Specific intronic p53 mutation in esophageal squamous cell carcinoma in Southern Thailand

AIM:To investigate p53 mutations in esophageal cancer in a high-risk population,and correlate them with smoking,alcohol consumption and betel chewing.METHODS:One hundred and sixty-five tumor samples of esophageal squamous cell carcinoma(ESCC) obtained from a university hospital in Songkhla province,Southern Thailand were investigated for p53 mutations in exons 5-8,using polymerase chain reaction-single strand conformation polymorphism analysis,followed by direct sequencing.A polymerase chain reactionrestriction fragment length polymorphism(RFLP) assay was additionally used to confirm possible germline mutation in intron 6.A history of risk habits was obtained by interviews.The association between risk habits and mutation frequency was evaluated using the χ 2 test.RESULTS:The studied specimens were from 139 male and 26 female patients with ESCC,treated at Songklanagarind Hospital.Most of the patients were smokers(86.7%) and alcohol consumers(72.73%),and 38.3% were betel chewers.Forty-three mutations of the p53 gene were detected in 25.5%(42/165) of tumor samples.Mutations were most commonly found in exon 5(25.6%) and exon 8(25.6%).Mutations in the hot-spot codon 248 were found in four cases(9.3% of all mutations).G:C→C:G(30.23%),G:C→A:T(27.90%) and G:C →T:A(16.28%) were the prevalent spectra of mutations.Unexpectedly,among 10 intronic mutations,eight cases harbored a similar mutation:G→C substitution in intron 6(nucleotide 12759,GenBank NC_000017).These were additionally confirmed by the RFLP technique.Similar mutations were also detected in their matched blood samples using RFLP and direct sequencing,which suggested germline mutations.There was no significant correlation between risk habits and p53 mutation frequency.CONCLUSION:A proportion of Thai ESCC patients harbored specific intronic p53 mutations,which might be germline mutations.Further studies are needed to explore this novel finding.

Voltage-Driven Adaptive Spintronic Neuron for Energy-Efficient Neuromorphic Computing

A spintronics neuron device based on voltage-induced strain is proposed.The stochastic switching behavior,which can mimic the firing behavior of neurons,is obtained by using two voltage signals to control the in-plane magnetization of a free layer of magneto-tunneling junction.One voltage signal is used as the input,and the other voltage signal can be used to tune the activation function(Sigmoid-like) of spin neurons.Therefore,this voltage-driven tunable spin neuron does not necessarily use energy-inefficient Oersted fields and spin-polarized current.Moreover,a voltage-control reading operation is presented,which can achieve the transition of activation function from Sigmoid-like to Re LU-like.A three-layer artificial neural network based on the voltage-driven spin neurons is constructed to recognize the handwritten digits from the MNIST dataset.For the MNIST handwritten dataset,the design achieves 97.75% recognition accuracy.The present results indicate that the voltage-driven adaptive spintronic neuron has the potential to realize energy-efficient well-adapted neuromorphic computing.

THE ROLE OF INTRONIC HSE IN THE HEAT SHOCK INDUCED EXPRESSION OF HUMAN hsp 90β GENE

The first intron of human hsp90β gene is not only essential in maintaining high constitutive expression but also critical for heat shock inducibility of the hsp90β gene. Typical HSEs in the first intron play a vital role in the heat induced expression of human hsp90β gene. Slot blot analysis shows that hsp90β gene mRNA transcripts initiated from the 3’ of the first intron dominates over that of the first exon. The intronic HSEs of the hsp90β gene show much higher binding affinity toward the recombinant heat shock factor HSF1 than that of the recombinant heat shock factor HSF2.

