Comparative transcriptome analysis provides insight into the molecular targets and signaling pathways of deer TGF-1 regulating chondrocytes proliferation and differentiation.

BACKGROUND: Chondrocytes are the only cell components in the cartilage, which has the poor regeneration ability. Thus, repairing damaged cartilage remains a huge challenge. Sika deer antlers are mainly composed of cartilaginous tissues that have an astonishing capacity for repair and renewal. Our previous study has demonstrated the transforming growth factor ß (TGF-ß1) is considered to be a key molecule involved in rapid growth, with the strongest expression in the cartilage layer. However, it remains to be clarified whether deer TGF-ß1 has significantly different function from other species such as mouse, and what is the molecular mechanism of regulating cartilage growth. METHODS: Primary chondrocytes was collected from new born mouse rib cartilage. The effect of TGF-ß1 on primary chondrocytes viability was elucidated by RNA sequencing (RNA-seq) technology combined with validation methods such as quantitative real-time polymerase chain reaction (qRT-PCR) and immunofluorescence assay (IFA). Differential expression genes were identified using the DEGseq package. RESULTS: Our results demonstrated that the overexpression of deer TGF-ß1 possibly promoted chondrocyte proliferation and extracellular matrix (ECM) synthesis, while simultaneously suppressing chondrocyte differentiation through regulating transcription factors, growth factors, ECM related genes, proliferation and differentiation marker genes, such as Comp, Fgfr3, Atf4, Stat1 etc., and signaling pathways such as the MAPK signaling pathway, inflammatory mediator regulation of TRP channels etc. In addition, by comparing the amino acid sequence and structures between the deer TGF-ß1 and mouse TGF-ß1, we found that deer TGF-ß1 and mouse TGF-ß1 proteins are mainly structurally different in arm domains, which is the main functional domain. Phenotypic identification results showed that deer TGF-ß1 may has stronger function than mouse TGF-ß1. CONCLUSION: ​These results suggested that deer TGF-ß1 has the ability to promote chondrogenesis by regulating chondrocyte proliferation, differentiation and ECM synthesis. This study provides insights into the molecular mechanisms underlying the effects of deer TGF-ß1 on chondrocyte viability.

Novel insights into the effect of deer IGF-1 on chondrocyte viability and IL-1ß-induced inflammation response.

Clinical treatment of Osteoarthritis (OA) remains a challenge due to the poor self-regeneration ability of cartilage. Deer antler is the only cartilage tissue that can completely regenerate each year. Insulin-like growth factor 1 (IGF-1) is one of the major active components in the deer antler that participate in regulating the rapid regeneration of deer antler cartilage. This has led us to speculate that deer IGF-1 might potentially become a candidate drug for reducing damage and inflammation of OA. Thus, we aimed to explore the underlying mechanism of deer IGF-1 in chondrocyte proliferation, differentiation, and inflammation response. Deer, mouse, and human IGF-1 amino acid sequences and protein structures were aligned using CLUSTAL and PSIPRED. The underlying molecular mechanism of deer IGF-1 on primary chondrocytes was investigated by RNA-sequencing (RNA-seq) technology combined with various experiments. Cytokine interleukin-1ß (IL-1ß) was used to induce the inflammation response of primary chondrocytes. We found that deer IGF-1 was more similar to human IGF-1 than mouse IGF-1. qRT-PCR and immunofluorescence assay indicated that deer IGF-1 had stronger effects than mouse IGF-1. We also found that the deer IGF-1 enhanced the expression of cell proliferation, differentiation, and extracellular matrix (ECM)-related genes, but decreased the expression of ECM-degrading genes. Deer IGF-1 also attenuated the IL-1ß-induced inflammatory and ECM degradation in chondrocytes. This study provides insight into the molecular mechanisms of deer IGF-1 on primary chondrocyte viability and presents a candidate for combatting inflammatory responses in OA development.

De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism.

