Limited allele-specific gene expression in highly polyploid sugarcane

Polyploidy is widespread in plants allowing the different copies of genes to be expressed differently in a tissue specific or developmental specific way. This allele-specific expression (ASE) has been widely reported but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole genome level in the highly polyploid sugarcane genome. Very high-depth whole genome sequencing and RNA sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single copy alleles to 12:0 for monomorphic sites. The rarer cases of ASE were more frequent in the expression of defense-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection for resistance to diseases in both nature and domestication.

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Limited allele-specific gene expression in highly polyploid sugarcane

10.21203/rs.3.rs-608681/v1 ◽

2021 ◽

Author(s):

Gabriel Rodrigues Alves Margarido ◽

Fernando Henrique Correr ◽

Agnelo Furtado ◽

Frederik Botha ◽

Robert Henry

Keyword(s):

Single Copy ◽

Specific Gene ◽

Whole Genome ◽

Strong Correlations ◽

Specific Expression ◽

Allele Specific ◽

Recent Origin ◽

Genome Level ◽

Very High ◽

High Depth

Abstract Polyploidy is widespread in plants allowing the different copies of genes to be expressed differently in a tissue specific or developmental specific way. This allele specific expression (ASE) has been widely reported but the proportion and nature of genes showing this characteristic has not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole genome level in the highly polyploid sugarcane genome. Very high-depth whole genome sequencing and RNA-sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single copy alleles to 12:0 for monomorphic sites. The rarer departures from allelic balance were more frequent in the expression of defence-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection in nature and domestication for resistance to diseases.

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Genetic influences on cell type specific gene expression and splicing during neurogenesis elucidate regulatory mechanisms of brain traits

10.1101/2020.10.21.349019 ◽

2020 ◽

Author(s):

Nil Aygün ◽

Angela L. Elwell ◽

Dan Liang ◽

Michael J. Lafferty ◽

Kerry E. Cheek ◽

...

Keyword(s):

Gene Expression ◽

Regulatory Elements ◽

Regulatory Mechanisms ◽

Specific Gene ◽

Cell Type ◽

Specific Expression ◽

Risk Variants ◽

Allele Specific ◽

Cell Type Specific ◽

Regulatory Effects

SummaryInterpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing is mainly performed in bulk post-mortem adult tissue. However, genetic risk loci are enriched in regulatory elements of cells present during neocortical differentiation, and regulatory effects of risk variants may be masked by heterogeneity in bulk tissue. Here, we map e/sQTLs and allele specific expression in primary human neural progenitors (n=85) and their sorted neuronal progeny (n=74). Using colocalization and TWAS, we uncover cell-type specific regulatory mechanisms underlying risk for these traits.

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A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

10.1101/2021.08.06.455380 ◽

2021 ◽

Author(s):

Richard J White ◽

Eirinn Mackay ◽

Stephen W Wilson ◽

Elisabeth M Busch-Nentwich

Keyword(s):

Differentially Expressed Genes ◽

Differentially Expressed Gene ◽

Transcript Abundance ◽

Differentially Expressed ◽

Model Organisms ◽

Specific Gene ◽

Wild Type ◽

Specific Expression ◽

Genomic Location ◽

Allele Specific

In model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation. Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that differentially expressed genes on the same chromosome as a mutation of interest may not be caused by that mutation. Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.

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Large structural variations in the haplotype-resolved African cassava genome.

10.1101/2021.06.25.450005 ◽

2021 ◽

Author(s):

Ben N Mansfeld ◽

Adam Boyher ◽

Jeffrey C Berry ◽

Mark Wilson ◽

Shujun Ou ◽

...

Keyword(s):

Gene Expression ◽

Genetic Load ◽

Specific Gene ◽

Stem Cuttings ◽

Structural Variations ◽

Manihot Esculenta Crantz ◽

Specific Expression ◽

Global Food Security ◽

Allele Specific ◽

Two Phases

Cassava (Manihot esculenta Crantz, 2n=36) is a global food security crop. Cassava has a highly heterozygous genome, high genetic load, and genotype-dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi-C to resolve each haplotype of the genome of a farmer-preferred cassava line, TME7 (Oko-iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON-Phase and Hi-C read data. The ultra-long-range information from Hi-C sequencing was also used for scaffolding. Comparison of the two phases revealed more than 5,000 large haplotype-specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele specific expression was further explored. RNA-seq data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy-to-use web-based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype-specific structural variation, gene hemizygosity, and allele specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.

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Parent of origin DNA methylation as a potential mechanism for genomic imprinting in bees.

10.1101/2021.12.17.473163 ◽

2021 ◽

Author(s):

Hollie Marshall ◽

Moi T Nicholas ◽

Jelle S van Zweden ◽

Felix Wäckers ◽

Laura Ross ◽

...

