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Distinct evolutionary pathways for the synthesis and function of tRNA modifications Brief. Funct. Genomics (IF 2.941) Pub Date : 2021-01-18 Satoshi Kimura
Transfer ribonucleicacids (RNAs) (tRNAs) are essential adaptor molecules for translation. The functions and stability of tRNAs are modulated by their post-transcriptional modifications (tRNA modifications). Each domain of life has a specific set of modifications that include ones shared in multiple domains and ones specific to a domain. In some cases, different tRNA modifications across domains have
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Deciphering RNA modifications at base resolution: from chemistry to biology Brief. Funct. Genomics (IF 2.941) Pub Date : 2021-01-18 Turja K Debnath; Blerta Xhemalçe
Nearly 200 distinct chemical modifications of RNAs have been discovered to date. Their analysis via direct methods has been possible in abundant RNA species, such as ribosomal, transfer or viral RNA, since several decades. However, their analysis in less abundant RNAs species, especially cellular messenger RNAs, was rendered possible only recently with the advent of high throughput sequencing techniques
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‘Green revolution’ dwarf gene sd1 of rice has gigantic impact Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-10-30 Gaur V, Channappa G, Chakraborti M, et al.
AbstractRice (Oryza sativa L.) is one of the most important cereal that has fed the world over a longer period. Before green revolution, cultivated rice is believed to have consisted of thousands of landraces each adapted to its specific climatic conditions by surviving against different abiotic and biotic selection pressure. However, owing to the low yield, photo-period sensitivity, late maturity
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The impact of epitranscriptomic marks on post-transcriptional regulation in plants Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-12-04 Xiang Yu; Bishwas Sharma; Brian D Gregory
Ribonucleotides within the various RNA molecules in eukaryotes are marked with more than 160 distinct covalent chemical modifications. These modifications include those that occur internally in messenger RNA (mRNA) molecules such as N6-methyladenosine (m6A) and 5-methylcytosine (m5C), as well as those that occur at the ends of the modified RNAs like the non-canonical 5′ end nicotinamide adenine dinucleotide
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An update: mechanisms of microRNA in primary open-angle glaucoma Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-11-09 Yuanping Wang; Lingzhi Niu; Jing Zhao; Mingxuan Wang; Ke Li; Yajuan Zheng
Glaucoma is a disease with characteristic optic neuropathy and loss of vision, leading to blindness, and primary open-angle glaucoma (POAG) is the most common glaucoma type throughout the world. Genetic susceptibility is the main factor in POAG, and most susceptibility genes cause changes in microRNA expression and function, thereby leading to POAG occurrence and development. Increasing evidence indicates
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Corrigendum to: CRISPR Cas9 for cancer treatment technology clinical applications and challenges. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-09-23 Xing Cheng,Shaoyi Fan,Chengcai Wen,Xianfa Du
In the originally published version of this manuscript, the spelling of the first author's name was incorrect. The name should be “Xing Cheng” instead of “Xing Chen”. This error has now been corrected online.
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Depositing annotated sequences in GenBank: there needs to be a better way. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-09-04 David Roy Smith
Submitting sequences to the National Center for Biotechnology Information (NCBI) is an integral part of research and the publication process for many disciplines within the life sciences, and it will only become more important as sequencing technologies continue to improve. Here, I argue that the available infrastructure and resources for uploading data to NCBI—especially the associated annotations
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CRISPR in medicine: applications and challenges. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-18 Jin-Yu Sun,Hai-Bo Hu,Yan-Xiang Cheng,Xiao-Jie Lu
Initially discovered in bacteria and archaea as adaptive immune strategies against invading nucleic acids, the clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) system has now been repurposed as a practical tool for genome editing and other applications [1]. Owing to its flexibility, simplicity, efficiency and precision, the application of CRISPR systems in medicine
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Erratum to: Advancing from protein interactomes and gene co-expression networks towards multi-omics-based composite networks: approaches for predicting and extracting biological knowledge. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-08-29 Vinay Randhawa,Shivalika Pathania
In the above article, Vinay Randhawa's affiliation was given as Department of Biotechnology, Panjab University, Chandigarh, 160014, India instead of Department of Biochemistry, Panjab University, Chandigarh, 160014, India. This has been corrected online. The publisher apologies for the error.
