GENOMICS 是一个描述基因组规模技术发展及其在所有生物学研究领域中的应用的论坛。解决广大观众可能感兴趣的基本问题。我们的目标是发表最高质量的研究，并为作者提供快速、公平和准确的审查和出版我们范围内的手稿。

GENOMICS is a forum dedicated to the development of genomics-scale technologies and their applications across all fields of biological research. We aim to address fundamental questions that may interest a broad audience. Our goal is to publish high-quality research and provide authors with a fast, fair, and accurate review and publication process.

GENOMICS 是一个专注于基因组规模技术发展及其在各个生物学研究领域应用的论坛。我们致力于解决广大读者可能感兴趣的基本问题。我们的目标是发表高质量的研究成果，并为作者提供快速、公平和准确的审稿与出版服务。

Genomics

Oral leukoplakia (OLK) is the most common potentially malignant disorders in the oral cavity. This study aimed to screen the key genes of OLK malignant transformation using the Gene Expression Omnibus (GEO) database and experiments. In this study, the GEO database was employed to screen OLK malignant transformation-related genes, which were subsequently identified with a series of bioinformatic analyses. External validation showed that the model based on LAPTM4B, NR3C1, and COX6A1 had high accuracy in diagnosing OLK malignant transformation. Furthermore, the DMBA-induced potentially malignant disorders and OSCC models in vivo and real-time PCR experiment in vitro further verified the database analysis results. In conclusion, three key genes (LAPTM4B, NR3C1, and COX6A1) were screened as potential biomarkers for the diagnosis and treatment of OLK malignant transformation.

Fengji Li

Lin Qiu

Qian Gao

Liguang Yu

Han Liu

Zhijun Xue

Anqi Tao

Comprehensive bioinformatics analysis combined with experimental validation to screen biomarkers for malignant transformation of oral leukoplakia

Large deletions in Xq21 often are associated with contiguous gene syndromes consisting of X-linked deafness type 3 (DFN3), mental retardation (MRX), and choroideremia (CHM). The identification of deletions associated with classic CHM or DFN3 facilitated the positional cloning of the underlying genes, REP-1 and POU3F4, respectively, and enabled the positioning of the MRX gene in between these genes. Here, we report the cloning and characterization of a novel gene, ribosomal S6-kinase 4 (RSK4; HGMW-approved symbol RPS6KA6), which maps in the MRX critical region. RSK4 is completely deleted in eight patients with the contiguous gene syndrome including MRX, partially deleted in a patient with DFN3 and present in patients with an Xq21 deletion and normal intellectual abilities. RSK4 is most abundantly expressed in brain and kidney. The predicted protein of 746 amino acids shows a high level of homology to three previously isolated members of the human RSK family. RSK2 is involved in Coffin-Lowry syndrome and nonspecific MRX. The localization of RSK4 in the interval that is commonly deleted in mentally retarded males together with the high degree of amino acid identity with RSK2 suggests that RSK4 plays a role in normal neuronal development. Further mutation analyses in males with X-linked mental retardation must prove that RSK4 is indeed a novel MRX gene.

Helger G. Yntema

Bellinda van den Helm

Johan Kissing

Gerard van Duijnhoven

Francis Poppelaars

Jamel Chelly

Claude Moraine

Jean-Pierre Fryns

Ben C.J. Hamel

Helmut Heilbronner

Hans-Jürgen Pander

Han G. Brunner

Hans-Hilger Ropers

Frans P.M. Cremers

Hans van Bokhoven

A Novel Ribosomal S6-Kinase (RSK4; RPS6KA6) Is Commonly Deleted in Patients with Complex X-Linked Mental Retardation

The NCBI database has >15 chloroplast (cp) genome sequences available for different Camellia species but none for C. assamica. There is no report of any mitochondrial (mt) genome in the Camellia genus or Theaceae family. With the strong believes that these organelle genomes can play a great tool for taxonomic and phylogenetic analysis, we successfully assembled and analyzed cp and mt genome of C. assamica. We assembled the complete mt genome of C. assamica in a single circular contig of 707,441 bp length comprising of a total of 66 annotated genes, including 35 protein-coding genes, 29 tRNAs and two rRNAs. The first ever cp genome of C. assamica resulted in a circular contig of 157,353 bp length with a typical quadripartite structure. Phylogenetic analysis based on these organelle genomes showed that C. assamica was closely related to C. sinensis and C. leptophylla. It also supports Caryophyllales as Superasterids.

Hukam C Rawal

P Mohan Kumar

Biswajit Bera

Nagendra Kumar Singh

Tapan Kumar Mondal

Decoding and analysis of organelle genomes of Indian tea (Camellia assamica) for phylogenetic confirmation.

DNA methylation governs gene regulation in plants in response to environmental conditions. Here, we analyzed role of DNA methylation under desiccation and salinity stresses in three (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) rice cultivars via bisulphite sequencing. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stresses, respectively, were correlated with higher expression of few abiotic stress response related genes. Most of the differentially methylated and differentially expressed genes (DMR-DEGs) were cultivar-specific, suggesting an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. DMR-DEGs harboring differentially methylated cytosines due to DNA polymorphisms between the sensitive and tolerant cultivars in their promoter regions and/or coding regions were identified, suggesting the role of epialleles in abiotic stress responses.

Mohan Singh Rajkumar

Rama Shankar

Rohini Garg

Mukesh Jain

Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars.

