scholarly journals DNA methylation patterns of protein-coding genes and long non-coding RNAs in males with schizophrenia

2015 ◽  
Vol 12 (5) ◽  
pp. 6568-6576 ◽  
Author(s):  
QI LIAO ◽  
YUNLIANG WANG ◽  
JIA CHENG ◽  
DONGJUN DAI ◽  
XINGYU ZHOU ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rnas ◽  
Methylation Patterns

scholarly journals Identification of the expressome by machine learning on omics data

2019 ◽  
Vol 116 (36) ◽  
pp. 18119-18125 ◽  
Author(s):  
Ryan C. Sartor ◽  
Jaclyn Noshay ◽  
Nathan M. Springer ◽  
Steven P. Briggs
Keyword(s):  
Machine Learning ◽  
Dna Methylation ◽  
Inbred Lines ◽  
Training Data ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Methylation Patterns

Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes.

scholarly journals Co‐regulation of long non‐coding RNAs and protein‐coding genes during cell quiescence

2021 ◽  
Vol 35 (S1) ◽  
Author(s):  
Hilary Coller ◽  
Huiling Huang ◽  
Mithun Mitra ◽  
Kaiser Atai ◽  
Kirthana Sarathy
Keyword(s):  
Protein Coding ◽  
Protein Coding Genes ◽  
Cell Quiescence ◽  
Non Coding Rnas

Expression changes in protein-coding genes and long non-coding RNAs in denatured dermis following thermal injury

Burns ◽  
2020 ◽  
Vol 46 (5) ◽  
pp. 1128-1135 ◽  
Author(s):  
Wenchang Yu ◽  
Zaiwen Guo ◽  
Pengfei Liang ◽  
Bimei Jiang ◽  
Le Guo ◽  
...  
Keyword(s):  
Thermal Injury ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rnas

scholarly journals Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Rui Chen ◽  
Ming Li ◽  
Huiyuan Zhang ◽  
Lijin Duan ◽  
Xianjun Sun ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Salt Stress ◽  
Bioinformatic Analysis ◽  
Protein Coding ◽  
Reduced Representation ◽  
Soybean Seedlings ◽  
A Genome ◽  
Whole Transcriptome Sequencing ◽  
Soybean Roots ◽  
Non Coding Rnas

Abstract Background Environmental stimuli can activate a series of physiological and biochemical responses in plants accompanied by extensive transcriptional reprogramming. Long non-coding RNAs (lncRNAs), as versatile regulators, control gene expression in multiple ways and participate in the adaptation to biotic and abiotic stresses. Results In this study, soybean seedlings were continuously cultured for 15 days with high salinity solutions started from seed germination. Strand-specific whole transcriptome sequencing and stringent bioinformatic analysis led to the identification of 3030 long intergenic non-coding RNAs (lincRNAs) and 275 natural antisense transcripts (lncNATs) in soybean roots. In contrast to mRNAs, newly identified lncRNAs exhibited less exons, similar AU content to UTRs, even distribution across the genome and low evolutionary conservation. Remarkably, more than 75% of discovered lncRNAs that were activated or up-regulated by continuous salt stress mainly targeted proteins with binding and catalytic activities. Furthermore, two DNA methylation maps with single-base resolution were generated by using reduced representation bisulfite sequencing, offering a genome-wide perspective and important clues for epigenetic regulation of stress-associated lncRNAs and protein-coding genes. Conclusions Taken together, our findings systematically demonstrated the characteristics of continuous salt stress-induced lncRNAs and extended the knowledge of corresponding methylation profiling, providing valuable evidence for a better understanding of how plants cope with long-term salt stress circumstances.

scholarly journals LncExpDB: an expression database of human long non-coding RNAs

2020 ◽  
Vol 49 (D1) ◽  
pp. D962-D968 ◽  
Author(s):  
Zhao Li ◽  
Lin Liu ◽  
Shuai Jiang ◽  
Qianpeng Li ◽  
Changrui Feng ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Biological Functions ◽  
Protein Coding ◽  
Web Interfaces ◽  
Functional Studies ◽  
Protein Coding Genes ◽  
Genes Expression ◽  
Wide Range ◽  
Non Coding Rnas ◽  
User Friendly

Abstract Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.

scholarly journals STEM-27. miR-10b-5p MODULATES 5hmC EXPRESSION AND THE STEM-LIKE PHENOTYPE IN GBM

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii202-ii202
Author(s):  
Harmon Khela ◽  
Sweta Sudhir ◽  
Maria Lugo-Fagundo ◽  
Bachchu Lal ◽  
Hernando Lopez-Bertoni ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cell Markers ◽  
Tumor Initiation ◽  
Epigenetic Alterations ◽  
Sox2 Expression ◽  
Initiation And Propagation ◽  
Xenograft Models ◽  
Non Coding Rnas ◽  
Methylation Patterns ◽  
Sphere Formation

Abstract Epigenetic alterations such as DNA methylation and dysregulation of non-coding RNAs (e.g. miRNAs) are found in all types of cancer and are thought to play important roles in tumorigenesis. GBM is characterized by small subsets of cells, referred to as glioma stem cells (GSCs), that display stem-like properties implicated in tumor initiation, therapeutic resistance, and recurrence. DNA methylation patterns are altered in GBM and GSCs and are thought to play critical roles in tumor initiation and propagation. DNA methylation is a reversible process catalyzed, in part, by the ten-eleven translocation (TET) family of enzymes. These enzymes function as deoxygenases that catalyze the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Multiple studies found negative correlations between 5hmC levels and glioma grade and loss of 5hmC correlates with poor prognosis of GBM patients. However, the mechanisms leading to the loss of 5hmC in glioma and the role this phenomenon plays in gliomagenesis remains poorly understood. We found that Sox2 expression decreases TET2 expression and its product 5hmC in GSCs and identified miR-10b-5p as a molecular intermediary of this process. We show that miR-10b-5p expression is high in GBM compared to non-tumor in clinical specimens and high levels of this miRNA correlate with poor patient outcome. Expression of transgenic miR-10b-5p enhanced sphere formation capacity of GSCs and the expression of stem cell markers and drivers. Additionally, using a combination of molecular and biochemical endpoints, we show that miR-10b-5p modifies 5hmC levels by regulating TET2 in GSCs. Finally, we show that repression of miR-10b-5p increases 5hmC levels and inhibits tumor propagation in GBM xenograft models. Taken together, these results present a new molecular mechanism that controls 5hmC and the tumor propagating capacity of GSCs and suggests that miR-10b-5p inhibition and other strategies for enhancing TET2 function can be developed to treat GBM.

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