Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

Abstract There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the ‘Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)’ to identify putative regulatory regions in flash frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest, average, and largest sized male piglets from each litter through five developmental time points. Of the 4,661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with down regulation of genes involved in muscle development that were present in small sized foetal piglets but absent in large foetal piglets at day 90 of gestation. The dataset that we have generated provides: a resource for studies of genome regulation in pigs, and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programmes.

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Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

10.1101/2021.01.21.426812 ◽

2021 ◽

Author(s):

Mazdak Salavati ◽

Shernae A. Woolley ◽

Yennifer Cortés Araya ◽

Michelle M. Halstead ◽

Claire Stenhouse ◽

...

Keyword(s):

Genetic Variants ◽

Sus Scrofa ◽

Prediction Models ◽

Developmental Time ◽

Open Chromatin ◽

Regulatory Sequences ◽

Specific Information ◽

Regulatory Regions ◽

Breeding Programmes ◽

Accessible Chromatin

AbstractThere is very little species-specific information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We have optimised the ‘Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-seq)’ to profile regions of open chromatin in flash frozen pig muscle tissue samples. This protocol has allowed us to identify putative regulatory regions in semitendinosus muscle from 24 male piglets. We collected samples from the smallest, average, and largest sized male piglets from each litter through five developmental time points. The ATAC-Seq data were mapped to Sscrofa11.1 with Bowtie2 and Genrich were used for post-alignment peak-calling. Of the 4661 putative regions of accessible chromatin identified, >50% were within 1 kb of known transcription start sites. The size of each open chromatin region varied according to the developmental time point. At day 90 of gestation, we investigated chromatin openness relative to foetal piglet size. In parallel we measured genome-wide gene expression and allele-specific expression using RNA-Seq analysis of the same muscle samples. We found regions of open chromatin associated with down regulation of genes involved in muscle development in small sized foetal piglets. The dataset that we have generated here provides: i) a resource for studies of genome regulation in pigs, and ii) contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programmes. Future work could leverage the ATAC-Seq data with very large datasets of genetic variants from phenotyped pigs. This approach could inform chromatin aware genomic prediction models and determine whether regions of open chromatin are enriched for trait-linked variants, and especially for muscle and meat traits.

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Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants

Science ◽

10.1126/science.aay3983 ◽

2020 ◽

Vol 369 (6503) ◽

pp. 561-565 ◽

Cited By ~ 6

Author(s):

Siwei Zhang ◽

Hanwen Zhang ◽

Yifan Zhou ◽

Min Qiao ◽

Siming Zhao ◽

...

Keyword(s):

Genetic Variants ◽

Target Genes ◽

Disease Risk ◽

Induced Pluripotent Stem Cell ◽

Open Chromatin ◽

Regulatory Sequences ◽

Functional Interpretation ◽

Neuropsychiatric Disease ◽

Risk Variants ◽

Allele Specific

Most neuropsychiatric disease risk variants are in noncoding sequences and lack functional interpretation. Because regulatory sequences often reside in open chromatin, we reasoned that neuropsychiatric disease risk variants may affect chromatin accessibility during neurodevelopment. Using human induced pluripotent stem cell (iPSC)–derived neurons that model developing brains, we identified thousands of genetic variants exhibiting allele-specific open chromatin (ASoC). These neuronal ASoCs were partially driven by altered transcription factor binding, overrepresented in brain gene enhancers and expression quantitative trait loci, and frequently associated with distal genes through chromatin contacts. ASoCs were enriched for genetic variants associated with brain disorders, enabling identification of functional schizophrenia risk variants and their cis-target genes. This study highlights ASoC as a functional mechanism of noncoding neuropsychiatric risk variants, providing a powerful framework for identifying disease causal variants and genes.

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Oocytes from gilts of domestic pig (Sus scrofa domesticus) and wild boar (Sus scrofa) species exhibit similar developmental potential during in vitro maturation

Proceedings of the British Society of Animal Science ◽

10.1017/s1752756200598305 ◽

1998 ◽

Vol 1998 ◽

pp. 178-178

Author(s):

N.S. Prathalingam ◽

K. Rust ◽

M.E. Staines ◽

G.J. McCallum ◽

S.A. Edwards ◽

...