A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants

Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching enzyme.However,increasing evidence showed that some lariat RNA could escape debranching.Little is known about how and why these lariat RNAs could be retained.By comparing the atlas of lariat RNAs between the non-dividing cell(mature pollen)and three actively dividing tissues(young shoot apex,young seeds,and young roots),we identified hundreds to thousands of lariat RNA naturally retained in each tissue,and the incidence of lariat RNA retention is much less in shoot apex while much more in pollen.Many lariat RNAs derived from the same intron or different lariat RNAs from the same pre-m RNA could be retained in one tissue while degraded in the other tissues.By deciphering lariat RNA sequences,we identified an AG-rich(RAAAAVAAAR)motif and a UC-rich(UCUCUYUCUC)motif for pollen-specific and the other three tissues-retained lariat RNAs,respectively.Reconstitution of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in plants.Biologically,hundreds of lariat RNAs harbored mi RNA binding sites,and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of mi RNA target genes.Collectively,our results uncover that selective retention of lariat RNA is an actively regulatory process,and provide new insights into understanding how lariat RNA metabolism may impact mi RNA activity.

Linking circular intronic RNA degradation and function in transcription by RNase H1

Circular intronic RNAs(ci RNAs) escaping from DBR1 debranching of intron lariats are co-transcriptionally produced from prem RNA splicing, but their turnover and mechanism of action have remained elusive. We report that RNase H1 degrades a subgroup of ci RNAs in human cells. Many ci RNAs contain high GC% and tend to form DNA:RNA hybrids(R-loops) for RNase H1 cleavage, a process that appears to promote Pol II transcriptional elongation at ci RNA-producing loci. One ci RNA, ciankrd52, shows a stronger ability of R-loop formation than that of its cognate pre-m RNA by maintaining a locally open RNA structure in vitro. This allows the release of pre-m RNA from R-loops by ci-ankrd52 replacement and subsequent ci RNA removal via RNase H1 for efficient transcriptional elongation. We propose that such an R-loop dependent ci RNA degradation likely represents a mechanism that on one hand limits ci RNA accumulation by recruiting RNase H1 and on the other hand resolves Rloops for transcriptional elongation at some GC-rich ci RNA-producing loci.

水稻中Intronic MicroRNA与其宿主基因功能关系分析

根据已有的水稻基因组注释,对水稻中已知的437个pre-miRNAs的基因组背景加以分析,有98个(～22%)与蛋白编码基因相重叠,其中69个(～16%)位于蛋白编码基因的内含子区域,即intronic microRNAs(in-miRNAs).对这些in-miRNAs的靶基因进行Gene Ontology(GO)富集分析,结果显示in-miRNAs对蛋白质氨基酸磷酸化,DNA整合,蛋白质水解,恒温保持,防御响应等生物学过程中的基因有明显的调控作用.最后,对宿主基因及靶基因的功能进行整合分析发现有4个in-miRNAs所调控的靶基因与其宿主基因参与了相同的生物过程.我们推断,in-miRNAs可能会在这些生物过程中,通过下调靶基因的表达来协助或抑制其宿主基因的功能.

A novel intronic circular RNA,circGNG7,inhibits head and neck squamous cell carcinoma progression by blocking the phosphorylation of heat shock protein 27 at Ser78 and Ser82

Background:There is increasing evidence that circular RNAs(circRNAs)play a significant role in pathological processes including tumorigenesis.In contrast to exonic circRNAs,which are the most frequently reported circRNAs in cancer so far,the studies of intronic circRNAs have been greatly lagged behind.Here,we aimed to investigate the regulatory role of intronic circRNAs in head and neck squamous cell carcinoma(HNSCC).Methods:We conducted whole-transcriptome sequencing with four pairs of primary tumor tissues and adjacent normal tissues from HNSCC patients.Then,we characterized circGNG7 expression in HNSCC tissues and cell lines and explored its association with the prognosis of HNSCC patients.We also identified interactions between circGNG7 and functional proteins,which alter downstream signaling that regulate HNSCC progression.Results:In this study,we identified a new intronic circRNA,circGNG7,and validated its functional roles in HNSCC progression.CircGNG7 was predominately localized to the cytoplasm,and its expression was downregulated in both HNSCC tissues andCAL27,CAL33,SCC4,SCC9,HN6,and HN30 cells.Low expression of circGNG7 was significantly correlated with poor prognosis in HNSCC patients.Consistent with this finding,overexpression of circGNG7 strongly inhibited tumor cell proliferation,colony formation,in vitro migration,and in vivo tumor growth.Mechanistically,the expression of circGNG7 in HNSCC cells was regulated by the transcription factor SMAD family member 4(SMAD4).Importantly,we discovered that circGNG7 could bind to serine residues 78 and 82 of the functional heat shock protein 27(HSP27),occupying its phosphorylation sites and hindering its phosphorylation,which reduced HSP27-JNK/P38 mitogen-activated protein kinase(MAPK)oncogenic signaling.Downregulation of circGNG7 expression in HNSCC increased HSP27-JNK/P38 MAPK signaling and promoted tumor progression.Conclusions:Our results revealed that a new intronic circRNA,circGNG7,functions as a strong tumor suppressor and that circGNG7/HSP27-JNK/P38 MAPK signaling is a novel mechanism by which HNSCC progression can be controlled.

