scholarly journals Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing

2018 ◽  
Author(s):  
Sandro Baldi ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
Peter B. Becker
Keyword(s):  
Illumina Sequencing ◽  
Nanopore Sequencing ◽  
New Approach ◽  
Chromatin States ◽  
Genome Wide ◽  
Chromatin Organisation ◽  
Regular Succession ◽  
Nucleosome Array ◽  
Iconic Status ◽  
Nucleosome Arrays

AbstractThe nature of chromatin as regular succession of nucleosomes has gained iconic status. However, since most nucleosomes in metazoans are poorly positioned it is unknown to which extent the bulk genomic nucleosome repeat length (NRL) reflects the regularity and spacing of nucleosome arrays at individual loci. We describe a new approach to map nucleosome array regularity and spacing through sequencing oligonucleosome-derived DNA by Illumina sequencing as well as emergent nanopore-technology. This revealed modulation of array regularity and NRL depending on functional chromatin states independently of nucleosome phasing and even in unmappable regions. We also found that nucleosome arrays downstream of silent promoters are considerably more regular than those downstream of highly expressed ones, despite more extensive nucleosome phasing of the latter. Our approach is generally applicable and provides an important parameter of chromatin organisation that so far had been missing.

scholarly journals Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing

2018 ◽  
Vol 25 (9) ◽  
pp. 894-901 ◽  
Author(s):  
Sandro Baldi ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
Peter B. Becker
Keyword(s):  
Nanopore Sequencing ◽  
Genome Wide ◽  
Nucleosome Array

scholarly journals Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Elisa Oberbeckmann ◽  
Vanessa Niebauer ◽  
Shinya Watanabe ◽  
Lucas Farnung ◽  
Manuela Moldt ◽  
...  
Keyword(s):  
Phased Arrays ◽  
Stable Steady State ◽  
Reference Sites ◽  
Chromatin Remodelers ◽  
Sliding Direction ◽  
Nucleosome Dynamics ◽  
Genome Wide ◽  
Sequence Elements ◽  
Nucleosome Array ◽  
Dna Ends

AbstractArrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the ‘ruler’ that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.

Analysis of yield and oil from a series of canola breeding trials. Part II. Exploring variety by environment interaction using factor analysisThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 1002-1016 ◽  
Author(s):  
B.R. Cullis ◽  
A.B. Smith ◽  
C.P. Beeck ◽  
W.A. Cowling
Keyword(s):  
Pedigree Information ◽  
Environment Interaction ◽  
Correlation Matrices ◽  
New Approach ◽  
Genome Wide ◽  
Selection Indices ◽  
New Varieties ◽  
Oilseed Brassicas ◽  
Analytic Models ◽  
Selection Of

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents.

scholarly journals Timing Polymerase Pausing with TV-PRO-seq

2018 ◽  
Author(s):  
Jie Zhang ◽  
Massimo Cavallaro ◽  
Daniel Hebenstreit
Keyword(s):  
High Resolution ◽  
Human Cells ◽  
Rrna Genes ◽  
Dna Motifs ◽  
Single Base ◽  
Chromatin States ◽  
Genome Wide ◽  
A Genome ◽  
Single Base Resolution ◽  
Polymerase Pausing

Transcription of many genes in metazoans is subject to polymerase pausing, which corresponds to the transient arrest of transcriptionally engaged polymerase. It occurs mainly at promoter proximal regions and is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking.We present here an extension of PRO-seq, time variant PRO-seq (TV-PRO-seq), that allowed us to estimate genome-wide pausing times at single base resolution. Its application to human cells reveals that promoter proximal pausing is surprisingly short compared to other regions and displays an intricate pattern. We also find precisely conserved pausing profiles at tRNA and rRNA genes and identified DNA motifs associated with pausing time. Finally, we show how chromatin states reflect differences in pausing times.

scholarly journals Chromatin Profiling of the Repetitive and Nonrepetitive Genomes of the Human Fungal Pathogen Candida albicans