Keyword(s):

Dna Methylation ◽

Genomic Imprinting ◽

Bombus Terrestris ◽

Experimental Manipulation ◽

Whole Genome ◽

Specific Expression ◽

Differentially Methylated Genes ◽

Allele Specific ◽

Parent Of Origin ◽

Functional Dna

Genomic imprinting is defined as parent-of-origin allele-specific expression. In order for genes to be expressed in this manner an `imprinting' mark must be present to distinguish the parental alleles within the genome. In mammals imprinted genes are primarily associated with DNA methylation. Genes exhibiting parent-of-origin expression have recently been identified in two species of Hymenoptera with functional DNA methylation systems; Apis mellifera and Bombus terrestris. We carried out whole genome bisulfite sequencing of parents and offspring from reciprocal crosses of two B. terrestris subspecies in order to identify parent-of-origin DNA methylation. We were unable to survey a large enough proportion of the genome to draw a conclusion on the presence of parent-of-origin DNA methylation however we were able to characterise the sex- and caste-specific methylomes of B. terrestris for the first time. We find males differ significantly to the two female castes, with differentially methylated genes involved in many histone modification related processes. We also analysed previously generated honeybee whole genome bisulfite data to see if genes previously identified as showing parent-of-origin DNA methylation in the honeybee show consistent allele-specific methylation in independent data sets. We have identified a core set of 12 genes in female castes which may be used for future experimental manipulation to explore the functional role of parent-of-origin DNA methylation in the honeybee. Finally, we have also identified allele-specific DNA methylation in honeybee male thorax tissue which suggests a role for DNA methylation in ploidy compensation in this species.

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Oocyte-specific expression of mouse Zp-2: developmental regulation of the zona pellucida genes

Molecular and Cellular Biology ◽

10.1128/mcb.10.4.1507-1515.1990 ◽

1990 ◽

Vol 10 (4) ◽

pp. 1507-1515

Author(s):

L F Liang ◽

S M Chamow ◽

J Dean

Keyword(s):

Dna Sequences ◽

Zona Pellucida ◽

Developmental Regulation ◽

Genetic Locus ◽

Single Copy ◽

Specific Gene ◽

Gene Transcript ◽

Developmentally Regulated ◽

Specific Expression ◽

Oocyte Growth

The zona pellucida surrounds all mammalian oocytes and plays a vital role at fertilization and in early development. The genes that code for two of the mouse zona proteins (ZP2 and ZP3) represent a developmentally regulated set of genes whose expression serves as markers of mouse oocyte growth and differentiation. We previously characterized the single-copy Zp-3 gene and showed that its expression is oocyte specific and restricted to a narrow window of oocyte development. We now define the Zp-2 gene transcript and show that it is coordinately expressed with Zp-3 only during the 2-week growth phase of oogenesis that occurs prior to ovulation. Like Zp-3, the expression of Zp-2 is restricted to oocytes, and, although not detectable in resting oocytes, both ZP2 and ZP3 transcripts accumulate to become very abundant messengers in 50-microns-diameter oocytes. Ovulated eggs contain ZP2 and ZP3 transcripts which are 200 nucleotides shorter than those found in growing oocytes and have an abundance of less than 5% of the peak levels. In an attempt to understand the molecular details associated with the developmentally regulated, tissue-specific gene expression of the zona genes, the Zp-2 genetic locus has been characterized and its 5' flanking sequences have been compared with those of Zp-3. Both genes contain three short (8- to 12-base-pair) DNA sequences of 80 to 88% identity located within 250 base pairs of their transcription start sites.

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The Transcriptional Aftermath in Two Independently Formed Hybrids of the Opportunistic Pathogen Candida orthopsilosis

mSphere ◽

10.1128/msphere.00282-20 ◽

2020 ◽

Vol 5 (3) ◽

Cited By ~ 1

Author(s):

Hrant Hovhannisyan ◽

Ester Saus ◽

Ewa Ksiezopolska ◽

Toni Gabaldón

Keyword(s):

Gene Expression ◽

Loss Of Heterozygosity ◽

Opportunistic Pathogen ◽

Specific Gene ◽

Specific Expression ◽

Allele Specific Expression ◽

Content Type ◽

Additional Layer ◽

Allele Specific ◽

Candida Orthopsilosis

ABSTRACT Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight into the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ∼4% of the genes studied. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ∼9.5% of the heterozygous genes in the hybrids. This effect was larger in the hybrid with more extensive loss of heterozygosity, which may indicate a tendency to avoid loss of heterozygosity in these genes. Consistently, the number of shared genes with allele-specific expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. Some of the imbalanced genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids. IMPORTANCE How new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to higher virulence is unclear. Here, we show that hybrids selectively retain gene regulation plasticity inherited from the two parents and that this plasticity affects genes involved in virulence.