An Intronic Variant of CHD7 Identified in Autism Patients Interferes with Neuronal Differentiation and Development

Genetic composition plays critical roles in the pathogenesis of autism spectrum disorder(ASD).Especially,inherited and de novo intronic variants are often seen in patients with ASD.However,the biological significance of intronic variants is difficult to address.Here,among a Chinese ASD cohort,we identified a recurrent inherited intronic variant in the CHD7 gene,which is specifically enriched in East Asian populations.CHD7 has been implicated in numerous developmental disorders including CHARGE syndrome and ASD.To investigate whether the ASD-associated CHD7 intronic variant affects neural development,we established human embryonic stem cells carrying this variant using CRISPR/Cas9 methods and found that the level of CHD7 mRNA significantly decreased compared to control.Upon differentiation towards the forebrain neuronal lineage,we found that neural cells carrying the CHD7 intronic variant exhibited developmental delay and maturity defects.Importantly,we found that TBR1,a gene also implicated in ASD,was significantly increased in neurons carrying the CHD7 intronic variant,suggesting the intrinsic relevance among ASD genes.Furthermore,the morphological defects found in neurons carrying CHD7 intronic mutations were rescued by knocking down TBR1,indicating that TBR1 may be responsible for the defects in CHD7-related disorders.Finally,the CHD7 intronic variant generated three abnormal forms of transcripts through alternative splicing,which all exhibited loss-of-function in functional assays.Our study provides crucial evidence supporting the notion that the intronic variant of CHD7 is potentially an autism susceptibility site,shedding new light on identifying the functions of intronic variants in genetic studies of autism.

Exploring Splicing Variants and Novel Genes in Sacred Lotus Based on RNA-seq Data

Sacred lotus(Nelumbo nucifera)is a typical aquatic plant,belonging to basal eudicot plant,which is ideal for genome and genetic evolutionary study.Understanding lotus gene diversity is important for the study of molecular genetics and breeding.In this research,public RNA-seq data and the annotated reference genome were used to identify the genes in lotus.A total of 26,819 consensus and 1,081 novel genes were identified.Meanwhile,a comprehensive analysis of gene alternative splicing events was conducted,and a total of 19,983“internal”alternative splicing(AS)events and 14,070“complete”AS events were detected in 5,878 and 5,881 multi-exon expression genes,respectively.Observations made from the AS events show the predominance of intron retention(IR)subtype of AS events representing 33%.IR is followed by alternative acceptor(AltA),alternative donor(AltD)and exon skipping(ES),highlighting the universality of the intron definition model in plants.In addition,functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process,showing the key role for alternative splicing in influencing the growth and development of lotus.The results contribute to a better understanding of the current gene diversity in lotus,and provide an abundant resource for future functional genome analysis in lotus.

