Article
Biochemical Research Methods
Stefan Gerber, Gerhard Schratt, Pierre-Luc Germain
Summary: The diffUTR Bioconductor package simplifies and improves differential exon usage analysis, enabling differential 3' UTR usage analysis as well. It is more flexible and accurate than current state-of-the-art alternatives, facilitating DEU and exploration of their results.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Shangling Lou, Xiang Guo, Lian Liu, Yan Song, Lei Zhang, Yuanzhong Jiang, Lushui Zhang, Pengchuan Sun, Bao Liu, Shaofei Tong, Ningning Chen, Meng Liu, Han Zhang, Ruyun Liang, Xiaoqin Feng, Yudan Zheng, Huanhuan Liu, Michael J. Holdsworth, Jianquan Liu
Summary: A study found that allelic changes in the cis-regulatory elements WT box and W box in the promoter of a key transcription factor RAP2.12 in Arabidopsis thaliana are responsible for differentially regulating tolerance to drought and flooding. These two cis-elements are regulated by different transcription factors, resulting in differential accumulation of hypoxia-responsive transcripts. This gene promotes both drought and flooding adaptation through an adaptive mechanism that diversifies its regulation through noncoding alleles.
Article
Microbiology
Maryam Hajikarimlou, Mohsen Hooshyar, Noor Sunba, Nazila Nazemof, Mohamed Taha Moutaoufik, Sadhena Phanse, Kamaledin B. B. Said, Mohan Babu, Martin Holcik, Bahram Samanfar, Myron Smith, Ashkan Golshani
Summary: Mitochondria possess their own DNA (mtDNA) and are capable of carrying out their transcription and translation. The presence of the 3'-UTR from OXA1 gene is correlated with mitochondrial translation in yeast.
Article
Multidisciplinary Sciences
Asia Mendelevich, Svetlana Vinogradova, Saumya Gupta, Andrey A. Mironov, Shamil R. Sunyaev, Alexander A. Gimelbrant
Summary: The study demonstrates that relying on a single RNA-seq library for allele-specific analysis can lead to variable error rates. Therefore, the development of a computational tool like Qllelic, which accurately accounts for technical noise by utilizing replicate RNA-seq libraries, greatly decreases false positive rates and improves reproducibility of AI estimates.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Yuri S. Van Ekelenburg, Karina S. Hornslien, Tom Van Hautegem, Matyas Fendrych, Gert Van Isterdael, Katrine N. Bjerkan, Jason R. Miller, Moritz K. Nowack, Paul E. Grini
Summary: Genomic imprinting refers to the differential expression of parental alleles in the endosperm of flowering plants, which is regulated by epigenetic modifications. This study used fluorescence-activated nuclear sorting (FANS) to capture parental-specific allelic expression and identified differential genomic imprinting in different developmental stages and specific endosperm domains. The findings challenge the canonical mechanisms for genomic imprinting and suggest dynamic regulation of imprinting in the endosperm.
Article
Biochemistry & Molecular Biology
Nguyet Le, Timothy M. Hufford, Jong S. Park, Rachel M. Brewster
Summary: Organisms rely on oxygen for cellular energy production, but severe hypoxia or excessive oxygen can lead to cell damage. To adapt to oxygen level fluctuations, organisms have evolved mechanisms. Zebrafish embryos exhibit hypoxia tolerance and the N-myc Downstream Regulated Gene (ndrg) family may play a role in this adaptation.
Article
Multidisciplinary Sciences
Hemant Chandru Naik, Kishore Hari, Deepshikha Chandel, Susmita Mandal, Mohit Kumar Jolly, Srimonta Gayen
Summary: Recent studies have shown the widespread presence of dynamic random monoallelic expression of autosomal genes during pregastrulation. The coordination of allelic bursting is lineage specific, with genes regulating development showing higher levels of coordination. This provides significant insights into the prevalence and origin of dynamic aRME during early development.
