MyMedR

Fulltext Complete Genome Sequence of Lignin-Degrading Streptomyces sp. Strain S6, Isolated from an Oil Palm Plantation in Malaysia

Yusof N, Abdullah Tahir A, Riyadi FA, Ahmad Sabri NS, Md Akhir FN, Othman N, et al.

Microbiol Resour Announc, 2020 Jan 30;9(5).

PMID: 32001560 DOI: 10.1128/MRA.01332-19

Streptomyces spp. are bacteria that are responsible for the degradation of aromatic compounds and produce secondary metabolites. Here, we present a complete genome sequence of Streptomyces sp. strain S6, which was isolated from an oil palm plantation, with a 7.8-Mbp liner chromosome, a GC content of 72%, and 4,266 coding sequences.

Matched MeSH terms: Exons

Fulltext Rare homozygous PRKN exon 8 and 9 deletion in Malay familial early-onset Parkinson's disease

Tay YW, Lim JL, Tan AH, Annuar AA, Lim SY

Ann Acad Med Singap, 2021 04;50(4):353-355.

PMID: 33990826 DOI: 10.47102/annals-acadmedsg.2020508

Matched MeSH terms: Exons/genetics

Choice of PCR microtube can impact on the success of long-range PCRs

Chua EW, Miller AL, Kennedy MA

Anal Biochem, 2015 May 15;477:115-7.

PMID: 25766577 DOI: 10.1016/j.ab.2015.02.023

We compared four brands of microtubes with respect to their suitability for long-range polymerase chain reactions (PCRs). One of the four brands was found to have an inhibitory effect, decreasing PCR yields. The effect was universal across different PCR or enzyme systems. Increased ultraviolet absorbance suggests leaching of unknown chemical species into PCR mixtures. However, this could not be confirmed by high-performance liquid chromatography-mass spectrometry analysis. Nevertheless, our article demonstrates a clear impact of the choice of microtubes on long-range PCR success. Due consideration should be given to the PCR microtubes when determining optimal reaction conditions for long-range PCR.

Matched MeSH terms: Exons/genetics

Fulltext Biological impact of mutually exclusive exon switching

Lam SD, Babu MM, Lees J, Orengo CA

PLoS Comput Biol, 2021 03;17(3):e1008708.

PMID: 33651795 DOI: 10.1371/journal.pcbi.1008708

Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch homologous exons and what are their biological impact? Here, we analyse the extent of sequence, structural and functional variability in MXEs and report the first large scale, structure-based analysis of the biological impact of MXE events from different genomes. MXE-specific residues tend to map to single domains, are highly enriched in surface exposed residues and cluster at or near protein functional sites. Thus, MXE events are likely to maintain the protein fold, but alter specificity and selectivity of protein function. This comprehensive resource of MXE events and their annotations is available at: http://gene3d.biochem.ucl.ac.uk/mxemod/. These findings highlight how small, but significant changes at critical positions on a protein surface are exploited in evolution to alter function.

Matched MeSH terms: Exons/genetics*

Fulltext Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2

Tharek M, Sim KS, Khairuddin D, Ghazali AH, Najimudin N

Genome Announc, 2017 May 11;5(19).

PMID: 28495774 DOI: 10.1128/genomeA.00305-17

Escherichia coli strain USML2 was originally isolated from the inner leaf tissues of surface-sterilized phytopathogenic-free oil palm (Elaeis guineensis Jacq.). We present here the whole-genome sequence of this plant-endophytic strain. The genome consists of a single circular chromosome of 4,502,758 bp, 4,315 predicted coding sequences, and a G+C content of 50.8%.

Matched MeSH terms: Exons

Identification of a recurrent BRCA1 exon 21-22 genomic rearrangement in Malay breast cancer patients

Hasmad HN, Sivanandan K, Lee V, Yip CH, Mohd Taib NA, Teo SH

Clin Genet, 2015 Apr;87(4):392-4.

PMID: 25066186 DOI: 10.1111/cge.12451

Matched MeSH terms: Exons/genetics

HLA-B*15:349:02, a novel variant of HLA-B*15, discovered in a Singaporean Malay bone marrow donor

Cho L, Kaur A, Cereb N, Lin PY, Yang KL

HLA, 2020 09;96(3):344-345.

