Characterization of brain cell nuclei with decondensed chromatin

Yu, Ping; McKinney, Elizabeth C.; Kandasamy, Muthugapatti M.; Albert, Alexandria L.; Meagher, Richard B.

doi:10.1002/dneu.22245

Cited by 23 publications

(32 citation statements)

References 122 publications

(170 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Approximately 0.2 g of whole seedlings or roots were collected and immediately chopped in 2 ml of pre-chilled lysis buffer (15 mM Tris-HCl pH7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 5 mM 2-ME, 0.2% TritonX-100). After chopping the total mixture was filtered with miracloth twice and then loaded on the surface of 2 mL dense sucrose buffer (20 mM Tris-HCl Ph8.0, 2 mM MgCl 2 , 2 mM EDTAl, 15 mM 2-ME, 1.7 M sucrose, 0.2% TritonX-100) in a 15 ml Falcon tube, as described before (21). The nuclei were centrifuged at 2200 g at 4C for 20 min and the pellets were resuspended in 500 µl pre-chilled lysis buffer.…”

Section: Methodsmentioning

confidence: 99%

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

Hofmeister

Vollmers

et al. 2016

Nucleic Acids Research

262

246

View full text Add to dashboard Cite

Chromatin structure plays a pivotal role in facilitating proper control of gene expression. Transcription factor (TF) binding of cis-elements is often associated with accessible chromatin regions. Therefore, the ability to identify these accessible regions throughout plant genomes will advance understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes. However, in plants, the existence of cell walls, subcellular organelles and the lack of stable cell lines have prevented routine application of this technique. Here, we describe an assay combining ATAC-seq with fluorescence-activated nuclei sorting (FANS) to identify and map open chromatin and TF-binding sites in plant genomes. FANS-ATAC-seq compares favorably with published DNaseI sequencing (DNase-seq) results and it requires less than 50 000 nuclei for accurate identification of accessible genomic regions.Summary: Application of ATAC-seq to sorted nuclei identifies accessible regions genome-wide.

show abstract

Section: Methodsmentioning

confidence: 99%

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

Hofmeister

Vollmers

et al. 2016

Nucleic Acids Research

262

246

View full text Add to dashboard Cite

show abstract

“…We used flow cytometry with propidium iodide staining to estimate the genome size of N. vespilloides using T. castaneum as a standard. Nuclei from insect heads and whole insects, respectively, were prepared as described in Yu et al . (2015) , stained as in Hare and Johnston (2011) , and analyzed with a CyAn Flow Cytometer (Beckman Coulter, Brea, CA) at the UGA’s Center for Tropical and Emerging Global Diseases Flow Cytometry Core Facility.…”

Section: Methodsmentioning

confidence: 99%

The Genome and Methylome of a Beetle with Complex Social Behavior,Nicrophorus vespilloides(Coleoptera: Silphidae)

Cunningham

Wiberg

et al. 2015

Genome Biol Evol

Self Cite

View full text Add to dashboard Cite

Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of methylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior.

show abstract

“…We used flow cytometry with propidium iodide staining to estimate the genome size of N. vespilloides using T. castaneum as a standard. Nuclei from insect heads and whole insects, respectively, were prepared as described in Yu et al (2015), stained as in Hare and Johnston (2011), and analyzed with a CyAn Flow Cytometer (Beckman Coulter, Brea, CA) at the UGA’s Center for Tropical and Emerging Global Diseases Flow Cytometry Core Facility. Data was processed with FlowJo software (Treestar, Inc., Ashland, Oregon).…”

Section: Methodsmentioning

confidence: 99%

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

Cunningham

Wiberg

et al. 2015

Preprint

View full text Add to dashboard Cite

22Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of 23 genomes available for comparison spanning multiple independent lineages. For example, complex social 24 behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are 25 Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa 26 that also vary in their levels of sociality. Here we present information on the genome of the subsocial beetle 27 Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social 28 behavior. We used this genome to address two questions. First, does life history predict overlap in gene 29 models more strongly than phylogenetic groupings? Second, like other insects with highly developed social 30 behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found the overlap in gene 31 models was similar between N. vespilloides and all other insect groups regardless of life history. Unlike 32 previous studies of beetles, we found strong evidence of DNA methylation, which allows this species to be 33 used to address questions about the potential role of methylation in social behavior. The addition of this 34 genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of 35 sociality. 36 37 Introduction 38Understanding phenotypic evolution necessitates investigating both the ultimate and proximate influences on 39 traits; however, these investigations require the appropriate tools. Social behavior is a particularly thorny 40 phenotype to study because of its complexity, variation, and its multi-level integration across an organism 41 (Boake et al., 2002). In addition, social behavior also often displays unusual evolutionary dynamics arising 42 from the genetic influences on interactions required for sociality (McGlothlin et al., 2010). Although single 43 genes can influence behavior (Fischman et al., 2011), social behavior is often multifaceted and can reflect a 44 complex genetic architecture (Walling et al., 2008; Mikheyev and Linksvayer, 2015) including influences 45 from epigenetic mechanisms (Cardoso et al., 2015). Genomes in particular are useful resources for 46 evolutionary questions of social behavior because they grant access to both broad scale and fine scale details 47 and mechanisms (Richards, 2015). For social behavior, while there are multiple Hymenopteran genomes 48 available to investigate fine scale detail, we lack sufficiently distantly related species to address broader 49 patterns. It is therefore important to develop genomic resources for organisms that are particularly 50 phenotypic models of social behavior but where genomic information is lacking. 51The genomes of several social insect are now available, including eusocial species such as honey 52 bees (Elsik et al., 2014), stingless bees (Kapheim et al., 2015), several ant species (Gadau et al., 2012), a 53 termite (Terrapon et al., 2...

show abstract

Characterization of brain cell nuclei with decondensed chromatin

Cited by 23 publications

References 122 publications

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

The Genome and Methylome of a Beetle with Complex Social Behavior,Nicrophorus vespilloides(Coleoptera: Silphidae)

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

Contact Info

Product

Resources

About