De Novo ACTG1 Variant Expands the Phenotype and Genotype of Partial Deafness and Baraitser–Winter Syndrome

Actin molecules are fundamental for embryonic structural and functional differentiation; γ-actin is specifically required for the maintenance and function of cytoskeletal structures in the ear, resulting in hearing. Baraitser–Winter Syndrome (B-WS, OMIM #243310, #614583) is a rare, multiple-anomaly genetic disorder caused by mutations in either cytoplasmically expressed actin gene, ACTB (β-actin) or ACTG1 (γ-actin). The resulting actinopathies cause characteristic cerebrofrontofacial and developmental traits, including progressive sensorineural deafness. Both ACTG1-related non-syndromic A20/A26 deafness and B-WS diagnoses are characterized by hypervariable penetrance in phenotype. Here, we identify a 28th patient worldwide carrying a mutated γ-actin ACTG1 allele, with mildly manifested cerebrofrontofacial B-WS traits, hypervariable penetrance of developmental traits and sensorineural hearing loss. This patient also displays brachycephaly and a complete absence of speech faculty, previously unreported for ACTG1-related B-WS or DFNA20/26 deafness, representing phenotypic expansion. The patient’s exome sequence analyses (ES) confirms a de novo ACTG1 variant previously unlinked to the pathology. Additional microarray analysis uncover no further mutational basis for dual molecular diagnosis in our patient. We conclude that γ-actin c.542C > T, p.Ala181Val is a dominant pathogenic variant, associated with mildly manifested facial and cerebral traits typical of B-WS, hypervariable penetrance of developmental traits and sensorineural deafness. We further posit and present argument and evidence suggesting ACTG1-related non-syndromic DFNA20/A26 deafness is a manifestation of undiagnosed ACTG1-related B-WS.

In Silico Analysis of Actin Gene as a Candidate for DNA Non-Halal Detection Base on Real-Time PCR

Actin genes are genes that are common in organisms, and their expression is constitutive. These genes are used for gene normalization and internal control of DNA extraction, but the actin gene is not widely used for halal certification tests. Bioinformatic studies help to analyze the experiment through in silico more deeply before the experiment is carried out in laboratory, making it more efficient and time effective. uMelt is an analysis to predict the melting curve of target amplification in real-time PCR. Real-time PCR has been widely used for screening and detection of pork content in a product. This research aimed to explore actin gene as a candidate for testing pork using qPCR. The study was carried out in two main stages, namely alignment of the DNA sequence and analysis of the melting curve using the uMelt approach. The results showed a set of actin genes containing conserved regions that can be used as degenerate primers with different family-type coverages. Melting curve prediction with uMelt shows differences in tm peaks so as the types of samples can be easily identified. The use of bioinformatic applications such as uMelt helps in the simulation of predicting the melting curve to increase the precision of the analysis.

The Development and Optimization of Primer Sets Used to Study the Relative Expression of Androgen Receptor Gene in Turkey (Meleagris gallopavo)

The Androgen Receptor (AR) Gene’s expression is essential during puberty and testes maturation, which is also used as a reference for Turkey’s breeding program. Therefore, this study aims to develop and optimize two primer sets for studying relative expression using qPCR technology. The primers were designed to amplify specific regions in the AR gene as the main target, and the β-actin gene as an internal control. They were tested using in-silico and amplicon sequencing, as well as efficiency calculation with a constructed standard curve from serially diluted reactions. Based on the sequencing methods, the primers amplified the corresponding regions of the respective targets. The primer for AR gene had an efficiency of 98.03%, a slope of -3.37, and an R2 of 0.995, while that of the β-actin gene had an efficiency of 98.01%, a slope of -3.371, and an R2 of 0.999. The two efficiencies exceeded the standard (93 -103%) value and the melting curve analysis showed that no non-specific amplification was discovered for both primers. According to the tests, the primers are suggested as acceptable to be used for the relative expression study of the AR gene in Turkey.

Genomic Amplification and Functional Dependency of the Gamma Actin Gene ACTG1 in Uterine Cancer

Sarcomere and cytoskeleton genes, or actomyosin genes, regulate cell biology including mechanical stress, cell motility, and cell division. While actomyosin genes are recurrently dysregulated in cancers, their oncogenic roles have not been examined in a lineage-specific fashion. In this report, we investigated dysregulation of nine sarcomeric and cytoskeletal genes across 20 cancer lineages. We found that uterine cancers harbored the highest frequencies of amplification and overexpression of the gamma actin gene, ACTG1. Each of the four subtypes of uterine cancers, mixed endometrial carcinomas, serous carcinomas, endometroid carcinomas, and carcinosarcomas harbored between 5~20% of ACTG1 gene amplification or overexpression. Clinically, patients with ACTG1 gains had a poor prognosis. ACTG1 gains showed transcriptional patterns that reflect activation of oncogenic signals, repressed response to innate immunity, or immunotherapy. Functionally, the CRISPR-CAS9 gene deletion of ACTG1 had the most robust and consistent effects in uterine cancer cells relative to 20 other lineages. Overall, we propose that ACTG1 regulates the fitness of uterine cancer cells by modulating cell-intrinsic properties and the tumor microenvironment. In summary, the ACTG1 functions relative to other actomyosin genes support the notion that it is a potential biomarker and a target gene in uterine cancer precision therapies.

