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Topic Review
Cupriavidus metallidurans CH34
Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 50 end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.
  • 1.3K
  • 14 Sep 2020
Topic Review
Megalencephaly-Polymicrogyria-Polydactyly-Hydrocephalus Syndrome
Megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome is a rare disorder that primarily affects the development of the brain.
  • 1.3K
  • 23 Dec 2020
Topic Review
Regulatory SNPs
Regulatory SNPs are genetic variants that associated with various human traits and diseases map to a noncoding part of the genome and are enriched in its regulatory compartment, suggesting that many causal variants may affect gene expression. The leading mechanism of action of these SNPs consists in the alterations in the transcription factor binding via creation or disruption of transcription factor binding sites (TFBSs) or some change in the affinity of these regulatory proteins to their cognate sites.
  • 1.3K
  • 29 Jun 2021
Topic Review
ADPEAF
Autosomal dominant partial epilepsy with auditory features (ADPEAF) is an uncommon form of epilepsy that runs in families. This disorder causes seizures usually characterized by sound-related (auditory) symptoms such as buzzing, humming, or ringing.
  • 1.3K
  • 04 Jan 2021
Topic Review
Tumor Heterogeneity in ESCC
Esophageal squamous cell carcinoma (ESCC) is a common and aggressive malignancy, with hitherto dismal clinical outcome. Genomic analyses of patient samples reveal a complex heterogeneous landscape for ESCC, which presents in both intertumor and intratumor forms, manifests at both genomic and epigenomic levels, and contributes significantly to tumor evolution, drug resistance, and metastasis.
  • 1.3K
  • 12 Oct 2021
Topic Review
Genome Editing Among Bioethics and Regulatory Practices
In the last decade, genome editing technologies became very effective and several clinical trials have been started in order to use them for treating some genetic diseases. Interestingly, despite more than 50 years of discussion about the frontiers of genetics in human health and evolution, the debate about the bioethics and the regulatory practices of genome editing is still far from satisfactory answers. This delay results from an excessive emphasis on the effectiveness of the genome editing technologies that is relevant for the regulatory practices, but not at a bioethical level. Indeed, other factors (such as accessibility and acceptability) could make these techniques not accepted at the bioethical level, even in the presence of their 100% effectiveness.
  • 1.3K
  • 31 Dec 2021
Topic Review
STRC Gene
Stereocilin: The STRC gene provides instructions for making a protein called stereocilin. 
  • 1.3K
  • 24 Dec 2020
Topic Review
Hand-Foot-Genital Syndrome
Hand-foot-genital syndrome is a rare condition that affects the development of the hands and feet, the urinary tract, and the reproductive system.
  • 1.3K
  • 23 Dec 2020
Topic Review
Congenital Hypothyroidism
Congenital hypothyroidism is a partial or complete loss of function of the thyroid gland (hypothyroidism) that affects infants from birth (congenital). The thyroid gland is a butterfly-shaped tissue in the lower neck. It makes iodine-containing hormones that play an important role in regulating growth, brain development, and the rate of chemical reactions in the body (metabolism). People with congenital hypothyroidism have lower-than-normal levels of these important hormones.
  • 1.3K
  • 07 Apr 2023
Topic Review
Chromosome 21
Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 21, one copy inherited from each parent, form one of the pairs.
  • 1.3K
  • 24 Dec 2020
Topic Review
ECM1 Gene
Extracellular matrix protein 1
  • 1.3K
  • 24 Dec 2020
Topic Review
PIWI-interacting RNAs
A set of key regulators whose function still needs to be fully elucidated are small non-coding RNAs (sncRNAs). Due to their broad range of unfolding functions in the regulation of gene expression during transcription and translation, sncRNAs are becoming vital to many cellular processes. Within the past decade, a novel class of sncRNAs called PIWI-interacting RNAs (piRNAs) have been implicated in various diseases, and understanding their complete function is of vital importance. Compounding evidence suggests that piRNAs encompass a wider functional range than small interfering RNAs (siRNAs) and microRNAs (miRNAs), which have been studied more in terms of cellular homeostasis and disease.
