A genome-wide screen for differentially methylated long noncoding RNAs identified that lncAC007255.8 is regulated by promoter DNA methylation in Beas-2B cells malignantly transformed by NNK

2021 ◽  
Author(s):  
Enzhao Chen ◽  
Jiaxin Zhou ◽  
Enwu Xu ◽  
Cheng Zhang ◽  
Jiayu Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide ◽  
A Genome ◽  
Promoter Dna Methylation ◽  
Promoter Dna

scholarly journals Genome-wide Mapping Reveals Conservation of Promoter DNA Methylation Following Chicken Domestication

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Qinghe Li ◽  
Yuanyuan Wang ◽  
Xiaoxiang Hu ◽  
Yaofeng Zhao ◽  
Ning Li
Keyword(s):  
Dna Methylation ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna

scholarly journals Transcriptomic and Genome-wide Association Study Reveal Long Noncoding RNAs Responding to Nitrogen Deficiency in Maize

2020 ◽  
Author(s):  
PENG MA ◽  
Xiao Zhang ◽  
Bowen Luo ◽  
Zhen Chen ◽  
Xuan He ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Snp Array ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome

Abstract Background: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.Results: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen and low-nitrogen conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability. An association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN resistance-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize regarding LN-responsive resistance.

scholarly journals Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Peng Ma ◽  
Xiao Zhang ◽  
Bowen Luo ◽  
Zhen Chen ◽  
Xuan He ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Nitrogen Deficiency ◽  
Snp Array ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Genome Wide Association ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome

Abstract Background Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited. Results Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. Conclusions These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress.

scholarly journals The activity of human enhancers is modulated by the splicing of their associated lncRNAs

2022 ◽  
Vol 18 (1) ◽  
pp. e1009722
Author(s):  
Jennifer Yihong Tan ◽  
Ana Claudia Marques
Keyword(s):  
Genetic Factors ◽  
Gene Expression Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Enhancer Activity ◽  
Highly Active ◽  
Genome Wide ◽  
A Genome ◽  
Enhancer Function ◽  
Outstanding Question

Pervasive enhancer transcription is at the origin of more than half of all long noncoding RNAs in humans. Transcription of enhancer-associated long noncoding RNAs (elncRNA) contribute to their cognate enhancer activity and gene expression regulation in cis. Recently, splicing of elncRNAs was shown to be associated with elevated enhancer activity. However, whether splicing of elncRNA transcripts is a mere consequence of accessibility at highly active enhancers or if elncRNA splicing directly impacts enhancer function, remains unanswered. We analysed genetically driven changes in elncRNA splicing, in humans, to address this outstanding question. We showed that splicing related motifs within multi-exonic elncRNAs evolved under selective constraints during human evolution, suggesting the processing of these transcripts is unlikely to have resulted from transcription across spurious splice sites. Using a genome-wide and unbiased approach, we used nucleotide variants as independent genetic factors to directly assess the causal relationship that underpin elncRNA splicing and their cognate enhancer activity. We found that the splicing of most elncRNAs is associated with changes in chromatin signatures at cognate enhancers and target mRNA expression. We provide evidence that efficient and conserved processing of enhancer-associated elncRNAs contributes to enhancer activity.

scholarly journals Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice

2014 ◽  
Vol 4 (10) ◽  
pp. e473-e473 ◽  
Author(s):  
K G Schraut ◽  
S B Jakob ◽  
M T Weidner ◽  
A G Schmitt ◽  
C J Scholz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Prenatal Stress ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
Deficient Mice

scholarly journals Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

2017 ◽  
Author(s):  
Ethan Ford ◽  
Matthew R. Grimmer ◽  
Sabine Stolzenburg ◽  
Ozren Bogdanovic ◽  
Alex de Mendoza ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fusion Protein ◽  
Rna Polymerase Ii ◽  
Zinc Finger ◽  
Gene Promoters ◽  
Natural Conditions ◽  
Promoter Regions ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna

AbstractIt is widely assumed that the addition of DNA methylation at CpG rich gene promoters silences gene transcription. However, this conclusion is largely drawn from the observation that promoter DNA methylation inversely correlates with gene expression in natural conditions. The effect of induced DNA methylation on endogenous promoters has yet to be comprehensively assessed. Here, we induced the simultaneous methylation of thousands of promoters in the genome of human cells using an engineered zinc finger-DNMT3A fusion protein, enabling assessment of the effect of forced DNA methylation upon transcription, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is frequently insufficient to transcriptionally repress promoters. Furthermore, DNA methylation deposited at promoter regions associated with H3K4me3 is rapidly erased after removal of the zinc finger-DNMT3A fusion protein. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. These findings suggest that promoter DNA methylation is not generally sufficient for transcriptional inactivation, with implications for the emerging field of epigenome engineering.One Sentence SummaryGenome-wide epigenomic manipulation of thousands of human promoters reveals that induced promoter DNA methylation is unstable and frequently does not function as a primary instructive biochemical signal for gene silencing and chromatin reconfiguration.

scholarly journals The activity of human enhancers is modulated by the splicing of their associated lncRNAs

2020 ◽  
Author(s):  
Jennifer Y. Tan ◽  
Ana C. Marques
Keyword(s):  
Genetic Factors ◽  
Gene Expression Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Enhancer Activity ◽  
Highly Active ◽  
Genome Wide ◽  
A Genome ◽  
Enhancer Function ◽  
Outstanding Question

ABSTRACTPervasive enhancer transcription is at the origin of more than half of all long noncoding RNAs in humans. Transcription of enhancer-associated long noncoding RNAs (elncRNA) contribute to their cognate enhancer activity and gene expression regulation in cis. Recently, splicing of elncRNAs was shown to be associated with elevated enhancer activity. However, whether splicing of elncRNA transcripts is a mere consequence of accessibility at highly active enhancers or if elncRNA splicing directly impacts enhancer function, remains unanswered.We analysed genetically driven changes in elncRNA expression, in humans, to address this outstanding question. We showed that splicing related motifs within multi-exonic elncRNAs evolved under selective constraints during human evolution, suggesting the processing of these transcripts is unlikely to have resulted from transcription across spurious splice sites. Using a genome-wide and unbiased approach, we used nucleotide variants as independent genetic factors to directly assess the causal relationship that underpin elncRNA splicing and their cognate enhancer activity. We found that the splicing of most elncRNAs is associated with changes in chromatin signatures at cognate enhancers and target mRNA expression.We conclude that efficient and conserved processing of enhancer-associated elncRNAs contributes to enhancer activity.

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