Intron Retention Fine-Tunes the Resistance of the Rice Mutant pls4 to Rice Sheath Blight(Rhizotonia solani AG I.1a)

OsPLS4 encodes aβ-ketoacyl carrier protein reductase(KAR).The role of OsPLS4 in rice sheath blight(Rhizoctonia solani)remains unclear.Our preliminary studies showed that premature leaf senescence mutants(pls4)were highly susceptive to sheath blight in the early stage of rice development.To explore the role of this gene in the development of rice sheath blight,the transcriptome profiles of the rice pls4 mutant and wild type were compared by RNA-seq.The results revealed 2,569 differentially expressed genes(DEGs).The down-regulated genes were significantly enriched in the defense response-related biological processes.These down-regulated genes included the chitinase genes and WRKY genes,which were significantly changed in pls4 mutants.Furthermore,467 genes induced significant alternative splicing(AS)events.Among them,intron retention(IR)affected gene expression levels and functions of the vitamin B6(VB6)metabolism pathway related to sheath blight.This result suggests that IR plays an important role in the sheath blight resistance of mutant pls4.Together,these results indicate that pls4 could be involved in the biological process of sheath blight via DEGs and the fine-tuning of IR.The present study provides a molecular basis for further investigation of the resistance of rice to sheath blight.

“Too Soon on Earth”: A Biophilosophical Model of Schizophrenia. Some Implications for Humanoid Robots

This paper presents a new explanatory model for schizophrenia based upon philosophical, molecular and neurobiological hypotheses as well as on years of experience in observing and treating these patients. To start with, a novel interpretation of the Hegelian concept of mediation is presented. Mediation is defined as the rejection of non-realizable programs, such as thoughts and ideas, at a certain point in time in the evolution of a living system. Whenever a system treats non-realizable programs as if they were realizable, its ability to “test the reality” is lost, and consequently a loss of ego-boundaries may occur. On the molecular level, I will try to show how “non-splicing” of introns during the mRNA splicing process is equivalent to a loss of the rejection function corresponding to mediation. At the cellular level in the brain, mediation can be explained in terms of glial-neuronal interactions. Glia exert a spatio-temporal boundary setting function determining the grouping of neurons into functional units. Mutations in genes that result in non-splicing of introns can produce truncated (“chimeric”) neurotransmitter receptors. I propose that such dysfunctional receptors are generated in glial cells and that they cannot interact properly with their cognate neurotransmitters. The glia will then lose their inhibitory-rejecting function with respect to the information processing within neuronal networks. This loss of glial boundary setting could be an explanation for the loss of ego or body boundaries in schizophrenia. Pertinent examples of case studies are given attempting to deduce the main symptoms of schizophrenia from the proposed hypothesis. Some implications for the design of delusional robots are also discussed. Finally, the evolutionary potency of non-coding introns is philosophically interpreted that schizophrenics may be “too soon on earth”.

The landscape and clinical relevance of intronic polyadenylation in human cancers

Intronic polyadenylation(IPA)is an RNA 3'end processing event which has been reported to play important roles in cancer development.However,the comprehensive landscape of IPA events across various cancer types is lacking.Here,we apply IPAFinder to identify and quantify IPA events in 10,383 samples covering all 33 cancer types from The Cancer Genome Atlas(TCGA)project.We identify a total of 21,835 IPA events,almost half of which are ubiquitously expressed.We identify 2761 unique dynamically changed IPA events across cancer types.Furthermore,we observe 8855 non-redundant clinically relevant IPA events,which could potentially be used as prognostic indicators.Our analysis also reveals that dynamic IPA usage within cancer signaling pathways may affect drug response.Finally,we develop a user-friendly data portal,IPACancer Atlas(http://www.tingni-lab.com/Pancan_IPA),to search and explore IPAs in cancer.

线粒体nad 1内含子2序列在石斛属植物分子鉴定中的应用(英文)

目的在兰科石斛属药用植物鉴定中应用新的分子标记。方法扩增并测定9种石斛属植物线粒体中NADH脱氢酶亚基1编码基因(nad 1)内含子2(in tron 2)的全长序列。结果比对后的nad 1 in tron 2序列长872bp,其中有17个变异位点,可以鉴别除粉花石斛D end robium lodd ig esii以外的8种植物。结论线粒体nad 1 in tron2序列可以作为一种新的分子标记用于石斛属植物的鉴定。