Keyword(s):

Wild Boar ◽

Sus Scrofa ◽

In Vitro Maturation ◽

Animal Species ◽

Genetic Material ◽

Developmental Potential ◽

In Captivity ◽

Breeding Programmes ◽

Sus Scrofa Domesticus

In vitro embryo production strategies have been considered as possible means to protect wild and endangered animal species through assisted breeding programmes. They also offer the possibility to preserve genetic material from such stock or to facilitate breeding in captivity. The relevant technologies, however, have been developed to meet the needs of oocytes and embryos of domesticated animals and their suitability for wild species remains largely unknown. This study investigated the ability of in vitro maturation procedures, designed for oocytes of domestic pigs (Sus scrofa domesticus), to support the development of oocytes from wild boar (Sus scrofa)gilts.

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Control of the expression of the bithorax complex genes abdominal-A and abdominal-B by cis-regulatory regions in Drosophila embryos

Development ◽

10.1242/dev.111.2.437 ◽

1991 ◽

Vol 111 (2) ◽

pp. 437-449 ◽

Cited By ~ 6

Author(s):

E. Sanchez-Herrero

Keyword(s):

Regulatory Sequences ◽

Bithorax Complex ◽

Regulatory Regions ◽

Drosophila Embryos

The abdominal-A (abd-A) and Abdominal-B (Abd-B) genes of the bithorax complex (BX-C) specify the identity of most of the Drosophila abdomen. Six different classes of infraabdominal (iab) mutations within the BX-C transform a subset of the parasegments affected by the lack of these two genes. It is thought that these mutations define parasegmental cis-regulatory regions that control the expression of abd-A and Abd-B. By staining embryos mutant for different iab mutations with anti-abd-A and anti-Abd-B antibodies I show here that the expression of Abd-B (and probably also abd-A) exhibit a parasegmental regulation. I have also studied the significance of the chromosomal order of parasegmental iab regulatory sequences, and the possible presence of chromosomal ‘boundaries’ between them, by looking at the expression of abd-A and Abd-B in embryos carrying the Uab and Mcp mutations. These data are discussed in the light of models of parasegmental-specific regulatory regions within the BX-C.

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Developmental atlas of the RNA editome in Sus scrofa skeletal muscle

DNA Research ◽

10.1093/dnares/dsz006 ◽

2019 ◽

Vol 26 (3) ◽

pp. 261-272 ◽

Cited By ~ 5

Author(s):

Yalan Yang ◽

Min Zhu ◽

Xinhao Fan ◽

Yilong Yao ◽

Junyu Yan ◽

...

Keyword(s):

Skeletal Muscle ◽

Rna Editing ◽

Sus Scrofa ◽

Muscle Development ◽

Rna Seq ◽

Sequencing Data ◽

Adenosine Deaminases ◽

Bisulphite Sequencing ◽

Highly Correlated ◽

Gain Loss

AbstractAdenosine-to-inosine (A-to-I) RNA editing meditated by adenosine deaminases acting on RNA (ADARs) enzymes is a widespread post-transcriptional event in mammals. However, A-to-I editing in skeletal muscle remains poorly understood. By integrating strand-specific RNA-seq, whole genome bisulphite sequencing, and genome sequencing data, we comprehensively profiled the A-to-I editome in developing skeletal muscles across 27 prenatal and postnatal stages in pig, an important farm animal and biomedical model. We detected 198,892 A-to-I editing sites and found that they occurred more frequently at prenatal stages and showed low conservation among pig, human, and mouse. Both the editing level and frequency decreased during development and were positively correlated with ADAR enzymes expression. The hyper-edited genes were functionally related to the cell cycle and cell division. A co-editing module associated with myogenesis was identified. The developmentally differential editing sites were functionally enriched in genes associated with muscle development, their editing levels were highly correlated with expression of their host mRNAs, and they potentially influenced the gain/loss of miRNA binding sites. Finally, we developed a database to visualize the Sus scrofa RNA editome. Our study presents the first profile of the dynamic A-to-I editome in developing animal skeletal muscle and provides evidences that RNA editing is a vital regulator of myogenesis.

