ApCPS2 contributes to medicinal diterpenoid biosynthesis and defense against insect herbivore in Andrographis paniculata

Kalmegh (Andrographis paniculata) spatiotemporally produces medicinally-important ent-labdane-related diterpenoids (ent-LRDs); andrographolide (AD), 14-deoxy-11,12-didehydroandrographolide (DDAD), neoandrographolide (NAD). ApCPS1 and ApCPS2, the ent-copalyl pyrophosphate (ent-CPP)-producing class II diterpene synthases (diTPSs) were identified, but their contributions to ent-CPP precursor supply for ent-LRD biosynthesis were not well understood. Here, we characterized ApCPS4, an additional ent-CPP-forming diTPS. Further, we elucidated in planta function of the ent-CPP-producing diTPSs (ApCPS1,2,4) by integrating transcript-metabolite co-profiles, biochemical analysis and gene functional characterization. ApCPS1,2,4 localized to the plastids, where diterpenoid biosynthesis occurs in plants, but ApCPS1,2,4 transcript expression patterns and ent-LRD contents revealed a strong correlation of ApCPS2 expression and ent-LRD accumulation in kalmegh. ApCPS1,2,4 upstream sequences differentially activated β-glucuronidase (GUS) in Arabidopsis and transiently-transformed kalmegh. Similar to higher expression of ApCPS1 in kalmegh stem, ApCPS1 upstream sequence activated GUS in stem/hypocotyl of Arabidopsis and kalmegh. However, ApCPS2,4 upstream sequences weakly activated GUS expression in Arabidopsis, which was not well correlated with ApCPS2,4 transcript expression in kalmegh tissues. Whereas, ApCPS2,4 upstream sequences could activate GUS expression at a considerable level in kalmegh leaf and roots/calyx, respectively, suggesting the involvement of transcriptional regulator(s) of ApCPS2,4 that might participate in kalmegh-specific diterpenoid pathway. Interestingly, ApCPS2-silenced kalmegh showed a drastic reduction in AD, DDAD and NAD contents and compromised defense against insect herbivore Spodoptera litura. However, ent-LRD contents and herbivore defense in ApCPS1 or ApCPS4-silenced plants remained largely unaltered. Overall, these results suggested an important role of ApCPS2 in producing ent-CPP for medicinal ent-LRD biosynthesis and defense against insect herbivore.

Comparative transcriptomic analysis delineates adaptation strategies of Rana kukunoris toward cold stress on the Qinghai-Tibet Plateau

BACKGROUND

Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to understand how the frogs survive in winter.

RESULTS

Transcriptome of liver and muscle of R. kukunoris collected in hibernation and spring were assisted by single molecule real-time (SMRT) sequencing technology. A total of 10,062 unigenes of R. kukunoris were obtained, and 9,924 coding sequences (CDS) were successfully annotated. Our examination of the mRNA response to whole body freezing and recover in the frogs revealed key genes concerning underlying antifreeze proteins and cryoprotectants (glucose and urea). Functional pathway analyses revealed differential regulated pathways of ribosome, energy supply, and protein metabolism which displayed a freeze-induced response and damage recover. Genes related to energy supply in the muscle of winter frogs were up-regulated compared with the muscle of spring frogs. The liver of hibernating frogs maintained modest levels of protein synthesis in the winter. In contrast, the liver underwent intensive high levels of protein synthesis and lipid catabolism to produce substantial quantity of fresh proteins and energy in spring. Differences between hibernation and spring were smaller than that between tissues, yet the physiological traits of hibernation were nevertheless passed down to active state in spring.

CONCLUSIONS

Based on our comparative transcriptomic analyses, we revealed the likely adaptive mechanisms of R. kukunoris. Ultimately, our study expands genetic resources for the freezing-tolerant frogs.

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identified conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at gega.sigenae.org.

Genetic effects of sequence-conserved enhancer-like elements on human complex traits

BACKGROUND

The vast majority of findings from human genome-wide association studies (GWAS) map to non-coding sequences, complicating their mechanistic interpretations and clinical translations. Non-coding sequences that are evolutionarily conserved and biochemically active could offer clues to the mechanisms underpinning GWAS discoveries. However, genetic effects of such sequences have not been systematically examined across a wide range of human tissues and traits, hampering progress to fully understand regulatory causes of human complex traits.

RESULTS

Here we develop a simple yet effective strategy to identify functional elements exhibiting high levels of human-mouse sequence conservation and enhancer-like biochemical activity, which scales well to 313 epigenomic datasets across 106 human tissues and cell types. Combined with 468 GWAS of European (EUR) and East Asian (EAS) ancestries, these elements show tissue-specific enrichments of heritability and causal variants for many traits, which are significantly stronger than enrichments based on enhancers without sequence conservation. These elements also help prioritize candidate genes that are functionally relevant to body mass index (BMI) and schizophrenia but were not reported in previous GWAS with large sample sizes.

CONCLUSIONS

Our findings provide a comprehensive assessment of how sequence-conserved enhancer-like elements affect complex traits in diverse tissues and demonstrate a generalizable strategy of integrating evolutionary and biochemical data to elucidate human disease genetics.

Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress

Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.

Changes in marker secondary metabolites revealed the medicinal parts, harvest time, and possible synthetic sites of Rubia cordifolia L

Rubia cordifolia L. is a significant medicinal plant. To investigate the changes of marker metabolites of R. cordifolia, the purpurin, mollugin, carbon, nitrogen contents, and the expression of genes involved in anthraquinones synthesis were examined. The findings indicated that the two secondary metabolites were only detected in stems and roots. Root purpurin content was 5-26 times higher than in stems, and root mollugin content was 92 times higher than in stems in June. These findings suggest that the potential of the roots as a medicinal part. The roots were found to have highest purpurin content in October (2.406 mg g-1), whereas the mollugin content was highest in August (6.193 mg g-1). However, the purpurin content in August was only 0.029 mg g-1 lower than that in October, making August a suitable harvest period for R. cordifolia. The expression 1-deoxy-D-xylulose 5-phosphate synthase (dxs) and 1-deoxy-D-xylulose-5-phosphate reductorisomerase (dxr) genes in roots showed an upward trend. However, the expression level of dxr gene was significantly higher than dxs with the range of 60-518 times higher, indicating the important role of dxr gene. Through correlation and redundancy analyses, it was found that mollugin showed positive correlation with carbon contents and carbon-nitrogen ratio of aerial parts. Additionally, purpurin showed a positive correlation with the expression of both genes. As a result, mollugin is likely to be synthesized in the aerial parts and then stored in the roots, whereas purpurin might be synthesized in the stems and roots. These findings could provide cultivation guidelines for R. cordifolia.

NeuroCNVscore: a tissue-specific framework to prioritise the pathogenicity of CNVs in neurodevelopmental disorders

BACKGROUND

Neurodevelopmental disorders (NDDs) are associated with altered development of the brain especially in childhood. Copy number variants (CNVs) play a crucial role in the genetic aetiology of NDDs by disturbing gene expression directly at linear sequence or remotely at three-dimensional genome level in a tissue-specific manner. Despite the substantial increase in NDD studies employing whole-genome sequencing, there is no specific tool for prioritising the pathogenicity of CNVs in the context of NDDs.

METHODS

Using an XGBoost classifier, we integrated 189 features that represent genomic sequences, gene information and functional/genomic segments for evaluating genome-wide CNVs in a neuro/brain-specific manner, to develop a new tool, neuroCNVscore. We used Human Phenotype Ontology to construct an independent NDD-related set.

RESULTS

Our neuroCNVscore framework (https://github.com/lxsbch/neuroCNVscore) achieved high predictive performance (precision recall=0.82; area under curve=0.85) and outperformed an existing reference method SVScore. Notably, the predicted pathogenic CNVs showed enrichment in known genes associated with autism.

