Book Chapter10.1016/B978-0-12-404729-7.00001-0
The Genome in Development
Eric H. Davidson,Isabelle S. Peter +1 more
- 01 Jan 2015
- pp 1-40
6
TL;DR: This chapter considers three major levels at which gene expression is controlled, with respect to their roles in the developmental process, including transcriptional regulation by sequence-specific transcription factors and their interaction with cis -regulatory modules.
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Abstract: Development is encoded in the genome by sequence-specific regulation of gene expression. In this chapter, we consider three major levels at which gene expression is controlled, with respect to their roles in the developmental process. The first is transcriptional regulation by sequence-specific transcription factors and their interaction with cis -regulatory modules. Secondly, micro RNAs modulate transcript prevalence, and a third level operates by means of chromatin modifications installed upon transcription factor–DNA interactions. While the expression of many genes is affected successively by all these mechanisms, the control of developmental complexity by means of spatially differential gene expression is executed by transcription factors and their sequence-specific interactions with the regulatory genome. Therefore, the primary key to the informational process of development lies in the control system regulating the expression of genes encoding transcription factors.
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Citations
MicroRNAs: Target Recognition and Regulatory Functions
David P. Bartel
- 01 Jan 2009
TL;DR: In this article, a review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.
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Enhancer sharing promotes neighborhoods of transcriptional regulation across eukaryotes
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Lineage specific conservation of cis-regulatory elements in Cytokinin Response Factors.
TL;DR: Over 300 promoter sequences from a small, well-conserved family of plant transcription factors known as Cytokinin Response Factors were examined for conserved motifs suggesting cis-regulatory regions have been conserved throughout CRF evolution.
Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes.
TL;DR: Cross-organismic evidence is presented suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions, and that EP distance is an important layer of information in gene regulation.
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Most mammalian mRNAs are conserved targets of microRNAs
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TL;DR: The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development.
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
Lee P. Lim,Nelson C. Lau,Philip W. Garrett-engele,Andrew Grimson,Janell M. Schelter,John C. Castle,David P. Bartel,Peter S. Linsley,Jason M. Johnson +8 more
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Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
John L. Rinn,Michael Kertesz,Jordon K. Wang,Sharon L. Squazzo,Xiao Xu,Samantha A. Brugmann,L. Henry Goodnough,Jill A. Helms,Peggy J. Farnham,Eran Segal,Howard Y. Chang +10 more
TL;DR: The transcriptional landscape of the four human HOX loci is characterized at five base pair resolution in 11 anatomic sites and 231 HOX ncRNAs are identified that extend known transcribed regions by more than 30 kilobases, suggesting transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance.
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