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Advancing from protein interactomes and gene co-expression networks towards multi-omics-based composite networks: approaches for predicting and extracting biological knowledge. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-07-17 Vinay Randhawa,Shivalika Pathania
Prediction of biological interaction networks from single-omics data has been extensively implemented to understand various aspects of biological systems. However, more recently, there is a growing interest in integrating multi-omics datasets for the prediction of interactomes that provide a global view of biological systems with higher descriptive capability, as compared to single omics. In this review
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Single-cell transcriptomics allows novel insights into aging and circadian processes. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-07-07 Sara S Fonseca Costa,Marc Robinson-Rechavi,Jürgen A Ripperger
Aging and circadian rhythms are two biological processes that affect an organism, although at different time scales. Nevertheless, due to the overlap of their actions, it was speculated that both interfere or interact with each other. However, to address this question, a much deeper insight into these processes is necessary, especially at the cellular level. New methods such as single-cell RNA-sequencing
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Machine learning-based approaches for disease gene prediction. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-06-22 Duc-Hau Le
Disease gene prediction is an essential issue in biomedical research. In the early days, annotation-based approaches were proposed for this problem. With the development of high-throughput technologies, interaction data between genes/proteins have grown quickly and covered almost genome and proteome; thus, network-based methods for the problem become prominent. In parallel, machine learning techniques
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Strandedness during cDNA synthesis, the stranded parameter in htseq-count and analysis of RNA-Seq data. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-16 Krishna A Srinivasan,Suman K Virdee,Andrew G McArthur
RNA sequencing (RNA-Seq) is a complicated protocol, both in the laboratory in generation of data and at the computer in analysis of results. Several decisions during RNA-Seq library construction have important implications for analysis, most notably strandedness during complementary DNA library construction. Here, we clarify bioinformatic decisions related to strandedness in both alignment of DNA sequencing
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Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-12 Mohd Amir,Taj Mohammad,Ravins Dohare,Asimul Islam,Faizan Ahmad,M D Imtaiyaz Hassan
Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins
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Challenges in the diagnosis and discovery of rare genetic disorders using contemporary sequencing technologies. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-12 Eleanor G Seaby,Sarah Ennis
Next generation sequencing (NGS) has revolutionised rare disease diagnostics. Concomitant with advancing technologies has been a rise in the number of new gene disorders discovered and diagnoses made for patients and their families. However, despite the trend towards whole exome and whole genome sequencing, diagnostic rates remain suboptimal. On average, only ~30% of patients receive a molecular diagnosis
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Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-04-29 Kimberly MacKay,Anthony Kusalik
The advent of high-resolution chromosome conformation capture assays (such as 5C, Hi-C and Pore-C) has allowed for unprecedented sequence-level investigations into the structure-function relationship of the genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these assays to predict 3D genome organization (the 3D genome
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A multifocal approach towards understanding the complexities of carotenoid biosynthesis and accumulation in rice grains. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-04-02 Upasna Chettry,Nikhil K Chrungoo
Carotenoids are mostly C40 terpenoids that participate in several important functions in plants including photosynthesis, responses to various forms of stress, signal transduction and photoprotection. While the antioxidant potential of carotenoids is of particular importance for human health, equally important is the role of β-carotene as the precursor for vitamin A in the human diet. Rice, which contributes
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Identifying cell types to interpret scRNA-seq data: how, why and more possibilities. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-03-31 Ziwei Wang,Hui Ding,Quan Zou
Single-cell RNA sequencing (scRNA-seq) has generated numerous data and renewed our understanding of biological phenomena at the cellular scale. Identification of cell types has been one of the most prevalent means for interpreting scRNA-seq data, based upon which connections are made between the transcriptome and phenotype. Herein, we attempt to review the methods and tools that dedicate to the task
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3D genome organization: setting the stage and introducing its players. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-03-23 Daan Noordermeer