CONCLUSIONS

NeuroCNVscore prioritises functional, deleterious and pathogenic CNVs in NDDs at whole genome-wide level, which is important for genetic studies and clinical genomic screening of NDDs as well as for providing novel biological insights into NDDs.

Tissue specificity of DNA damage and repair

DNA is a remarkable biochemical macromolecule tasked with storing the genetic information that instructs life on planet Earth. However, its inherent chemical instability within the cellular milieu is incompatible with the accurate transmission of genetic information to subsequent generations. Therefore, biochemical pathways that continuously survey and repair DNA are essential to sustain life, and the fundamental mechanisms by which different DNA lesions are repaired have remained well conserved throughout evolution. Nonetheless, the emergence of multicellular organisms led to profound differences in cellular context and physiology, leading to large variations in the predominant sources of DNA damage between different cell types, and in the relative contribution of different DNA repair pathways towards genome maintenance in different tissues. While we continue to make large strides into understanding how individual DNA repair mechanisms operate on a molecular level, much less attention is given to these cell type-specific differences. This short review aims to provide a broad overview of DNA damage and repair mechanism to non-specialists, and to highlight some fundamental open questions in tissue and cell-type-specificity of these processes, which may have profound implications for our understanding of important pathophysiological processes such as cancer, neurodegeneration and aging.

3D culture of the spinal cord with roots as an ex vivo model for comparative studies of motor and sensory nerve regeneration

Motor and sensory nerves exhibit tissue-specific structural and functional features. However, in vitro models designed to reflect tissue-specific differences between motor and sensory nerve regeneration have rarely been reported. Here, by embedding the spinal cord with roots (SCWR) in a 3D hydrogel environment, we compared the nerve regeneration processes between the ventral and dorsal roots. The 3D hydrogel environment induced an outward migration of neurons in the gray matter of the spinal cord, which allowed the long-term survival of motor neurons. Tuj1 immunofluorescence labeling confirmed the regeneration of neurites from both the ventral and dorsal roots. Next, we detected asymmetric ventral and dorsal root regeneration in response to nerve growth factor (NGF) and glial cell line-derived neurotrophic factor (GDNF), and we observed motor and sensory Schwann cell phenotypes in the regenerated ventral and dorsal roots, respectively. Moreover, based on the SCWR model, we identified a targeted effect of collagen VI on sensory nerve fasciculation and characterized the protein expression profiles correlating to motor/sensory-specific nerve regeneration. These results suggest that the SCWR model can serve as a valuable ex vivo model for comparative study of motor and sensory nerve regeneration and for pharmacodynamic evaluations.

EccBase: A high-quality database for exploration and characterization of extrachromosomal circular DNAs in cancer

Extrachromosomal circular DNAs (eccDNAs) are widely observed in eukaryotes. Previous studies have demonstrated that eccDNAs are essential to cancer progression, and found that they can not only express in normal cells to regulate RNA, but also function differently in different tissues. It is of major interest to conduct computational or experiments assay to elucidate the mechanisms of eccDNA function, uncover key eccDNAs associated with diseases, and even develop related algorithms for liquid biopsy. Naturally, a comprehensive eccDNAs data resource is urgently needed to provide annotation and analysis more in-depth research. In this study, we constructed the eccBase (http://www.eccbase.net) in literature curation and database retrieval, which was the first database mainly collecting eccDNAs from Homo sapiens (n = 754,391) and Mus musculus (n = 481,381). Homo sapiens eccDNAs were taken from 50 kinds of cancer tissue and/or cell line, and 5 kinds of healthy tissues. The Mus musculus eccDNAs were sourced from 13 kinds of healthy tissue and/or cell line. We thoroughly annotated all eccDNA molecules in terms of basic information, genomic composition, regulatory elements, epigenetic modifications, and raw data. EccBase provided users with the ability to browse, search, download for targets of interest, as well as similarity alignment by the integrated BLAST. Further, comparative analysis suggested the cancer eccDNA is composed of nucleosomes and is prominently derived from the gene-dense regions. We also initially revealed that eccDNAs are strongly tissue-specific. In short, we have started a robust database for eccDNA resource utilization, which may facilitate studying the role of eccDNA in cancer development and therapy, cell function maintenance, and tissue differentiation.

Hydrogel-complexed small-diameter vascular graft loaded with tissue-specific vascular extracellular matrix components used for tissue engineering

Tissue engineering is thought to the most promising strategy to develop successful small diameter vascular grafts (SDVG) to meet clinical demand. The introduction of natural substances into the SDVG made from synthetic biomaterials can improve the biocompatibility to promote the regeneration of SDVG in vivo. Due to that natural materials from different sources may have property deviation, it is vital to determine the source of natural materials to optimize SDVG fabrication for tissue engineering applications. In this study, bioactive SDVGs were prepared via coating of heparin-modified poly-(ε-caprolactone) scaffolds with a precursor solution containing vascular extracellular matrix (VECM) components and subsequent in situ gelation. The mechanical properties, degradation behaviors, and morphologies of the SDVGs were thoroughly characterized and evaluated. Cell experiments demonstrated the in vitro tissue specificity of the VECM that could promote the proliferation of endothelial cells better than skin-derived collagen. Furthermore, three types of SDVGs, SDVGs with blank hydrogel, SDVGs with skin-derived collagen, and SDVGs with vascular extracellular matrix (VECM-SDVGs), were implanted into the abdominal aorta of rats for one month. The explanted SDVGs were then comprehensively evaluated using hematoxylin and eosin, Masson, von Kossa staining, and immunohistochemical staining for CD31, α-SMA, and MHC. The results showed that the VECM-SDVGs showed the best endothelium regeneration, appropriate intima regeneration, and no calcification, indicating the in vivo specificity of the fabricated VECM-SDVGs. Thus, long-term implantation of VECM-SDVGs was performed. The results showed that a complete endothelial layer formed after 6 months of implantation, and the amount of contractile SMCs in the regenerative smooth muscle layer approached the amount of native aorta at the 12th month. Consequently, relying on vascular tissue specificity, VECM-SDVGs can modulate the regenerative behavior of the implanted SDVGs in vivo to achieve satisfactory vascular regeneration both in short- and long-term implantation.

Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?

Gene expression differences between distinct cell types are orchestrated by specific sets of transcription factors and epigenetic regulators acting upon the genome. In plants, the mechanisms underlying tissue-specific gene activity remain largely unexplored. Although transcriptional and epigenetic profiling of individual organs, tissues, and more recently, of single cells can easily detect the molecular signatures of different biological samples, how these unique cell identities are established at the mechanistic level is only beginning to be decoded. Computational methods, including machine learning, used in combination with experimental approaches, enable the identification and validation of candidate cis-regulatory elements driving cell-specific expression. Synthetic biology shows great promise not only as a means of testing candidate DNA motifs but also for establishing the general rules of nature driving promoter architecture and for the rational design of genetic circuits in research and agriculture to confer tissue-specific expression to genes or molecular pathways of interest.

Diversity of endophytic fungi in Coptis chinensis Franch. and their activity against methicillin-resistant Staphylococcus aureus

This study aimed at investigating the diversity of endophytic fungi from Coptis chinensis and their activity against methicillin-resistant Staphylococcus aureus (MRSA). Seventy-nine fungal isolates obtained from C. chinensis were identified to belong to 27 species based on morphological features and internal transcript spacer (ITS) gene sequencing analysis. Comparing relative frequency values, the most frequent genera were Colletotrichum and Fusarium, while most frequent species were C. gloeosporioides and F. avenaceum. Analysis of diversity indices indicated that C. chinensis harbored abundant fungal resources. Methanol extracts of fungal endophyte cultures were evaluated for antibacterial activity against S. aureus ATCC 25923 and two other MRSA clinical strains. Nine of 27 endophytic fungi exhibited inhibitory activities against S. aureus ATCC 25923. Among them, Paraboeremia litseae HL-17, Fusarium sp. HL-23, and Fusarium sp. HL-27 exhibited obvious inhibition against the three S. aureus strains. Our findings suggest that the endophytic fungi in C. chinensis have a high diversity and an obvious tissue specificity, and could be of potential interest in screening anti-MRSA agents. To the best of our knowledge, this is the first report on the diversity and anti-MRSA activity of fungal endophytes from C. chinensis.