SOX4, together with SOX11 and SOX12, forms group C of SRY-related (SOX) transcription factors. They play key roles, often in redundancy, in multiple developmental pathways, including neurogenesis and skeletogenesis. De novo SOX11 heterozygous mutations have been shown to cause intellectual disability, growth deficiency, and dysmorphic features compatible with mild Coffin-Siris syndrome. Using trio-based exome sequencing, we here identify de novo SOX4 heterozygous missense variants in four children who share developmental delay, intellectual disability, and mild facial and digital morphological abnormalities. SOX4 is highly expressed in areas of active neurogenesis in human fetuses, and sox4 knockdown in Xenopus embryos diminishes brain and whole-body size. The SOX4 variants cluster in the highly conserved, SOX family-specific HMG domain, but each alters a different residue. In silico tools predict that each variant affects a distinct structural feature of this DNA-binding domain, and functional assays demonstrate that these SOX4 proteins carrying these variants are unable to bind DNA in vitro and transactivate SOX reporter genes in cultured cells. These variants are not found in the gnomAD database of individuals with presumably normal development, but 12 other SOX4 HMG-domain missense variants are recorded and all demonstrate partial to full activity in the reporter assay. Taken together, these findings point to specific SOX4 HMG-domain missense variants as the cause of a characteristic human neurodevelopmental disorder associated with mild facial and digital dysmorphism.

Comparison of Gene Expression Patterns in Articular Cartilage and Xiphoid Cartilage.

Cartilage is a resilient and smooth connective tissue that is found throughout the body. Among the three major types of cartilage, namely hyaline cartilage, elastic cartilage, and fibrocartilage, hyaline cartilage is the most widespread type of cartilage predominantly located in the joint surfaces (articular cartilage, AC). It remains a huge challenge for orthopedic surgeons to deal with AC damage since it has limited capacity for self-repair. Xiphoid cartilage (XC) is a vestigial cartilage located in the distal end of the sternum. XC-derived chondrocytes exhibit strong chondrogenic differentiation capacity. Thus, XC could become a potential donor site of chondrocytes for cartilage repair and regeneration. However, the underlying gene expression patterns between AC and XC are still largely unknown. In the present study, we used state-of-the-art RNA-seq technology combined with validation method to investigate the gene expression patterns between AC and XC, and identified a series of differentially expressed genes (DEGs) involved in chondrocyte commitment and differentiation including growth factors, transcription factors, and extracellular matrices. We demonstrated that the majority of significantly up-regulated DEGs (XC vs. AC) in XC were involved in regulating cartilage regeneration and repair, whereas the majority of significantly up-regulated DEGs (XC vs. AC) in AC were involved in regulating chondrocyte differentiation and maturation. This study has increased our knowledge of transcriptional networks in hyaline cartilage and elastic cartilage. It also supports the use of XC-derived chondrocytes as a potential cell resource for cartilage regeneration and repair.

Nfib promotes chondrocyte proliferation and inhibits differentiation by mildly regulating Sox9 and its downstream genes.

BACKGROUND: Chondrocyte proliferation and differentiation play pivotal roles in regulating cartilage formation, endochondral bone formation, and repair. Cartilage damage and underdevelopment may cause severe joint diseases. Various transcription factors regulate cartilage development. Nuclear factor 1 B (Nfib) is a transcription factor that plays a regulatory role in various organs. However, the effect and mechanism of Nfib on the proliferation and differentiation of chondrocytes in cartilage are still largely unknown. METHODS AND RESULTS: In the present study, we investigated the gene expression patterns in primary chondrocytes with Nfib overexpression or silencing by RNA sequencing (RNA-seq) technology. The results showed that Nfib overexpression significantly up-regulated genes that are related to chondrocyte proliferation and extracellular matrix (ECM) synthesis and significantly down-regulated genes related to chondrocyte differentiation and ECM degradation. However, with Nfib silencing, the genes involved in promoting chondrocyte differentiation were significantly up-regulated, whereas those involved in promoting chondrocyte proliferation were significantly down-regulated. Furthermore, quantitative real-time PCR (qRT-PCR), western blot, alcian blue staining and immunofluorescence staining assays further confirmed that Nfib potentially promotes chondrocyte proliferation and extracellular synthesis but inhibits differentiation. CONCLUSIONS: The molecular mechanism of Nfib in promoting chondrocyte proliferation and inhibiting differentiation was probably achieved by stimulating Sox9 and its downstream genes. Thus, this study adds new insights regarding the underlying molecular mechanism of transcriptional regulation in cartilage.

Comprehensive RNA sequencing in primary murine keratinocytes and fibroblasts identifies novel biomarkers and provides potential therapeutic targets for skin-related diseases.