  • 1.3K
  • 11 Jun 2021
Topic Review
Actin-accumulation Myopathy
Actin-accumulation myopathy is a disorder that primarily affects skeletal muscles, which are muscles that the body uses for movement. People with actin-accumulation myopathy have severe muscle weakness (myopathy) and poor muscle tone (hypotonia) throughout the body. Signs and symptoms of this condition are apparent in infancy and include feeding and swallowing difficulties, a weak cry, and difficulty with controlling head movements. Affected babies are sometimes described as "floppy" and may be unable to move on their own.
  • 1.3K
  • 23 Dec 2020
Topic Review
22q11.2 Microdeletion
Chromosomal 22q11.2 deletion syndrome (22q11.2DS) (ORPHA:567) caused by microdeletion in chromosome 22 is the most common chromosomal microdeletion disorder in humans. Despite the same change on the genome level like in case of monozygotic twins, phenotypes are expressed differently in 22q11.2 deletion individuals. The rest of the genome, as well as epigenome and environmental factors, are not without influence on the variability in phenotypes. The penetrance seems to be more genotype-specific than deleted locus-specific. The transcript levels of deleted genes are not usually reduced by 50% as assumed due to haploinsufficiency. 22q11.2DS is often undiagnosed condition, as each patient may have a different set out of 180 possible clinical manifestations. Diverse dysmorphic traits are present in patients from different ethnicities, which makes diagnosis even more difficult. 22q11.2 deletion syndrome serve as an example of genetic syndrome that is not easy to manage at all stages: diagnosis, consulting and dealing with.
  • 1.3K
  • 08 Sep 2020
Topic Review
Smith-Kingsmore Syndrome
Smith-Kingsmore syndrome is a neurological disorder characterized by a head that is larger than normal (macrocephaly), intellectual disability, and seizures.
  • 1.3K
  • 25 Dec 2020
Topic Review
1q21.1 Microdeletion
1q21.1 microdeletion is a chromosomal change in which a small piece of chromosome 1 is deleted in each cell. The deletion occurs on the long (q) arm of the chromosome in a region designated q21.1. This chromosomal change increases the risk of delayed development, intellectual disability, physical abnormalities, and neurological and psychiatric problems. However, some people with a 1q21.1 microdeletion do not appear to have any associated features.
  • 1.3K
  • 23 Dec 2020
Topic Review
Vitiligo
Vitiligo is a condition that causes patchy loss of skin coloring (pigmentation). The average age of onset of vitiligo is in the mid-twenties, but it can appear at any age. It tends to progress over time, with larger areas of the skin losing pigment. Some people with vitiligo also have patches of pigment loss affecting the hair on their scalp or body.
  • 1.3K
  • 04 Jan 2021
Topic Review
X-linked adrenal Hypoplasia Congenita
X-linked adrenal hypoplasia congenita is a disorder that mainly affects males. It involves many hormone-producing (endocrine) tissues in the body, particularly a pair of small glands on top of each kidney called the adrenal glands. These glands produce a variety of hormones that regulate many essential functions in the body.
  • 1.3K
  • 24 Dec 2020
Topic Review
Poly ADP-Ribose Polymerases
Poly ADP-ribose polymerases (PARP) are specialized enzymes that catalyze the addition of ADP ribose units from “nicotinamide adenine dinucleotide-donor molecules” to their target substrates.
  • 1.3K
  • 02 Jul 2021
Topic Review
Interstitial Telomeric-like Repeats (ITR)
Interstitial telomeric repeat (ITR) sites, also known as interstitial telomeric sequences (ITSs), consist of tandem repeats of telomeric motifs that are located within intrachromosomal regions, including repeats located close to the centromeres and the ones found between the centromeres and the telomeres.
  • 1.3K
  • 10 Dec 2021
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