The introduction of Chromosome Conformation Capture (3C) by Job Dekker and colleagues in 2002, followed by derivatives that incorporate high-throughput sequencing—most notably Hi-C—have transformed the study of eukaryotic 3D genome organization [1,2]. Whereas prior imaging-based studies mostly focused on the positioning of genomic regions within the cell nucleus or relative to other structures, 3C-based
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Three-dimensional chromosome organization in flowering plants. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-03-23 Stefan Grob
Research on plant three-dimensional (3D) genome architecture made rapid progress over the past 5 years. Numerous Hi-C interaction data sets were generated in a wide range of plant species, allowing for a comprehensive overview on 3D chromosome folding principles in the plant kingdom. Plants lack important genes reported to be vital for chromosome folding in animals. However, similar 3D structures such
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Genome anchoring to nuclear landmarks drives functional compartmentalization of the nuclear space. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-02-12 Antoine Canat,Adeline Veillet,Amandine Bonnet,Pierre Therizols
The spatial organization of the genome contributes to essential functions such as transcription and chromosome integrity maintenance. The principles governing nuclear compartmentalization have been the focus of considerable research over the last decade. In these studies, the genome-nuclear structure interactions emerged as a main driver of this particular 3D genome organization. In this review, we
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Order and disorder: abnormal 3D chromatin organization in human disease. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-02-05 Chiara Anania,Darío G Lupiáñez
A precise three-dimensional (3D) organization of chromatin is central to achieve the intricate transcriptional patterns that are required to form complex organisms. Growing evidence supports an important role of 3D chromatin architecture in development and delineates its alterations as prominent causes of disease. In this review, we discuss emerging concepts on the fundamental forces shaping genomes
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Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-01-23 C A Brackley,D Marenduzzo
We review the mechanism and consequences of the 'bridging-induced attraction', a generic biophysical principle that underpins some existing models for chromosome organization in 3D. This attraction, which was revealed in polymer physics-inspired computer simulations, is a generic clustering tendency arising in multivalent chromatin-binding proteins, and it provides an explanation for the biogenesis
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Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-12-26 Zhichao Xu,Jesse R Dixon
Genomic analysis of individuals or organisms is predicated on the availability of high-quality reference and genotype information. With the rapidly dropping costs of high-throughput DNA sequencing, this is becoming readily available for diverse organisms and for increasingly large populations of individuals. Despite these advances, there are still aspects of genome sequencing that remain challenging
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3D genome organization during lymphocyte development and activation. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-12-10 Anne van Schoonhoven,Danny Huylebroeck,Rudi W Hendriks,Ralph Stadhouders
Chromosomes have a complex three-dimensional (3D) architecture comprising A/B compartments, topologically associating domains and promoter–enhancer interactions. At all these levels, the 3D genome has functional consequences for gene transcription and therefore for cellular identity. The development and activation of lymphocytes involves strict control of gene expression by transcription factors (TFs)
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3D genome organisation in Drosophila. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-12-03 Charlotte Moretti,Isabelle Stévant,Yad Ghavi-Helm
Ever since Thomas Hunt Morgan’s discovery of the chromosomal basis of inheritance by using Drosophila melanogaster as a model organism, the fruit fly has remained an essential model system in studies of genome biology, including chromatin organisation. Very much as in vertebrates, in Drosophila, the genome is organised in territories, compartments and topologically associating domains (TADs). However
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Genome organization via loop extrusion, insights from polymer physics models. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-08 Surya K Ghosh,Daniel Jost
Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play
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Small regulatory noncoding RNAs in Drosophila melanogaster: biogenesis and biological functions. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-03-27 Saeed Soleimani,Zahra Valizadeh Arshad,Sharif Moradi,Ali Ahmadi,Seyed Javad Davarpanah,Sadegh Azimzadeh Jamalkandi
RNA interference (RNAi) is an important phenomenon that has diverse genetic regulatory functions at the pre- and posttranscriptional levels. The major trigger for the RNAi pathway is double-stranded RNA (dsRNA). dsRNA is processed to generate various types of major small noncoding RNAs (ncRNAs) that include microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) in Drosophila
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Plant carotenoid cleavage oxygenases: structure–function relationships and role in development and metabolism Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-12-26 Dhar M, Mishra S, Bhat A, et al.