BACKGROUND: Keratinocytes and fibroblasts represent the major cell types in the epidermis and dermis of the skin and play a significant role in maintenance of skin homeostasis. However, the biological characteristics of keratinocytes and fibroblasts remain to be elucidated. The purpose of this study was to compare the gene expression pattern between keratinocytes and fibroblasts and to explore novel biomarker genes so as to provide potential therapeutic targets for skin-related diseases such as burns, wounds, and aging. METHODS: Skin keratinocytes and fibroblasts were isolated from newborn mice. To fully understand the heterogeneity of gene expression between keratinocytes and fibroblasts, differentially expressed genes (DEGs) between the two cell types were detected by RNA-seq technology. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the known genes of keratinocytes and fibroblasts and verify the RNA-seq results. RESULTS: Transcriptomic data showed a total of 4309 DEGs (fold-change > 1.5 and q-value < 0.05). Among them, 2197 genes were highly expressed in fibroblasts and included 10 genes encoding collagen, 16 genes encoding transcription factors, and 14 genes encoding growth factors. Simultaneously, 2112 genes were highly expressed in keratinocytes and included 7 genes encoding collagen, 14 genes encoding transcription factors, and 8 genes encoding growth factors. Furthermore, we summarized 279 genes specifically expressed in keratinocytes and 33 genes specifically expressed in fibroblasts, which may represent distinct molecular signatures of each cell type. Additionally, we observed some novel specific biomarkers for fibroblasts such as Plac8 (placenta-specific 8), Agtr2 (angiotensin II receptor, type 2), Serping1 (serpin peptidase inhibitor, clade G, member 1), Ly6c1 (lymphocyte antigen 6 complex, locus C1), Dpt (dermatopontin), and some novel specific biomarkers for keratinocytes such as Ly6a (lymphocyte antigen 6 complex, locus A) and Lce3c (late cornified envelope 3C), Ccer2 (coiled-coil glutamate-rich protein 2), Col18a1 (collagen, type XVIII, alpha 1) and Col17a1 (collagen type XVII, alpha 1). In summary, these data provided novel identifying biomarkers for two cell types, which can provide a resource of DEGs for further investigations.

Runx3 regulates chondrocyte phenotype by controlling multiple genes involved in chondrocyte proliferation and differentiation.

Chondrocytes are the sole cell type present within cartilage, and play pivotal roles in controlling the formation and composition of health cartilage. Chondrocytes maintain cartilage homeostasis through proliferating, differentiating and synthesizing different types of extracellular matrices. Thus, the coordinated proliferation and differentiation of chondrocytes are essential for cartilage growth, repair and the conversion from cartilage to bone during the processes of bone formation and fracture healing. Runx3, a transcription factor that belongs to the Runx family, is significantly upregulated at the onset of cartilage mineralization and regulates both early and late markers of chondrocyte maturation. Therefore, Runx3 may serve as an accelerator of chondrocyte differentiation and maturation. However, the underlying molecular mechanism of Runx3 in regulating chondrocyte proliferation and differentiation remains largely to be elucidated. In the present study, we used state-of-the-art RNA-seq technology combined with validation methods to investigate the effect of Runx3 overexpression or silencing on primary chondrocyte proliferation and differentiation, and demonstrated that Runx3 overexpression possibly inhibited chondrocyte proliferation but accelerated differentiation, whereas Runx3 silencing possibly promoted chondrocyte proliferation but suppressed differentiation. Furthermore, Runx3 overexpression possibly decreased the expression levels of Sox9 and its downstream genes via Sox9 cartilage-specific enhancers, and vice versa for Runx3 silencing.

Comparative transcriptome analysis of the main beam and brow tine of sika deer antler provides insights into the molecular control of rapid antler growth.

