4.7 Article

Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

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

Mazdak Salavati et al.

Summary: This research identified regulatory sequences in the pig genome through Omni-ATAC-Seq analysis of semitendinosus muscle from 24 male piglets. Over 50% of the open chromatin regions were found near known transcription start sites. Differential analysis revealed genomic regions with significantly different chromatin accessibility across developmental time points.

G3-GENES GENOMES GENETICS (2022)

Article Cell Biology

Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver

Luxi Chen et al.

Summary: Researchers generated high-resolution maps of chromatin architecture to investigate the dynamic chromatin structure during liver development and metabolic stress. They found that the plasticity of chromatin structure played a role in the rapid functional transitions in the liver, and its changes were associated with the transition of hepatic functions.

CELL DISCOVERY (2022)

Article Agriculture, Dairy & Animal Science

Differences in liver microRNA profiling in pigs with low and high feed efficiency

Yuanxin Miao et al.

Summary: Feed cost is a major factor affecting the economic benefits of the pig industry. Improving feed efficiency can reduce costs and improve economic benefits. This study identified key liver miRNAs that regulate feed efficiency by analyzing miRNA profiling in high-feed efficiency and low-feed efficiency pigs.

JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY (2022)

Article Cardiac & Cardiovascular Systems

Human apolipoprotein A-II reduces atherosclerosis in knock-in rabbits

Tomonari Koike et al.

Summary: Using a novel rabbit model, the study revealed the specific roles of apoAII in lipoprotein metabolism and atherosclerosis. Rabbits with human apoAII gene insertion showed lower plasma triglycerides, higher HDL cholesterol, resistance to cholesterol-rich diet, and reduced aortic atherosclerosis compared to wild-type rabbits. These findings suggest that apoAII may serve as a potential target for the treatment of atherosclerosis.

ATHEROSCLEROSIS (2021)

Article Multidisciplinary Sciences

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

Zhangyuan Pan et al.

Summary: This study provides a comprehensive catalogue of regulatory elements in the pig genome, highlighting the enrichment of genomic variants associated with complex traits and adaptive evolution in active promoters and enhancers. Tissue-specific regulatory selection differs between Asian and European pig domestication processes, with porcine regulatory elements showing greater conservation in DNA sequence compared to human and mouse genomes. Integrating human genome-wide association studies reveals that mice or pigs may be more suitable biomedical models for different complex traits and diseases, based on tissue-specific regulatory conservation.

NATURE COMMUNICATIONS (2021)

Article Nutrition & Dietetics

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

Weiwei Miao et al.

Summary: The study identified the potential transcription factors affecting muscle growth and development and revealed the classical pathways regulating skeletal muscle development. Additionally, candidate genes associated with muscle development were identified, and differential regulation of chromatin openness and transcription factors were found to be involved in the regulation of gene expression.

FRONTIERS IN NUTRITION (2021)

Article Agriculture, Dairy & Animal Science

The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

Jingwei Yue et al.

Summary: Chromatin accessibility plays a crucial role in the regulation of embryonic muscle development in pigs by influencing the binding of transcription factors and controlling the temporal and spatial expression patterns of key genes involved in muscle development. The study highlights the importance of understanding the regulatory dynamics of genes in pig embryonic skeletal muscle development.

JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY (2021)

Review Biochemistry & Molecular Biology

Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin

Olivia Morrison et al.

Summary: Chromatin is composed of DNA and histone proteins and is important for packaging DNA and regulating DNA metabolic pathways. It is categorized into euchromatin (active transcription), heterochromatin (silencing), and centromeric chromatin (chromosome segregation).

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Multidisciplinary Sciences

A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription

Long Jin et al.

Summary: A comprehensive transcriptomic survey of pigs can provide insight into tissue specialization processes and facilitate their use as a biomedical model. The study reveals transcriptomic variability among different tissues in pigs, shedding light on tissue physiology.

NATURE COMMUNICATIONS (2021)

Review Cell Biology

Regulation of active and quiescent somatic stem cells by Notch signaling

Risa Sueda et al.

DEVELOPMENT GROWTH & DIFFERENTIATION (2020)

Review Cell Biology

Chromatin replication and epigenetic cell memory

Kathleen R. Stewart-Morgan et al.

NATURE CELL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Multiple Signaling Roles of CD3ε and Its Application in CAR-T Cell Therapy

Wei Wu et al.

Article Biotechnology & Applied Microbiology

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Michelle M. Halstead et al.

BMC GENOMICS (2020)

Article Multidisciplinary Sciences

Comparison of differential accessibility analysis strategies for ATAC-seq data

Paul Gontarz et al.

SCIENTIFIC REPORTS (2020)

Article Multidisciplinary Sciences

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

Yingyao Zhou et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes

Madhusudhan Bysani et al.

