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Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos.

Liu T, Yu L, Ding G, Wang Z, Liu L, Li H, Li Y - Biomed Res Int (2015)

Bottom Line: The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages.Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development.Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.

ABSTRACT
Evolutionary developmental biology (EVO-DEVO) tries to decode evolutionary constraints on the stages of embryonic development. Two models--the "funnel-like" model and the "hourglass" model--have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED) were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA). Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

No MeSH data available.


Related in: MedlinePlus

(a) Distributions of transcription factors (TFs) in stage-specific modules. (b) Distributions of genes with highly conserved noncoding elements (HCNEs) in their cis-regulatory regions. For each stage, the vertical axis shows the observed proportions minus expected proportions of TF and genes with HCNEs, respectively. The asterisks denote significant enrichment (P < 0.01).
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fig6: (a) Distributions of transcription factors (TFs) in stage-specific modules. (b) Distributions of genes with highly conserved noncoding elements (HCNEs) in their cis-regulatory regions. For each stage, the vertical axis shows the observed proportions minus expected proportions of TF and genes with HCNEs, respectively. The asterisks denote significant enrichment (P < 0.01).

Mentions: Conservation of cis-regulatory sequences is also a critical standard for measuring the selective pressure on genes [14, 32], and highly conserved noncoding elements (HCNEs) are often considered to be associated with developmental regulatory genes or transcription factors (TFs) [23, 33]. Therefore, we determined the transcriptional importance of stage-specific genes by analyzing their potential to become TFs and the distribution of HCNEs in their promoter regions (Figure 6).


Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos.

Liu T, Yu L, Ding G, Wang Z, Liu L, Li H, Li Y - Biomed Res Int (2015)

(a) Distributions of transcription factors (TFs) in stage-specific modules. (b) Distributions of genes with highly conserved noncoding elements (HCNEs) in their cis-regulatory regions. For each stage, the vertical axis shows the observed proportions minus expected proportions of TF and genes with HCNEs, respectively. The asterisks denote significant enrichment (P < 0.01).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4530217&req=5

fig6: (a) Distributions of transcription factors (TFs) in stage-specific modules. (b) Distributions of genes with highly conserved noncoding elements (HCNEs) in their cis-regulatory regions. For each stage, the vertical axis shows the observed proportions minus expected proportions of TF and genes with HCNEs, respectively. The asterisks denote significant enrichment (P < 0.01).
Mentions: Conservation of cis-regulatory sequences is also a critical standard for measuring the selective pressure on genes [14, 32], and highly conserved noncoding elements (HCNEs) are often considered to be associated with developmental regulatory genes or transcription factors (TFs) [23, 33]. Therefore, we determined the transcriptional importance of stage-specific genes by analyzing their potential to become TFs and the distribution of HCNEs in their promoter regions (Figure 6).

Bottom Line: The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages.Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development.Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.

ABSTRACT
Evolutionary developmental biology (EVO-DEVO) tries to decode evolutionary constraints on the stages of embryonic development. Two models--the "funnel-like" model and the "hourglass" model--have been proposed by investigators to illustrate the fluctuation of selective pressure on these stages. However, selective indices of stages corresponding to mammalian preimplantation embryonic development (PED) were undetected in previous studies. Based on single cell RNA sequencing of stages during human PED, we used coexpression method to identify gene modules activated in each of these stages. Through measuring the evolutionary indices of gene modules belonging to each stage, we observed change pattern of selective constraints on PED for the first time. The selective pressure decreases from the zygote stage to the 4-cell stage and increases at the 8-cell stage and then decreases again from 8-cell stage to the late blastocyst stages. Previous EVO-DEVO studies concerning the whole embryo development neglected the fluctuation of selective pressure in these earlier stages, and the fluctuation was potentially correlated with events of earlier stages, such as zygote genome activation (ZGA). Such oscillation in an earlier stage would further affect models of the evolutionary constraints on whole embryo development. Therefore, these earlier stages should be measured intensively in future EVO-DEVO studies.

No MeSH data available.


Related in: MedlinePlus