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Novel association of genetic variants in non-coding regulatory regions with HIV-1 infection

Infection Genetics and Evolution ◽

10.1016/j.meegid.2020.104514 ◽

2020 ◽

Vol 85 ◽

pp. 104514

Author(s):

Walifa Waqar ◽

Saba Altaf ◽

Sadia Nazir ◽

Aneela Javed

Keyword(s):

Genetic Variants ◽

Regulatory Regions ◽

Novel Association ◽

Hiv 1

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The influence of pre-weaning nutrition on biochemical and myofibre characteristics of bovine semitendinosus muscle

Australian Journal of Agricultural Research ◽

10.1071/ar00162 ◽

2001 ◽

Vol 52 (9) ◽

pp. 891 ◽

Cited By ~ 6

Author(s):

Peter G. Allingham ◽

Gregory S. Harper ◽

David W. Hennessy ◽

V. Hutton Oddy

Keyword(s):

Muscle Development ◽

Late Pregnancy ◽

High Energy ◽

Eating Quality ◽

Growth Path ◽

Semitendinosus Muscle ◽

Calf Growth ◽

Treatment Groups ◽

Sarcoplasmic Protein ◽

Biophysical Attributes

This study investigates pre-weaning growth of cattle and its effect on biochemical and histochemical markers of muscle development and subsequent biophysical attributes of eating quality. Combinations of cow (late pregnancy to mid-lactation) and pre-weaning (varying duration of access to a high-energy ration) supplementation were used to vary calf growth to weaning in 6 treatment groups. After weaning, calves were grazed together on pasture (backgrounding) and then grown rapidly on a feedlot ration (finishing) until slaughter. Biochemical and myofibre characteristics were determined in semitendinosus muscle samples collected just prior to weaning (7 months), at the end of backgrounding (13 months), and at slaughter (17 months). The concentration of sarcoplasmic protein and the activity of lactate dehydrogenase in the muscle at weaning were associated with differences in pre-weaning growth and both variables correlated positively with liveweight at weaning. Isocitrate dehydrogenase activity varied with sex, not treatment, at weaning and at the end of backgrounding. The size of myofibres at weaning related to differences in growth path and correlated positively with liveweight. Pre-weaning growth effects on these characteristics were not evident at slaughter. Biophysical properties of the meat were not affected by earlier growth path treatment, and were not correlated with biochemical characteristics or myofibre type profile. Variation in both shear peak force and adhesion was related to sex. We conclude that the effects of divergent early life growth do not persist 10 months after weaning, at least in meat quality characteristics.

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Analysis of transgenic mosaicism in microinjected mouse embryos using fluorescence in situ hybridization at various developmental time points

Theriogenology ◽

10.1016/0093-691x(96)84808-4 ◽

1996 ◽

Vol 45 (1) ◽

pp. 335 ◽

Cited By ~ 4

Author(s):

J. Lewis-Williams ◽

M. Harvey ◽

B. Wilburn ◽

M. Destrempes ◽

Y. Echelard

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Developmental Time ◽

Mouse Embryos ◽

Time Points

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A high-resolution mRNA expression time course of embryonic development in zebrafish

eLife ◽

10.7554/elife.30860 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 82

Author(s):

Richard J White ◽

John E Collins ◽

Ian M Sealy ◽

Neha Wali ◽

Christopher M Dooley ◽

...

Keyword(s):

Mrna Expression ◽

Time Course ◽

Expression Profiles ◽

Developmental Time ◽

Rna Seq ◽

Time Points ◽

New Genes ◽

Expression Atlas ◽

Genome Activation ◽

Expression Time

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.

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