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Robert Jordan Price ◽  
Esther Weindling ◽  
Judith Berman ◽  
Alessia Buscaino
Keyword(s):  
Gene Expression ◽  
Candida Albicans ◽  
Histone Modifications ◽  
Chromatin Structure ◽  
Fungal Pathogen ◽  
Histone H3 ◽  
Content Type ◽  
Chromatin States ◽  
Genome Wide ◽  
Chromatin Profiling

ABSTRACT Eukaryotic genomes are packaged into chromatin structures that play pivotal roles in regulating all DNA-associated processes. Histone posttranslational modifications modulate chromatin structure and function, leading to rapid regulation of gene expression and genome stability, key steps in environmental adaptation. Candida albicans, a prevalent fungal pathogen in humans, can rapidly adapt and thrive in diverse host niches. The contribution of chromatin to C. albicans biology is largely unexplored. Here, we generated the first comprehensive chromatin profile of histone modifications (histone H3 trimethylated on lysine 4 [H3K4me3], histone H3 acetylated on lysine 9 [H3K9Ac], acetylated lysine 16 on histone H4 [H4K16Ac], and γH2A) across the C. albicans genome and investigated its relationship to gene expression by harnessing genome-wide sequencing approaches. We demonstrated that gene-rich nonrepetitive regions are packaged into canonical euchromatin in association with histone modifications that mirror their transcriptional activity. In contrast, repetitive regions are assembled into distinct chromatin states; subtelomeric regions and the ribosomal DNA (rDNA) locus are assembled into heterochromatin, while major repeat sequences and transposons are packaged in chromatin that bears features of euchromatin and heterochromatin. Genome-wide mapping of γH2A, a marker of genome instability, identified potential recombination-prone genomic loci. Finally, we present the first quantitative chromatin profiling in C. albicans to delineate the role of the chromatin modifiers Sir2 and Set1 in controlling chromatin structure and gene expression. This report presents the first genome-wide chromatin profiling of histone modifications associated with the C. albicans genome. These epigenomic maps provide an invaluable resource to understand the contribution of chromatin to C. albicans biology and identify aspects of C. albicans chromatin organization that differ from that of other yeasts. IMPORTANCE The fungus Candida albicans is an opportunistic pathogen that normally lives on the human body without causing any harm. However, C. albicans is also a dangerous pathogen responsible for millions of infections annually. C. albicans is such a successful pathogen because it can adapt to and thrive in different environments. Chemical modifications of chromatin, the structure that packages DNA into cells, can allow environmental adaptation by regulating gene expression and genome organization. Surprisingly, the contribution of chromatin modification to C. albicans biology is still largely unknown. For the first time, we analyzed C. albicans chromatin modifications on a genome-wide basis. We demonstrate that specific chromatin states are associated with distinct regions of the C. albicans genome and identify the roles of the chromatin modifiers Sir2 and Set1 in shaping C. albicans chromatin and gene expression.

scholarly journals FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis

2018 ◽  
Vol 115 (20) ◽  
pp. E4720-E4729 ◽  
Author(s):  
Jennifer M. Frost ◽  
M. Yvonne Kim ◽  
Guen Tae Park ◽  
Ping-Hung Hsieh ◽  
Miyuki Nakamura ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Nucleosome Occupancy ◽  
Dna Demethylation ◽  
Embryo Viability ◽  
Chromatin States ◽  
Specific Recognition ◽  
Genome Wide ◽  
Target Sites ◽  
Recognition Protein

The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.

scholarly journals A new view of transcriptome complexity and regulation through the lens of local splicing variations

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Jorge Vaquero-Garcia ◽  
Alejandro Barrera ◽  
Matthew R Gazzara ◽  
Juan González-Vallinas ◽  
Nicholas F Lahens ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Alternative Splicing ◽  
Gene Function ◽  
Specific Protein ◽  
Mrna Splicing ◽  
New Approach ◽  
Genome Wide ◽  
Mouse Tissues ◽  
Splice Variation ◽  
Novel Isoforms