PMID: 32212215 DOI: 10.1111/tan.13879

One nucleotide substitution in codon 112 of HLA-B*15:349:01 results in a novel allele, HLA-B*15:349:02.

Matched MeSH terms: Exons/genetics

HLA-DQB1*06:132, an HLA-DQB1*06 variant, discovered in a Singaporean Malay bone marrow donor

Cho L, Kaur A, Cereb N, Lin PY, Yang KL

HLA, 2020 08;96(2):243-244.

PMID: 32250029 DOI: 10.1111/tan.13889

One nucleotide substitution in codon 38 of HLA-DQB1*06:01:01:01 results in a novel allele, HLA-DQB1*06:132.

Matched MeSH terms: Exons/genetics

HLA-DQB1*05:66:01, a novel variant of HLA-DQB1*05, identified in a Singaporean Malay bone marrow donor

Cho L, Kaur A, Cereb N, Lin PY, Yang KL

HLA, 2020 08;96(2):240-241.

PMID: 32246584 DOI: 10.1111/tan.13887

Nucleotide substitutions in codon 38 of HLA-DQB1*05:03:01:01 result in a novel allele, HLA-DQB1*05:66:01.

Matched MeSH terms: Exons/genetics

HLA-B*38:64, an HLA-B*38 variant, detected in a Singaporean Malay unrelated hematopoietic stem cell donor

Cho L, Kaur A, Cereb N, Lin PY, Yang KL

HLA, 2020 08;96(2):217-218.

PMID: 32227685 DOI: 10.1111/tan.13873

One nucleotide substitution in codon 89 of HLA-B*38:02:01:01 results in a novel allele, HLA-B*38:64.

Matched MeSH terms: Exons/genetics

Discovery of HLA-B*35:368, a novel HLA-B*35 variant, in a Singaporean Malay hematopoietic stem cell donor

Kaur A, Cho L, Cereb N, Lin PY, Yang KL

HLA, 2020 07;96(1):94-95.

PMID: 32166893 DOI: 10.1111/tan.13862

DNA substitutions from codons 69 to 71 of HLA-B*35:05:01:01 result in a novel allele, HLA-B*35:368.

Matched MeSH terms: Exons/genetics

Fulltext Improved ontology for eukaryotic single-exon coding sequences in biological databases

Jorquera R, González C, Clausen P, Petersen B, Holmes DS

Database (Oxford), 2018 01 01;2018:1-6.

PMID: 30239665 DOI: 10.1093/database/bay089

Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases.

Matched MeSH terms: Exons/genetics*

Sequencing analysis of exons 5 and 6 in RUNX2 in non-syndromic patients with supernumerary tooth in Kelantan, Malaysia

Saharudin S, Sanusi SY, Ponnuraj KT

Clin Oral Investig, 2022 Feb;26(2):1261-1268.

PMID: 34453594 DOI: 10.1007/s00784-021-04098-x

OBJECTIVE: The aim of this study is to do a sequencing analysis of RUNX2 in non-syndromic patients with supernumerary tooth.

MATERIALS AND METHODS: Fifty-three patients with supernumerary tooth were identified retrospectively from 1,275 radiographic reviews who attended the Hospital Universiti Sains Malaysia (USM) Dental Clinic. Informed consent was obtained from the patients prior to the study. Blood samples were collected from 41 patients and DNA extractions were performed out of which 10 samples were chosen randomly for PCR amplification using designated primers for RUNX2 followed by DNA sequencing analysis.

RESULTS: This study involved 28 male patients (68.3%) and 13 female patients (31.7%) with a gender ratio of 2.2:1 and mean age of 15.9 ± 6.2 years. DNA extraction yielded ~ 40 ng/μl of concentrated DNA, and each DNA sample had more than 1500 bp of DNA length. The purity ranged between 1.8 and 2.0. DNA sequencing analysis did not reveal any mutations in exons 5 and 6 of RUNX2.

CONCLUSION: This study did not reveal any mutations in exons 5 and 6 of RUNX2 in non-syndromic patients with supernumerary tooth.

CLINICAL RELEVANCE: Analysis of mutations in RUNX2 is important to enhance the understanding of tooth development in humans.

Matched MeSH terms: Exons/genetics

Fulltext Identification and characterization of a novel Epstein-Barr Virus-encoded circular RNA from LMP-2 Gene

Tan KE, Ng WL, Marinov GK, Yu KH, Tan LP, Liau ES, et al.

