Epigenomics analysis of miRNA cis-regulatory elements in pig muscle and fat tissues

A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

(2021) Yunxia Zhao et al.   Nature Communications

High-throughput Transcriptome Analysis Reveals Potentially Important Relationships Between LncRNAs and Genes in Broilers Affected by Valgus-varus Deformity (Gallus gallus)

(2020) Yaping Guo et al.   GENE

Deciphering the miRNA transcriptome of Rongchang pig longissimus dorsi at weaning and slaughter time points

(2020) Xiaochang Chen et al.   JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION

The scaffold protein p62 regulates adaptive thermogenesis through ATF2 nuclear target activation

(2020) Katrin Fischer et al.   Nature Communications

Adipose Tissue and FoxO1: Bridging Physiology and Mechanisms

(2020) Laura Ioannilli et al.   Cells

miRDB: an online database for prediction of functional microRNA targets

(2019) Yuhao Chen et al.   NUCLEIC ACIDS RESEARCH

Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

(2018) R. Davoli et al.   ANIMAL GENETICS

Dynamic transcriptional control of macrophage miRNA signature via inflammation responsive enhancers revealed using a combination of next generation sequencing-based approaches

(2018) Zsolt Czimmerer et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A Huntingtin Knockin Pig Model Recapitulates Features of Selective Neurodegeneration in Huntington’s Disease

(2018) Sen Yan et al.   CELL

MiR-122 marks the differences between subcutaneous and visceral adipose tissues and associates with the outcome of bariatric surgery

(2018) Chien-Hung Liao et al.   Obesity Research & Clinical Practice

CDK6 inhibits white to beige fat transition by suppressing RUNX1

(2018) Xiaoli Hou et al.   Nature Communications

An overview of microRNAs: Biology, functions, therapeutics, and analysis methods

(2018) Kioomars Saliminejad et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Differential expression profile of miRNAs in porcine muscle and adipose tissue during development

(2017) Qi Wang et al.   GENE

Advances in the understanding of adipose tissue biology

(2017) Shingo Kajimura   Nature Reviews Endocrinology

IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions

(2017) Martin Mann et al.   NUCLEIC ACIDS RESEARCH

Function of the myogenic regulatory factors Myf5, MyoD, Myogenin and MRF4 in skeletal muscle, satellite cells and regenerative myogenesis

(2017) Peter S. Zammit   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

MicroRNA-95 promotes myogenic differentiation by down-regulation of aminoacyl-tRNA synthase complex-interacting multifunctional protein 2

(2017) Biao Li et al.   Oncotarget

Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle

(2017) Yuntao Guo et al.   Scientific Reports

MicroRNAs in metabolism

(2016) S. Vienberg et al.   Acta Physiologica

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Comparative genomic analysis of upstream miRNA regulatory motifs inCaenorhabditis

(2016) Richard Jovelin et al.   RNA

Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors

(2015) Jason Piper et al.   BMC GENOMICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

MicroRNA regulatory networks in human adipose tissue and obesity

(2015) Peter Arner et al.   Nature Reviews Endocrinology

The Role of Six1 in the Genesis of Muscle Cell and Skeletal Muscle Development

(2014) Wangjun Wu et al.   International Journal of Biological Sciences

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Foxk proteins repress the initiation of starvation-induced atrophy and autophagy programs

(2014) Christopher John Bowman et al.   NATURE CELL BIOLOGY

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

(2014) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

MicroRNA-143 Regulates Adipogenesis by Modulating the MAP2K5–ERK5 Signaling

(2014) Lin Chen et al.   Scientific Reports

An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury

(2013) Li-Wei Chang et al.   BMC GENOMICS

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

(2012) Jiyuan An et al.   NUCLEIC ACIDS RESEARCH

New insights into adipocyte-specific leptin gene expression

(2012) Christiane D. Wrann et al.   Adipocyte

MicroRNAs in skeletal myogenesis

(2011) Yejing Ge et al.   CELL CYCLE

microRNAs in the Regulation of Adipogenesis and Obesity

(2011) R. A. McGregor et al.   CURRENT MOLECULAR MEDICINE

MicroRNAs in adipogenesis and as therapeutic targets for obesity

(2011) Ryan Alexander et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A Brief Review on the Mechanisms of miRNA Regulation

(2010) Yimei Cai et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

MicroRNA control of muscle development and disease

(2009) Andrew H Williams et al.   CURRENT OPINION IN CELL BIOLOGY

Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data

(2009) David L. Corcoran et al.   PLoS One

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Chromatin structure analyses identify miRNA promoters

(2008) F. Ozsolak et al.   GENES & DEVELOPMENT

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH