TY - JOUR
T1 - Native elongating transcript sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast
AU - Wery, Maxime
AU - Gautier, Camille
AU - Descrimes, Marc
AU - Yoda, Mayuko
AU - Vennin-Rendos, Hervé
AU - Migeot, Valérie
AU - Gautheret, Daniel
AU - Hermand, Damien
AU - Morillon, Antonin
N1 - © 2018 Wery et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
PY - 2018/2/1
Y1 - 2018/2/1
N2 - Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long noncoding (aslnc)RNAs by RNA-seq and/or microarrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used native elongating transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-seq analyses showed that antisense (as)XUT's expression is associated with specific histone modification patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional nonpromoter determinant of gene regulation complexity.
AB - Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long noncoding (aslnc)RNAs by RNA-seq and/or microarrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used native elongating transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-seq analyses showed that antisense (as)XUT's expression is associated with specific histone modification patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional nonpromoter determinant of gene regulation complexity.
KW - Gene Expression Regulation, Fungal
KW - Histone Chaperones/metabolism
KW - Histone Code
KW - Meiosis/genetics
KW - Peptide Chain Elongation, Translational
KW - RNA Interference
KW - RNA Stability
KW - RNA, Antisense/biosynthesis
KW - Schizosaccharomyces pombe Proteins/metabolism
KW - Schizosaccharomyces/genetics
KW - Sequence Analysis, RNA
KW - Transcription, Genetic
UR - http://www.scopus.com/inward/record.url?scp=85040976623&partnerID=8YFLogxK
U2 - 10.1261/rna.063446.117
DO - 10.1261/rna.063446.117
M3 - Article
C2 - 29114019
SN - 1355-8382
VL - 24
SP - 196
EP - 208
JO - RNA
JF - RNA
IS - 2
ER -