Correction to: The coding and noncoding transcriptome of Neurospora crassa.
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ABSTRACT:
SUBMITTER: Cemel IA
PROVIDER: S-EPMC5935966 | biostudies-literature | 2018 May
REPOSITORIES: biostudies-literature
Publications
Correction to: The coding and noncoding transcriptome of Neurospora crassa.
Cemel Ibrahim Avi IA Ha Nati N Schermann Geza G Yonekawa Shusuke S Brunner Michael M
BMC genomics 20180504 1
After publication of the original article [1], the authors noted that Additional files 6, 8 and 9 and their legends were incorrect. ...[more]
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Project description:BackgroundLong non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncRNAs is incomplete.ResultsWe have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, RNA-seq and polysome fractionation datasets. We have annotated and characterized 1478 long intergenic noncoding RNAs (lincRNAs) and 1056 natural antisense transcripts, indicating that 20% of the RNA Polymerase II transcripts of Neurospora are not coding for protein. Both classes of lncRNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. Our analysis showed that the vast majority of lincRNAs and antisense transcripts do not contain introns and carry less H3K4me2 modifications than similarly expressed protein coding genes. In contrast, H3K27me3 modifications inversely correlate with transcription of protein coding and lincRNA genes. We show furthermore most lincRNA sequences evolve rapidly, even between phylogenetically close species.ConclusionsOur transcriptome analyses revealed distinct features of Neurospora lincRNAs and antisense transcripts in comparison to mRNAs and showed that the prevalence of noncoding transcripts in this organism is higher than previously anticipated. The study provides a broad repertoire and a resource for further studies of lncRNAs.
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Project description:We present the NEUTRA database, a catalogue of the Neurospora transcriptome, based on RNA-Seq, RNAPII ChIP-Seq and ribosome fractionation studies. The database also includes genome-wide binding sites of transcription factors involved in regulation of circadian gene expression. In a comprehensive analysis of the transcriptome we identified and characterized 1478 long intergenic non-coding RNAs (lincRNAs) and 1056 natural antisense transcripts. Both classes of long non-coding RNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. We also confirmed annotated splice sites and identified new splice junctions and alternative splice sites, which are rare in Neurospora. Our analysis revealed that the vast majority of lincRNAs and antisense transcripts do not contain introns. NEUTRA is the first database to provide a collection of genome-wide deep sequencing data for the model organism Neurospora crassa and thus provides a tool that facilitates future research.
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Project description:The prevalence of long non-coding RNAs (lncRNA) and natural antisense transcripts (NATs) has been reported in a variety of organisms. While a consensus has yet to be reached on their global importance, an increasing number of examples have been shown to be functional, regulating gene expression at the transcriptional and post-transcriptional level. Here, we use RNA sequencing data from the ABI SOLiD platform to identify lncRNA and NATs obtained from samples of the filamentous fungus Neurospora crassa grown under different light and temperature conditions. We identify 939 novel lncRNAs, of which 477 are antisense to annotated genes. Across the whole dataset, the extent of overlap between sense and antisense transcripts is large: 371 sense/antisense transcripts are complementary over 500 nts or more and 236 overlap by more than 1000 nts. Most prevalent are 3' end overlaps between convergently transcribed sense/antisense pairs, but examples of divergently transcribed pairs and nested transcripts are also present. We confirm the expression of a subset of sense/antisense transcript pairs by qPCR. We examine the size, types of overlap and expression levels under the different environmental stimuli of light and temperature, and identify 11 lncRNAs that are up-regulated in response to light. We also find differences in transcript length and the position of introns between protein-coding transcripts that have antisense expression and transcripts with no antisense expression. These results demonstrate the ability of N. crassa lncRNAs and NATs to be regulated by different environmental stimuli and provide the scope for further investigation into the function of NATs.