Tissue-Specific Analysis of Alternative Splicing Events and Differential Isoform Expression in Large Yellow Croaker (Larimichthys crocea) After Cryptocaryon irritans Infection

The large yellow croaker (Larimichthys crocea) is one of the most important mariculture fish in China. Recently, cryptocaryonosis caused by Cryptocryon irritans infection has brought huge economic losses and threatens the healthy and sustainable development of the L. crocea industry. However, the molecular mechanism and regulation process for L. crocea resistance to C. irritans infection has not been fully researched. Alternative splicing (AS) is an important post-transcriptional regulatory mechanism that allows cells to produce transcriptional and proteomic diversity. The results of AS are tissue dependent, and the expression of tissue-specific transcription subtype genes is determined by AS and transcriptional regulation. However, studies on the tissue specificity of AS events in L. crocea following infection with C. irritans have not been performed. In this study, the L. crocea were artificially infected with C. irritans; their skin and gill were collected at 0 h, 24 h, 48 h, 72 h, and 96 h post infection. After sequencing and differential expression analysis, a set of 452, 692, 934, 711, 534, and 297 differential alternative splicing (DAS) events were identified in 0 h, 12 h, 24 h, 48 h, 72 h, and 96 h post infection respectively. Furthermore, 4160 differentially expressed isoforms (DEIs) and 4209 DEI genes were identified from all time point groups. GO enrichment and pathway analysis indicated that many genes of DAS and DEIs were rich in immune-related GO terms and KEGG pathways, such as the Toll and Imd signaling pathway, NOD-like receptor signaling pathway, TNF signaling pathway, and TNF signaling pathway. Among hub DEI genes, alternative splicing-related genes (cwc25, prpf8, and sf3a3), skin function-related gene (fa2h), and oxygen deprivation-related gene (hyo1) were found in DEI genes. This study provided insight into the temporal change of DAS and DEIs between skin and gill of L. crocea against C. irritans infection and revealed that these differences might play immune-related roles in the infection process.

Comparative transcriptome analysis of leaf, stem, and root tissues of Semiliquidambar cathayensis reveals candidate genes involved in terpenoid biosynthesis

BACKGROUND

Semiliquidambar cathayensis is a traditional medicinal plant and endemic species in China. Its roots, branches, leaves, bark, and nectar are known to have therapeutic effects against rheumatoid arthritis, lumbar muscle strain, and several other diseases. However, limited knowledge regarding the molecular properties of S. cathayensis highlights the need for further research in order to elucidate the underlying pathways governing the synthesis of its active ingredients and regulation of its accumulation processes.

METHODS

We conducted transcriptome sequencing of the leaf, stem and root epidermises, and stem and root xylems of S. cathayensis with three biological replicates. Moreover, candidate genes involved in terpenoid biosynthesis, such as IDI, FPPS, DXR, SQS, GPPS, and HMGR were selected for quantitative real-time PCR analysis.

RESULTS

We identified 88,582 unigenes. Among which, 36,144 unigenes were annotated to the nr protein database, 21,981 to the Gene Ontology database, 11,565 to the Clusters of Orthologous Groups database, 24,209 to the Pfam database, 21,685 to the SWISS-PROT database, and 12,753 to the Kyoto Encyclopedia of Genes and Genomes (KEGG), with 5072 unigenes common to all six databases. Of those annotated using the KEGG database, 187 unigenes were related to the terpenoid metabolism pathway, and expression analysis of the related genes indicated that the mevalonate and methylerythritol 4-phosphate pathways play different roles in terpenoid biosynthesis in different tissues of S. cathayensis.

CONCLUSIONS

These findings greatly expand gene resources of S. cathayensis and provide basic data for the study of the biosynthetic pathways and molecular mechanisms of terpenoids.

Interplay between gene expression and gene architecture as a consequence of gene and genome duplications: evidence from metabolic genes of Arabidopsis thaliana

Gene and genome duplications have been widespread during the evolution of flowering plant which resulted in the increment of biological complexity as well as creation of plasticity of a genome helping the species to adapt to changing environments. Duplicated genes with higher evolutionary rates can act as a mechanism of generating novel functions in secondary metabolism. In this study, we explored duplication as a potential factor governing the expression heterogeneity and gene architecture of Primary Metabolic Genes (PMGs) and Secondary Metabolic Genes (SMGs) of Arabidopsis thaliana. It is remarkable that different types of duplication processes controlled gene expression and tissue specificity differently in PMGs and SMGs. A complex relationship exists between gene architecture and expression patterns of primary and secondary metabolic genes. Our study reflects, expression heterogeneity and gene structure variation of primary and secondary metabolism in Arabidopsis thaliana are partly results of duplication events of different origins. Our study suggests that duplication has differential effect on PMGs and SMGs regarding expression pattern by controlling gene structure, epigenetic modifications, multifunctionality and subcellular compartmentalization. This study provides an insight into the evolution of metabolism in plants in the light of gene and genome scale duplication.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01188-2.

Factors That Determine Microsporidia Infection and Host Specificity

Microsporidia are a large phylum of obligate intracellular parasites that infect an extremely diverse range of animals and protists. In this chapter, we review what is currently known about microsporidia host specificity and what factors influence microsporidia infection. Extensive sampling in nature from related hosts has provided insight into the host range of many microsporidia species. These field studies have been supported by experiments conducted in controlled laboratory environments which have helped to demonstrate host specificity. Together, these approaches have revealed that, while examples of generalist species exist, microsporidia specificity is often narrow, and species typically infect one or several closely related hosts. For microsporidia to successfully infect and complete their life cycle within a compatible host, several steps must occur, including spore germination, host cell invasion, and proliferation of the parasite within the host tissue. Many factors influence infection, including temperature, seasonality, nutrient availability, and the presence or absence of microbes, as well as the developmental stage, sex, and genetics of the host. Several studies have identified host genomic regions that influence resistance to microsporidia, and future work is likely to uncover molecular mechanisms of microsporidia host specificity in more detail.

Noncoding RNAs in Papillary Thyroid Cancer: Interaction with Cancer-Associated Fibroblasts (CAFs) in the Tumor Microenvironment (TME) and Regulators of Differentiation and Lymph Node Metastasis

A large majority of all thyroid cancers are papillary thyroid carcinomas (PTC), named for the specific papillary architecture observed histologically. Despite the high rate of success with modern diagnostic and therapeutic algorithms, there are significant areas where the management of PTC can be improved. Aggressive PTC subtypes that are refractory to radioactive iodine (RAI) therapy carry a more severe prognosis and account for most of PTC-related deaths. As lymph node metastasis is present in roughly 40% of all adult PTC cases, higher specificity in these tests is a clinical need, especially since lymph node metastases are associated with reduced survival and higher recurrence rates. Additionally, this cancer can progress to more dedifferentiated and aggressive variants, such as poorly differentiated papillary thyroid cancer (PDPTC) and anaplastic thyroid cancer (ATC). Therefore, development of more sensitive and specific detection methods that allow unnecessary surgeries to be avoided is of the utmost importance. The body of large-scale, unbiased gene expression analysis in PTC has focused on the coding transcriptome, specifically mRNAs and microRNAs. However, there have been implications for the potential use of long noncoding RNAs (lncRNAs) in PTC diagnosis, prognosis, and treatment via the utilization of genome-wide studies of patient samples. lncRNAs have diverse regulatory potential in gene expression, alternative splicing, posttranscriptional mRNA modification, and epigenomic alterations. Many lncRNAs have tissue-specific expression and are demonstrated to play key roles in cancer progression and prognosis. However, lncRNAs are not being exploited as biomarkers or therapeutic targets currently, despite their elucidated effects on oncogenesis. These potent biomarkers would be revolutionary in detection at early stages, as this significantly increases the chances of survival. Their aberrant expression in cancer and correlation with steps in tumorigenesis as well as their role in differentiation would allow for a promising role as a prognostic and diagnostic biomarker in thyroid cancer. This would help prevent the more aggressive ATC that derives from dedifferentiation of the less aggressive PTC and FTC. The targeting of the specific lncRNAs could also pose a valuable treatment option via preventing or reversing this dedifferentiation process and making this usually refractory form of thyroid cancer more responsive to standard treatment options.