Alternative splicing (AS) can critically affect gene function and disease, yet mapping splicing variations remains a challenge. Here, we propose a new approach to define and quantify mRNA splicing in units of local splicing variations (LSVs). LSVs capture previously defined types of alternative splicing as well as more complex transcript variations. Building the first genome wide map of LSVs from twelve mouse tissues, we find complex LSVs constitute over 30% of tissue dependent transcript variations and affect specific protein families. We show the prevalence of complex LSVs is conserved in humans and identify hundreds of LSVs that are specific to brain subregions or altered in Alzheimer's patients. Amongst those are novel isoforms in the Camk2 family and a novel poison exon in Ptbp1, a key splice factor in neurogenesis. We anticipate the approach presented here will advance the ability to relate tissue-specific splice variation to genetic variation, phenotype, and disease.

scholarly journals Epigenetic Inheritance is Gated by Naive Pluripotency and Dppa2

2021 ◽  
Author(s):  
Valentina Carlini ◽  
Cristina Policarpi ◽  
Jamie A Hackett
Keyword(s):  
De Novo ◽  
Epigenetic Inheritance ◽  
Developmental Model ◽  
Lineage Specification ◽  
Chromatin States ◽  
Genome Wide ◽  
Mechanistic Basis ◽  
Endogenous Loci ◽  
Epigenetic Editing

Environmental factors can trigger cellular responses that propagate across mitosis or even generations. Perturbations to the epigenome could underpin such acquired changes, however, the extent and contexts in which modified chromatin states confer heritable memory in mammals is unclear. Here we exploit a modular epigenetic editing strategy to establish de novo heterochromatin domains (epialleles) at endogenous loci and track their inheritance in a developmental model. We find that naive pluripotent phases systematically erase ectopic domains of heterochromatin via active mechanisms, which acts as an intergenerational safeguard against transmission of epialleles. Upon lineage specification however, acquired chromatin states can be probabilistically inherited under selectively favourable conditions, including propagation of p53 silencing through in vivo development. Using genome-wide CRISPR screening, we identify the mechanisms that block heritable silencing memory in pluripotent cells, and demonstrate removal of Dppa2 unlocks the potential for epigenetic inheritance uncoupled from DNA sequence. Our study outlines a mechanistic basis for how epigenetic inheritance is restricted in mammals, and reveals genomic- and developmental- contexts in which heritable memory is feasible.

scholarly journals SLOW5: a new file format enables massive acceleration of nanopore sequencing data analysis

2021 ◽  
Author(s):  
Hasindu Gamaarachchi ◽  
Hiruna Samarakoon ◽  
Sasha P. Jenner ◽  
James M Ferguson ◽  
Timothy G. Amos ◽  
...  
Keyword(s):  
Data Analysis ◽  
High Performance ◽  
Nanopore Sequencing ◽  
File Format ◽  
Sequencing Data ◽  
Genome Wide ◽  
Wide Range ◽  
File Structure ◽  
Order Of Magnitude ◽  
Methylation Profiling

Nanopore sequencing is an emerging genomic technology with great potential. However, the storage and analysis of nanopore sequencing data have become major bottlenecks preventing more widespread adoption in research and clinical genomics. Here, we elucidate an inherent limitation in the file format used to store raw nanopore data, known as FAST5, that prevents efficient analysis on high-performance computing (HPC) systems. To overcome this we have developed SLOW5, an alternative file format that permits efficient parallelisation and, thereby, acceleration of nanopore data analysis. For example, we show that using SLOW5 format, instead of FAST5, reduces the time and cost of genome-wide DNA methylation profiling by an order of magnitude on common HPC systems, and delivers consistent improvements on a wide range of different architectures. With a simple, accessible file structure and a ~25% reduction in size compared to FAST5, SLOW5 format will deliver substantial benefits to all areas of the nanopore community.

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