Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Origination and Function of Plant Pseudogenes.

ABSTRACT: Pseudogenes, nonfunctional genomic sequences derived from functional protein-coding genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Studies on the evolution and functional aspects of plant pseudogenes are limited, despite their abundance in the plant genome. To date, most researches on pseudogenes focus on mammals. Here, we summarized current knowledge on pseudogenes including the historical and recent progress, analyzes their essential roles in gene regulation in hope of further stimulating researches in plant species for understanding gene regulation and evolution.

SUBMITTER: Xie J

PROVIDER: S-EPMC6619919 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Origination and Function of Plant Pseudogenes.

Xie Jianbo J Chen Sisi S Xu Weijie W Zhao Yiyang Y Zhang Deqiang D

Plant signaling & behavior 20190604 8

Pseudogenes, nonfunctional genomic sequences derived from functional protein-coding genes, form by duplication or retrotransposition, and loss of gene function by disabling mutations. Studies on the evolution and functional aspects of plant pseudogenes are limited, despite their abundance in the plant genome. To date, most researches on pseudogenes focus on mammals. Here, we summarized current knowledge on pseudogenes including the historical and recent progress, analyzes their essential roles i ...[more]

PMID: 31161861

Similar Datasets

Hybrid sequencing characterizes expression and function of mouse pseudogenes

Project description:Pseudogenes are defined as regions of the genome that resemble functional genes but contain disabling mutations and lack regulatory elements needed for transcription or translation. They are excellent markers for genome evolution and are emerging as crucial regulators of the development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogene remain largely unexplored. In particular, the contribution of pseudogene to organ development is still unknown. Meanwhile, studies of pseudogene transcription, which is the first step for generating functional RNA, is precluded by the limited capacity of short-read sequencing. To address these issues, we systematically inferred the origin time and characterized the evolution pattern of pseudogenes. We leveraged PacBio full-length sequencing in combination with deep Illumina data as well as public developmental time-course RNA-seq, we dramatically expanded the analyzed samples and profiled genome-wide pseudogene expression paradigm. Additionally, we prioritized functional pseudogenes at multiple regulatory layers and determined their implications in disease and cancer biology.

2022-02-18 | GSE176018 | GEO

Evolution and function of developmentally dynamic pseudogenes in mammals.

Project description:Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogenes remain largely unexplored. To systematically characterize pseudogenes, we date the origin of human and mouse pseudogenes across vertebrates and observe a burst of pseudogene gain in these two lineages. Based on a hybrid sequencing dataset combining full-length PacBio sequencing, sample-matched Illumina sequencing, and public time-course transcriptome data, we observe that abundant mammalian pseudogenes could be transcribed, which contribute to the establishment of organ identity. Our analyses reveal that developmentally dynamic pseudogenes are evolutionarily conserved and show an increasing weight during development. Besides, they are involved in complex transcriptional and post-transcriptional modulation, exhibiting the signatures of functional enrichment. Coding potential evaluation suggests that 19% of human pseudogenes could be translated, thus serving as a new way for protein innovation. Moreover, pseudogenes carry disease-associated SNPs and conduce to cancer transcriptome perturbation. Our discovery reveals an unexpectedly high abundance of mammalian pseudogenes that can be transcribed and translated, and these pseudogenes represent a novel regulatory layer. Our study also prioritizes developmentally dynamic pseudogenes with signatures of functional enrichment and provides a hybrid sequencing dataset for further unraveling their biological mechanisms in organ development and carcinogenesis in the future.

| S-EPMC9641868 | biostudies-literature

CircRNA-derived pseudogenes.

Project description: Not available

| S-EPMC4897178 | biostudies-literature

Probing the Evolutionary History of Human Bitter Taste Receptor Pseudogenes by Restoring Their Function.

Project description:Lineage-specific gene losses can be driven by selection or environmental adaptations. However, a lack of studies on the original function of species-specific pseudogenes leaves a gap in our understanding of their role in evolutionary histories. Pseudogenes are of particular relevance for taste perception genes, which encode for receptors that confer the ability to both identify nutritionally valuable substances and avoid potentially harmful substances. To explore the role of bitter taste pseudogenization events in human origins, we restored the open reading frames of the three human-specific pseudogenes and synthesized the reconstructed functional hTAS2R2, hTAS2R62 and hTAS2R64 receptors. We have identified ligands that differentially activate the human and chimpanzee forms of these receptors and several other human functional TAS2Rs. We show that these receptors are narrowly tuned, suggesting that bitter-taste sensitivities evolved independently in different species, and that these pseudogenization events occurred because of functional redundancy. The restoration of function of lineage-specific pseudogenes can aid in the reconstruction of their evolutionary history, and in understanding the forces that led to their pseudogenization.

| S-EPMC5850805 | biostudies-literature

Pseudogenes in Human Cancer.

