significantly different patterns in nucleosome/regulator binding to ecDNA at a single-molecule resolution. Conclusions These results deepen the understanding of ecDNA regulatory mechanisms.

scholarly journals CDCA-seq resolve the different chromatin structure on integral circular DNAs

2021 ◽  
Author(s):  
Weitian Chen ◽  
Zhe Weng ◽  
Zhe Xie ◽  
Yeming Xie ◽  
Chen Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
Single Molecule ◽  
Chromatin Structure ◽  
Regulatory Mechanism ◽  
Underlying Mechanism ◽  
Open Chromatin ◽  
Nanopore Sequencing ◽  
Research Activity ◽  
Long Read ◽  
Circular Dnas

Although ecDNAs have been a subject of sustained research activity for some years, the underlying mechanism driving the ecDNAs tumorigenesis has begun to unfold recently. Overall, from the results presented in conventional research, the high throughput short reads sequencing largely ignores the epigenetic status on most ecDNA regions except the junctional areas. We developed a method named CDCA-seq by using methylase to label the open chromatin without fragmentation, and exonuclease to enrich the ecDNA sequencing depth, followed by the long-read nanopore sequencing. Using this technology, the significantly different patterns of nucleosome/regulator binding were observed in ecDNAs at single-molecule resolution. These results further the understanding of the different regulatory mechanism on ecDNAs.

Use of Metallomics in Environmental Pollution Assessment Using Mice Mus musculus/Mus spretus as Bioindicators

2013 ◽  
Vol 9 (2) ◽  
pp. 229-243
Author(s):  
M. Gonzalez-Fernandez ◽  
M. Angel Garcia-Sevillano ◽  
R. Jara-Biedma ◽  
F. Navarro- Roldn ◽  
T. Garcia-Barrera ◽  
...  
Keyword(s):  
Environmental Pollution ◽  
Mus Musculus ◽  
Pollution Assessment ◽  
Mus Spretus

scholarly journals Analysis of HLA-G long-read genomic sequences in mother–offspring pairs with preeclampsia

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ayako Nishizawa ◽  
Kazuki Kumada ◽  
Keiko Tateno ◽  
Maiko Wagata ◽  
Sakae Saito ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Polymorphisms ◽  
Genomic Dna ◽  
Genomic Sequences ◽  
Genomic Sequencing ◽  
Public Database ◽  
Coding Sequences ◽  
Pacbio Rs Ii ◽  
Potential Association ◽  
Long Read

AbstractPreeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.

scholarly journals MBRS-47. RAPID MOLECULAR SUBGROUPING OF MEDULLOBLASTOMA BASED ON DNA METHYLATION BY NANOPORE SEQUENCING

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii406-iii406
Author(s):  
Julien Masliah-Planchon ◽  
Elodie Girard ◽  
Philipp Euskirchen ◽  
Christine Bourneix ◽  
Delphine Lequin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Molecule ◽  
Nanopore Sequencing ◽  
Molecular Subgroup ◽  
Group Assignment ◽  
Group 4 ◽  
Methylation Assay ◽  
Tumor Group ◽  
Long Read ◽  
Group 3

Abstract Medulloblastoma (MB) can be classified into four molecular subgroups (WNT group, SHH group, group 3, and group 4). The gold standard of assignment of molecular subgroup through DNA methylation profiling uses Illumina EPIC array. However, this tool has some limitation in terms of cost and timing, in order to get the results soon enough for clinical use. We present an alternative DNA methylation assay based on nanopore sequencing efficient for rapid, cheaper, and reliable subgrouping of clinical MB samples. Low-depth whole genome with long-read single-molecule nanopore sequencing was used to simultaneously assess copy number profile and MB subgrouping based on DNA methylation. The DNA methylation data generated by Nanopore sequencing were compared to a publicly available reference cohort comprising over 2,800 brain tumors including the four subgroups of MB (Capper et al. Nature; 2018) to generate a score that estimates a confidence with a tumor group assignment. Among the 24 MB analyzed with nanopore sequencing (six WNT, nine SHH, five group 3, and four group 4), all of them were classified in the appropriate subgroup established by expression-based Nanostring subgrouping. In addition to the subgrouping, we also examine the genomic profile. Furthermore, all previously identified clinically relevant genomic rearrangements (mostly MYC and MYCN amplifications) were also detected with our assay. In conclusion, we are confirming the full reliability of nanopore sequencing as a novel rapid and cheap assay for methylation-based MB subgrouping. We now plan to implement this technology to other embryonal tumors of the central nervous system.

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