Review
Genetics & Heredity
Kiran Kumar Kolathur
Summary: Alternative splicing is crucial for enhancing proteome complexity in higher eukaryotes, with almost all multi intron-containing genes undergoing AS in humans. RNA polymerase II plays a crucial role in coordinating transcription and pre-mRNA splicing. Specific epigenetic changes at promoter regions may regulate alternative splicing.
Article
Multidisciplinary Sciences
Yanjun Zhang, Yuan Fang, Yin Tang, Shixun Han, Junqi Jia, Xinyi Wan, Jiaqi Chen, Ying Yuan, Bin Zhao, Dong Fang
Summary: SETD2 methylates histone H3K36me3 in gene bodies in mammalian cells. In this study, the authors demonstrate that H3K36me3 is also enriched at promoter regions and is catalyzed by SMYD5, recruited by RNA polymerase II. They further show that SMYD5 is elevated in liver cancer, with a correlation to changes in gene expression. These findings provide insights into the localization and function of H3K36me3.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Liliana Villao-Uzho, Tatiana Chavez-Navarrete, Ricardo Pacheco-Coello, Eduardo Sanchez-Timm, Efren Santos-Ordonez
Summary: One strategy to overcome crop diseases or abiotic stress is through the use of improved varieties achieved by genetic improvement methods such as conventional breeding, induced mutation, genetic transformation, or gene editing. Promoters, which regulate gene expression, are crucial for transgenic crops to improve specific traits. Many techniques, including RT-PCR, genetic libraries, cloning, and sequencing, are used to identify and isolate promoters for biotechnological crops. Promoter analysis through plant genetic transformation allows for understanding gene regulation and development, highlighting the importance of promoters in ensuring correct gene expression in biotechnological processes.
Article
Multidisciplinary Sciences
Jingyao Wang, Shihe Zhang, Hongfang Lu, Heng Xu
Summary: Many eukaryotic genes have alternative promoters with distinct expression patterns, but how these promoters are regulated is still not well understood. Researchers have studied the regulation of alternative promoters of the Drosophila embryonic gene hunchback and found that they are regulated by different action modes of two enhancers.
NATURE COMMUNICATIONS
(2022)
Article
Psychology, Multidisciplinary
Amy Scott, Gail Gillon, Brigid McNeill, Alex Kopach
Summary: Oral narrative abilities are important indicators of children's language competency and academic performance. New Zealand is developing an innovative online tool that uses audio recordings, speech-to-text software, and language analysis to monitor and analyze children's oral narrative and listening comprehension. The tool aims to support teachers in data interpretation and improve teaching practices through online professional development. The tool has gone through three phases of development and the current version utilizes automatic speech recognition with assistance from research assistants for transcription and analysis.
FRONTIERS IN PSYCHOLOGY
(2022)
Article
Zoology
Jing-Song Zhang, Hai-Quan Wang, Jie Xia, Kun Sha, Shu-Tao He, Hao Dai, Xiao-Hu Hao, Yi-Wei Zhou, Qiu Wang, Ke-Ke Ding, Zhang-Lei Ju, Wen Wang, Luo-Nan Chen
Summary: The divergence and evolution of plants and animals have contributed to ecological diversity. An extensive analysis of multi-omics sequences in animal and plant species revealed different evolutionary trends in promoter and transcription factor features. Promoters and TFs exhibited antagonistic coevolution in the animal kingdom but mutualistic coevolution in the plant kingdom. These distinct coevolutionary patterns potentially drive the divergence, divergent evolution, and ecological diversity of plants and animals.
ZOOLOGICAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Bo Bae Lee, Hyeonju Woo, Min Kyung Lee, SeoJung Youn, Sumin Lee, Jae-Seok Roe, Soo Young Lee, TaeSoo Kim
Summary: Chromatin-based regulation of internal cryptic promoters is mediated by core promoter strength as well as transcription elongation factors.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Jonas Kretz, Vera Israel, Matthew McIntosh
Summary: Inducible gene expression is valuable for biotechnological applications and gene regulation studies in bacteria. However, many systems that work well in model organisms like Escherichia coli show poor performance in other biotechnologically relevant bacteria due to weak or leaky expression. To address this, a new invention named ACIT (Alphaproteobacteriahromosomally integrating transcription-control cassette) is described, which allows tight transcription control over any gene or gene cluster of interest through homologous recombination.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hyung Joo Lee, Yiran Hou, Ju Heon Maeng, Nakul M. Shah, Yujie Chen, Heather A. Lawson, Hongbo Yang, Feng Yue, Ting Wang
Summary: This study systematically investigates the epigenomic and transcriptomic profile of transposable elements (TEs) in zebrafish tissues. The results show that TEs significantly contribute to gene regulation in zebrafish, with a portion of TEs being in active regulatory states. Specific TE subfamilies are found to be enriched in different tissues, and TE-derived transcriptional units are expressed across tissues.
Article
Microbiology
Jan Blumenstein, Robert Radisch, Vaclav Stepanek, Michal Grulich, Hana Dostalova, Miroslav Patek
Summary: The bacterium Rhodococcus erythropolis CCM2595 has the ability to degrade toxic aromatic compounds, with its genes being controlled by sigma factors. Experiments have revealed the gene activation mechanism of R. erythropolis under various extreme conditions, providing insights into the complex stress responses induced by substances like phenol.