重亚硫酸盐测序揭示水稻品种在干旱和盐胁迫下的动态DNA甲基化。

Controlled proteolytic activation of membrane-bound transcription factors (MTFs) is recently emerging as a versatile way of rapid transcriptional responses to environmental changes in plants. Here, we report genome-scale identification of putative MTFs in the Arabidopsis and rice genomes. The Arabidopsis and rice genomes have at least 85 and 45 MTFs, respectively, in virtually all major transcription factor families. Of particular interest is the NAC MTFs (designated NTLs): there are at least 18 NTLs in Arabidopsis and 5 NTL members (OsNTLs) in rice. While the full-size OsNTL forms are associated with the membranes, truncated forms lacking the transmembrane domains are detected exclusively in the nucleus. Furthermore, transcript levels of the OsNTL genes were elevated after treatments with abiotic stresses, supporting their roles in plant stress responses. We propose that membrane-mediated transcriptional control is a critical component of gene regulatory network that serves as an adaptive strategy under unfavorable growth conditions.

Sang-Gyu Kim

Sangmin Lee

Pil Joon Seo

Soon-Kap Kim

Jeong-Kook Kim

Chung-Mo Park

Genome-scale screening and molecular characterization of membrane-bound transcription factors in Arabidopsis and rice.

拟南芥和水稻中膜结合转录因子的全基因组筛选与分子特征分析。

The significance of the adaptive immune response in Alzheimer's disease (AD) is increasingly recognized. We analyzed scRNA-Seq data from AD patients, revealing a notable rise in CD4 cytotoxic T cells (CD4-CTLs) in peripheral blood mononuclear cells (PBMCs), validated in vivo and in vitro. This rise correlates with cognitive decline in AD patients. We also identified transcription factors TBX21 and MYBL1 as key drivers of CD4-CTL expansion. Further analyses indicate these cells are terminally differentiated, showing clonal expansion, metabolic changes, and unique communication patterns. Mendelian randomization identified risk genes SRGN and ITGB1, suggesting their genetic regulation in CD4-CTLs may contribute to AD. To summarize, our findings characterize the expansion of CD4-CTLs in the PBMCs of AD patients, providing valuable understanding into the possible mechanisms involved in the expansion of CD4-CTLs in AD.

Jiongxue Chen

Jiatian Xie

Fuyin Deng

Jinhua Cai

Sitai Chen

Xingrong Song

Shangzhou Xia

Qingyu Shen

Xinying Guo

Yamei Tang

Expansion of peripheral cytotoxic CD4+ T cells in Alzheimer's disease: New insights from multi-omics evidence

阿尔茨海默病中外周细胞毒性CD4+ T细胞的扩展：多组学证据的新见解

Na Zhang

Puguang Zhao

Wenda Zhang

Huiying Wang

Kaixuan Wang

Xiangyu Wang

Zhanjing Zhang

Ninghua Tan

Lingyun Chen

A chromosome-level genome of Lobelia seguinii provides insights into the evolution of Campanulaceae and the lobeline biosynthesis

条叶级半边莲基因组为桔梗科演化及洛贝林生物合成提供新见解

Ziyuan Feng

Xiaoyu Wang

Zihan Luo

Aihua Liu

Caixia Wen

Qi Ma

Wenyong Liu

Xuemei Li

Lianju Ma

Yueying Li

Bin Yang

Lanlan Wang

Identification and expression analysis of lncRNAs in rice roots (Oryza sativa L.) under elevated CO2 concentration and/or cadmium stress

水稻根系（Oryza sativa L.）在 elevated CO2 浓度和/或镉胁迫下长链非编码RNAs的鉴定与表达分析

Abnormal programmed cell death (PCD) plays a central role in spermatogenic dysfunction. However, the molecular mechanisms and biomarkers of PCD in patients with nonobstructive azoospermia (NOA) remain unclear.

Shuqiang Huang

Cuiyu Tan

Wanru Chen

Tongtong Zhang

Liying Xu

Zhihong Li

Miaoqi Chen

Xiaojun Yuan

Cairong Chen

Qiuxia Yan

Multiomics identification of programmed cell death-related characteristics for nonobstructive azoospermia based on a 675-combination machine learning computational framework

基于675组合机器学习计算框架的无阻塞性无精症程序性细胞死亡相关特征的多组学识别

Minghui Ye

Deying Wang

Ruixin Li

Kunyang Zhuang

Hongjiao Wang

Xinyin Cao

Tengfei Qin

Hengjia Zhang

Shangjing Guo

Bingjie Wu

SlAN2 overexpression improves cold resistance in tomato (Solanum lycopersicum L.) by regulating glycolysis and ascorbic acid metabolism

SlAN2 过表达通过调节糖酵解和抗坏血酸代谢提高番茄（Solanum lycopersicum L.）的耐冷性

Abbreviation
Journal Impact	3.52
Quartiles(Global)	GENETICS & HEREDITY(Q2)

ISSN	0888-7543, 1089-8646
h-index	156

Publication Information	Publisher: Academic Press Inc.，Publishing cycle: Monthly，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 1987，Proportion of original research papers: 97.17%，Self Citation Rate:0.00%， Gold OA Rate: 97.93%
Journal Fees	$2410Details
Average review cycle	网友分享经验：平均1.5月
Average recruitment ratio	网友分享经验：约40%

Genomics

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