Sci Rep, 2021 Jul 13;11(1):14392.

PMID: 34257379 DOI: 10.1038/s41598-021-93781-w

Epstein-Barr virus (EBV) has been recently found to generate novel circular RNAs (circRNAs) through backsplicing. However, comprehensive catalogs of EBV circRNAs in other cell lines and their functional characterization are still lacking. In this study, we have identified a list of putative EBV circRNAs in GM12878, an EBV-transformed lymphoblastoid cell line, with a significant majority encoded from the EBV latent genes. A novel EBV circRNA derived from the exon 5 of LMP-2 gene which exhibited highest prevalence, was further validated using RNase R assay and Sanger sequencing. This circRNA, which we term circLMP-2_e5, can be universally detected in a panel of EBV-positive cell lines modelling different latency programs. It ranges from lower expression in nasopharyngeal carcinoma (NPC) cells to higher expression in B cells, and is localized to both the cytoplasm and the nucleus. We provide evidence that circLMP-2_e5 is expressed concomitantly with its cognate linear LMP-2 RNA upon EBV lytic reactivation, and may be produced as a result of exon skipping, with its circularization possibly occurring without the involvement of cis elements in the short flanking introns. Furthermore, we show that circLMP-2_e5 is not involved in regulating cell proliferation, host innate immune response, its linear parental transcripts, or EBV lytic reactivation. Taken together, our study expands the current repertoire of putative EBV circRNAs, broadens our understanding of the biology of EBV circRNAs, and lays the foundation for further investigation of their function in the EBV life cycle and disease development.

Matched MeSH terms: Exons/genetics

Fulltext Griscelli syndrome

Ariffin H, Geikowski A, Chin TF, Chau D, Arshad A, Abu Bakar K, et al.

Med J Malaysia, 2014 Aug;69(4):193-4.

PMID: 25500851 MyJurnal

We report a case of Griscelli Syndrome (GS). Our patient initially presented with a diagnosis of haemophagocytic lymphistiocytosis (HLH). Subsequent microscopic analysis of the patient's hair follicle revealed abnormal distribution of melanosomes in the shaft, which is a hallmark for GS. Analysis of RAB27A gene in this patient revealed a homozygous mutation in exon 6, c.550C>T, p.R184X . This nonsense mutation causes premature truncation of the protein resulting in a dysfunctional RAB27A. Recognition of GS allows appropriate institution of therapy namely chemotherapy for HLH and curative haemotopoeitic stem cell transplantation.

Matched MeSH terms: Exons

Fulltext Draft Genome Sequence of Burkholderia sp. Strain CCA53, Isolated from Leaf Soil

Akita H, Kimura Z, Yusoff MZ, Nakashima N, Hoshino T

Genome Announc, 2016;4(4).

PMID: 27389268 DOI: 10.1128/genomeA.00630-16

Burkholderia sp. strain CCA53 was isolated from leaf soil collected in Higashi-Hiroshima City in Hiroshima Prefecture, Japan. Here, we present a draft genome sequence of this strain, which consists of a total of 4 contigs containing 6,647,893 bp, with a G+C content of 67.0% and comprising 9,329 predicted coding sequences.

Matched MeSH terms: Exons

Fulltext Infantile Progressive Hepatoencephalomyopathy with Combined OXPHOS Deficiency due to Mutations in the Mitochondrial Translation Elongation Factor Gene GFM1

Balasubramaniam S, Choy YS, Talib A, Norsiah MD, van den Heuvel LP, Rodenburg RJ

JIMD Rep, 2012;5:113-22.

