scholarly journals Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens

2018 ◽  
Author(s):  
Bhaven B. Patel ◽  
Andres M. Lebensohn ◽  
Jan E. Carette ◽  
Julia Salzman ◽  
Rajat Rohatgi
Keyword(s):  
Gene Expression ◽  
Wnt Signaling ◽  
Insertional Mutagenesis ◽  
Bioinformatics Analysis ◽  
Regulatory Elements ◽  
Gene Trap ◽  
Genetic Screens ◽  
Control Gene ◽  
Protein Coding ◽  
Control Gene Expression

AbstractThe systematic identification of regulatory elements that control gene expression remains a challenge. Genetic screens that use untargeted mutagenesis have the potential to identify protein-coding genes, non-coding RNAs and regulatory elements, but their analysis has mainly focused on identifying the former two. To identify regulatory elements, we conducted a new bioinformatics analysis of insertional mutagenesis screens interrogating WNT signaling in haploid human cells. We searched for specific patterns of retroviral gene trap integrations (used as mutagens in haploid screens) in short genomic intervals overlapping with introns and regions upstream of genes. We uncovered atypical patterns of gene trap insertions that were not predicted to disrupt coding sequences, but caused changes in the expression of two key regulators of WNT signaling, suggesting the presence of cis-regulatory elements. Our methodology extends the scope of haploid genetic screens by enabling the identification of regulatory elements that control gene expression.

scholarly journals Cis-regulatory elements used to control gene expression in plants

2016 ◽  
Vol 127 (2) ◽  
pp. 269-287 ◽  
Author(s):  
Róża Biłas ◽  
Katarzyna Szafran ◽  
Katarzyna Hnatuszko-Konka ◽  
Andrzej K. Kononowicz
Keyword(s):  
Gene Expression ◽  
Regulatory Elements ◽  
Control Gene ◽  
Control Gene Expression

scholarly journals Virus-Induced Changes in mRNA Secondary Structure Uncover cis-Regulatory Elements that Directly Control Gene Expression

2018 ◽  
Vol 72 (5) ◽  
pp. 862-874.e5 ◽  
Author(s):  
Orel Mizrahi ◽  
Aharon Nachshon ◽  
Alina Shitrit ◽  
Idit A. Gelbart ◽  
Martina Dobesova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Secondary Structure ◽  
Regulatory Elements ◽  
Mrna Secondary Structure ◽  
Control Gene ◽  
Control Gene Expression ◽  
Induced Changes

scholarly journals Src acts with WNT/FGFRL signaling to pattern the planarian anteroposterior axis

2021 ◽  
Author(s):  
Nicolle A. Bonar ◽  
David I. Gittin ◽  
Christian P. Petersen
Keyword(s):  
Gene Expression ◽  
Wnt Signaling ◽  
Posterior Pole ◽  
Control Gene ◽  
Downstream Signaling ◽  
Control Gene Expression ◽  
Signaling Mechanisms ◽  
Positional System ◽  
Canonical Wnt ◽  
Positional Control

Tissue identity determination is critical for regeneration, and the planarian anteroposterior (AP) axis uses positional control genes expressed from bodywall muscle to determine body regionalization. Canonical Wnt signaling establishes anterior versus posterior pole identities through notum and wnt1 signaling, and two Wnt/FGFRL signaling pathways control head and trunk domains, but their downstream signaling mechanisms are not fully understood. Here we identify a planarian Src homolog that restricts head and trunk identities to anterior positions. src-1(RNAi) animals formed enlarged brains and ectopic eyes and also duplicated trunk tissue, similar to a combination of Wnt/FGFRL RNAi phenotypes. src-1 was required for establishing territories of positional control gene expression, indicating it acts at an upstream step in patterning the AP axis. Double RNAi experiments and eye regeneration assays suggest src-1 can act in parallel to at least some Wnt and FGFRL factors. Co-inhibition of src-1 with other posterior-promoting factors led to dramatic patterning changes and a reprogramming of Wnt/FGFRLs into controlling new positional outputs. These results identify src-1 as a factor that promotes robustness of the AP positional system that instructs appropriate regeneration.

Building the heart piece by piece: modularity of cis-elements regulating Nkx2-5 transcription

Development ◽  
1999 ◽  
Vol 126 (19) ◽  
pp. 4187-4192 ◽  
Author(s):  
R.J. Schwartz ◽  
E.N. Olson
Keyword(s):  
Gene Expression ◽  
Homeobox Gene ◽  
Regulatory Elements ◽  
Mouse Heart ◽  
Cis Elements ◽  
Control Gene ◽  
Control Gene Expression ◽  
Developing Heart ◽  
Heart Formation ◽  
Vertebrate Embryos

Heart formation in Drosophila is dependent on the homeobox gene tinman. The homeobox gene Nkx2-5 is closely related to tinman and is the earliest known marker for cardiogenesis in vertebrate embryos. Recent studies of cis-regulatory elements required for Nkx2-5 expression in the developing mouse heart have revealed an extraordinary array of independent cardiac enhancers, and associated negative regulatory elements, that direct transcription in distinct regions of the embryonic heart. These studies demonstrate the modularity in cardiac transcription, in which different regulatory elements respond to distinct sets of transcription factors to control gene expression in different compartments of the developing heart. We consider the potential mechanisms underlying such transcriptional complexity, its possible significance for cardiac function, and the implications for evolution of the multichambered heart.