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Project description:Neurospora crassa has a long history as an excellent model for genetic, cellular, and biochemical research. Although this fungus is known as a saprotroph, it normally appears on burned vegetations or trees after forest fires. However, due to a lack of experimental evidence, the nature of its association with living plants remains enigmatic. Here we report that Scots pine (Pinus sylvestris) is a host plant for N. crassa. The endophytic lifestyle of N. crassa was found in its interaction with Scots pine. Moreover, the fungus can switch to a pathogenic state when its balanced interaction with the host is disrupted. Our data reveal previously unknown lifestyles of N. crassa, which are likely controlled by both environmental and host factors. Switching among the endophytic, pathogenic, and saprotrophic lifestyles confers upon fungi phenotypic plasticity in adapting to changing environments and drives the evolution of fungi and associated plants.
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Project description:This study demonstrates the utility of Lifeact for the investigation of actin dynamics in Neurospora crassa and also represents the first report of simultaneous live-cell imaging of the actin and microtubule cytoskeletons in filamentous fungi. Lifeact is a 17-amino-acid peptide derived from the nonessential Saccharomyces cerevisiae actin-binding protein Abp140p. Fused to green fluorescent protein (GFP) or red fluorescent protein (TagRFP), Lifeact allowed live-cell imaging of actin patches, cables, and rings in N. crassa without interfering with cellular functions. Actin cables and patches localized to sites of active growth during the establishment and maintenance of cell polarity in germ tubes and conidial anastomosis tubes (CATs). Recurrent phases of formation and retrograde movement of complex arrays of actin cables were observed at growing tips of germ tubes and CATs. Two populations of actin patches exhibiting slow and fast movement were distinguished, and rapid (1.2 microm/s) saltatory transport of patches along cables was observed. Actin cables accumulated and subsequently condensed into actin rings associated with septum formation. F-actin organization was markedly different in the tip regions of mature hyphae and in germ tubes. Only mature hyphae displayed a subapical collar of actin patches and a concentration of F-actin within the core of the Spitzenkörper. Coexpression of Lifeact-TagRFP and beta-tubulin-GFP revealed distinct but interrelated localization patterns of F-actin and microtubules during the initiation and maintenance of tip growth.
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Project description:Purpose: We utilised high-throughput genomic approache to investigate transcriptional changes in two Neurospora strains (74A [wild-type] and mutant Δmus-52), under different phosphate availability conditions to evaluate the effects of mus-52 deletion in gene transcriptional modulation, and thus, infer its influence regarding metabolic response to changing extracellular levels of inorganic phosphate (Pi). Methods: All N. crassa strains were maintained on Vogel’s minimal medium, pH 5.8, at 30°C. Conidia from each strain were germinated for 5 h at 30°C in an orbital shaker (200 rpm), in low-Pi (10µM) and high-Pi (10mM) media. Total RNA was isolated from both strains and a total of 4 cDNA libraries were sequenced, with their respective biological triplicates corresponding to the paired libraries, using an Illumina HiSeq2000 sequencer, to generate 100 bp paired-end reads. FastQC software was used to visualize the library quality before and after trimming. For quality and sequence filtering, a Phred score lower than 20 was employed to remove sequencing bases from the read ends. Filtered reads were mapped onto the N. crassa genome using Bowtie2 software. The reads count values were obtained and used to calculate the expression variation of the transcripts from different conditions, considering the statistical significance of the differential gene expression. qRT–PCR validation was performed using SYBR Green assays. Results: extracellular Pi availability influenced the expression of genes involved in several biological functions. The main affected gene groups were those associated with integral components of the membrane, such as transport, regulation, and cell signalling pathways, as well as genes involved with the nucleolus and protein synthesis. The absence of mus-52 affected global gene transcription in all conditions tested, highlighting the expression of some specific gene groups, such as transcription factors, kinase proteins, circadian clock-related genes, oxi-reduction balance, phosphate pathways, and general metabolism. Conclusions: The consequences of N. crassa mus-52 disruption to the cell may be deeper than the obvious phenotypic aspect. It may affect canonical and non-canonical pathways, leading to alternative adaptive processes, altering the perception and response to the environmental changes.
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