scholarly journals The natural antisense transcript DONE40 derived from the lncRNA ENOD40 locus interacts with SET domain protein ASHR3 during inception of symbiosis in Arachis hypogaea

2021 ◽  
Author(s):  
Pritha Ganguly ◽  
Dipan Roy ◽  
Troyee Das ◽  
Anindya Kundu ◽  
Zhumur Ghosh ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Antisense Transcript ◽  
Cortical Cell ◽  
Nodule Formation ◽  
Phylogenetic Distance ◽  
Natural Antisense Transcript ◽  
Set Domain ◽  
Cell Extracts ◽  
Family Protein ◽  
Rna Immunoprecipitation

The lncRNA ENOD40 is required for cortical cell division during root nodule symbiosis (RNS) of legumes, though it is not essential for actinorhizal RNS. Our objective was to understand whether ENOD40 was required for aeschynomenoid nodule formation in Arachis hypogaea. AhENOD40 express from chr5 (AhENOD40-1) and chr15 (AhENOD40-2) during symbiosis, and RNA interference of these transcripts drastically affected nodulation indicating the importance of ENOD40 in A.hypogaea. Furthermore, we demonstrated several distinct characteristics of ENOD40: (i) Natural antisense transcript of ENOD40 was detected from the AhENOD40-1 locus (designated as NAT-AhDONE40). (ii) Both AhENOD40-1 and AhENOD40-2 had two exons, whereas NAT-AhDONE40 was monoexonic. RT-qPCR analysis indicated both sense and antisense transcripts to be present in both cytoplasm and nucleus, and their expression increased with the progress of symbiosis. (iii) RNA Pulldown from whole cell extracts of infected roots at 4DPI indicated NAT-AhDONE40 to interact with the SET (Su(var)3-9, Enhancer-of-zeste and Trithorax) domain containing Ash (Absent Small homeotic disc) family protein AhASHR3 and this interaction was further validated using RNA immunoprecipitation and EMSA. (iv) ChIP assays indicate deposition of ASHR3 specific histone marks H3K36me3 and H3K4me3 in both the ENOD40 loci during the progress of symbiosis. ASHR3 is known for its role in optimizing cell proliferation and reprogramming. Since both ASHR3 and ENOD40 from legumes cluster away from those in actinorhizal plants and other nonlegumes in phylogenetic distance trees, we hypothesize that the interaction of DONE40 with ASHR3 could have evolved for adapting the nodule organogenesis program for legumes.

scholarly journals Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 759
Author(s):  
Zhongjing Su ◽  
Guangyu Liu ◽  
Bin Zhang ◽  
Ze Lin ◽  
Dongyang Huang
Keyword(s):  
Dna Methylation ◽  
Alternative Splicing ◽  
Histone Modification ◽  
Antisense Rna ◽  
Noncoding Rna ◽  
Antisense Transcript ◽  
Natural Antisense Transcript ◽  
Regulation Of Expression ◽  
Splicing Isoforms ◽  
Intron 2

The leukocyte common antigen CD45 is a transmembrane phosphatase expressed on all nucleated hemopoietic cells, and the expression levels of its splicing isoforms are closely related to the development and function of lymphocytes. PEBP1P3 is a natural antisense transcript from the opposite strand of CD45 intron 2 and is predicted to be a noncoding RNA. The genotype-tissue expression and quantitative PCR data suggested that PEBP1P3 might be involved in the regulation of expression of CD45 splicing isoforms. To explore the regulatory mechanism of PEBP1P3 in CD45 expression, DNA methylation and histone modification were detected by bisulfate sequencing PCR and chromatin immunoprecipitation assays, respectively. The results showed that after the antisense RNA PEBP1P3 was knocked down by RNA interference, the DNA methylation of CD45 intron 2 was decreased and histone H3K9 and H3K36 trimethylation at the alternative splicing exons of CD45 DNA was increased. Knockdown of PEBP1P3 also increased the binding levels of chromatin conformation organizer CTCF at intron 2 and the alternative splicing exons of CD45. The present results indicate that the natural antisense RNA PEBP1P3 regulated the alternative splicing of CD45 RNA, and that might be correlated with the regulation of histone modification and DNA methylation.

Effects of a Nod-factor-overproducing strain of Sinorhizobium meliloti on the expression of the ENOD40 gene in Melilotus alba

2002 ◽  
Vol 80 (9) ◽  
pp. 907-915 ◽  
Author(s):  
Walter F Giordano ◽  
Michelle R Lum ◽  
Ann M Hirsch
Keyword(s):  
Lateral Root ◽  
Sinorhizobium Meliloti ◽  
Cortical Cell ◽  
Host Cells ◽  
Nodule Development ◽  
Nodule Formation ◽  
Additional Increase ◽  
Nod Factor ◽  
Melilotus Alba ◽  
Different Strains