scholarly journals The central role of RNA in the genetic programming of complex organisms

2010 ◽  
Vol 82 (4) ◽  
pp. 933-939 ◽  
Author(s):  
John S. Mattick
Keyword(s):  
Gene Expression ◽  
Control Gene ◽  
Animal Kingdom ◽  
Protein Coding ◽  
Coding Sequences ◽  
Protein Coding Genes ◽  
Control Gene Expression ◽  
Large Numbers ◽  
The Brain

Notwithstanding lineage-specific variations, the number and type of protein-coding genes remain relatively static across the animal kingdom. By contrast there has been a massive expansion in the extent of genomic non-proteincoding sequences with increasing developmental complexity. These non-coding sequences are, in fact, transcribed in a regulated manner to produce large numbers of large and small non-protein-coding RNAs that control gene expression at many levels including chromatin architecture, post-transcriptional processing and translation. Moreover, many RNAs are edited, especially in the nervous system, which may be the basis of epigenome-environment interactions and the function of the brain.

scholarly journals Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

2019 ◽  
Author(s):  
Claudia Racioppi ◽  
Keira A Wiechecki ◽  
Lionel Christiaen
Keyword(s):  
Gene Expression ◽  
Specific Activity ◽  
Expression Profiles ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Control Gene ◽  
Specific Expression ◽  
Pharyngeal Muscle ◽  
Control Gene Expression ◽  
Multipotent Progenitors

ABSTRACTIn embryos, lineage-specific profiles of chromatin accessibility control gene expression by modulating transcription, and thus impact multipotent progenitor states and subsequent fate choices. Subsets of cardiac and pharyngeal/head muscles share a common origin in the cardiopharyngeal mesoderm, but the chromatin landscapes that govern multipotent progenitors’ competence and early fate choices remain largely elusive. Here, we leveraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereotyped transitions from naive Mesp+ mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors. An FGF-Foxf pathway acts in multipotent progenitors to establish cardiopharyngeal-specific patterns of accessibility, which govern later heart vs. pharyngeal muscle-specific expression profiles, demonstrating extensive spatiotemporal decoupling between early cardiopharyngeal enhancer accessibility and late cell-type-specific activity. Combinations of cis-regulatory elements with distinct chromatin accessibility profiles are required to activate of Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that this higher order combinatorial logic increases the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity, thus fostering spatially and temporally accurate fate choices.

scholarly journals Epigenetics, Wnt signaling, and stem cells: the Pygo2 connection

2009 ◽  
Vol 185 (5) ◽  
pp. 761-763 ◽  
Author(s):  
Valerie Horsley
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Wnt Signaling ◽  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Mammary Epithelial ◽  
Epigenetic Mechanisms ◽  
Control Gene ◽  
Epithelial Stem Cells ◽  
Control Gene Expression

Stem cells use both transcriptional and epigenetic mechanisms to control gene expression and regulate tissue development and homeostasis. In this issue, Gu et al. (Gu, B., P. Sun, Y. Yuan, R.C. Moraes, A. Li, A. Teng, A. Agrawal, C. Rhéaume, V. Bilanchone, J.M. Veltmaat, et al. 2009. J. Cell Biol. 185:811–826) reveal an important link between these two mechanisms in mammary epithelial stem cells by showing that transcriptional activation of β-catenin downstream of Wnt signaling can be regulated epigenetically through a chromatin remodeling factor, Pygo2.

LEC1 (NF-YB9) directly interacts with LEC2 to control gene expression in seed

2018 ◽  
Vol 1861 (5) ◽  
pp. 443-450 ◽  
Author(s):  
C. Boulard ◽  
J. Thévenin ◽  
O. Tranquet ◽  
V. Laporte ◽  
L. Lepiniec ◽  
...  
Keyword(s):  
Gene Expression ◽  
Control Gene ◽  
Control Gene Expression

scholarly journals Nonhistone Proteins Control Gene Expression in Reconstituted Chromatin

1974 ◽  
Vol 71 (12) ◽  
pp. 5057-5061 ◽  
Author(s):  
T. Barrett ◽  
D. Maryanka ◽  
P. H. Hamlyn ◽  
H. J. Gould
Keyword(s):  
Gene Expression ◽  
Control Gene ◽  
Nonhistone Proteins ◽  
Control Gene Expression

scholarly journals A Quantitative Optogenetic Tool to Control Gene Expression during Embryonic Development

2021 ◽  
Vol 120 (3) ◽  
pp. 354a
Author(s):  
Anand P. Singh ◽  
Ping Wu ◽  
Eric F. Wieschaus ◽  
Jared E. Toettcher ◽  
Thomas Gregor
Keyword(s):  
Gene Expression ◽  
Embryonic Development ◽  
Control Gene ◽  
Control Gene Expression
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