Developmental progression is driven by specific spatiotemporal domains of gene expression, which give rise to stereotypically patterned embryos even in the presence of environmental and genetic variation. Views of how transcription factors regulate gene expression are changing owing to recent genome-wide studies of transcription factor binding and RNA expression. Such studies reveal patterns that, at first glance, seem to contrast with the robustness of the developmental processes they encode. Here, we review our current knowledge of transcription factor function from genomic and genetic studies and discuss how different strategies, including extensive cooperative regulation (both direct and indirect), progressive priming of regulatory elements, and the integration of activities from multiple enhancers, confer specificity and robustness to transcriptional regulation during development.

http://materiais.dbio.uevora.pt/BD/Crescimento/TFs_2012.pdf

Transcription factors: from enhancer binding to developmental control.

INTRODUCTION: The copy number and in- tracellular localization of RNA are important regulators of gene expression. Measurement of these properties at the transcriptome scale in single cells will give answers to many ques- tions related to gene expression and regulation. Single-molecule RNA imaging approaches, such as single-molecule fluorescence in situ hybrid- ization(smFISH), are powerful toolsforcount- ing and mappingRNA; however, the number of RNA species that can be simultaneously im- aged in individual cells has been limited. This makes it challenging to perform transcriptomic analysis of single cells in a spatially resolved manner. Here, we report multiplexed error- robust FISH (MERFISH), a single-molecule im- aging method that allows thousands of RNA species to be imaged in single cells by using combinatorial FISH labeling with encoding schemes capable of detecting and/or correct- ing errors. RATIONALE: We labeled each cellular RNA with a set of encoding probes, which contain targeting sequences that bind the RNA and readout sequences that bind fluorescently la- beled readout probes. Each RNA species is encodedwithaparticular combinationofread- out sequences. We used successive rounds of hybridization and imaging, each with a differ- ent readout probe, to identify the readout se- quences bound to each RNA and to decode the RNA. In principle, combinatorial labeling al- lows the number of detectable RNA species to

http://science.sciencemag.org/content/sci/348/6233/aaa6090.full.pdf

Spatially resolved, highly multiplexed RNA profiling in single cells

eMedicine创建于1996年，由近万名临床医师作为作者或编辑参与此临床医学知识库的建设，其中编辑均是来自美国哈佛、耶鲁、斯坦福、芝加哥、德克萨斯、加州大学等各分校医学院的教授或副教授。

eMedicine

Cis-regulatory sequences, such as enhancers and promoters, control development and physiology by regulating gene expression. Mutations that affect the function of these sequences contribute to phenotypic diversity within and between species. With many case studies implicating divergent cis-regulatory activity in phenotypic evolution, researchers have recently begun to elucidate the genetic and molecular mechanisms that are responsible for cis-regulatory divergence. Approaches include detailed functional analysis of individual cis-regulatory elements and comparing mechanisms of gene regulation among species using the latest genomic tools. Despite the limited number of mechanistic studies published to date, this work shows how cis-regulatory activity can diverge and how studies of cis-regulatory divergence can address long-standing questions about the genetic mechanisms of phenotypic evolution.

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

Genomic enhancers are important regulators of gene expression, but their identification is a challenge, and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, which enables screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell type–specific enhancers across a broad continuum of strengths, links differential gene expression to differences in enhancer activity, and creates a genome-wide quantitative enhancer map. This map reveals the highly complex regulation of transcription, with several independent enhancers for both developmental regulators and ubiquitously expressed genes. STARR-seq can be used to identify and quantify enhancer activity in other eukaryotes, including humans.

Genome-wide quantitative enhancer activity maps identified by STARR-seq.

Book reviewSurgical approaches to the facial skeleton, 2nd edition, Edward Ellis III, Michael F. Zide, Lippincott Williams & Wilkins, 2 edition (December 1, 2005) ISBN-10: 0781754992, ISBN-13: 978-0781754996

Colias butterflies (the “clouded sulphurs”) often occur in mixed populations where females exhibit two color morphs, yellow/orange or white White females, known as Alba [A-], reallocate resources from colored pigment synthesis to reproductive and somatic development Due to this tradeoff Alba females develop faster and have higher fecundity than orange females However while colored pigments are costly to produce, males preferentially mate with orange females and transfer nutrient rich spermatophores during mating Thus the wing color morphs represent alternative life history strategies (ALHS) that are female-limited, wherein tradeoffs, due to divergent resource investment, result in distinct phenotypes with associated fitness consequences Here we map the genetic basis of Alba in Colias croceus to a transposable element insertion downstream of the Colias homolog of BarH-1 We use CRISPR/Cas9 to validate BarH-1’s functional role in the wing color switch and antibody staining confirms expression differences in the scale building cells of pupal wings We use scanning electron microscopy to determine that BarH-1 expression in the wings causes a reduction in pigment granules within wing scales, and thereby gives rise to the white color Further lipid and transcriptome analyses reveal additional physiological differences that arise due to the Alba, suggesting pleiotropic effects beyond the wing color While male-limited ALHS are well documented, comparatively few examples of female-limited ALHS are known This is either due to biological reality or our lack of understanding of how ALHS manifest in females, highlighting the need for mechanistic insights, as none currently exist These findings provide, to our knowledge, the first known mechanism for a female ALHS and support an alternative view of color polymorphism as indicative of pleiotropic effects with life history consequences

https://biorxiv.org/content/biorxiv/early/2018/09/24/424879.full-text.pdf

A female alternative life-history strategy arose via novel recruitment of homeobox gene, BarH-1

Tradeoffs affect resource allocation during development and result in fitness consequences that drive the evolution of life history strategies. Yet despite their importance, we know little about the mechanisms underlying life history tradeoffs in wild populations. Many species of Colias butterflies exhibit an alternative life history strategy (ALHS) where females divert resources from wing pigment synthesis to reproductive and somatic development. Due to this reallocation, a wing color polymorphism is associated with the ALHS: individuals have either yellow/orange or white wings. Here we map the genetic basis of the ALHS switch in Colias crocea to a transposable element insertion downstream of the Colias homolog of BarH-1, a homeobox transcription factor. Using CRISPR/Cas9 gene editing, antibody staining, and electron microscopy we find morph-specific specific expression of BarH-1 suppresses the formation of pigment granules in wing scales. Lipid and transcriptome analyses reveal physiological differences associated with the ALHS. These findings characterize a novel mechanism for a female-limited ALHS and show that the switch arises via recruitment of a transcription factor previously known for its function in cell fate determination in pigment cells of the retina.

/pdf/a-transposable-element-insertion-is-the-switch-between-oxfmaim59w.pdf

Michael Perry

Papers

Book reviewSurgical approaches to the facial skeleton, 2nd edition, Edward Ellis III, Michael F. Zide, Lippincott Williams & Wilkins, 2 edition (December 1, 2005) ISBN-10: 0781754992, ISBN-13: 978-0781754996

A female alternative life-history strategy arose via novel recruitment of homeobox gene, BarH-1

A transposable element insertion is the switch between alternative life history strategies

The Inclusion of Mandibular Condyles in Orthopantomogram radiographs for Trauma cases: a retrospective audit at a Regional Maxillofacial Unit

Iliac bone grafts for orbital wall reconstruction.