Faculty Opinions recommendation of A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes.

Abstract Background As one of the novel molecules, circRNA has been identified closely involved in the pathogenesis of many diseases. However, the function of circRNA in acute myeloid leukemia (AML) still remains unknown. Methods In the current study, the RNA expression profiles were obtained from Gene Expression Omnibus (GEO) datasets. The differentially expressed RNAs were identified using R software and the competing endogenous RNA (ceRNA) network was constructed using Cytoscape. Functional and pathway enrichment analyses were performed to identify the candidate circRNA-mediated aberrant signaling pathways. The hub genes were identified by MCODE and CytoHubba plugins of Cytoscape, and then a subnetwork regulatory module was established. Results A total of 27 circRNA-miRNA pairs and 208 miRNA-mRNA pairs, including 12 circRNAs, 24 miRNAs and 112 mRNAs were included in the ceRNA network. Subsequently, a subnetwork, including 4 circRNAs, 5 miRNAs and 6 mRNAs, was established based on related circRNA-miRNA-mRNA regulatory modules. Conclusions In summary, this work analyzes the characteristics of circRNA as competing endogenous RNA in AML pathogenesis, which would provide hints for developing novel prognostic, diagnostic and therapeutic strategy for AML.

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Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa

Nature Communications ◽

10.1038/s41467-021-22821-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Mary Elizabeth Mathyer ◽

Erin A. Brettmann ◽

Alina D. Schmidt ◽

Zane A. Goodwin ◽

Inez Y. Oh ◽

...

Keyword(s):

Selective Sweep ◽

Skin Barrier ◽

Human Migration ◽

Epidermal Differentiation ◽

Human Populations ◽

Epidermal Differentiation Complex ◽

Regulatory Module ◽

Reporter Assays ◽

Out Of Africa

AbstractThe genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.

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Dog colour patterns explained by modular promoters of ancient canid origin

Nature Ecology & Evolution ◽

10.1038/s41559-021-01524-x ◽

2021 ◽

Author(s):

Danika L. Bannasch ◽

Christopher B. Kaelin ◽

Anna Letko ◽

Robert Loechel ◽

Petra Hug ◽

...

Keyword(s):

Colour Pattern ◽

Hair Cycle ◽

Temporal And Spatial Distribution ◽

Multiple Alleles ◽

Haplotype Combination ◽

Regulatory Modules ◽

Regulatory Module ◽

Temporal And Spatial ◽

Selection For ◽

Colour Patterns

AbstractDistinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.

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Cis regulatory module discovery in immune cell development

Proceedings of the International Symposium on Biocomputing - ISB '10 ◽

10.1145/1722024.1722039 ◽

2010 ◽

Author(s):

Satishkumar Ranganathan Ganakammal ◽

Mark H. Kaplan ◽

Narayanan B. Perumal

Keyword(s):

Immune Cell ◽

Cell Development ◽

Regulatory Module ◽

Module Discovery

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The LARGE2-APO1/APO2 regulatory module controls panicle size and grain number in rice

The Plant Cell ◽

10.1093/plcell/koab041 ◽

2021 ◽

Author(s):

Luojiang Huang ◽

Kai Hua ◽

Ran Xu ◽

Dali Zeng ◽

Ruci Wang ◽

...

Keyword(s):

Agronomic Traits ◽

Loss Of Function ◽

Grain Number ◽

Hect Domain ◽

Regulatory Module ◽

Promising Target ◽

Meristematic Activity ◽

Positive Regulators ◽

Genetic Mechanisms ◽

Biochemical Analyses

Abstract Panicle size and grain number are important agronomic traits and influence grain yield in rice (Oryza sativa), but the molecular and genetic mechanisms underlying panicle size and grain number control remain largely unknown in crops. Here we report that LARGE2 encodes a HECT-domain E3 ubiquitin ligase OsUPL2 and regulates panicle size and grain number in rice. The loss of function large2 mutants produce large panicles with increased grain number, wide grains and leaves, and thick culms. LARGE2 regulates panicle size and grain number by repressing meristematic activity. LARGE2 is highly expressed in young panicles and grains. Biochemical analyses show that LARGE2 physically associates with ABERRANT PANICLE ORGANIZATION1 (APO1) and APO2, two positive regulators of panicle size and grain number, and modulates their stabilities. Genetic analyses support that LARGE2 functions with APO1 and APO2 in a common pathway to regulate panicle size and grain number. These findings reveal a novel genetic and molecular mechanism of the LARGE2-APO1/APO2 module-mediated control of panicle size and grain number in rice, suggesting that this module is a promising target for improving panicle size and grain number in crops.

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