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

Background

Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects.

Results

Here, we present a two-step computational framework MAGAR (https://bioconductor.org/packages/MAGAR), which fully supports the identification of methQTLs from matched genotyping and DNA methylation data, and additionally allows for illuminating cell type-specific methQTL effects. In a pilot analysis, we apply MAGAR on data in four tissues (ileum, rectum, T cells, B cells) from healthy individuals and demonstrate the discrimination of common from cell type-specific methQTLs. We experimentally validate both types of methQTLs in an independent data set comprising additional cell types and tissues. Finally, we validate selected methQTLs located in the PON1, ZNF155, and NRG2 genes by ultra-deep local sequencing. In line with previous reports, we find cell type-specific methQTLs to be preferentially located in enhancer elements.

Conclusions

Our analysis demonstrates that a systematic analysis of methQTLs provides important new insights on the influences of genetic variants to cell type-specific epigenomic variation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13072-021-00415-6.

REDESCRIPTION OF CATHARIOTREMA SELACHII (MACCALLUM, 1916) JOHNSTON AND TIEGS, 1922 (MONOGENOIDEA: MONOCOTYLIDAE), EMENDATION OF MONOTYPIC CATHARIOTREMA JOHNSTON AND TIEGS, 1922, AND PROPOSAL OF CATHARIOTREMATINAE N. SUBFAM. BASED ON MORPHOLOGICAL AND NUCLEOTIDE EVIDENCE

We herein redescribe the enigmatic Cathariotrema selachii (MacCallum, 1916) Johnston and Tiegs, 1922 based on the holotype, paratypes, and newly collected specimens infecting the olfactory organ of 5 shark species from the Gulf of Mexico (all new host records): scalloped hammerhead shark, Sphyrna lewini (Griffith and Smith, 1834) (Carcharhiniformes: Sphyrnidae); great hammerhead shark, Sphyrna mokarran (Rüppell, 1837); blacktip shark, Carcharhinus limbatus (Müller and Henle, 1839) (Carcharhiniformes: Carcharhinidae); spinner shark, Carcharhinus brevipinna (Müller and Henle, 1839); and Atlantic sharpnose shark, Rhizoprionodon terraenovae (Richardson, 1836) (Carcharhinidae). These specimens were morphologically indistinguishable from each other and from MacCallum's holotype and paratypes. Those sequenced had identical first internal transcribed spacer (ITS1) and large subunit ribosomal DNA (28S) nucleotide sequences. As such, C. selachii infects sharks of 2 orders (Carcharhiniformes, Lamniformes) and 3 families (Carcharhinidae, Sphyrnidae, Lamnidae) in the Northwestern Atlantic Ocean (type locality) and Gulf of Mexico (new records herein). This report is the first of new specimens of C. selachii in the Atlantic Ocean Basin in 95 yr and corrects long-standing error cascades and ambiguities concerning the morphology and systematic placement of C. selachii. Considering morphology and nucleotide-based phylogenetic evidence (28S, Bayesian analysis), we herein emend monotypic CathariotremaJohnston and Tiegs, 1922 and propose Cathariotrematinae Bullard n. subfam. for it and 4 other genera (all formerly assigned to Merizocotylinae Johnston and Tiegs, 1922). These genera comprise species infecting only the nose of sharks (monotypic Cathariotrema, SqualotremaKearn and Green, 1983 and SeptitremaKheddam, Chisholm, and Tazerouti, 2020 plus 3 species of TriloculotremaKearn, 1993) and nose of a chimaera (monotypic HolocephalocotyleDerouiche, Neifar, Gey, Justine, and Tazerouti, 2019). Cathariotrematinae differs from Merizocotylinae by having a 3-part attachment organ and by lacking open loculi that symmetrically encircle a cluster of >2 loculi in the center of the haptor. Monophyletic Cathariotrematinae (with sequences representing species of Cathariotrema, Triloculotrema, and Holocephalocotyle only) was sister to monophyletic Merizocotylinae, which together were sister to monophyletic Calicotylinae Monticelli, 1903. These subfamilies comprise a monophyletic group of monocotylids that have a double vagina and infect extrabranchial, enclosed niches (urogenital system, body cavity, olfactory chamber/nose) on their shark, ray, and chimaera hosts (all other monocotylids have a single vagina and infect the gill or body surfaces of rays only). Monocotylinae Taschenberg, 1879 and Decacotylinae Chisholm, Wheeler, and Beverley-Burton, 1995 were recovered as monophyletic. Heterocotylinae Chisholm, Wheeler, and Beverley-Burton, 1995 remained paraphyletic. We accept ParacalicotyleSzidat, 1970.

The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content

Background

Extensive molecular differences exist between proliferative and differentiated cells. Here, we conduct a meta-analysis of publicly available transcriptomic datasets from preimplantation and differentiation stages examining the architectural properties and content of genes whose abundance changes significantly across developmental time points.

Results

Analysis of preimplantation embryos from human and mouse showed that short genes whose introns are enriched in Alu (human) and B (mouse) elements, respectively, have higher abundance in the blastocyst compared to the zygote. These highly expressed genes encode ribosomal proteins or metabolic enzymes. On the other hand, long genes whose introns are depleted in repetitive elements have lower abundance in the blastocyst and include genes from signaling pathways. Additionally, the sequences of the genes that are differentially expressed between the blastocyst and the zygote contain distinct collections of pyknon motifs that differ between up- and down-regulated genes. Further examination of the genes that participate in the stem cell-specific protein interaction network shows that their introns are short and enriched in Alu (human) and B (mouse) elements. As organogenesis progresses, in both human and mouse, we find that the primarily short and repeat-rich expressed genes make way for primarily longer, repeat-poor genes. With that in mind, we used a machine learning-based approach to identify gene signatures able to classify human adult tissues: we find that the most discriminatory genes comprising these signatures have long introns that are repeat-poor and include transcription factors and signaling-cascade genes. The introns of widely expressed genes across human tissues, on the other hand, are short and repeat-rich, and coincide with those with the highest expression at the blastocyst stage.

Conclusions

Protein-coding genes that are characteristic of each trajectory, i.e., proliferation/pluripotency or differentiation, exhibit antithetical biases in their intronic and exonic lengths and in their repetitive-element content. While the respective human and mouse gene signatures are functionally and evolutionarily conserved, their introns and exons are enriched or depleted in organism-specific repetitive elements. We posit that these organism-specific repetitive sequences found in exons and introns are used to effect the corresponding genes’ regulation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-020-00928-8.