Phototaxis of the Unicellular Red Alga Cyanidioschyzon merolae Is Mediated by Novel Actin-Driven Tentacles

Phototaxis, which is the ability to move towards or away from a light source autonomously, is a common mechanism of unicellular algae. It evolved multiple times independently in different plant lineages. As of yet, algal phototaxis has been linked mainly to the presence of cilia, the only known locomotive organelle in unicellular algae. Red algae (Rhodophyta), however, lack cilia in all stages of their life cycle. Remarkably, multiple unicellular red algae like the extremophile Cyanidioschyzon merolae (C. merolae) can move towards light. Remarkably, it has remained unclear how C. merolae achieves movement, and the presence of a completely new mechanism has been suggested. Here we show that the basis of this movement are novel retractable projections, termed tentacles due to their distinct morphology. These tentacles could be reproducibly induced within 20 min by increasing the salt concentration of the culture medium. Electron microscopy revealed filamentous structures inside the tentacles that we identified to be actin filaments. This is surprising as C. merolae’s single actin gene was previously published to not be expressed. Based on our findings, we propose a model for C. merolae’s actin-driven but myosin-independent motility. To our knowledge, the described tentacles represent a novel motility mechanism.

OPTIMASI SUHU ANNEALING UNTUK AMPLIFIKASI GEN AKTIN PADA PANDAN (Pandanus sp)

ABSTRACT Genes expression information involved in Pandanus sp. adaptation in Kajuik Lake sp. to environmental stress is unknown. The genes expression analysis requires the internal control gene such as actin. Actin gene is one of the genes that can be expressed continuously at all stages of plant development. Before obtaining genetic information, it is necessary to isolate and amplify DNA. The purpose of this study was to determine the annealing temperature for actin gene amplification in Pandan (Pandanus sp.). The DNA amplification uses two primer pairs with 20 annealing temperatures. The annealing temperatures were calculated based on the mean values of Tm which were then reduced and added with 5, 4, 3, 2 and 1. The annealing temperature of 53.4 ºC (Tm +1) yielded single thick clear using. The annealing temperature of 53.4 ºC (Tm +1) using P_act_F / P_act_R1 primer pair yielded single, thick and firm DNA band. It was concluded that the annealing temperature for actinin gene amplification in Pandanussp was 53.4 ºC with primer P_act_F / P_act_R1. Keywords: Actin gene, Annealing temperatures, PCR

Giant viruses encode novel types of actins possibly related to the origin of eukaryotic actin: the viractins

Actin is a major component of the eukaryotic cytoskeleton. Many related actin homologues can be found in eukaryotes1, some of them being present in most or all eukaryotic lineages. The gene repertoire of the Last Eukaryotic Common Ancestor (LECA) therefore would have harbored both actin and various actin-related proteins (ARPs). A current hypothesis is that the different ARPs originated by gene duplication in the proto-eukaryotic lineage from an actin gene that was inherited from Asgard archaea. Here, we report the first detection of actin-related genes in viruses (viractins), encoded by 19 genomes belonging to the Imitervirales, a viral order encompassing the giant Mimiviridae. Most viractins were closely related to the actin, contrasting with actin-related genes of Asgard archaea and Bathyarchaea (a newly discovered clade). Our phylogenetic analysis suggests viractins could have been acquired from proto-eukaryotes and possibly gave rise to the conventional eukaryotic actin after being reintroduced into the pre-LECA eukaryotic lineage.

The 5’ regulatory region of the β actin gene in Clarias species is complex and variable in relation to ecological needs

The β actin gene is involved in various cellular housekeeping processes including transcription, mRNA processing, cell signaling and chromosome remodeling. For regulating the expression of this gene under different environmental conditions, the promoter region of the β actin gene is structurally dynamic with multiple regulatory features in the upstream region. Most previous information about the 5’ regulatory region of the β actin gene has been limited to in vitro laboratory experiments. Considering the need for functional versatility of expression of this gene in the Catfish Clarias batrachus in different environments, here we have analyzed the 5’ regulatory region of β actin and identified numerous elements that are variable. We have made comparisons of individuals from three populations found in three different diverse ecological systems, as well as in three sister species, to elucidate its structural diversity. Our results show that the 5’ regulatory region has considerable diversity and changes in architecture with respect Cis-acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5’ regulatory region of a housekeeping gene like β actin, modify its architecture as per the environmental conditions. These modifications specifically includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5’ regulatory region is conserved which was yet not highlighted.Author summaryPromoter is a regulatory region where the basal transcription machinery assembles to initiate the process of transcription. It plays crucial role in controlling the gene expression. The 5’ regulatory region includes TATA box, CAAT box, GC box and Cis -acting regulatory elements. Most previous information about the 5’ regulatory region of the β actin gene has been limited to in vitro laboratory experiments. Our study results show that the 5’ regulatory region has considerable diversity and changes in architecture with respect Cis-acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5’ regulatory region of a housekeeping gene like β actin, modify its architecture as per the environmental requirements. These modifications precisely includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5’ regulatory region is conserved. These findings clearly define a novel role of promotor of β actin gene which was yet not highlighted. These findings can broaden our understanding in linking TF in 5’ regulatory regions to a specific environmental variable/disease conditions. This may become a simple strategy in understanding complex gene-environment interactions.