Article
Biochemistry & Molecular Biology
Monika Vilimova, Maud Contrant, Ramy Randrianjafy, Philippe Dumas, Endrit Elbasani, Paivi M. Ojala, Sebastien Pfeffer, Aurelie Fender
Summary: miRNAs are small regulatory RNAs involved in almost all biological processes, and little is known about the impact of their co-expression from clusters. This study focused on the regulatory mechanism controlling the expression of ten clustered pre-miRNAs from KSHV, identifying the importance of pre-miR-K1 and -K3 in the cleavage efficiency. Mutational analysis showed that the presence of a canonical pre-miRNA at the location is crucial, and the cluster is cleaved in a sequential manner, providing insights for inhibiting the expression of the whole set of miRNAs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Andrea Cipriano, Martina Macino, Giulia Buonaiuto, Tiziana Santini, Beatrice Biferali, Giovanna Peruzzi, Alessio Colantoni, Chiara Mozzetta, Monica Ballarino
Summary: This study identified a novel lncRNA, Lnc-Rewind, which regulates MuSC proliferation and expansion by influencing the expression of skeletal muscle genes and components of the WNT signaling pathway in mouse. The interaction of Lnc-Rewind with the G9a histone lysine methyltransferase mediates the repression of the Wnt7b gene, providing insights into the epigenetic regulation of adult muscle stem cells fate by lncRNAs.
Article
Plant Sciences
Marta Budziszewska, Przemyslaw Wieczorek
Summary: Research described the genetic variability of necrosis-inducing ToTV-Wal'17 derived from ToTV-Wal'03 after long-term passages in plants, including single nucleotide substitutions, amino acid changes in viral polyproteins, and a shorter 3'UTR compared to Wal'03. Sequence analyses revealed that the 3'UTR of RNA1 of ToTV-Wal'17 is the most divergent among all previously described European isolates.
Article
Biochemistry & Molecular Biology
Fernanda Wisnieski, Jaqueline Cruz Geraldis, Leonardo Caires Santos, Mariana Ferreira Leal, Danielle Queiroz Calcagno, Carolina Oliveira Gigek, Elizabeth Suchi Chen, Ana Carolina Anauate, Ricardo Artigiani, Samia Demachki, Paulo Pimentel Assumpcao, Laercio Gomes Lourenco, Carlos Haruo Arasaki, Julie Krainer, Stephan Pabinger, Rommel Rodriguez Burbano, Marilia Arruda Cardoso Smith
Summary: In this study, the research group identified a list of 83 genes potentially modulated by DNA methylation in GC cell lines, with LRRC37A2 playing a role in undifferentiated and poorly differentiated tumors. The study showed that reduced LRRC37A2 mRNA levels and increased LRRC37A2 exon methylation are associated with GC progression, emphasizing the potential utility of gene-related stratification for epigenetic therapy in GC patients.
Article
Biochemistry & Molecular Biology
Emma Price, Olympia Gianfrancesco, Patrick T. Harrison, Bernhard Frank, Vivien J. Bubb, John P. Quinn
Summary: In this study, SVA retrotransposons were shown to have cis-regulatory activity through CRISPR deletion, affecting the expression of TRPV1 and TRPV3 genes. The human-specific SVA insertion between TRPV1 and TRPV3 was found to disrupt their co-expression, highlighting the role of SVA retrotransposons in species-specific gene expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Bingnan Li, Patrice Zeis, Yujie Zhang, Alisa Alekseenko, Eliska Fuerst, Yerma Pareja Sanchez, Gen Lin, Manu M. Tekkedil, Ilaria Piazza, Lars M. Steinmetz, Vicent Pelechano
Summary: Transcriptional memory is crucial for cellular adaptation. Differences in mRNA stability and mRNA degradation machinery between naive and primed cells facilitate faster gene expression response to repeated stimuli.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael Love
Summary: The study introduces a statistical method called airpart for identifying differential cell-type-specific allelic imbalance from single-cell RNA-sequencing data, or dynamics allelic imbalance from other spatially or time-resolved datasets. The method accurately detects common mechanisms of cis-genetic regulation and shows lower error rates in single-cell data.