Genome-Wide Investigation of Major Enzyme-Encoding Genes in the Flavonoid Metabolic Pathway in Tartary Buckwheat (Fagopyrum tataricum)

Key enzymes play a vital role in plant growth and development. However, the evolutionary relationships between genes encoding key enzymes in the metabolic pathway of Tartary buckwheat flavonoids are poorly understood. Based on the published Tartary buckwheat genome sequence and related Tartary buckwheat transcriptome data, 48 key enzyme-encoding genes involved in flavonoid metabolism were screened from the Tartary buckwheat genome in this study; the chromosome localization, gene structure and promoter elements of these enzyme-encoding gene were also investigated. Gene structure analysis revealed relatively conserved 5' exon sequences among the 48 genes, indicating that the structural diversity of key enzyme-encoding genes is low in Tartary buckwheat. Through promoter analysis, these key enzyme-encoding genes were found to contain a large number of light-response elements and hormone-response elements. In addition, some genes could bind MYB transcription factors, participating in the regulation of flavonoid biosynthesis. The transcription level of the 48 key enzyme-encoding gene varied greatly among tissues. In this study, we identified 48 key enzyme-encoding genes involved in flavonoid metabolic pathways, and elucidated the structure, evolution and tissue-specific expression patterns of these genes. These results lay a foundation for further understanding the functional characteristics and evolutionary relationships of key enzyme-encoding genes involved in the flavonoid metabolic pathway in Tartary buckwheat.

Decellularized Disc Hydrogels for hBMSCs tissue-specific differentiation and tissue regeneration

Tissue specificity, a key factor in the decellularized tissue matrix (DTM), has shown bioactive functionalities in tuning cell fate-e.g., the differentiation of mesenchymal stem cells. Notably, cell fate is also determined by the living microenvironment, including material composition and spatial characteristics. Herein, two neighboring tissues within intervertebral discs, the nucleus pulposus (NP) and annulus fibrosus (AF), were carefully processed into DTM hydrogels (abbreviated DNP-G and DAF-G, respectively) to determine the tissue-specific effects on stem cell fate, such as specific components and different culturing methods, as well as in vivo regeneration. Distinct differences in their protein compositions were identified by proteomic analysis. Interestingly, the fate of human bone marrow mesenchymal stem cells (hBMSCs) also responds to both culturing methods and composition. Generally, hBMSCs cultured with DNP-G (3D) differentiated into NP-like cells, while hBMSCs cultured with DAF-G (2D) underwent AF-like differentiation, indicating a close correlation with the native microenvironments of NP and AF cells, respectively. Furthermore, we found that the integrin-mediated RhoA/LATS/YAP1 signaling pathway was activated in DAF-G (2D)-induced AF-specific differentiation. Additionally, the activation of YAP1 determined the tendency of NP- or AF-specific differentiation and played opposite regulatory effects. Finally, DNP-G and DAF-G specifically promoted tissue regeneration in NP degeneration and AF defect rat models, respectively. In conclusion, DNP-G and DAF-G can specifically determine the fate of stem cells through the integrin-mediated RhoA/LATS/YAP1 signaling pathway, and this tissue specificity is both compositional and spatial, supporting the utilization of tissue-specific DTM in advanced treatments of intervertebral disc degeneration.

Circular RNA expression profiles and features in NAFLD mice: a study using RNA-seq data

Background

Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously.

Methods

A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

Results

The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development.

Conclusions

Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

Understanding the role of tissue-specific decellularized spinal cord matrix hydrogel for neural stem/progenitor cell microenvironment reconstruction and spinal cord injury

The repair of spinal cord injury (SCI) highly relies on microenvironment remodeling and facilitating the recruitment and neuronal differentiation of endogenous stem/progenitor cells. Decellularized tissue matrices (DTMs) have shown their unique and beneficial characteristics in promoting neural tissue regeneration, especially those derived from the nervous system. Herein, we present a comparative analysis of a DTM hydrogel derived from spinal cord (DSCM-gel) and a decellularized matrix hydrogel derived from peripheral nerves (DNM-gel). The tissue-specificity of DSCM-gel was evaluated both in vitro, using neural stem/progenitor cell (NSPC) culture, and in vivo, using various materials and biological analyses, including transcriptome and proteomics. It was found that DSCM-gel retained an extracellular matrix-like nanofibrous structure but exhibited higher porosity than DNM-gel, which potentiated NSPCs viability, proliferation, and migration in the early stage of 3D culturing, followed by facilitation of the NSPCs differentiation into neurons. Transcriptome analysis indicated that DSCM-gel regulates NSPCs behavior by modulating integrin α2, α9, and β1 expression profiles along with AKT/ERK related signaling pathways. Proteomics analyses suggest that DSCM specific extracellular matrix proteins, such as the tenascin family (TNC) and some soluble growth factor (FGF2) may contribute to these regulations. Furthermore, in vivo assessments confirmed that DSCM-gel provides a suitable microenvironment for endogenous stem/progenitor cell recruitment and axonal regeneration for bridging the lesion site after a completely transected SCI. Thus, this systematic study provides key insights useful for the development of the tissue-specific DTM biomaterials for translational microenvironment replacement therapies and tissue repair.

Chinese herbal medicine promote tissue differentiation in colorectal cancer by activating HSD11B2

BACKGROUND

Colorectal cancer is a common malignant tumor of the digestive tract. In recent years, the incidence rate has increased year by year and is showing a younger trend. The application of Chinese herbal medicine (CHM) is one of the important methods for the treatment of colorectal cancer. CHM refers to the main therapeutic drugs based on traditional Chinese medicine (TCM), which is still valued. Many effective anticancer small-molecule compounds are derived from CHMs, and their effective anticancer ingredients and targets must be clarified and to further understand the molecular mechanisms by which CHM affects cancer.

METHODS

We analyzed the ingredients in CHM that were found to be effective against colorectal cancer and constructed an interaction network among these ingredients and the target protein. By analyzing the number of connections in the network and their type of interaction, we identified the key target protein Corticosteroid 11-beta-dehydrogenase isozyme 2, the enzyme encoded by HSD11B2. Analyses of HSD11B2 expression, survival curve, and co-expressed genes helped clarify the correlation between HSD11B2 and colorectal cancer as well as its underlying molecular mechanism.

RESULTS

We determined that the anticancer ingredients contained in Sanguisorba officinalis, Patrinia scabiosaefolia, and Smilax china had more connections to the target proteins found in colorectal cancer. In the interaction network, eight small-molecule compounds had an activating effect on HSD11B2. The expression of the HSD11B2 was markedly decreased in colorectal cancer tissues and was positively correlated with the overall survival time of patients. In addition, co-expression analyses showed a close relationship between HSD11B2 and tissue-specific genes in colorectal tissues. The expression levels of HSD11B2 in well-, moderately, and poorly differentiated tissues progressively decreased.

CONCLUSION

The HSD11B2 protein was a key CHM target for treating colorectal cancer. The key role of CHM may lie in activating HSD11B2 and further promoting tissue differentiation in colorectal cancer.

Identification and expression profile of microRNA in seven tissues of the Golden snub-nosed monkey (Rhinopithecus roxellanae)

MicroRNAs (miRNAs) are key in the post-transcriptional regulation of gene expression and thus characterization of miRNAs and investigation of the relative abundance and specificity of tissue expression are essential for understanding gene expression in the golden snub-nosed monkey (GSM, Rhinopithecus roxellanae). Here, we report the first dataset of GSM miRNAs where we identified 460 miRNAs in seven tissues, with 246 conserved known mature miRNAs and 214 novel mature miRNAs. We determined miRNA abundance and expression in the seven tissues using a Tissue Specificity Index score and found that most novel GSM miRNAs showed a highly tissue-specific expression pattern. In particular, 67 novel miRNAs and the miR-34 family were expressed in abundance only in the lung. Five known miRNAs were highly abundant in digestive organs such as the pancreas and liver, and four novel miRNAs were highly expressed in the heart and muscle. Annotation of target genes of GSM miRNAs indicated that target genes were enriched in many important pathways, such as the HIF-1 signaling pathway and xenobiotic biodegradation-related pathways. Collectively, these results emphasize that miRNAs play important roles in GSM diet and high-elevation adaptation regulation. In summary, this study provides essential information on GSM miRNAs and will benefit further investigations of the function and mechanism of miRNAs in controlling gene expression in the GSM.