BACKGROUND: Deer antlers have become a valuable model for biomedical research due to the capacities of regeneration and rapid growth. However, the molecular mechanism of rapid antler growth remains to be elucidated. The aim of the present study was to compare and explore the molecular control exerted by the main beam and brow tine during rapid antler growth. METHODS: The main beams and brow tines of sika deer antlers were collected from Chinese sika deer (Cervus nippon) at the rapid growth stage. Comparative transcriptome analysis was conducted using RNA-Seq technology. Differential expression was assessed using the DEGseq package. Functional Gene Ontology (GO) enrichment analysis was accomplished using a rigorous algorithm according to the GO Term Finder tool, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis was accomplished with the R function phyper, followed by the hypergeometric test and Bonferroni correction. Quantitative real-time polymerase chain reaction (qRT-PCR) was carried out to verify the RNA levels for differentially expressed mRNAs. RESULTS: The expression levels of 16 differentially expressed genes (DEGs) involved in chondrogenesis and cartilage development were identified as significantly upregulated in the main beams, including transcription factor SOX-9 (Sox9), collagen alpha-1(II) chain (Col2a1), aggrecan core protein (Acan), etc. However, the expression levels of 17 DEGs involved in endochondral ossification and bone formation were identified as significantly upregulated in the brow tines, including collagen alpha-1(X) chain (Col10a1), osteopontin (Spp1) and bone sialoprotein 2 (Ibsp), etc. CONCLUSION: These results suggest that the antler main beam has stronger growth capacity involved in chondrogenesis and cartilage development compared to the brow tine during rapid antler growth, which is mainly achieved through regulation of Sox9 and its target genes, whereas the antler brow tine has stronger capacities of endochondral bone formation and resorption compared to the main beam during rapid antler growth, which is mainly achieved through the genes involved in regulating osteoblast and osteoclast activities. Thus, the current research has deeply expanded our understanding of the intrinsic molecular regulation displayed by the main beam and brow tine during rapid antler growth.

Proteomic analysis of the effects of antler extract on chondrocyte proliferation, differentiation and apoptosis.

Deer antlers are unique cranial appendages capable of regeneration and rapid growth. In addition, deer antlers have been widely used in traditional Chinese medicine to promote the function of the kidneys, reproductive system, bones and nervous system. It has been shown that water-soluble substances are the major bioactive components within the deer antlers. In this study, we prepared aqueous extracts from deer antlers during a rapid growth stage. We investigated the effects of antler extracts on primary chondrocytes by analyzing their protein expression patterns using isobaric tags for relative and absolute quantitation technology. We demonstrated that antler extracts promote chondrocyte proliferation and prevent chondrocyte differentiation and apoptosis by controlling multiple cellular processes involved in genomic stability, epigenetic alterations, ribosome biogenesis, protein synthesis and cytoskeletal reorganization. Antler extracts significantly increased the expression levels of proliferation markers Mki67 and Stmn1 and differentiation inhibitor Acp5 as well as cellular apoptosis inhibitors Ndufa4l2 and Rcn1. Thus, this study has greatly expanded our current knowledge of the molecular effects of antler extracts on chondrocytes. It has also shed new light on possible strategies to prevent damage to and to treat cartilage and its related diseases by using aqueous extracts from growing Sika deer antlers.

Identification of potential therapeutic targets of deer antler extract on bone regulation based on serum proteomic analysis.

Traditional Chinese medicine has been proven to be effective in treating human diseases according to a long-term observation for more than 2000 years. However, the precise molecular mechanisms of a majority of the medications are still largely unknown. Deer antler has been clinically used as an effective animal medication in traditional Chinese medicine for many centuries. Previous studies have demonstrated that antler extracts play crucial roles in promoting bone and cartilage development, growth and repair. However, the underlying molecular mechanism remains to be elucidated. In the present study, we applied isobaric tags for relative and absolute quantitation (iTRAQ) technology and a systematic bioinformatics analysis accompanied with validation method to obtain a full spectrum of the serum protein profiles under deer antler extract treatment. We identified a complex interaction network formed by the positive regulation of Tropomyosins (Tpm1, 2 and 4), WD repeat-containing protein 1 (Wdr1), Alpha-actinin-1 (Actn1) and Destrin (Dstn) and the negative regulation of Alpha-2-macroglobulin (A2m), Serine protease inhibitor A3 N (Serpina3n) and Apolipoproteins (Apoh and Apof), which coordinately interact with multiple proteins and signaling pathways. Our results suggest that the therapeutic effects of deer antler extract on treating bone diseases might achieved though the regulation of bone formation and remodeling by controlling a series of serum proteins and signaling pathways that were essential for osteoblast and osteoclast activities. Thus, this study has greatly deepened the current knowledge about the molecular mechanism of therapeutic effects of deer antler extract on bone diseases such as osteoporosis.

Transcriptomic characterization elucidates a signaling network that controls antler growth.