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Influence of epigenetic changes during oocyte growth on nuclear reprogramming after nuclear transfer

Reproduction Fertility and Development ◽

10.1071/rd98056 ◽

1998 ◽

Vol 10 (8) ◽

pp. 593 ◽

Cited By ~ 17

Author(s):

Tomohiro Kono

Keyword(s):

Gene Expression ◽

Genomic Imprinting ◽

Epigenetic Mechanism ◽

Specific Gene ◽

Paternal Genome ◽

Specific Expression ◽

Oocyte Growth ◽

Specific Gene Expression ◽

Mammalian Embryos ◽

Allele Specific

Genomic imprinting is the epigenetic mechanism that distinguishes whether the loci that are inherited from the maternal or paternal genome lead to parent-specific gene expression. The mechanism also regulates development in mammalian embryos. Genomic imprinting is established after implantation according to the specific markers that are imposed on the genome during gametogenesis; the allele-specific gene expression is then maintained throughout embryogenesis. The genomic imprinting markers are erased and renewed on an own-sex basis only in cells that differentiate into germline cells. This report shows that the epigenetic modifications that occur during oogenesis perform the crucial function of establishing the allele-specific expression of imprinted genes, and also suggests that the epigenetic DNA modification is related to the reprogramming and aberrant development seen in manipulated embryos.

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Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

10.1101/192344 ◽

2017 ◽

Cited By ~ 2

Author(s):

Bo Zhou ◽

Steve S. Ho ◽

Stephanie U. Greer ◽

Xiaowei Zhu ◽

John M. Bell ◽

...

Keyword(s):

Functional Genomics ◽

Genome Analysis ◽

Large Scale ◽

Wide Spectrum ◽

Whole Genome ◽

Sequencing Data ◽

Whole Genome Analysis ◽

Multiple Allele ◽

Specific Expression ◽

Allele Specific

ABSTRACTK562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensively studied, its genome sequence and genomic structural features have never been comprehensively analyzed. Such information is essential for the correct interpretation and understanding of the vast troves of existing functional genomics and epigenomics data for K562. We performed and integrated deep-coverage whole-genome (short-insert), mate-pair, and linked-read sequencing as well as karyotyping and array CGH analysis to identify a wide spectrum of genome characteristics in K562: copy numbers (CN) of aneuploid chromosome segments at high-resolution, SNVs and Indels (both corrected for CN in aneuploid regions), loss of heterozygosity, mega-base-scale phased haplotypes often spanning entire chromosome arms, structural variants (SVs) including small and large-scale complex SVs and non-reference retrotransposon insertions. Many SVs were phased, assembled, and experimentally validated. We identified multiple allele-specific deletions and duplications within the tumor suppressor geneFHIT. Taking aneuploidy into account, we re-analyzed K562 RNA-seq and whole-genome bisulfite sequencing data for allele-specific expression and allele-specific DNA methylation. We also show examples of how deeper insights into regulatory complexity are gained by integrating genomic variant information and structural context with functional genomics and epigenomics data. Furthermore, using K562 haplotype information, we produced an allele-specific CRISPR targeting map. This comprehensive whole-genome analysis serves as a resource for future studies that utilize K562 as well as a framework for the analysis of other cancer genomes.

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DNA Methylation Profile of the Mouse Skeletal α-Actin Promoter during Development and Differentiation

Molecular and Cellular Biology ◽

10.1128/mcb.19.1.164 ◽

1999 ◽

Vol 19 (1) ◽

pp. 164-172 ◽

Cited By ~ 59

Author(s):

Peter M. Warnecke ◽

Susan J. Clark

Keyword(s):

Dna Methylation ◽

Single Copy ◽

Methylation Profile ◽

Specific Gene ◽

Specific Expression ◽

Tissue Specific ◽

Methylation State ◽

Dna Methylation Profile ◽

Development And Differentiation ◽

Actin Promoter

ABSTRACT Genomic levels of DNA methylation undergo widespread alterations in early embryonic development. However, changes in embryonic methylation have proven difficult to study at the level of single-copy genes due to the small amount of tissue available for assay. This study provides the first detailed analysis of the methylation state of a tissue-specific gene through early development and differentiation. Using bisulfite sequencing, we mapped the methylation profile of the tissue-specific mouse skeletal α-actin promoter at all stages of development, from gametes to postimplantation embryos. We show that the α-actin promoter, which is fully methylated in the sperm and essentially unmethylated in the oocyte, undergoes a general demethylation from morula to blastocyst stages, although the blastula is not completely demethylated. Remethylation of the α-actin promoter occurs after implantation in a stochastic pattern, with some molecules being extensively methylated and others sparsely methylated. Moreover, we demonstrate that tissue-specific expression of the skeletal α-actin gene in the adult mouse does not correlate with the methylation state of the promoter, as we find a similar low level of methylation in both expressing and one of the two nonexpressing tissues tested. However, a subset of CpG sites within the skeletal α-actin promoter are preferentially methylated in liver, a nonexpressing tissue.

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