A plant communicates within itself and with the outside world by deploying an array of agents that include several attractants by virtue of their color and smell. In this category, the contribution of ‘carotenoids and apocarotenoids’ is very significant. Apocarotenoids, the carotenoid-derived compounds, show wide representation among organisms. Their biosynthesis occurs by oxidative cleavage of carotenoids
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Machine learning and its applications in plant molecular studies Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-12-23 Sun S, Wang C, Ding H, et al.
The advent of high-throughput genomic technologies has resulted in the accumulation of massive amounts of genomic information. However, biologists are challenged with how to effectively analyze these data. Machine learning can provide tools for better and more efficient data analysis. Unfortunately, because many plant biologists are unfamiliar with machine learning, its application in plant molecular
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A broad survey of DNA sequence data simulation tools Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-12-23 Alosaimi S, Bandiang A, van Biljon N, et al.
In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools
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Functions of short lifetime biological structures at large: the case of intrinsically disordered proteins. Brief. Funct. Genomics (IF 2.941) Pub Date : 2018-07-03 Vladimir N Uversky
Although for more than a century a protein function was intimately associated with the presence of unique structure in a protein molecule, recent years witnessed a skyrocket rise of the appreciation of protein intrinsic disorder concept that emphasizes the importance of the biologically active proteins without ordered structures. In different proteins, the depth and breadth of disorder penetrance are
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Molecular breeding approaches for production of disease-resilient commercially important tobacco. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-01-14 Kaleem U Kakar,Zarqa Nawaz,Zhouqi Cui,Nazeer Ahemd,Xueliang Ren
Tobacco is one of the most widely cultivated nonfood cash crops, a source of income, model organism for plant molecular research, a natural pesticide and of pharmaceutical importance. First domesticated in South Americas, the modern-day tobacco (Nicotiana tabacum) is now cultivated in more than 125 countries to generate revenues worth billions of dollars each year. However, the production of this crop
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CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-01-08 Shakeel Ahmad,Xiangjin Wei,Zhonghua Sheng,Peisong Hu,Shaoqing Tang
Several plant pathogens severely affect crop yield and quality, thereby threatening global food security. In order to cope with this challenge, genetic improvement of plant disease resistance is required for sustainable agricultural production, for which conventional breeding is unlikely to do enough. Luckily, genome editing systems that particularly clustered regularly interspaced short palindromic
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Applications and advances of CRISPR/Cas9 in animal cancer model. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Min Xu,Qiaoyou Weng,Jiansong Ji
The recent developments of clustered regularly interspaced short palindromic repeats(CRISPR)/-associate protein 9 (CRISPR/Cas9) have got scientific interests due to the straightforward, efficient and versatile talents of it. Furthermore, the CRISPR/Cas9 system has democratized access to gene editing in many biological fields, including cancer. Cancer development is a multistep process caused by innate
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Human embryo gene editing: God's scalpel or Pandora's box? Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Qi Zhou,Yan Zhang,Yujie Zou,Tailang Yin,Jing Yang
Gene editing refers to the site-specific modification of the genome, which mainly focuses on basic research, model organism construction and treatment and prevention of disease. Since the first application of CRISPR/Cas9 on the human embryo genome in 2015, the controversy over embryo gene editing (abbreviated as EGE in the following text) has never stopped. At present, the main contradictions focus
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CRISPR/Cas9 for cancer treatment: technology, clinical applications and challenges. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Xing Chen,Shaoyi Fan,Chengcai Wen,Xianfa Du
Clustered regularly interspaced short palindromic repeats (CRISPR) is described as RNA mediated adaptive immune system defense, which is naturally found in bacteria and archaea. CRISPR-Cas9 has shown great promise for cancer treatment in cancer immunotherapy, manipulation of cancer genome and epigenome and elimination or inactivation of carcinogenic viral infections. However, many challenges remain
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Application of CRISPR/Cas9 technology in sepsis research. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Miao Wu,Niandan Hu,Xianjin Du,Jie Wei
CRISPR/Cas9, as a new genome-editing tool, offers new approaches to understand and treat diseases, which is being rapidly applied in various areas of biomedical research including sepsis field. The type II prokaryotic CRISPR/Cas system uses a single-guide RNA (sgRNA) to target the Cas9 nuclease to a specific genomic sequence, which is introduced into disease models for functional characterization and
