The role of enhancer RNAs in epigenetic regulation of gene expression

Rahnamoun, Homa; Orozco, Paola; Lauberth, Shannon

doi:10.1080/21541264.2019.1698934

Cited by 10 publications

(8 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To help substantiate this premise, the interactome associated with NAC TFs in A. thaliana was analysed. Results indicated that NAC TFs are potentially involved in a least 289 different (1) Fbox domain followed by protein kinase and NAC domain (2) NAC domain followed by G_TR_2 domain (3) RDRP domain followed by NAC (4) NAC domain followed by CHCH domain (5) TPR repeats followed by NAC domain (6) F-box domain followed by NAC and F-box domain (7) NAC domain followed by YJEF_N domain (8) NAC domain followed by HTH domain (9) Homeobox domain followed by NAC domain (10) NAC domain followed by three GH6.2 domain (11) ANK repeat domain followed by NAC domain (12) NAC domain followed by peroxidase domain (13) NAC domain followed by LONGIN and V_SNA domain (14) NAC domain followed by RECA_2 and RECA_3 domain (15) KH_TY repeats followed by NAC domain (16) NAC domain followed by RAB domain (17) JMJN domain followed by NAC domain (18) NAC domain followed by APAG domain (19) two RRM domain followed by NAC domain (20) carrier domain followed by NAC domain and (21) NAC domain followed by DCO domain. The identification of chimeric NAC domain sequences was determined using the ScanProsite and InterProScan server.…”

Section: Nac Tfs Are Involved In Diverse Cellular Processesmentioning

confidence: 99%

“…Some TFs bind to a DNA promoter region located near the transcription start site of a gene and help to form the transcription initiation complex [13][14][15][16]. Other TFs bind to regulatory enhancer sequences and stimulate or repress transcription of the related genes [17][18][19]. Regulating transcription is of paramount importance to controlling gene expression and TFs enable the expression of an individual gene in a unique manner, such as during different stages of development or in response to biotic or abiotic stress [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomics, molecular and evolutionary perspective of NAC transcription factors

et al. 2020

View full text Add to dashboard Cite

NAC (NAM, ATAF1,2, and CUC2) transcription factors are one of the largest transcription factor families found in the plants and are involved in diverse developmental and signalling events. Despite the availability of comprehensive genomic information from diverse plant species, the basic genomic, biochemical, and evolutionary details of NAC TFs have not been established. Therefore, NAC TFs family proteins from 160 plant species were analyzed in the current study. Study revealed, Brassica napus (410) encodes highest number and Klebsormidium flaccidum (3) encodes the lowest number of TFs. The study further revealed the presence of NAC TF in the Charophyte algae K. flaccidum. On average, the monocot plants encode higher number (141.20) of NAC TFs compared to the eudicots (125.04), gymnosperm (75), and bryophytes (22.66). Furthermore, our analysis revealed that several NAC TFs are membrane bound and contain monopartite, bipartite, and multipartite nuclear localization signals. NAC TFs were also found to encode several novel chimeric proteins and regulate a complex interactome network. In addition to the presence of NAC domain, several NAC proteins were found to encode other functional signature motifs as well. Relative expression analysis of NAC TFs in A. thaliana revealed root tissue treated with urea and ammonia showed higher level of expression and leaf tissues treated with urea showed lower level of expression. The synonymous codon usage is absent in the NAC TFs and it appears that they have evolved from orthologous ancestors and undergone vivid duplications to give rise to paralogous NAC TFs. The presence of novel chimeric NAC TFs are of particular interest and the presence of chimeric NAC domain with other functional signature motifs in the NAC TF might encode novel functional properties in the plants.

show abstract

Section: Nac Tfs Are Involved In Diverse Cellular Processesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomics, molecular and evolutionary perspective of NAC transcription factors

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Transcription of enhancers most likely results from the accumulation of TFs and the consequent recruitment of pol II. However, accumulating evidence over the last decade indicates that at least some eRNAs contribute to enhancer function [8,[14][15][16][17]. Whereas most eRNAs are unstable and rapidly subjected to exosome-dependent degradation, some are more stable and even polyadenylated [11,18], which could underpin their function (Figure 2).…”

Section: Ernas Direct the Actorsmentioning

confidence: 99%

Noncoding RNAs Set the Stage for RNA Polymerase II Transcription

Studniarek¹,

Egloff²,

Murphy³

2021

Trends in Genetics

View full text Add to dashboard Cite

“…Small ncRNAs are less than 30 bp and they include: microRNA (miRNA), short interfering RNA (siRNA), piwi-interacting RNAs (piRNA), tRNA-derived fragments (tRFs), and tRNA halves (tiRNAs). lncRNAs are greater than 200 nucleotides [ 91 , 92 , 93 , 94 ]. With respect to post-transcriptional processing, A-to-I editing has been most studied in miRNAs and lncRNAs [ 32 ].…”

Section: Editing Of Non-coding Rna In Cancermentioning

confidence: 99%

Non-Coding RNA Editing in Cancer Pathogenesis

Romano

Saviana

et al. 2020

Cancers

View full text Add to dashboard Cite

In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.

show abstract

The role of enhancer RNAs in epigenetic regulation of gene expression

Cited by 10 publications

References 81 publications

Genomics, molecular and evolutionary perspective of NAC transcription factors

Genomics, molecular and evolutionary perspective of NAC transcription factors

Noncoding RNAs Set the Stage for RNA Polymerase II Transcription

Non-Coding RNA Editing in Cancer Pathogenesis

Contact Info

Product

Resources

About