PMID: 23430926 DOI: 10.1007/8904_2011_107

Mitochondrial disorders are a heterogeneous group of often multisystemic and early fatal diseases caused by defects in the oxidative phosphorylation (OXPHOS) system. Given the complexity and intricacy of the OXPHOS system, it is not surprising that the underlying molecular defect remains unidentified in many patients with a mitochondrial disorder. Here, we report the clinical features and diagnostic workup leading to the elucidation of the genetic basis for a combined complex I and IV OXPHOS deficiency secondary to a mitochondrial translational defect in an infant who presented with rapidly progressive liver failure, encephalomyopathy, and severe refractory lactic acidemia. Sequencing of the GFM1 gene revealed two inherited novel, heterozygous mutations: a.539delG (p.Gly180AlafsX11) in exon 4 which resulted in a frameshift mutation, and a second c.688G > A (p.Gly230Ser) mutation in exon 5. This missense mutation is likely to be pathogenic since it affects an amino acid residue that is highly conserved across species and is absent from the dbSNP and 1,000 genomes databases. Review of literature and comparison were made with previously reported cases of this recently identified mitochondrial disorder encoded by a nuclear gene. Although limited in number, nuclear gene defects causing mitochondrial translation abnormalities represent a new, rapidly expanding field of mitochondrial medicine and should potentially be considered in the diagnostic investigation of infants with progressive hepatoencephalomyopathy and combined OXPHOS disorders.

Matched MeSH terms: Exons

Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter

Mohamed Hashim EK, Abdullah R

J Theor Biol, 2015 Dec 21;387:88-100.

PMID: 26427337 DOI: 10.1016/j.jtbi.2015.09.014

Empirical analysis on k-mer DNA has been proven as an effective tool in finding unique patterns in DNA sequences which can lead to the discovery of potential sequence motifs. In an extensive study of empirical k-mer DNA on hundreds of organisms, the researchers found unique multi-modal k-mer spectra occur in the genomes of organisms from the tetrapod clade only which includes all mammals. The multi-modality is caused by the formation of the two lowest modes where k-mers under them are referred as the rare k-mers. The suppression of the two lowest modes (or the rare k-mers) can be attributed to the CG dinucleotide inclusions in them. Apart from that, the rare k-mers are selectively distributed in certain genomic features of CpG Island (CGI), promoter, 5' UTR, and exon. We correlated the rare k-mers with hundreds of annotated features using several bioinformatic tools, performed further intrinsic rare k-mer analyses within the correlated features, and modeled the elucidated rare k-mer clustering feature into a classifier to predict the correlated CGI and promoter features. Our correlation results show that rare k-mers are highly associated with several annotated features of CGI, promoter, 5' UTR, and open chromatin regions. Our intrinsic results show that rare k-mers have several unique topological, compositional, and clustering properties in CGI and promoter features. Finally, the performances of our RWC (rare-word clustering) method in predicting the CGI and promoter features are ranked among the top three, in eight of the CGI and promoter evaluations, among eight of the benchmarked datasets.

Matched MeSH terms: Exons

Fulltext Comparative Genetic Analyses of Human Rhinovirus C (HRV-C) Complete Genome from Malaysia

Khaw YS, Chan YF, Jafar FL, Othman N, Chee HY

Front Microbiol, 2016;7:543.

PMID: 27199901 DOI: 10.3389/fmicb.2016.00543

Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5' and 3' non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63-81% among themselves and 63-96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection.

Matched MeSH terms: Exons

Whole exome sequencing is an efficient, sensitive and specific method for determining the genetic cause of short-rib thoracic dystrophies

McInerney-Leo AM, Harris JE, Leo PJ, Marshall MS, Gardiner B, Kinning E, et al.

Clin Genet, 2015 Dec;88(6):550-7.

PMID: 25492405 DOI: 10.1111/cge.12550

Short-rib thoracic dystrophies (SRTDs) are congenital disorders due to defects in primary cilium function. SRTDs are recessively inherited with mutations identified in 14 genes to date (comprising 398 exons). Conventional mutation detection (usually by iterative Sanger sequencing) is inefficient and expensive, and often not undertaken. Whole exome massive parallel sequencing has been used to identify new genes for SRTD (WDR34, WDR60 and IFT172); however, the clinical utility of whole exome sequencing (WES) has not been established. WES was performed in 11 individuals with SRTDs. Compound heterozygous or homozygous mutations were identified in six confirmed SRTD genes in 10 individuals (IFT172, DYNC2H1, TTC21B, WDR60, WDR34 and NEK1), giving overall sensitivity of 90.9%. WES data from 993 unaffected individuals sequenced using similar technology showed two individuals with rare (minor allele frequency <0.005) compound heterozygous variants of unknown significance in SRTD genes (specificity >99%). Costs for consumables, laboratory processing and bioinformatic analysis were

Matched MeSH terms: Exons

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