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Aberrant DNA methylation and miRNAs in coronary artery diseases and stroke: a systematic review. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-07-29 Anu Radha Sharma,Umakanth Shashikiran,Abdul Razak Uk,Ranjan Shetty,Kapaettu Satyamoorthy,Padmalatha S Rai
Coronary artery disease (CAD) and ischemic stroke are the two most predominant forms of cardiovascular diseases (CVDs) caused by genetic, epigenetic and environmental risk factors. Although studies on the impact of 'epigenetics' in CVDs is not new, its effects are increasingly being realized as a key regulatory determinant that may drive predisposition, pathophysiology and therapeutic outcome. The
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Applications and explorations of CRISPR/Cas9 in CAR T-cell therapy. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Chenggong Li,Heng Mei,Yu Hu
Chimeric antigen receptor(CAR) T-cell therapy has shown remarkable effects and promising prospects in patients with refractory or relapsed malignancies, pending further progress in the next-generation CAR T cells with more optimized structure, enhanced efficacy and reduced toxicities. The clustered regulatory interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology
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CRISPR/Cas9 technology: towards a new generation of improved CAR-T cells for anticancer therapies. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Guillermo Ureña-Bailén,Andrés Lamsfus-Calle,Alberto Daniel-Moreno,Janani Raju,Patrick Schlegel,Christian Seitz,Daniel Atar,Justin S Antony,Rupert Handgretinger,Markus Mezger
Chimeric antigen receptor (CAR)-modified T cells have raised among other immunotherapies for cancer treatment, being implemented against B-cell malignancies. Despite the promising outcomes of this innovative technology, CAR-T cells are not exempt from limitations that must yet to be overcome in order to provide reliable and more efficient treatments against other types of cancer. The purpose of this
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Epigenome editing by CRISPR/Cas9 in clinical settings: possibilities and challenges. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Wen-Di Pei,Yan Zhang,Tai-Lang Yin,Yang Yu
Epigenome editing is a promising approach for both basic research and clinical application. With the convergence of techniques from different fields, regulating gene expression artificially becomes possible. From a clinical point of view, targeted epigenome editing by CRISPR/Cas9 of disease-related genes offers novel therapeutic avenues for many diseases. In this review, we summarize the EpiEffectors
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CRISPR-Cas9 genome editing for cancer immunotherapy: opportunities and challenges. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Ming Chen,Jiang Xu,Yang Zhou,Silin Zhang,Di Zhu
Cancer immunotherapy, consisting of antibodies, adoptive T-cell transfer, vaccines and cytokines, is a novel strategy for fighting cancer by artificially stimulating the immune system. It has developed rapidly in recent years, and its efficacy in hematological malignancies and solid tumors has been remarkable. It is regarded as one of the most promising methods for cancer therapy. The current trend
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Advances in therapeutic application of CRISPR-Cas9. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Jinyu Sun,Jianchu Wang,Donghui Zheng,Xiaorong Hu
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is one of the most versatile and efficient gene editing technologies, which is derived from adaptive immune strategies for bacteria and archaea. With the remarkable development of programmable nuclease-based genome engineering these years, CRISPR-Cas9 system has developed quickly in recent 5 years and has
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CRISPR therapy towards an HIV cure. Brief. Funct. Genomics (IF 2.941) Pub Date : 2020-05-20 Elena Herrera-Carrillo,Zongliang Gao,Ben Berkhout
Tools based on RNA interference (RNAi) and the recently developed clustered regularly short palindromic repeats (CRISPR) system enable the selective modification of gene expression, which also makes them attractive therapeutic reagents for combating HIV infection and other infectious diseases. Several parallels can be drawn between the RNAi and CRISPR-Cas9 platforms. An ideal RNAi or CRISPR-Cas9 therapeutic
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Polycomb proteins as organizers of 3D genome architecture in embryonic stem cells. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Tomas Pachano,Giuliano Crispatzu,Alvaro Rada-Iglesias
Polycomb group proteins (PcGs) control the epigenetic and transcriptional state of developmental genes and regulatory elements during mammalian embryogenesis. Moreover, PcGs can also contribute to 3D genome organization, adding an additional layer of complexity to their regulatory functions. Understanding the mechanistic basis and the dynamics of PcG-dependent chromatin structures will help us untangle
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A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Xiaolei Zhu,Jingjing He,Shihao Zhao,Wei Tao,Yi Xiong,Shoudong Bi