Dynamic changes impact the plum pox virus population structure during leaf and bud development

Plum pox virus (PPV) is a worldwide threat to stone fruit production. Its woody perennial hosts provide a dynamic environment for virus evolution over multiple growing seasons. To investigate the impact seasonal host development plays in PPV population structure, next generation sequencing of ribosome associated viral genomes, termed translatome, was used to assess PPV variants derived from phloem or whole leaf tissues over a range of plum leaf and bud developmental stages. Results show that translatome PPV variants occur at proportionately higher levels in bud and newly developing leaf tissues that have low infection levels while more mature tissues with high infection levels display proportionately lower numbers of viral variants. Additional variant analysis identified distinct groups based on population frequency as well as sets of phloem and whole tissue specific variants. Combined, these results indicate PPV population dynamics are impacted by the tissue type and developmental stage of their host.

Genome-wide identification, characterization and expression profiling of gibberellin metabolism genes in jute

BACKGROUND

Gibberellin (GA) is one of the most essential phytohormones that modulate plant growth and development. Jute (Corchorus sp.) is the second most important source of bast fiber. Our result has shown that exogenous GA can positively regulate jute height and related characteristics which mean increasing endogenous GA production will help to get a jute variety with improved characteristics. However, genes involved in jute GA biosynthesis have not been analyzed precisely.

RESULTS

Genome-wide analysis identified twenty-two candidate genes involved in jute GA biosynthesis pathway. Among them, four genes- CoCPS, CoKS, CoKO and CoKAO work in early steps. Seven CoGA20oxs, three CoGA3oxs, and eight GA2oxs genes work in the later steps. These genes were characterized through phylogenetic, motif, gene structure, and promoter region analysis along with chromosomal localization. Spatial gene expression analysis revealed that 11 GA oxidases were actively related to jute GA production and four of them were marked as key regulators based on their expression level. All the biosynthesis genes both early and later steps showed tissue specificity. GA oxidase genes were under feedback regulation whereas early steps genes were not subject to such regulation.

CONCLUSION

Enriched knowledge about jute GA biosynthesis pathway and genes will help to increase endogenous GA production in jute by changing the expression level of key regulator genes. CoGA20ox7, CoGA3ox2, CoGA2ox3, and CoGA2ox5 may be the most important genes for GA production.

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

BACKGROUND

RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification-related proteins (RMPs) may be dysregulated in each cancer type.

RESULTS

Here, we perform a comprehensive annotation and evolutionary analysis of human RMPs, as well as an integrative analysis of their expression patterns across 32 tissues, 10 species, and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. We uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO are not significantly upregulated in most cancer types, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers.

CONCLUSIONS

Our analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviors that are orchestrated by RNA modifications.

Spatial and temporal control of gene manipulation in Drosophila via drug-activated Cas9 nucleases

Advances in CRISPR/Cas9 have revolutionized molecular biology and greatly facilitated the ability to manipulate gene function through the creation of precisely engineered mutants. We recently reported a collection of modular gateway-compatible Cas9/gRNA Drosophila lines to interfere with gene expression in a tissue-specific manner, including polytene tissues. However, most current in vivo CRISPR/Cas9 tools cannot temporally control the induction of Cas9 or gRNAs via external stimuli such as RU486. A drug-inducible CRISPR/Cas9 system would allow studying genes at later stages where early lethality is an issue. This would be especially useful when combined with tissue-specific expression of Cas9 or gRNAs, allowing for full spatiotemporal control. Here, we present a RU486-inducible version of Cas9 and also show that a Rapamycin-inducible Cas9, previously used in mammalian cell culture, works in Drosophila as well. Both RU486 and rapamycin-inducible Cas9 work in vivo and in Drosophila cell culture. We also present split Cas9 constructs for rapamycin-dependent gene disruption and activation. These approaches establish drug-inducible and thus temporally controlled CRISPR/Cas9 tools for gene disruption and expression in a living model organism. Our CRISPR/Cas9 vector collection can be easily adapted for any tissue and provides higher fidelity compared to RNAi approaches.

Tissue-specific effects of temperature on proteasome function

Variation in ambient growth temperature can cause changes in normal animal physiology and cellular functions such as control of protein homeostasis. A key mechanism for maintaining proteostasis is the selective degradation of polyubiquitinated proteins, mediated by the ubiquitin-proteasome system (UPS). It is still largely unsolved how temperature changes affect the UPS at the organismal level. Caenorhabditis elegans nematodes are normally bred at 20 °C, but for some experimental conditions, 25 °C is often used. We studied the effect of 25 °C on C. elegans UPS by measuring proteasome activity and polyubiquitinated proteins both in vitro in whole animal lysates and in vivo in tissue-specific transgenic reporter strains. Our results show that an ambient temperature shift from 20 to 25 °C increases the UPS activity in the intestine, but not in the body wall muscle tissue, where a concomitant accumulation of polyubiquitinated proteins occurs. These changes in the UPS activity and levels of polyubiquitinated proteins were not detectable in whole animal lysates. The exposure of transgenic animals to 25 °C also induced ER stress reporter fluorescence, but not the fluorescence of a heat shock responsive reporter, albeit detection of a mild induction in hsp-16.2 mRNA levels. In conclusion, C. elegans exhibits tissue-specific responses of the UPS as an organismal strategy to cope with a rise in ambient temperature.

REPIC: a database for exploring the N6-methyladenosine methylome

The REPIC (RNA EPItranscriptome Collection) database records about 10 million peaks called from publicly available m6A-seq and MeRIP-seq data using our unified pipeline. These data were collected from 672 samples of 49 studies, covering 61 cell lines or tissues in 11 organisms. REPIC allows users to query N6-methyladenosine (m6A) modification sites by specific cell lines or tissue types. In addition, it integrates m6A/MeRIP-seq data with 1418 histone ChIP-seq and 118 DNase-seq data tracks from the ENCODE project in a modern genome browser to present a comprehensive atlas of m6A methylation sites, histone modification sites, and chromatin accessibility regions. REPIC is accessible at https://repicmod.uchicago.edu/repic.

Not all cancers are created equal: Tissue specificity in cancer genes and pathways

Tumors arise through waves of genetic alterations and clonal expansion that allow tumor cells to acquire cancer hallmarks, such as genome instability and immune evasion. Recent genomic analyses showed that the vast majority of cancer driver genes are mutated in a tissue-dependent manner, that is, are altered in some cancers but not others. Often the tumor type also affects the likelihood of therapy response. What is the origin of tissue specificity in cancer? Recent studies suggest that both cell-intrinsic and cell-extrinsic factors play a role. On one hand, cell type-specific wiring of the cell signaling network determines the outcome of cancer driver gene mutations. On the other hand, the tumor cells' exposure to tissue-specific microenvironments (e.g. immune cells) also contributes to shape the tissue specificity of driver genes and of therapy response. In the future, a more complete understanding of tissue specificity in cancer may inform methods to better predict and improve therapeutic outcomes.

Expression Quantitative Trait Loci Analysis in Multiple Tissues

Expression quantitative trait loci (eQTL) analysis identifies genetic variants that regulate the expression level of a gene. The genetic regulation may persist or vary in different tissues. When data are available on multiple tissues, it is often desired to borrow information across tissues and conduct an integrative analysis. Here we describe a multi-tissue eQTL analysis procedure, which improves the identification of different types of eQTL and facilitates the assessment of tissue specificity.

Human gene expression variability and its dependence on methylation and aging

BACKGROUND

Phenotypic variability of human populations is partly the result of gene polymorphism and differential gene expression. As such, understanding the molecular basis for diversity requires identifying genes with both high and low population expression variance and identifying the mechanisms underlying their expression control. Key issues remain unanswered with respect to expression variability in human populations. The role of gene methylation as well as the contribution that age, sex and tissue-specific factors have on expression variability are not well understood.

