Genome Biology最新文献_第7页

ReSeq simulates realistic Illumina high-throughput sequencing data. ReSeq模拟真实的Illumina高通量测序数据。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-19 DOI: 10.1186/s13059-021-02265-7

Stephan Schmeing, Mark D Robinson

引用次数: 5

Promoting reproducibility with Code Ocean. 使用代码海洋提高可再现性。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-19 DOI: 10.1186/s13059-021-02299-x

Barbara Cheifet

引用次数: 8

iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks. iMAP：通过对抗性配对转移网络整合多个单细胞数据集。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-18 DOI: 10.1186/s13059-021-02280-8

Dongfang Wang, Siyu Hou, Lei Zhang, Xiliang Wang, Baolin Liu, Zemin Zhang

引用次数: 0

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions. LINE 反转座子是哺乳动物组织特异性和进化动态调控区域的特征。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-18 DOI: 10.1186/s13059-021-02260-y

Maša Roller, Ericca Stamper, Diego Villar, Osagie Izuogu, Fergal Martin, Aisling M Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T Odom, Paul Flicek

{"title":"LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.","authors":"Maša Roller, Ericca Stamper, Diego Villar, Osagie Izuogu, Fergal Martin, Aisling M Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T Odom, Paul Flicek","doi":"10.1186/s13059-021-02260-y","DOIUrl":"10.1186/s13059-021-02260-y","url":null,"abstract":"Background: To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals.Results: The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species.Conclusions: Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"22 1","pages":"62"},"PeriodicalIF":12.3,"publicationDate":"2021-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25381713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Assembly of hundreds of novel bacterial genomes from the chicken caecum. 作者更正:来自鸡盲肠的数百种新型细菌基因组的组装。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-12 DOI: 10.1186/s13059-021-02284-4

Laura Glendinning, Robert D Stewart, Mark J Pallen, Kellie A Watson, Mick Watson

引用次数: 4

The data-hypothesis relationship. 数据-假设关系。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-10 DOI: 10.1186/s13059-021-02276-4

Teppo Felin, Jan Koenderink, Joachim I Krueger, Denis Noble, George F R Ellis

引用次数: 10

Data bias. 数据偏差。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-10 DOI: 10.1186/s13059-021-02278-2

Teppo Felin, Jan Koenderink, Joachim I Krueger, Denis Noble, George F R Ellis

引用次数: 7

3 ^'-5 ^' crosstalk contributes to transcriptional bursting. 3 '-5 '串扰有助于转录突变。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-04 DOI: 10.1186/s13059-020-02227-5

Massimo Cavallaro, Mark D Walsh, Matt Jones, James Teahan, Simone Tiberi, Bärbel Finkenstädt, Daniel Hebenstreit

{"title":"3 '-5 ' crosstalk contributes to transcriptional bursting.","authors":"Massimo Cavallaro, Mark D Walsh, Matt Jones, James Teahan, Simone Tiberi, Bärbel Finkenstädt, Daniel Hebenstreit","doi":"10.1186/s13059-020-02227-5","DOIUrl":"10.1186/s13059-020-02227-5","url":null,"abstract":"Background: Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different numbers of an mRNA species in isogenic cell populations. Several factors contributing to transcriptional bursting have been identified, usually classified as intrinsic, in other words local to single genes, or extrinsic, relating to the macroscopic state of the cell. However, some possible contributors have not been explored yet. Here, we focus on processes at the 3 ' and 5 ' ends of a gene that enable reinitiation of transcription upon termination.Results: Using Bayesian methodology, we measure the transcriptional bursting in inducible transgenes, showing that perturbation of polymerase shuttling typically reduces burst size, increases burst frequency, and thus limits transcriptional noise. Analysis based on paired-end tag sequencing (PolII ChIA-PET) suggests that this effect is genome wide. The observed noise patterns are also reproduced by a generative model that captures major characteristics of the polymerase flux between the ends of a gene and a phase-separated compartment.Conclusions: Interactions between the 3 ' and 5 ' ends of a gene, which facilitate polymerase recycling, are major contributors to transcriptional noise.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"22 1","pages":"56"},"PeriodicalIF":12.3,"publicationDate":"2021-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7860045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25332581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GeneWalk identifies relevant gene functions for a biological context using network representation learning. GeneWalk 利用网络表征学习技术识别生物背景下的相关基因功能。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-02-02 DOI: 10.1186/s13059-021-02264-8

Robert Ietswaart, Benjamin M Gyori, John A Bachman, Peter K Sorger, L Stirling Churchman

引用次数: 0

A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis. 一项全面的增强子筛选确定了TRAM2是YAP肿瘤发生的关键和新的介质。

IF 12.3 1区生物学

Genome Biology Pub Date : 2021-01-29 DOI: 10.1186/s13059-021-02272-8

Li Li, Alejandro P Ugalde, Colinda L G J Scheele, Sebastian M Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gozde Korkmaz, Ran Elkon, Miao-Ping Chien, Li You, Pin-Rui Su, Onno B Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber, Ruiqi Han, Pieter C van Breugel, Rui Lopes, Peter Ten Dijke, Jacco van Rheenen, Reuven Agami

{"title":"A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis.","authors":"Li Li, Alejandro P Ugalde, Colinda L G J Scheele, Sebastian M Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gozde Korkmaz, Ran Elkon, Miao-Ping Chien, Li You, Pin-Rui Su, Onno B Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber, Ruiqi Han, Pieter C van Breugel, Rui Lopes, Peter Ten Dijke, Jacco van Rheenen, Reuven Agami","doi":"10.1186/s13059-021-02272-8","DOIUrl":"10.1186/s13059-021-02272-8","url":null,"abstract":"Background: Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiveness. Although thousands of YAP/TEAD4 binding-sites are annotated, their functional importance is unknown. Here, we aim at further identification of enhancer elements that are required for YAP functions.Results: We first apply genome-wide ChIP profiling of YAP to systematically identify enhancers that are bound by YAP/TEAD4. Next, we implement a genetic approach to uncover functions of YAP/TEAD4-associated enhancers, demonstrate its robustness, and use it to reveal a network of enhancers required for YAP-mediated proliferation. We focus on EnhancerTRAM2, as its target gene TRAM2 shows the strongest expression-correlation with YAP activity in nearly all tumor types. Interestingly, TRAM2 phenocopies the YAP-induced cell proliferation, migration, and invasion phenotypes and correlates with poor patient survival. Mechanistically, we identify FSTL-1 as a major direct client of TRAM2 that is involved in these phenotypes. Thus, TRAM2 is a key novel mediator of YAP-induced oncogenic proliferation and cellular invasiveness.Conclusions: YAP is a transcription co-factor that binds to thousands of enhancer loci and stimulates tumor aggressiveness. Using unbiased functional approaches, we dissect YAP enhancer network and characterize TRAM2 as a novel mediator of cellular proliferation, migration, and invasion. Our findings elucidate how YAP induces cancer aggressiveness and may assist diagnosis of cancer metastasis.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"22 1","pages":"54"},"PeriodicalIF":12.3,"publicationDate":"2021-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13059-021-02272-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25310983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1