Article
Biology
Alejandro Prieto, Manuel Bernabeu, Jose Francisco Sanchez-Herrero, Anna Perez-Bosque, Lluisa Mir, Christine Bauer, Carmen Colladcy, Mario Huttener, Antonio Juarez
Summary: Research on Enteroaggregative Escherichia coli (EAEC) has uncovered a novel mechanism involving the 3' UTR of the gene that encodes the transcriptional activator AggR, which affects aggR transcript stability and AggR levels, ultimately impacting EAEC virulence. Additionally, the study has identified new AggR-regulated genes that could play significant roles in EAEC virulence.
COMMUNICATIONS BIOLOGY
(2021)
Article
Genetics & Heredity
Choongwon Jeong, Shigeki Nakagome, Anna Di Rienzo
Article
Biochemistry & Molecular Biology
Shigeki Nakagome, Gorka Alkorta-Aranburu, Roberto Amato, Bryan Howie, Benjamin M. Peter, Richard R. Hudson, Anna Di Rienzo
MOLECULAR BIOLOGY AND EVOLUTION
(2016)
Editorial Material
Cell Biology
Joshua M. Akey, Anna Di Rienzo
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2016)
Article
Multidisciplinary Sciences
Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon, Pontus Skoglund, Iosif Lazaridis, Sriram Sankararaman, Qiaomei Fu, Nadin Rohland, Gabriel Renaud, Yaniv Erlich, Thomas Willems, Carla Gallo, Jeffrey P. Spence, Yun S. Song, Giovanni Poletti, Francois Balloux, George van Driem, Peter de Knijff, Irene Gallego Romero, Aashish R. Jha, Doron M. Behar, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Andres Moreno-Estrada, Olga L. Posukh, Elena Balanovska, Oleg Balanovsky, Sena Karachanak-Yankova, Hovhannes Sahakyan, Draga Toncheva, Levon Yepiskoposyan, Chris Tyler-Smith, Yali Xue, M. Syafiq Abdullah, Andres Ruiz-Linares, Cynthia M. Beall, Anna Di Rienzo, Choongwon Jeong, Elena B. Starikovskaya, Ene Metspalu, Juri Parik, Richard Villems, Brenna M. Henn, Ugur Hodoglugil, Robert Mahley, Antti Sajantila, George Stamatoyannopoulos, Joseph T. S. Wee, Rita Khusainova, Elza Khusnutdinova, Sergey Litvinov, George Ayodo, David Comas, Michael F. Hammer, Toomas Kivisild, William Klitz, Cheryl A. Winkler, Damian Labuda, Michael Bamshad, Lynn B. Jorde, Sarah A. Tishkoff, W. Scott Watkins, Mait Metspalu, Stanislav Dryomov, Rem Sukernik, Lalji Singh, Kumarasamy Thangaraj, Svante Paeaebo, Janet Kelso, Nick Patterson, David Reich
Article
Multidisciplinary Sciences
Silvia N. Kariuki, Joseph C. Maranville, Shaneen S. Baxter, Choongwon Jeong, Shigeki Nakagome, Cara L. Hrusch, David B. Witonsky, Anne I. Sperling, Anna Di Rienzo
Article
Biochemistry & Molecular Biology
Yi Peng, Chaoying Cui, Yaoxi He, Ouzhuluobu, Hui Zhang, Deying Yang, Qu Zhang, Bianbazhuoma, Lixin Yang, Yibo He, Kun Xiang, Xiaoming Zhang, Sushil Bhandari, Peng Shi, Yangla, Dejiquzong, Baimakangzhuo, Duojizhuoma, Yongyue Pan, Cirenyangji, Baimayangji, Gonggalanzi, Caijuan Bai, Bianba, Basang, Ciwangsangbu, Shuhua Xu, Hua Chen, Shiming Liu, Tianyi Wu, Xuebin Qi, Bing Su
MOLECULAR BIOLOGY AND EVOLUTION
(2017)
Article
Multidisciplinary Sciences