RESULTS

Here we used a novel method that accounts for sampling error to classify human genes based on their expression variability in normal human breast and brain tissues. We find that high expression variability is almost exclusively unimodal, indicating that variance is not the result of segregation into distinct expression states. Genes with high expression variability differ markedly between tissues and we find that genes with high population expression variability are likely to have age-, but not sex-dependent expression. Lastly, we find that methylation likely has a key role in controlling expression variability insofar as genes with low expression variability are likely to be non-methylated.

CONCLUSIONS

We conclude that gene expression variability in the human population is likely to be important in tissue development and identity, methylation, and in natural biological aging. The expression variability of a gene is an important functional characteristic of the gene itself and the classification of a gene as one with Hyper-Variability or Hypo-Variability in a human population or in a specific tissue should be useful in the identification of important genes that functionally regulate development or disease.

PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders

De novo variants (DNVs) are one of the most significant contributors to severe early-onset genetic disorders such as autism spectrum disorder, intellectual disability, and other developmental and neuropsychiatric (DNP) disorders. Presently, a plethora of DNVs have been identified using next-generation sequencing, and many efforts have been made to understand their impact at the gene level. However, there has been little exploration of the effects at the isoform level. The brain contains a high level of alternative splicing and regulation, and exhibits a more divergent splicing program than other tissues. Therefore, it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP disorders. To facilitate a better usage and improve the isoform-level interpretation of variants, we developed NeuroPsychiatric Mutation Knowledge Base (PsyMuKB). It contains a comprehensive, carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoform-specific mutations. PsyMuKB allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations, such as expression, transcript genomic structures, protein interactions, and the mutation sites mapped on the protein structures. It also provides an easy-to-use web interface, allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and isoforms. PsyMuKB thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related disorders. PsyMuKB is freely accessible at http://psymukb.net.

Decoding regulatory structures and features from epigenomics profiles: A Roadmap-ENCODE Variational Auto-Encoder (RE-VAE) model

The development of chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing (ChIP-seq) technologies has promoted generation of large-scale epigenomics data, providing us unprecedented opportunities to explore the landscape of epigenomic profiles at scales across both histone marks and tissue types. In addition to many tools directly for data analysis, advanced computational approaches, such as deep learning, have recently become promising to deeply mine the data structures and identify important regulators from complex functional genomics data. We implemented a neural network framework, a Variational Auto-Encoder (VAE) model, to explore the epigenomic data from the Roadmap Epigenomics Project and the Encyclopedia of DNA Elements (ENCODE) project. Our model is applied to 935 reference samples, covering 28 tissues and 12 histone marks. We used the enhancer and promoter regions as the annotation features and ChIP-seq signal values in these regions as the feature values. Through a parameter sweep process, we identified the suitable hyperparameter values and built a VAE model to represent the epigenomics data and to further explore the biological regulation. The resultant Roadmap-ENCODE VAE (RE-VAE) model contained data compression and feature representation. Using the compressed data in the latent space, we found that the majority of histone marks were well clustered but not for tissues or cell types. Tissue or cell specificity was observed only in some histone marks (e.g., H3K4me3 and H3K27ac) and could be characterized when the number of tissue samples is large (e.g., blood and brain). In blood, the contributive regions and genes identified by RE-VAE model were confirmed by tissue-specificity enrichment analysis with an independent tissue expression panel. Finally, we demonstrated that RE-VAE model could detect cancer cell lines with similar epigenomics profiles. In conclusion, we introduced and implemented a VAE model to represent large-scale epigenomics data. The model could be used to explore classifications of histone modifications and tissue/cell specificity and to classify new data with unknown sources.

tRNA-derived fragments from the Sus scrofa tissues provide evidence of their conserved role in mammalian development

The recently discovered group of noncoding RNAs, which are fragments of tRNA molecules (tRFs), has not been fully characterized and its potential functions still require investigation. Porcine tRFs were characterized and compared to mouse and human tRFs. Two tRFs, 5' 32-33 nt and 3' 41-42 nt that are derived from the mature tRNAVal(CAC) and tRNAGly(GCC) were detected with the use of bioinformatics and the Northern blot method. The abundance of these tRFs in the case of Sus scrofa is restricted to the ovary and the kidney. The same tRFs were found in human cancer cells and in mouse sperm, circulating blood and its serum. The binding of selected sncRNAs (piRNA, 5'tRFVal(CAC) and miRNA) to the overexpressed PAZ domain of the PIWIL4 protein was also studied. It is noteworthy that porcine 5'tRFVal(CAC) and human 5'tRFVal(CAC)as well as 5'tRFGly(GCC) are bound to the PIWIL4 protein. The potential role of the analyzed tRFs in the development of mammals is also discussed.

Directed differential behaviors of multipotent adult stem cells from decellularized tissue/organ extracellular matrix bioinks. Biomaterials. 2019;224:119496. [PMID: 31557592 DOI: 10.1016/j.biomaterials.2019.119496]

The decellularized tissue/organ extracellular matrix (dECM) is a naturally derived biomaterial that inherits various functional components from the native tissue or organ. Recently, various kinds of tissue/organ dECM bioinks capable of encapsulating cells, combined with 3D cell printing, have enabled remarkable progress in tissue engineering and regenerative medicine. However, the way in which the dECM component compositions of each tissue of different origins interact with cells and dictate tissue-specific cell behavior in the 3D microenvironment remains mostly unknown. To address this issue, in-depth differential proteomic analyses of four porcine dECMs were performed. Specifically, the differential variations of matrisome protein composition in each decellularized tissue type were also uncovered, which can play a significant role by affecting the resident cells in specific tissues. Furthermore, microarray analyses of human bone marrow mesenchymal stem cells (hBMMSCs) printed with various dECM bioinks were conducted to reveal the effect of compositional variations in a tissue-specific manner at the cellular level depending on the multipotency of MSCs. Through whole transcriptome analysis, differential expression patterns of genes were observed in a tissue-specific manner, and this research provides strong evidence of the tissue-specific functionalities of dECM bioinks.

Promoter conservation in HDACs points to functional implications

Background

Histone deacetylases (HDACs) are the proteins responsible for removing the acetyl group from lysine residues of core histones in chromosomes, a crucial component of gene regulation. Eleven known HDACs exist in humans and most other vertebrates. While the basic function of HDACs has been well characterized and new discoveries are still being made, the transcriptional regulation of their corresponding genes is still poorly understood.

Results

Here, we conducted a computational analysis of the eleven HDAC promoter sequences in 25 vertebrate species to determine whether transcription factor binding sites (TFBSs) are conserved in HDAC evolution, and if so, whether they provide useful information about HDAC expression and function. Furthermore, we used tissue-specific information of transcription factors to investigate the potential expression patterns of HDACs in different human tissues based on their transcription factor binding sites. We found that the TFBS profiles of most of the HDACs were well conserved in closely related species for all HDAC promoters except HDAC7 and HDAC10. HDAC5 had particularly strong conservation across over half of the species studied, with nearly identical profiles in the primate species. Our comparisons of TFBSs with the tissue specific gene expression profiles of their corresponding TFs showed that most HDACs had the ability to be ubiquitously expressed. A few HDAC promoters exhibited the potential for preferential expression in certain tissues, most notably HDAC11 in gall bladder, while HDAC9 seemed to have less propensity for expression in the nervous system.

Conclusions

In general, we found evolutionary conservation in HDAC promoters that seems to be more prominent for the ubiquitously expressed HDACs. In turn, when conservation did not follow usual phylogeny, human TFBS patterns indicated possible functional relevance. While we found that HDACs appear to uniformly expressed, we confirm that the functional differences in HDACs may be less a matter of location of activity than a question of which proteins and which acetyl groups they may be acting on.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5973-x) contains supplementary material, which is available to authorized users.

