Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nascent Y Chromosome Evolution in Guppies

ABSTRACT: Shared and Species specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species

PROVIDER: PRJEB26489 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

Project description:Nuclear chromosomes transcribe far more RNA than required to code for protein. Here we investigate whether non-coding RNA broadly contributes to cytological-scale chromosome territory architecture. We develop a procedure that depletes soluble proteins, chromatin and most nuclear RNA from the nucleus, but does not delocalize XIST, a known architectural RNA, from an insoluble chromosome “scaffold.” RNA-seq analysis reveals most RNA in the nuclear scaffold is repeat-rich, non-coding, and predominantly derived from introns of nascent transcripts. This repeat-rich (C0T-1) RNA inversely correlates with chromatin compaction in normal and experimentally manipulated nuclei, demonstrating RNA physically antagonizes a propensity for chromatin to condense. C0T-1 hnRNA co-distributes on euchromatin with several known scaffold proteins including scaffold attachment factor A (SAF-A). We further show that RNA is required for SAF-A to interact with chromatin and to form structurally embedded scaffold-attachment regions (SARs) in the nuclear genome. Collectively, results indicate nascent transcripts serve a dynamic structural role in the open architecture of active chromosome territories

2021-07-06 | GSE124979 | GEO

Sex chromosome evolution in the guppy, Poecilia reticulata

Project description:Genome sequencing of fish from a natural population of the guppy, Poecilia reticulata, for studying sex chromosome evolution

| PRJEB22221 | ENA

Topoisomerase II-induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity [Nascent RNA]

Project description:Topoisomerase II-induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity [Nascent RNA]

| PRJNA531666 | ENA

Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

Project description:Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

| PRJNA514731 | ENA

Global transgenerational gene expression dynamics in two nascent allohexaploid wheat lines analogous in genome constitution to common wheat (Triticum aestivum)

Project description:Alteration in gene expression accompanying initial stages of allopolyploidy is a prominent feature in plants, but its spectrum and model are highly idiosyncratic. We used multi-colour GISH to identify individuals from two nascent allohexaploid wheat lines between Triticum turgidum and Aegilops tauschii, which had a transgenerationally stable chromosomal constitution mimicking that of common wheat. We performed genomewide analysis of gene expression for these plants along with their parental species using the Affymetrix GeneChip Wheat Genome-Array. Comparison with parental species coupled with inclusion of empirical mid-parent values (MPVs) revealed two patterns of alteration in gene expression in the allohexaploid lines: parental dominance expression and nonadditive expression. Genes involved in each altered pattern could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes is stochastic, consistent with the involvement of diverse Gene Ontology (GO) terms. Nonetheless, those genes showing nonadditive expression exhibited a significant enrichment for vesicle-function. Our results suggest global alteration in gene expression conditioned by nascent allopolyploidy likely play functional roles in stabilization and establishment of the newly formed plants, and consequential to evolution. We used Affymetrix GeneChip Wheat Genome-Array to compare the expression difference of newly synthetic wheat allopolyploid lines and their parental lines.

2012-04-30 | E-GEOD-29882 | biostudies-arrayexpress

Comparative analysis of nascent transcription among plant species

Project description:Comparative analysis of nascent transcription among plant species

2023-09-28 | GSE233927 | GEO

Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

Project description:Here we describe the principles of 3D genome folding dynamics in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (i) identified different patterns of chromosome folding across vertebrate species, (ii) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of 10 species representative of the major therian phylogroups, (iii) detected lineage-specific chromosome rearrangements and (iv) identified the dynamics of the structural properties of genome reshuffling through therian evolution.

2022-12-08 | GSE206075 | GEO

Global transgenerational gene expression dynamics in two nascent allohexaploid wheat lines analogous in genome constitution to common wheat (Triticum aestivum)

2012-05-01 | GSE29882 | GEO

Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin structures

Project description:To investigate the mechanisms underlying the rearrangement patterns,we compared the rearrangement map with local chromatin structures and the three-dimensional genome architecture via assay for transposase-accessible chromatin using sequencing (ATAC-seq) and genome-wide chromosome conformation capture (Hi-C), respectively

2022-06-10 | GSE168182 | GEO

Revealing nascent RNA processing dynamics with nano-COP

Project description:During maturation, eukaryotic precursor RNAs undergo processing events including intron splicing, 3’-end cleavage, and polyadenylation. Here, we describe nanopore analysis of CO-transcriptional Processing (nano-COP), a method for probing the timing and patterns of RNA processing. An extension of native elongating transcript sequencing (NET-seq), which quantifies transcription genome-wide through short-read sequencing of nascent RNA 3’ ends, nano-COP uses long-read nascent RNA sequencing to observe global patterns of RNA processing. First, nascent RNA is stringently purified through a combination of 4-thiouridine metabolic labeling and cellular fractionation. In contrast to cDNA or short-read–based approaches relying on reverse transcription or amplification, the sample is sequenced directly through nanopores to reveal the native context of nascent RNA. nano-COP identifies both active transcription sites and splice isoforms of single RNA molecules during synthesis, providing insight into patterns of intron removal and the physical coupling between transcription and splicing. The nano-COP protocol yields data within 3 days.

2021-01-06 | GSE154079 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data