藏鸡和隐性白羽鸡GH基因的SNP检测及其与生长性状间的关联分析

利用改良等位基因特异性PCR(Modified Allele Specific PCR,M-ASP)结合PCR-RFLP以及直接测序方法对藏鸡和隐性白羽鸡生长激素(Growth Hormone,GH)基因内含子4(Intron4)的一个位点进行了SNP检测,并进行了该基因与藏鸡生长性状的关联分析。检测结果显示,GH基因Intron4的这个位点同时具有M-ASP和SacI-RFLP多态。测序结果表明,该位点发生了C→G的碱基突变,产生了CC、CG和GG三种基因型。两个等位基因和三种基因型在两鸡种中的分布基本一致。其中,基因型CC和等位基因C的频率最高。χ2检验结果表明,基因型频率或者等位基因频率在两鸡种之间没有显著差异(P>0.05),而分别在两鸡种内部却存在显著(P<0.05)或极显著(P<0.01)差异。方差分析结果表明,基因型与藏鸡的2周龄体重等12个生长性状有显著(P<0.05)或极显著(P<0.01)关联;基因型CC与藏鸡的7周龄体重存在显著关联(P<0.05)。这暗示了GH基因是影响藏鸡生长的主效基因或者它与主效基因相关,而该位点的碱基突变可以作为筛选藏鸡高的7周龄体重的分子标记。

内含子的进化及基因表达调节

由于内含子(intron)的进化目前还没有一致的观点,一般认为内含子的进化是基因进化的重要部分,是与物种形成相适应的过程。内含子参与基因的组织特异性表达、蛋白质变异、基因转录等多种生物学过程。

Cloning and Expression Patterns of a Metallothionein-like GenehtMT2 of Helianthus tuberosus

A novel cDNA sequencehtMT2, which encodes a type 2 metallothionein_like protein, was isolated from Helianthus tuberosus L. tuber cDNA library. The whole sequence is 509 bp, including an open reading frame (ORF) of 240 bp, a 5′ UTR of 62 bp and a 3′ UTR of 207 bp. Two genomic sequences covering the coding region ofhtMT2were cloned by PCR reaction. Sequence analysis revealed that the genomic sequences htMTG_1 of 986 bp and htMTG_2 of 982 bp were both composed of three exons and two introns. The deduced protein consisted of 79 amino acid residues with a predicted molecular weight of 7.8 ku (kD). Amino_terminal and carboxy_terminal domains contained 8 and 7 cysteine residues respectively, separated by a central cysteine free spacer. Sequence alignment revealed that the predicted protein ofhtMT2 was homologous to type 2 metallothioneins (MTs) of plants. Southern blotting analysis indicated that htMT2was encoded by a small multi_gene family in H. tuberosus genome. Northern blotting analysis showed that htMT2 transcripts were detected in stems, leaves and leafstalks, but no transcripts were detected in roots. The expression level in stems was the highest among the above tissues. Transcripts in stems were significantly reduced by Cu 2+ treatment. Judging from the homologies between the deduced HtMT2 and other type 2 plant metallothioneins as well as responses to metal ions, we believe thatwere cloned by PCR reaction. Sequence analysis revealed that the genomic sequences htMTG_1 of 986 bp and htMTG_2 of 982 bp were both composed of three exons and two introns. The deduced protein consisted of 79 amino acid residues with a predicted molecular weight of 7.8 ku (kD). Amino_terminal and carboxy_terminal domains contained 8 and 7 cysteine residues respectively, separated by a central cysteine free spacer. Sequence alignment revealed that the predicted protein ofhtMT2 was homologous to type 2 metallothioneins (MTs) of plants. Southern blotting analysis indicated that htMT2was encoded by a small multi_gene family in H. tuberosus genome. Northern blotting analysis showed that htMT2 transcripts were detected in stems, leaves and leafstalks, but no transcripts were detected in roots. The expression level in stems was the highest among the above tissues. Transcripts in stems were significantly reduced by Cu 2+ treatment. Judging from the homologies between the deduced HtMT2 and other type 2 plant metallothioneins as well as responses to metal ions, we believe that[ShtMT2 encodes a new type 2 metallothionein.