CURRENT MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Tao Jiang, Tianshuang Xia, Fangliang Qiao, Nani Wang, Yiping Jiang, Hailiang Xin
Summary: Bones serve mechanical and defensive functions, as well as regulating calcium ions and housing bone marrow. The qualities of bones fluctuate throughout life, with functions increasing in some situations while deteriorating in others. Excessive osteoclast differentiation can lead to various bone pathologies, and the transcription factors and developmental/environmental signals play crucial roles in this process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Chi-Nga Chow, Kuan-Chieh Tseng, Ping-Fu Hou, Nai-Yun Wu, Tzong-Yi Lee, Wen -Chi Chang
Summary: This study characterized the cis-regulatory regions of TFs and histone marks in Arabidopsis, revealing that promoters and regions around the transcription termination sites of protein-coding genes recruit the most TFs, with diverse histone combinations. Comparative analysis between genes with distinct functions showed substantial differences in cis-regulatory regions, histone regulation, and TAD boundary organization. Integration of multiple high-throughput sequencing datasets generated regulatory models to explain the complexity of transcriptional regulation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Plant Sciences
Norbert Andrasi, Aladar Pettko-Szandtner, Laszlo Szabados
Summary: Plant heat shock factors (HSFs) are encoded by large gene families and are involved in responses to high temperatures and various abiotic stresses. They are regulated primarily at the transcript level, with alternative splicing and post-translational modifications providing additional variability. Plant HSFs participate in a complex network of protein-protein interactions and play crucial roles in transcriptional control.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Psychology, Multidisciplinary
Floriana Costanzo, Elisa Fuca, Cristina Caciolo, Deborah Rua, Sara Smolley, Danny Weissberg, Stefano Vicari
Summary: This study evaluated the usability and satisfaction of the Talkitt application and its impact on adaptive behavior and communication in individuals with Down syndrome (DS). The results showed good usability and high satisfaction with the application, as well as improvement in linguistic abilities, particularly naming. These findings suggest that Talkitt could potentially serve as a supportive and rehabilitative tool for individuals with DS.
FRONTIERS IN PSYCHOLOGY
(2023)
Article
Plant Sciences
Yuxin Shen, Zhengrui Qin, Gaojie Ren, Pingchuan Deng, Wanquan Ji, Chen Jiao, Liang Wu
Summary: Alternative splicing mediated by SCL33, SCL33L, and miR156 is involved in phase transitions in Brachypodium, regulating intron assembly and miR156 targets in growth transitions.
Article
Substance Abuse
Valentina Medici, Diane I. Schroeder, Rima Woods, Janine M. LaSalle, Yongzhi Geng, Noreene M. Shibata, Janet Peerson, Emir Hodzic, Sanjana Dayal, Hidekazu Tsukamoto, Kusum K. Kharbanda, Brittany Tillman, Samuel W. French, Charles H. Halsted
ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH
(2014)
Article
Biochemistry & Molecular Biology
Kristen Martins-Taylor, Diane I. Schroeder, Janine M. LaSalle, Marc Lalande, Ren-He Xu
Article
Biochemistry & Molecular Biology
Diane I. Schroeder, Paul Lott, Ian Korf, Janine M. LaSalle
Article
Biochemistry & Molecular Biology
Dag H. Yasui, Haley A. Scoles, Shin-ichi Horike, Makiko Meguro-Horike, Keith W. Dunaway, Diane I. Schroeder, Janine M. LaSalle
HUMAN MOLECULAR GENETICS
(2011)
Article
Biochemistry & Molecular Biology
Makiko Meguro-Horike, Dag H. Yasui, Weston Powell, Diane I. Schroeder, Mitsuo Oshimura, Janine M. LaSalle, Shin-ichi Horike
HUMAN MOLECULAR GENETICS
(2011)
Article
Neurosciences
Malaika K. Singleton, Michael L. Gonzales, Karen N. Leung, Dag H. Yasui, Diane I. Schroeder, Keith Dunaway, Janine M. LaSalle
NEUROBIOLOGY OF DISEASE
(2011)
Article
Multidisciplinary Sciences
Diane I. Schroeder, John D. Blair, Paul Lott, Hung On Ken Yu, Danna Hong, Florence Crary, Paul Ashwood, Cheryl Walker, Ian Korf, Wendy P. Robinson, Janine M. LaSalle
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2013)
Article
Genetics & Heredity
Diane I. Schroeder, Janine M. LaSalle
Meeting Abstract
Gastroenterology & Hepatology
Valentina Medici, Diane I. Schroeder, Rima Woods, Janine M. LaSalle, Sanjana Dayal, Hidekazu Tsukamoto, Kusum K. Kharbanda, Samuel W. French, Charles H. Halsted
Meeting Abstract
Environmental Sciences
K. Dunaway, D. Schroeder, P. Lott, M. S. Islam, R. Woods, M. M. Mitchell, D. H. Yasui, I Korf, J. LaSalle
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2013)
Article
Computer Science, Information Systems
XY Wang, D Schroeder, D Dobbs, V Honavar
INFORMATION SCIENCES
(2003)
Article
Biochemistry & Molecular Biology
Y Ji, D Schroeder, D Byrne, B Zipser, J Jellies, KM Johansen, J Johansen
BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION
(2001)
Article
Microbiology
BJ Feilmeier, G Iseminger, D Schroeder, H Webber, GJ Phillips
JOURNAL OF BACTERIOLOGY
(2000)
Article
Biochemistry & Molecular Biology
ND Trinklein, SF Aldred, SJ Hartman, DI Schroeder, RP Otillar, RM Myers
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.