eprintid: 24270
rev_number: 12
eprint_status: archive
userid: 1589
dir: disk0/00/02/42/70
datestamp: 2018-04-20 09:06:44
lastmod: 2024-04-08 07:58:02
status_changed: 2018-04-20 09:06:44
type: article
metadata_visibility: show
creators_name: Cemel, Ibrahim Avi
creators_name: Ha, Nati
creators_name: Schermann, Geza
creators_name: Yonekawa, Shusuke
creators_name: Brunner, Michael
title: The coding and noncoding transcriptome of Neurospora crassa
subjects: 570
divisions: 711000
abstract: Background: Long 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.

Results: We 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.

Conclusions: Our 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.
date: 2017
publisher: BioMed Central ; Springer
id_scheme: DOI
ppn_swb: 1656463075
own_urn: urn:nbn:de:bsz:16-heidok-242706
language: eng
bibsort: CEMELIBRAHTHECODINGA2017
full_text_status: public
publication: BMC Genomics
volume: 18
number: 978
place_of_pub: London ; Berlin ; Heidelberg
pagerange: 1-11
issn: 1471-2164
citation:   Cemel, Ibrahim Avi ; Ha, Nati ; Schermann, Geza ; Yonekawa, Shusuke ; Brunner, Michael  (2017) The coding and noncoding transcriptome of Neurospora crassa.  BMC Genomics, 18 (978).  pp. 1-11.  ISSN 1471-2164     
document_url: https://archiv.ub.uni-heidelberg.de/volltextserver/24270/1/12864_2017_Article_4360.pdf