Application of Mitochondria DNA Hypervariable Region in Identification of Genetic Relationships among Different Varieties in Musa paradisiaca

[Objective] The aim was to establish an effective method for the identification of genetic relationships among different varieties in Musa paradisaca. [Method] Based on the diversity of mitochondria DNA intron sequence among different varieties of M. paradisaca,an intron of cytochrome oxidase subunit II gene in mitochondria DNA genome was amplified and sequenced. And then the cluster analysis was used to classify 16 varieties of M. paradisaca,which belonged to five genotypes （AAA,AA,AAB,ABB and BB）. [Result] The 16 varieties of M. paradisaca could be divided to three classes：the first class contained one variety,the genotype of which was BB; the second class contained seven varieties,the genotype of which was ABB; the third class contained eight varieties,the genotypes of which included AA,AAA,AAB and BB. The new varieties YiXian 1,2 and 3 showed the nearest relationship with FenZa. [Conclusion] The result of classification was consistent with the genotypes,thus verified the feasibility and effectiveness of the new method in the genetic relationship identification of M. paradisaca germplasm.

Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum

MicroRNAs （miRNAs） are endogenous 22-nt RNAs, which play important regulatory roles by post-transcriptional gene silencing. A computational strategy has been developed for the identification of conserved miRNAs based on features of known metazoan miRNAs in red flour beetle （Tribolium castaneum）, which is regarded as one of the major laboratory models of arthropods. Among 118 putative miRNAs, 47% and 53% of the predicted miRNAs from the red flour beetle are harbored by known protein-coding genes （intronic） and genes located outside （intergenic miRNA）, respectively. There are 31 intronic miRNAs in the same transcriptional orientation as the host genes, which may share RNA polymerase II and spliceosomal machinery with their host genes for their biogenesis. A hypothetical feed-back model has been proposed based on the analysis of the relationship between intronic miRNAs and their host genes in the development of red flour beetle.

A Chinese family with Axenfeld-Rieger syndrome:report of the clinical and genetic findings

AIM： To describe a Chinese family affected by a severe form of Axenfeld-Rieger syndrome （ARS） and characterize the molecular defect in PITX2 in the family. METHODS： Patients presented with typical ARS from a Chinese family were investigated. We performed genome- wide linkage scan and exome sequencing to identify the pathogenic mutations, Candidate mutations were verified for co-segregation in the whole pedigree using Sanger sequencing, Real-time polymerase chain reaction （RT- PCR） and Western blotting were performed to verify the expression of the pathogenic gene. RESULTS： Genome-wide linkage and exome sequencing analyses showed PITX2 as the disease candidate gene. A〉G substitution at position -11 of 3＇ss of exon 5 （IVS5- 11A〉G） that co-segregated with the disease phenotype was discovered in the family. The PITX2 messenger ribonucleic acid and protein levels were about 50% lower in patients with ARS than in unaffected family members in the family, CONCLUSION： Our findings implicate the first intronic mutation of the PITX2 gene in the pathogenesis of a severe form of ARS in a Chinese family. This study highlights the importance of a systematic search for intronic mutation in ARS cases for which no mutations in the exons of PITX2 have been found.

CYP11B2基因第2内含子转位与醛固酮瘤发病的关系

目的探讨醛固酮瘤CYP11B2基因第2内含子(intron 2)转位与醛固酮瘤患者发病之间的关系。方法应用PCR检测醛固酮瘤(66例)、醛固酮瘤肿瘤旁腺瘤组织(38例)和正常肾上腺组织(14例)CYP11B2基因intron2多态性(野生型/转位型)。结果在醛固酮瘤CYP11B2基因intron 2转位发生率为31.81%,醛固酮瘤肿瘤旁腺瘤组织为20.05%,正常肾上腺组织为14.29%,三者之间无统计学差异。结论醛固酮瘤CYP11B2基因intron 2转位与醛固酮瘤的发生无显著关联。