Project description:Recent advances in the analysis of RNA sequencing data have shown that pseudogenes are highly specific markers of cell identity and can be used as diagnostic and prognostic markers. Furthermore, genetically engineered mouse models have recently provided compelling support for a causal link between altered pseudogene expression and cancer. In this review, we discuss the most recent milestones reached in the pseudogene field and the use of pseudogenes as cancer classifiers.

| S-EPMC4585173 | biostudies-literature

Olfactory receptor pseudo-pseudogenes.

Project description:Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. Although certain pseudogene-derived RNAs have regulatory roles, and some pseudogene fragments are translated, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species. Here we report the characterization of a pseudogene in the chemosensory variant ionotropic glutamate receptor repertoire of Drosophila sechellia, an insect endemic to the Seychelles that feeds almost exclusively on the ripe fruit of Morinda citrifolia. This locus, D. sechellia Ir75a, bears a premature termination codon (PTC) that appears to be fixed in the population. However, D. sechellia Ir75a encodes a functional receptor, owing to efficient translational read-through of the PTC. Read-through is detected only in neurons and is independent of the type of termination codon, but depends on the sequence downstream of the PTC. Furthermore, although the intact Drosophila melanogaster Ir75a orthologue detects acetic acid-a chemical cue important for locating fermenting food found only at trace levels in Morinda fruit-D. sechellia Ir75a has evolved distinct odour-tuning properties through amino-acid changes in its ligand-binding domain. We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such 'pseudo-pseudogenes' could represent a widespread phenomenon.

| S-EPMC5164928 | biostudies-literature

Hybrid sequencing characterizes expression and function of mouse pseudogenes

Project description:Hybrid sequencing characterizes expression and function of mouse pseudogenes

| PRJNA734591 | ENA

Higher origination and extinction rates in larger mammals.

Project description:Do large mammals evolve faster than small mammals or vice versa? Because the answer to this question contributes to our understanding of how life-history affects long-term and large-scale evolutionary patterns, and how microevolutionary rates scale-up to macroevolutionary rates, it has received much attention. A satisfactory or consistent answer to this question is lacking, however. Here, we take a fresh look at this problem using a large fossil dataset of mammals from the Neogene of the Old World (NOW). Controlling for sampling biases, calculating per capita origination and extinction rates of boundary-crossers and estimating survival probabilities using capture-mark-recapture (CMR) methods, we found the recurring pattern that large mammal genera and species have higher origination and extinction rates, and therefore shorter durations. This pattern is surprising in the light of molecular studies, which show that smaller animals, with their shorter generation times and higher metabolic rates, have greater absolute rates of evolution. However, higher molecular rates do not necessarily translate to higher taxon rates because both the biotic and physical environments interact with phenotypic variation, in part fueled by mutations, to affect origination and extinction rates. To explain the observed pattern, we propose that the ability to evolve and maintain behavior such as hibernation, torpor and burrowing, collectively termed "sleep-or-hide" (SLOH) behavior, serves as a means of environmental buffering during expected and unexpected environmental change. SLOH behavior is more common in some small mammals, and, as a result, SLOH small mammals contribute to higher average survivorship and lower origination probabilities among small mammals.

| S-EPMC2329699 | biostudies-literature

Systematic functional interrogation of human pseudogenes

Project description:Human genome encodes >14,000 pseudogenes that are evolutionary relics and have long been considered as nonfunctional genomic elements. Emerging evidence suggests that pseudogene can exert important regulatory function. However, function of most pseudogenes remains unknown. To fill this gap, we developed an integrated computational pipeline and performed to date the first set of pseudogene-focused CRISPRi screens in human cells. Our screens identified >100 pseudogenes that are important for cell fitness, with a more cell-type specific function compared to parent genes. In addition, we discovered a cancer-testis unitary pseudogene MGAT4EP that interacts with FOXA1, a key regulator in luminal A breast cancer.

2021-08-01 | GSE155510 | GEO

Role of Pseudogenes in Tumorigenesis.

Project description:Functional genomics has provided evidence that the human genome transcribes a large number of non-coding genes in addition to protein-coding genes, including microRNAs and long non-coding RNAs (lncRNAs). Among the group of lncRNAs are pseudogenes that have not been paid attention in the past, compared to other members of lncRNAs. However, increasing evidence points the important role of pseudogenes in diverse cellular functions, and dysregulation of pseudogenes are often associated with various human diseases including cancer. Like other types of lncRNAs, pseudogenes can also function as master regulators for gene expression and thus, they can play a critical role in various aspects of tumorigenesis. In this review we discuss the latest developments in pseudogene research, focusing on how pseudogenes impact tumorigenesis through different gene regulation mechanisms. Given the high sequence homology with the corresponding parent genes, we also discuss challenges for pseudogene research.

| S-EPMC6115995 | biostudies-literature

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