N6-methyladenosine (m6A) modification, as one of the commonest post-transcription modifications in RNAs, has been reported to be highly related to many biological processes. Over the past decade, several tools for m6A sites prediction of Saccharomyces cerevisiae have been developed and are freely available online. However, the quality of predictions by these tools is difficult to quantify and compare
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Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Anne H Klein,Kaylene R Ballard,Kenneth B Storey,Cherie A Motti,Min Zhao,Scott F Cummins
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites
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Technologies to study spatial genome organization: beyond 3C. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Nadine Übelmesser,Argyris Papantonis
The way that chromatin is organized in three-dimensional nuclear space is now acknowledged as a factor critical for the major cell processes, like transcription, replication and cell division. Researchers have been armed with new molecular and imaging technologies to study this structure-to-function link of genomes, spearheaded by the introduction of the 'chromosome conformation capture' technology
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Human core duplicon gene families: game changers or game players? Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Cemalettin Bekpen,Diethard Tautz
Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available
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Prediction of tumor metastasis from sequencing data in the era of genome sequencing. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Linlin Yuan,Fei Guo,Lei Wang,Quan Zou
Tumor metastasis is the key reason for the high mortality rate of tumor. Growing number of scholars have begun to pay attention to the research on tumor metastasis and have achieved satisfactory results in this field. The advent of the era of sequencing has enabled us to study cancer metastasis at the molecular level, which is essential for understanding the molecular mechanism of metastasis, identifying
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Corrigendum to: Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Andreas Kloetgen,Philipp C Münch,Arndt Borkhardt,Jessica I Hoell,Alice C McHardy
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Microfluidic devices for embryonic and larval zebrafish studies. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Arezoo Khalili,Pouya Rezai
Zebrafish or Danio rerio is an established model organism for studying the genetic, neuronal and behavioral bases of diseases and for toxicology and drug screening. The embryonic and larval stages of zebrafish have been used extensively in fundamental and applied research due to advantages offered such as body transparency, small size, low cost of cultivation and high genetic homology with humans.
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Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-19 Vilas Menon
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Plasmodium comparative genomics. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-11-07 Lisa Ranford-Cartwright,Elena Gómez-Díaz
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The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-09-24 Steven Abel,Karine G Le Roch
Due to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence
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Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-08-01 Marcus C S Lee,Scott E Lindner,Jose-Juan Lopez-Rubio,Manuel Llinás
CRISPR/Cas9 approaches are revolutionizing our ability to perform functional genomics across a wide range of organisms, including the Plasmodium parasites that cause malaria. The ability to deliver single point mutations, epitope tags and gene deletions at increased speed and scale is enabling our understanding of the biology of these complex parasites, and pointing to potential new therapeutic targets
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Functional genomics of simian malaria parasites and host-parasite interactions. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-06-27 Mary R Galinski
Two simian malaria parasite species, Plasmodium knowlesi and Plasmodium cynomolgi, cause zoonotic infections in Southeast Asia, and they have therefore gained recognition among scientists and public health officials. Notwithstanding, these species and others including Plasmodium coatneyi have served for decades as sources of knowledge on the biology, genetics and evolution of Plasmodium, and the diverse
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Bioinoculant capability enhancement through metabolomics and systems biology approaches. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-06-25 Twinkle Chaudhary,Pratyoosh Shukla
Bioinoculants are eco-friendly microorganisms, and their products are utilized for improving the potential of soil and fulfill the nutrients requirement for the host plant. The agricultural yield has increased due to the use of bioinoculants over chemical-based fertilizers, and thus it generates interest in understanding the innovation process by various methods. By gene-editing tool, the desired gene
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What functional genomics has taught us about transcriptional regulation in malaria parasites. Brief. Funct. Genomics (IF 2.941) Pub Date : 2019-06-21 Christa G Toenhake,Richárd Bártfai
Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights
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