Deer antlers are amazing appendages with the fastest growth rate among mammalian organs. Antler growth is driven by the growth center through a modified endochondral ossification process. Thus, identification of signaling pathways functioning in antler growth center would help us to uncover the underlying molecular mechanism of rapid antler growth. Furthermore, exploring and dissecting the molecular mechanism that regulates antler growth is extremely important and helpful for identifying methods to enhance long bone growth and treat cartilage- and bone-related diseases. In this study, we build a comprehensive intercellular signaling network in antler growth centers from both the slow growth stage and rapid growth stage using a state-of-art RNA-Seq approach. This network includes differentially expressed genes that regulate the activation of multiple signaling pathways, including the regulation of actin cytoskeleton, calcium signaling, and adherens junction. These signaling pathways coordinately control multiple biological processes, including chondrocyte proliferation and differentiation, matrix homeostasis, mechanobiology, and aging processes, during antler growth in a comprehensive and efficient manner. Therefore, our study provides novel insights into the molecular mechanisms regulating antler growth and provides valuable and powerful insight for medical research on therapeutic strategies targeting skeletal disorders and related cartilage and bone diseases.

The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers.

Two decades after the discovery that heterozygous mutations within and around SOX9 cause campomelic dysplasia, a generalized skeleton malformation syndrome, it is well established that SOX9 is a master transcription factor in chondrocytes. In contrast, the mechanisms whereby translocations in the --350/-50-kb region 5' of SOX9 cause severe disease and whereby SOX9 expression is specified in chondrocytes remain scarcely known. We here screen this upstream region and uncover multiple enhancers that activate Sox9-promoter transgenes in the SOX9 expression domain. Three of them are primarily active in chondrocytes. E250 (located at -250 kb) confines its activity to condensed prechondrocytes, E195 mainly targets proliferating chondrocytes, and E84 is potent in all differentiated chondrocytes. E84 and E195 synergize with E70, previously shown to be active in most Sox9-expressing somatic tissues, including cartilage. While SOX9 protein powerfully activates E70, it does not control E250. It requires its SOX5/SOX6 chondrogenic partners to robustly activate E195 and additional factors to activate E84. Altogether, these results indicate that SOX9 expression in chondrocytes relies on widely spread transcriptional modules whose synergistic and overlapping activities are driven by SOX9, SOX5/SOX6 and other factors. They help elucidate mechanisms underlying campomelic dysplasia and will likely help uncover other disease mechanisms.

Comparative analysis of differentially expressed genes in Sika deer antler at different stages.

Deer antlers serve as useful models of rapid growth and mineralization in mammals. During the period of rapid growth, the antlers of many species of deer will elongate by more than 2 cm per day, after which the antlers gradually ossify. However, little is known about the genes that are involved in their development, particularly the molecular mechanisms responsible for rapid growth and ossification. In our previous studies, we have reported on the transcriptome analysis of deer antlers at rapid growth and ossification stages. With the aim to get a comprehensive understanding of gene expression patterns during antler growth, in the present study, we performed a rigorous algorithm to identify differentially expressed genes between two different stages (60 and 90 days) during antler growth. A total of 16,905 significantly changed transcripts were identified. Those sequences were mapped to 5,573 genes with 2,217 genes up-regulated and 3,356 genes down-regulated (60 days vs. 90 days), including ribosomal proteins, translation initiation and elongation factors, transcription factors, signaling molecules and extracellular matrix proteins. We also performed the gene ontology (GO) functional enrichment and pathway enrichment analysis of gene expression patterns with hypergeometric test and Bonferroni Correction. Both the two stages were enriched with members of GO categories and distinct pathways. Our data represent the most comprehensive sequence resource available for the deer antler and provide a basis for further research on deer antler molecular genetics and functional genomics.

Function and regulation of nuclear factor 1 X-type on chondrocyte proliferation and differentiation.