We have initiated studies on the molecular biology and genetics of white sweetclover (Melilotus alba Desr.) and its responses to inoculation with the nitrogen-fixing symbiont Sinorhizobium meliloti. Early nodulin genes such as ENOD40 serve as markers for the transition from root to nodule development even before visible stages of nodule formation are evident. Using Northern blot analysis, we found that the ENOD40 gene was expressed within 6 h after inoculation with two different strains of S. meliloti, one of which overproduces symbiotic Nod factors. Inoculation with this strain resulted in an additional increase in ENOD40 gene expression over a typical wild-type S. meliloti strain. Moreover, the increase in mRNA brought about by the Nod-factor-overproducing strain 24 h after inoculation was correlated with lateral root formation by using whole-mount in situ hybridization to localize ENOD40 transcripts in lateral root meristems and by counting lateral root initiation sites. Cortical cell divisions were not detected. We also found that nodulation occurred more rapidly on white sweetclover in response to the Nod-factor-overproducing strain, but ultimately there was no difference in nodulation efficiency in terms of nodule number or the number of roots nodulated by the two strains. Also, the two strains could effectively co-colonize the host when inoculated together, although a few host cells were occupied by both strains.Key words: ENOD40, Nod factor, Melilotus, Sinorhizobium, symbiosis.

Long noncoding RNA FGFR3-AS1 promotes osteosarcoma growth through regulating its natural antisense transcript FGFR3

2016 ◽  
Vol 43 (5) ◽  
pp. 427-436 ◽  
Author(s):  
Jiabing Sun ◽  
Xuming Wang ◽  
Chunjiang Fu ◽  
Xiaoyu Wang ◽  
Jilong Zou ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Antisense Transcript ◽  
Natural Antisense Transcript

P4-264: A GENE THERAPY APPROACH FOR REDUCTION OF TAU BY TAU LONG NON-CODING RNA GENE (MAPT-AS1 ) NATURAL ANTISENSE TRANSCRIPT

2006 ◽  
Vol 14 (7S_Part_29) ◽  
pp. P1547-P1548
Author(s):  
Rohan de Silva ◽  
Justyna Zareba-Paslawska ◽  
Filipa Almeida ◽  
Per Svenningsson ◽  
Tom Warner ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Antisense Transcript ◽  
Natural Antisense Transcript ◽  
Therapy Approach ◽  
Gene Therapy Approach ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals Chicken GHR natural antisense transcript regulates GHR mRNA in LMH cells

Oncotarget ◽  
2016 ◽  
Vol 7 (45) ◽  
pp. 73607-73617 ◽  
Author(s):  
Li Zhang ◽  
Shudai Lin ◽  
Lilong An ◽  
Jinge Ma ◽  
Fengfang Qiu ◽  
...  
Keyword(s):  
Antisense Transcript ◽  
Natural Antisense Transcript ◽  
Lmh Cells

scholarly journals Nod Factor-Induced Expression of Leghemoglobin to Study the Mechanism of NH4NO3 Inhibition on Root Hair Deformation

1997 ◽  
Vol 10 (2) ◽  
pp. 215-220 ◽  
Author(s):  
Renze Heidstra ◽  
Gerd Nilsen ◽  
Francisco Martinez-Abarca ◽  
Ab van Kammen ◽  
Ton Bisseling
Keyword(s):  
Gene Expression ◽  
Root Hair ◽  
Rhizobium Leguminosarum ◽  
Cortical Cell ◽  
Brefeldin A ◽  
Marker Genes ◽  
Nodule Formation ◽  
Cdna Clones ◽  
Nod Factor ◽  
Root Hair Deformation

Nod factors secreted by Rhizobium leguminosarum bv. viciae induce root hair deformation, the formation of nodule primordia, and the expression of early nodulin genes in Vicia sativa (vetch). Root hair deformation is induced within 3 h in a small, susceptible zone (±2 mm) of the root. NH4NO3, known to be a potent blocker of nodule formation, inhibits root hair deformation, initial cortical cell divisions, and infection thread formation. To test whether NH4NO3 affects the formation of a component of the Nod factor perception-transduction system, we studied Nod factor-induced gene expression. The differential display technique was used to search for marker genes, which are induced within 1 to 3 h after Nod factor application. Surprisingly, one of the isolated cDNA clones was identified as a leghemoglobin gene (VsLb1), which is induced in vetch roots within 1 h after Nod factor application. By using the drug brefeldin A, it was then shown that VsLb1 activation does not require root hair deformation. The pVsLb1 clone was used as a marker to show that in vetch plants grown in the presence of NH4NO3 Nod factor perception and transduction leading to gene expression are unaffected.

scholarly journals Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family

2016 ◽  
Vol 29 (12) ◽  
pp. 950-964 ◽  
Author(s):  
Md Shakhawat Hossain ◽  
Arina Shrestha ◽  
Sihui Zhong ◽  
Mandana Miri ◽  
Ryan S. Austin ◽  
...  
Keyword(s):  
Gene Family ◽  
Lotus Japonicus ◽  
Cortical Cell ◽  
Plant Evolution ◽  
Nodule Formation ◽  
Functional Diversification ◽  
Nuclear Factor Y ◽  
Functional Analyses ◽  
Transcription Factor Gene Family ◽  
Selection Of

Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell divisions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.

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