Sequenciando o mRNA de embriões de Drosophila crio-fatiados para determinar os padrões espaciais de expressão de genes através do genoma

terça-feira, março 12, 2013

Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression

Peter A. Combs, Michael B. Eisen

(Submitted on 19 Feb 2013 (v1), last revised 20 Feb 2013 (this version, v2))


Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial patterns of gene expression. {\em In situ} imaging of transcripts and proteins is the gold-standard, but is difficult and time consuming to apply to an entire genome, even when highly automated. Sequencing, in contrast, is fast and genome-wide, but generally applied to homogenized tissues, thereby discarding spatial information. At some point, these methods will converge, and we will be able to sequence RNAs {\em in situ}, simultaneously determining their identity and location. As a step along this path, we developed methods to cryosection individual blastoderm stage {\em Drosophila melanogaster} embryos along the anterior-posterior axis and sequence the mRNA isolated from each 60\micron{} slice. The spatial patterns of gene expression we infer closely match patterns determined by {\em in situ} hybridization and microscopy, where such data exist, and thus we conclude that we have generated the first genome-wide map of spatial patterns in the {\em Drosophila} embryo. We identify numerous genes with spatial patterns that have not yet been screened in the several ongoing systematic in situ based projects, the majority of which are localized to the posterior end of the embryo, likely in the pole cells. This simple experiment demonstrates the potential for combining careful anatomical dissection with high-throughput sequencing to obtain spatially resolved gene expression on a genome-wide scale.

Comments: 6 pages, 2 figures, 3 supplemental figures (available on request from

Subjects: Genomics (q-bio.GN)

Cite as: arXiv:1302.4693 [q-bio.GN]
  (or arXiv:1302.4693v2 [q-bio.GN] for this version)

Submission history

From: Peter Combs [view email] 
[v1] Tue, 19 Feb 2013 17:44:59 GMT (1760kb)
[v2] Wed, 20 Feb 2013 18:28:21 GMT (1760kb,D)