Nuclear factor 1 X-type (Nfix) is a transcription factor related to mental and physical development. However, very few studies have reported the effects of Nfix on cartilage. This study aims to reveal the influence of Nfix on the proliferation and differentiation of chondrocytes, and to explore its potential action mechanism. We isolated primary chondrocytes from the costal cartilage of newborn C57BL/6 mice and with Nfix overexpression or silencing treatment. We used Alcian blue staining and found that Nfix overexpression significantly promoted ECM synthesis in chondrocytes while silencing inhibited ECM synthesis. Using RNA-seq technology to study the expression pattern of Nfix in primary chondrocytes. We found that Nfix overexpression significantly up-regulated genes that are related to chondrocyte proliferation and extracellular matrix (ECM) synthesis and significantly down-regulated genes related to chondrocyte differentiation and ECM degradation. Nfix silencing, however, significantly up-regulated genes associated with cartilage catabolism and significantly down-regulated genes associated with cartilage growth promotion. Furthermore, Nfix exerted a positive regulatory effect on Sox9, and we propose that Nfix may promote chondrocyte proliferation and inhibit differentiation by stimulating Sox9 and its downstream genes. Our findings suggest that Nfix may be a potential target for the regulation of chondrocyte proliferation and differentiation.

BuShen JianGu Fang alleviates cartilage degeneration via regulating multiple genes and signaling pathways to activate NF-κB/Sox9 axis.

BACKGROUND: Osteoarthritis (OA) is an inflammatory response in chondrocytes, causing extracellular matrix (ECM) degradation and cartilage destruction, affecting millions of people worldwide. Chinese herbal formulae BuShen JianGu Fang (BSJGF) has been clinically applied for treating OA-related syndromes, but the underlying mechanism still unclear. METHODS: The components of BSJGF were analyzed by liquid chromatography-mass spectrometry (LC-MS). To make a traumatic OA model, the anterior cruciate ligament of 6-8-week-old male SD rats were cut and then the 0.4 mm metal was used to destroy the knee joint cartilage. OA severity was assessed by histological and Micro-CT. Mouse primary chondrocytes were utilized to investigate the mechanism of BSJGF alleviate osteoarthritis, which was examined by RNA-seq technology combined with a series of functional experiments. RESULTS: A total 619 components were identified by LC-MS. In vivo, BSJGF treatment result in a higher articular cartilage tissue area compared to IL-1ß group. Treatment also significantly increased Tb.Th, BV/TV and BMD of subchondral bone (SCB), which implied a protective effect on maintaining the stabilization of SCB microstructure. In vitro results indicated BSJGF promoted chondrocyte proliferation, increased the expression level of cartilage-specific genes (Sox9, Col2a1, Acan) and synthesized acidic polysaccharide, while inhibiting the release of catabolic enzymes and production of reactive oxygen species (ROS) induced by IL-1ß. Transcriptome analysis showed that there were 1471 and 4904 differential genes between IL-1ß group and blank group, BSJGF group and IL-1ß group, respectively, including matrix synthesis related genes (Col2a1, H19, Acan etc.), inflammation related genes (Comp, Pcsk6, Fgfr3 etc.) and oxidative stress related genes (Gm26917, Bcat1, Sod1 etc.). Furthermore, KEGG analysis and validation results showed that BSJGF reduces OA-mediated inflammation and cartilage damaged due to modulation of NF-κB/Sox9 signaling axis. CONCLUSION: The innovation of the present study was the elucidation of the alleviating cartilage degradation effect of BSJGF in vivo and in vitro and discovery of its mechanism through RNA-seq combined with function experiments, which provides a biological rationale for the clinical application of BSJGF for OA treatment.

De novo characterization of the antler tip of Chinese Sika deer transcriptome and analysis of gene expression related to rapid growth.

Deer antlers are well known for their regeneration and rapid growth. However, little is known about the genes that are involved in their development, especially the molecular mechanisms responsible for rapid growth. In the present study, we produced more than 41 million sequencing reads using the Illumina sequencing platform. These reads were assembled into 89,001 unique sequences (mean size: 450 bp), representing more than 58 times as many Sika deer sequences previously available in the NCBI database (as of Sep 15, 2011). Based on a similarity search with known proteins, we identified 40,088 sequences with a cut-off E value of 10(-5). Assembled sequences were then annotated using Gene ontology terms, Clusters of Orthologous Groups classifications, and Kyoto Encyclopedia of Genes and Genomes pathways. In addition, we found a number of highly expressed genes involved in the regulation of Sika deer antler rapid growth, including transcription factors, signaling molecules, and extracellular matrix proteins. Our data represent the most comprehensive sequence resource available for the deer antler and provide a basis for new research on deer antler molecular genetics and functional genomics.

