Cultured Myoblasts Derived from Rat Soleus Muscle Show Altered Regulation of Proliferation and Myogenesis during the Course of Mechanical Unloading

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Abstract

The structure and function of soleus muscle fibers undergo substantial remodeling under real or simulated microgravity conditions. However, unloading-induced changes in the functional activity of skeletal muscle primary myoblasts remain poorly studied. The purpose of our study was to investigate how short-term and long-term mechanical unloading would affect cultured myoblasts derived from rat soleus muscle. Mechanical unloading was simulated by rat hindlimb suspension model (HS). Myoblasts were purified from rat soleus at basal conditions and after 1, 3, 7, and 14 days of HS. Myoblasts were expanded in vitro, and the myogenic nature was confirmed by their ability to differentiate as well as by immunostaining/mRNA expression of myogenic markers. The proliferation activity at different time points after HS was analyzed, and transcriptome analysis was performed. We have shown that soleus-derived myoblasts differently respond to an early and later stage of HS. At the early stage of HS, the proliferative activity of myoblasts was slightly decreased, and processes related to myogenesis activation were downregulated. At the later stage of HS, we observed a decrease in myoblast proliferative potential and spontaneous upregulation of the pro-myogenic program.

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

Y. Liao, G K Smyth, W Shi (2014)

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.

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Gene Set Knowledge Discovery with Enrichr

Zhuorui Xie, Allison A. Bailey, Maxim Kuleshov … (2021)

Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of genes and proteins that need to be further analyzed and integrated in the context of known biology. Enrichr (Chen et al., 2013; Kuleshov et al., 2016) is a gene set search engine that enables the querying of hundreds of thousands of annotated gene sets. Enrichr uniquely integrates knowledge from many high-profile projects to provide synthesized information about mammalian genes and gene sets. The platform provides various methods to compute gene set enrichment, and the results are visualized in several interactive ways. This protocol provides a summary of the key features of Enrichr, which include using Enrichr programmatically and embedding an Enrichr button on any website. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Analyzing lists of differentially expressed genes from transcriptomics, proteomics and phosphoproteomics, GWAS studies, or other experimental studies Basic Protocol 2: Searching Enrichr by a single gene or key search term Basic Protocol 3: Preparing raw or processed RNA-seq data through BioJupies in preparation for Enrichr analysis Basic Protocol 4: Analyzing gene sets for model organisms using modEnrichr Basic Protocol 5: Using Enrichr in Geneshot Basic Protocol 6: Using Enrichr in ARCHS4 Basic Protocol 7: Using the enrichment analysis visualization Appyter to visualize Enrichr results Basic Protocol 8: Using the Enrichr API Basic Protocol 9: Adding an Enrichr button to a website.

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Satellite cells and the muscle stem cell niche.

Hang Yin, Feodor Price, Michael A Rudnicki (2013)

Adult skeletal muscle in mammals is a stable tissue under normal circumstances but has remarkable ability to repair after injury. Skeletal muscle regeneration is a highly orchestrated process involving the activation of various cellular and molecular responses. As skeletal muscle stem cells, satellite cells play an indispensible role in this process. The self-renewing proliferation of satellite cells not only maintains the stem cell population but also provides numerous myogenic cells, which proliferate, differentiate, fuse, and lead to new myofiber formation and reconstitution of a functional contractile apparatus. The complex behavior of satellite cells during skeletal muscle regeneration is tightly regulated through the dynamic interplay between intrinsic factors within satellite cells and extrinsic factors constituting the muscle stem cell niche/microenvironment. For the last half century, the advance of molecular biology, cell biology, and genetics has greatly improved our understanding of skeletal muscle biology. Here, we review some recent advances, with focuses on functions of satellite cells and their niche during the process of skeletal muscle regeneration.