Choongwon Jeong, Benjamin M. Peter, Buddha Basnyat, Maniraj Neupane, Cynthia M. Beall, Geoff Childs, Sienna R. Craig, John Novembre, Anna Di Rienzo
Article
Multidisciplinary Sciences
Guido A. Gnecchi-Ruscone, Choongwon Jeong, Sara De Fanti, Stefania Sarno, Michela Trancucci, Davide Gentilini, Anna M. Di Blasio, Mingma G. Sherpa, Phurba T. Sherpa, Giorgio Marinelli, Marco Di Marcello, Luca Natali, Davide Peluzzi, Davide Pettener, Anna Di Rienzo, Donata Luiselli, Marco Sazzini
SCIENTIFIC REPORTS
(2017)
Article
Genetics & Heredity
Choongwon Jeong, David B. Witonsky, Buddha Basnyat, Maniraj Neupane, Cynthia M. Beall, Geoff Childs, Sienna R. Craig, John Novembre, Anna Di Rienzo
Article
Multidisciplinary Sciences
Matthew D. Krause, Ru-Ting Huang, David Wu, Tzu-Pin Shentu, Devin L. Harrison, Michael B. Whalen, Lindsey K. Stolze, Anna Di Rienzo, Ivan P. Moskowitz, Mete Civelek, Casey E. Romanoski, Yun Fang
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Multidisciplinary Sciences
John Lindo, Randall Haas, Courtney Hofman, Mario Apata, Mauricio Moraga, Ricardo A. Verdugo, James T. Watson, Carlos Viviano Llave, David Witonsky, Cynthia Beall, Christina Warinner, John Novembre, Mark Aldenderfer, Anna Di Rienzo
Article
Biology
Shigeki Nakagome, Richard R. Hudson, Anna Di Rienzo
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2019)
Article
Multidisciplinary Sciences
Chi-Chun Liu, David Witonsky, Anna Gosling, Ju Hyeon Lee, Harald Ringbauer, Richard Hagan, Nisha Patel, Raphaela Stahl, John Novembre, Mark Aldenderfer, Christina Warinner, Anna Di Rienzo, Choongwon Jeong
Summary: Present-day Tibetans have genetically and culturally adapted to the high altitude environment of the Tibetan Plateau, with recent research suggesting an early population entering the area within the past 40 thousand years and subsequent groups arriving within the past 10 thousand years. Ancient individuals from high elevation sites in Nepal are most closely related to present-day Tibetans, deriving their ancestry from Late Neolithic populations at the northeastern edge of the Plateau with a minor genetic component from a distinct Paleolithic Eurasian ancestry. Compared to Tibetans, non-Tibetan Tibeto-Burman speakers living at mid-elevations along the Plateau form a distinct genetic cline, and ongoing positive selection of high altitude adaptive alleles is confirmed through a comparison of ancient and present-day highlanders.
NATURE COMMUNICATIONS
(2022)
Article
Evolutionary Biology
Jang Ik Cho, Buddha Basnyat, Choongwon Jeong, Anna Di Rienzo, Geoff Childs, Sienna R. Craig, Jiayang Sun, Cynthia M. Beall
EVOLUTION MEDICINE AND PUBLIC HEALTH
(2017)
Article
Biotechnology & Applied Microbiology
Amy M. Cole, Sean Cox, Choongwon Jeong, Nayia Petousi, Dhana R. Aryal, Yunden Droma, Masayuki Hanaoka, Masao Ota, Nobumitsu Kobayashi, Paolo Gasparini, Hugh Montgomery, Peter Robbins, Anna Di Rienzo, Gianpiero L. Cavalleri
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.