Tissue specificity and differential effects on in vitro plant growth of single bacterial endophytes isolated from the roots, leaves and rhizospheric soil of Echinacea purpurea

BACKGROUND

Echinacea-endophyte interaction might affect plant secondary metabolites content and influence bacterial colonization specificity and plant growth, but the underlying mechanisms need deepening. An in vitro model, in which E. purpurea axenic plants as host species and E. angustifolia and Nicotiana tabacum as non-host species inoculated with single endophytes isolated from stem/leaf, root and rhizospheric soil, were used to investigate bacterial colonization.

RESULTS

Colonization analysis showed that bacteria tended to reach tissues from which they were originally isolated (tissue-specificity) in host plants but not in non-host ones (species-specificity). Primary root elongation inhibition as well as the promotion of the growth of E. purpurea and E. angustifolia plants were observed and related to endophyte-produced indole-3-Acetic Acid. Bacteria-secreted substances affected plant physiology probably interacting with plant regulators. Plant metabolites played an important role in controlling the endophyte growth.

CONCLUSIONS

The proposed in vitro infection model could be, generally used to identify novel bioactive compounds and/or to select specific endophytes contributing to the host metabolism properties.

In Situ Localization of Small RNAs in Plants

Small RNAs have vital roles in numerous aspects of plant biology. Deciphering their precise contributions requires knowledge of a small RNA's spatiotemporal pattern of accumulation. The in situ hybridization protocol described here takes advantage of locked nucleic acid (LNA) oligonucleotide probes to visualize small RNA expression at the cellular level with high sensitivity and specificity. The procedure is optimized for paraffin-embedded plant tissue sections, is applicable to a wide range of plants and tissues, and can be completed within 2-6 days.

Detection of condition-specific marker genes from RNA-seq data with MGFR

The identification of condition-specific genes is key to advancing our understanding of cell fate decisions and disease development. Differential gene expression analysis (DGEA) has been the standard tool for this task. However, the amount of samples that modern transcriptomic technologies allow us to study, makes DGEA a daunting task. On the other hand, experiments with low numbers of replicates lack the statistical power to detect differentially expressed genes. We have previously developed MGFM, a tool for marker gene detection from microarrays, that is particularly useful in the latter case. Here, we have adapted the algorithm behind MGFM to detect markers in RNA-seq data. MGFR groups samples with similar gene expression levels and flags potential markers of a sample type if their highest expression values represent all replicates of this type. We have benchmarked MGFR against other methods and found that its proposed markers accurately characterize the functional identity of different tissues and cell types in standard and single cell RNA-seq datasets. Then, we performed a more detailed analysis for three of these datasets, which profile the transcriptomes of different human tissues, immune and human blastocyst cell types, respectively. MGFR’s predicted markers were compared to gold-standard lists for these datasets and outperformed the other marker detectors. Finally, we suggest novel candidate marker genes for the examined tissues and cell types. MGFR is implemented as a freely available Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.MGFR), which facilitates its use and integration with bioinformatics pipelines.

Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

BACKGROUND

Promoters and enhancers are cis-regulatory DNA sequences that control specificity and quantity of transcription. Both are rich on clusters of cis-acting sites that interact with sequence-specific DNA-binding transcription factors (TFs). At the level of chromatin, these regions display increased nuclease sensitivity, reduced nucleosome density, including nucleosome-free regions, and specific combinations of posttranslational modifications of core histone proteins. Together, "open" and "closed" chromatins represent transcriptionally active and repressed states of individual genes, respectively. Cellular differentiation is marked by changes in local chromatin structure. Lens morphogenesis, regulated by TF Pax6, includes differentiation of epithelial precursor cells into lens fibers in parallel with differentiation of epithelial precursors into the mature lens epithelium.

RESULTS

Using ATAC-seq, we investigated dynamics of chromatin changes during mouse lens fibers and epithelium differentiation. Tissue-specific features of these processes are demonstrated via comparative studies of embryonic stem cells, forebrain, and liver chromatins. Unbiased analysis reveals cis-regulatory logic of lens differentiation through known (e.g., AP-1, Ets, Hsf4, Maf, and Pax6 sites) and novel (e.g., CTCF, Tead, and NF1) motifs. Twenty-six DNA-binding TFs, recognizing these cis-motifs, are markedly up-regulated in differentiating lens fibers. As specific examples, our ATAC-seq data uncovered both the regulatory regions and TF binding motifs in Foxe3, Prox1, and Mip loci that are consistent with previous, though incomplete, experimental data. A cross-examination of Pax6 binding with ATAC-seq data demonstrated that Pax6 bound to both open (H3K27ac and P300-enriched) and closed chromatin domains in lens and forebrain.

CONCLUSIONS

Our study has generated the first lens chromatin accessibility maps that support a general model of stage-specific chromatin changes associated with transcriptional activities of batteries of genes required for lens fiber cell formation. Analysis of active (or open) promoters and enhancers reveals important cis-DNA motifs that establish the molecular foundation for temporally and spatially regulated gene expression in lens. Together, our data and models open new avenues for the field to conduct mechanistic studies of transcriptional control regions, reconstruction of gene regulatory networks that govern lens morphogenesis, and identification of cataract-causing mutations in noncoding sequences.

Comparative sequence and methylation analysis of chloroplast and amyloplast genomes from rice

Grain amyloplast and leaf chloroplast DNA sequences are identical in rice plants but are differentially methylated. The leaf chloroplast DNA becomes more methylated as the rice plant ages. Rice is an important crop worldwide. Chloroplasts and amyloplasts are critical organelles but the amyloplast genome is poorly studied. We have characterised the sequence and methylation of grain amyloplast DNA and leaf chloroplast DNA in rice. We have also analysed the changes in methylation patterns in the chloroplast DNA as the rice plant ages. Total genomic DNA from grain, old leaf and young leaf tissues were extracted from the Oryza sativa ssp. indica cv. MR219 and sequenced using Illumina Miseq. Sequence variant analysis revealed that the amyloplast and chloroplast DNA of MR219 were identical to each other. However, comparison of CpG and CHG methylation between the identical amyloplast and chloroplast DNA sequences indicated that the chloroplast DNA from rice leaves collected at early ripening stage was more methylated than the amyloplast DNA from the grains of the same plant. The chloroplast DNA became more methylated as the plant ages so that chloroplast DNA from young leaves was less methylated overall than amyloplast DNA. These differential methylation patterns were primarily observed in organelle-encoded genes related to photosynthesis followed by those involved in transcription and translation.

Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities

Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.

Genetics and epigenetics in obesity

Obesity is among the most threatening health burdens worldwide and its prevalence has markedly increased over the last decades. Obesity maybe considered a heritable trait. Identifications of rare cases of monogenic obesity unveiled that hypothalamic circuits and the brain-adipose axis play an important role in the regulation of energy homeostasis, appetite, hunger and satiety. For example, mutations in the leptin gene cause obesity through almost unsuppressed overeating. Common (multifactorial) obesity, most likely resulting from a concerted interplay of genetic, epigenetic and environmental factors, is clearly linked to genetic predisposition by multiple risk variants, which, however only account for a minor part of the general BMI variability. Although GWAS opened new avenues in elucidating the complex genetics behind common obesity, understanding the biological mechanisms relative to the specific risk contributing to obesity remains poorly understood. Non-genetic factors such as eating behavior or physical activity strongly modulate the individual risk for developing obesity. These factors may interact with genetic predisposition for obesity through epigenetic mechanisms. Thus, here, we review the current knowledge about monogenic and common (multifactorial) obesity highlighting the important recent advances in our knowledge on how epigenetic regulation is involved in the etiology of obesity.