SCIENTIFIC REPORTS (2019)

Review Genetics & Heredity

Chromatin accessibility and the regulatory epigenome

Sandy L. Klemm et al.

NATURE REVIEWS GENETICS (2019)

Article Endocrinology & Metabolism

Lipid and glucose metabolism in hepatocyte cell lines and primary mouse hepatocytes: a comprehensive resource for in vitro studies of hepatic metabolism

Shilpa R. Nagarajan et al.

AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM (2019)

Article Multidisciplinary Sciences

Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle

Leydiana D. Fonseca et al.

SCIENTIFIC REPORTS (2019)

Review Gastroenterology & Hepatology

Development of the liver: Insights into organ and tissue morphogenesis

Elke A. Ober et al.

JOURNAL OF HEPATOLOGY (2018)

Article Biochemical Research Methods

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

M. Ryan Corces et al.

NATURE METHODS (2017)

Article Gastroenterology & Hepatology

Drug Metabolism in the Liver

Omar Abdulhameed Almazroo et al.

CLINICS IN LIVER DISEASE (2017)

Article Multidisciplinary Sciences

Fetal liver hematopoietic stem cell niches associate with portal vessels

Jalal A. Khan et al.

SCIENCE (2016)

Article Anesthesiology

Alterations in coagulation following major liver resection

S. V. Mallett et al.

ANAESTHESIA (2016)

Article Biotechnology & Applied Microbiology

Near-optimal probabilistic RNA-seq quantification

Nicolas L. Bray et al.

NATURE BIOTECHNOLOGY (2016)

Article Biochemistry & Molecular Biology

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Cell Biology

SERCA1 overexpression minimizes skeletal muscle damage in dystrophic mouse models

Davi A. G. Mazala et al.

AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY (2015)

Article Biochemical Research Methods

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

Guangchuang Yu et al.

BIOINFORMATICS (2015)

Article Medicine, Research & Experimental

Quadriceps muscle weakness and atrophy are associated with a differential epigenetic profile in advanced COPD

Ester Puig-Vilanova et al.

CLINICAL SCIENCE (2015)

Review Developmental Biology

Orchestrating liver development

Miriam Gordillo et al.

DEVELOPMENT (2015)

Article Biochemistry & Molecular Biology

MEF2D Deficiency in Neonatal Cardiomyocytes Triggers Cell Cycle Re-entry and Programmed Cell Death in Vitro

Nelsa L. Estrella et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2015)

Article Biochemistry & Molecular Biology

The MEME Suite

Timothy L. Bailey et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Surgery

Current status of pig liver xenotransplantation

Burcin Ekser et al.

INTERNATIONAL JOURNAL OF SURGERY (2015)

Article Biochemistry & Molecular Biology

Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPK-MEF2 signaling

Stephanie Wales et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Physiology

Energy Metabolism in the Liver

Liangyou Rui

COMPREHENSIVE PHYSIOLOGY (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Hematology

Transcriptional regulation of the Ikzf1 locus

Toshimi Yoshida et al.

BLOOD (2013)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Endocrinology & Metabolism

SERCA1 protein expression in muscle of patients with Brody disease and Brody syndrome and in cultured human muscle fibers

Valeria Guglielmi et al.

MOLECULAR GENETICS AND METABOLISM (2013)

Article Multidisciplinary Sciences

The accessible chromatin landscape of the human genome

Robert E. Thurman et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Identifying ChIP-seq enrichment using MACS

Jianxing Feng et al.

NATURE PROTOCOLS (2012)

Review Biochemistry & Molecular Biology

The pig: a model for human infectious diseases

Francois Meurens et al.

TRENDS IN MICROBIOLOGY (2012)

Article Statistics & Probability

MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT EXPERIMENTS

Qunhua Li et al.

ANNALS OF APPLIED STATISTICS (2011)

Article Biochemical Research Methods

Assigning roles to DNA regulatory motifs using comparative genomics

Fabian A. Buske et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription

Adam N. Yadon et al.

MOLECULAR AND CELLULAR BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

GREAT improves functional interpretation of cis-regulatory regions

Cory Y. McLean et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Review Medicine, Research & Experimental

Selected physiologic compatibilities and incompatibilities between human and porcine organ systems

Zuhaib Ibrahim et al.

XENOTRANSPLANTATION (2006)

Article Biotechnology & Applied Microbiology

Pigs in sequence space:: A 0.66X coverage pig genome survey based on shotgun sequencing -: art. no. 70

R Wernersson et al.

BMC GENOMICS (2005)

Article Biochemistry & Molecular Biology

Mitochondrial deficiency and cardiac sudden death in mice lacking the MEF2A transcription factor

FJ Naya et al.

NATURE MEDICINE (2002)

Review Gastroenterology & Hepatology

Coagulation disorders in liver disease

L Amitrano et al.

SEMINARS IN LIVER DISEASE (2002)