Generation and analysis of expressed sequence tags from the bone marrow of Chinese Sika deer.

Sika deer is one of the best-known and highly valued animals of China. Despite its economic, cultural, and biological importance, there has not been a large-scale sequencing project for Sika deer to date. With the ultimate goal of sequencing the complete genome of this organism, we first established a bone marrow cDNA library for Sika deer and generated a total of 2,025 reads. After processing the sequences, 2,017 high-quality expressed sequence tags (ESTs) were obtained. These ESTs were assembled into 1,157 unigenes, including 238 contigs and 919 singletons. Comparative analyses indicated that 888 (76.75%) of the unigenes had significant matches to sequences in the non-redundant protein database, In addition to highly expressed genes, such as stearoyl-CoA desaturase, cytochrome c oxidase, adipocyte-type fatty acid-binding protein, adiponectin and thymosin beta-4, we also obtained vascular endothelial growth factor-A and heparin-binding growth-associated molecule, both of which are of great importance for angiogenesis research. There were 244 (21.09%) unigenes with no significant match to any sequence in current protein or nucleotide databases, and these sequences may represent genes with unknown function in Sika deer. Open reading frame analysis of the sequences was performed using the getorf program. In addition, the sequences were functionally classified using the gene ontology hierarchy, clusters of orthologous groups of proteins and Kyoto encyclopedia of genes and genomes databases. Analysis of ESTs described in this paper provides an important resource for the transcriptome exploration of Sika deer, and will also facilitate further studies on functional genomics, gene discovery and genome annotation of Sika deer.

Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology.

Deer antlers are the only mammalian appendages capable of repeated rounds of regeneration. Every year, deer antlers are shed and regrown from blastema into large branched structures of cartilage and bone. Little is known about the genes involved in antler development particularly during the later stages of ossification. We have produced more than 39 million sequencing reads in a single run using the Illumina sequencing platform. These were assembled into 138,642 unique sequences (mean size: 405 bp) representing 50 times the number of Sika deer sequences previously available in the NCBI database (as of Nov 2, 2011). Based on a similarity search of a database of known proteins, we identified 43,937 sequences with a cut-off E-value of 10(-5). Assembled sequences were annotated using Gene Ontology terms, Clusters of Orthologous Groups classifications and Kyoto Encyclopedia of Genes and Genomes pathways. A number of highly expressed genes involved in the regulation of Sika deer antler ossification, including growth factors, transcription factors and extracellular matrix components were found. This is the most comprehensive sequence resource available for the deer antler and provides a basis for the molecular genetics and functional genomics of deer antler.

Integrated RNA-Seq Analysis Uncovers the Potential Mechanism of the "Kidney Governing Bones" Theory of TCM.

Background: As in philosophy of traditional Chinese medicine (TCM), the theory of "kidney governing bones" has been demonstrated by a series of scientific studies. Furthermore, many groups including ours have explored the molecular mechanisms related to bone development, growth, and regeneration using modern biology technologies, such as RNA sequencing (RNA-Seq) and isobaric tags for relative and absolute quantification (ITRAQ), and have demonstrated that the underlying molecular mechanisms were highly consistent with the "kidney governing bones" theory. Objective: Kidney-yang deficiency (YD), as a pathological condition, has a passive effect on the skeleton growth; more specifically, it is a state of skeletal metabolic disorder. However, the exact molecular mechanisms related to the "kidney governing bones" theory under the control of multiple organs and systems are still unknown. Methods: In this study, we performed RNA-Seq analysis to investigate and compare the gene expression patterns of six types of tissue (bone, cartilage, kidney, testicle, thyroid gland, and adrenal gland) from YD rats and normal rats and analyzed the interaction effects controlled by multiple functional genes and signaling pathways between those tissues. Results: Our results showed that, in the state of YD, the functions of bone and cartilage were inhibited. Furthermore, multiple organs involving the reproductive, endocrine, and urinary systems were also investigated, and our results showed that YD could cause dysfunctions of these systems by downregulating multiple functional genes and signaling pathways that positively regulate the homeostasis of these tissues. Conclusion: We ensure that "kidney governing bones" was not a simple change in a single gene but the changes in complex biological networks caused by functional changes in multiple genes. This also coincides with the holistic view of TCM, which holds that the human body itself is an organic whole and the functional activities of each organ coordinate with each other.