High-resolution analysis of gene activity during the Xenopus mid-blastula transition.
The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here, we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilisation wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the seventh cleavage and extending beyond the MBT at the twelfth cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal mRNAs that are deadenylated shortly after fertilisation, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organisation of gene regulatory networks in the early Xenopus embryo.
Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
Clara
C
Collart
Nick D L
ND
Owens
Leena
L
Bhaw-Rosun
Brook
B
Cooper
Elena
E
De Domenico
Ilya
I
Patrushev
Abdul K
AK
Sesay
James N
JN
Smith
James C
JC
Smith
Michael J
MJ
Gilchrist
D000818:Animals; D036703:Blastula / Q000378:metabolism*; D004625:Embryo, Nonmammalian / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D058977:Molecular Sequence Annotation; D011061:Poly A / Q000378:metabolism; D026723:Polyadenylation / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D023121:RNA, Messenger, Stored / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014981:Xenopus / Q000196:embryology* / Q000235:genetics*; D029867:Xenopus Proteins / Q000235:genetics / Q000378:metabolism; D015027:Zebrafish / Q000235:genetics
D023121:RNA, Messenger, Stored; D014157:Transcription Factors; D029867:Xenopus Proteins; D011061:Poly A
Gene regulatory networks; Maternal zygotic transition; Midblastula transition; Polyadenylation; RNA-seq; Transcription; Xenopus tropicalis