Genome Biology最新文献_第3页

Author Correction: Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG. 作者更正:使用scREG对单细胞多组基因表达和染色质可及性数据进行调控分析。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-10-13 DOI: 10.1186/s13059-022-02786-9

Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong

引用次数: 2

Enhanced mitochondrial DNA editing in mice using nuclear-exported TALE-linked deaminases and nucleases. 利用核输出的 TALE 链接脱氨酶和核酸酶加强小鼠线粒体 DNA 编辑。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-10-12 DOI: 10.1186/s13059-022-02782-z

Seonghyun Lee, Hyunji Lee, Gayoung Baek, Eunji Namgung, Joo Min Park, Sanghun Kim, Seongho Hong, Jin-Soo Kim

引用次数: 0

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels. KAGE:快速无比对图的snp和短索引基因分型。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-10-04 DOI: 10.1186/s13059-022-02771-2

Ivar Grytten, Knut Dagestad Rand, Geir Kjetil Sandve

引用次数: 1

H3K18 lactylation marks tissue-specific active enhancers. H3K18乳酸化标志着组织特异性活性增强剂。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-10-03 DOI: 10.1186/s13059-022-02775-y

Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R Ruiz, Ferdinand von Meyenn

{"title":"H3K18 lactylation marks tissue-specific active enhancers.","authors":"Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R Ruiz, Ferdinand von Meyenn","doi":"10.1186/s13059-022-02775-y","DOIUrl":"https://doi.org/10.1186/s13059-022-02775-y","url":null,"abstract":"Background: Histone lactylation has been recently described as a novel histone post-translational modification linking cellular metabolism to epigenetic regulation.Results: Given the expected relevance of this modification and current limited knowledge of its function, we generate genome-wide datasets of H3K18la distribution in various in vitro and in vivo samples, including mouse embryonic stem cells, macrophages, adipocytes, and mouse and human skeletal muscle. We compare them to profiles of well-established histone modifications and gene expression patterns. Supervised and unsupervised bioinformatics analysis shows that global H3K18la distribution resembles H3K27ac, although we also find notable differences. H3K18la marks active CpG island-containing promoters of highly expressed genes across most tissues assessed, including many housekeeping genes, and positively correlates with H3K27ac and H3K4me3 as well as with gene expression. In addition, H3K18la is enriched at active enhancers that lie in proximity to genes that are functionally important for the respective tissue.Conclusions: Overall, our data suggests that H3K18la is not only a marker for active promoters, but also a mark of tissue specific active enhancers.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"23 1","pages":"207"},"PeriodicalIF":12.3,"publicationDate":"2022-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33486751","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: 12

Repeated turnovers keep sex chromosomes young in willows. 在柳树中，反复的循环使性染色体保持年轻。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-09-23 DOI: 10.1186/s13059-022-02769-w

Deyan Wang, Yiling Li, Mengmeng Li, Wenlu Yang, Xinzhi Ma, Lei Zhang, Yubo Wang, Yanlin Feng, Yuanyuan Zhang, Ran Zhou, Brian J Sanderson, Ken Keefover-Ring, Tongming Yin, Lawrence B Smart, Stephen P DiFazio, Jianquan Liu, Matthew Olson, Tao Ma

{"title":"Repeated turnovers keep sex chromosomes young in willows.","authors":"Deyan Wang, Yiling Li, Mengmeng Li, Wenlu Yang, Xinzhi Ma, Lei Zhang, Yubo Wang, Yanlin Feng, Yuanyuan Zhang, Ran Zhou, Brian J Sanderson, Ken Keefover-Ring, Tongming Yin, Lawrence B Smart, Stephen P DiFazio, Jianquan Liu, Matthew Olson, Tao Ma","doi":"10.1186/s13059-022-02769-w","DOIUrl":"https://doi.org/10.1186/s13059-022-02769-w","url":null,"abstract":"Background: Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively.Results: Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the \"deleterious mutation load\" and \"sexually antagonistic selection\" theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration.Conclusions: Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"23 1","pages":"200"},"PeriodicalIF":12.3,"publicationDate":"2022-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9502649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33479701","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: 6

Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation. 脊椎动物 CPEB 蛋白的比较分析确定了两个亚家族，它们在转录后基因调控中具有协调但不同的功能。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-09-12 DOI: 10.1186/s13059-022-02759-y

Berta Duran-Arqué, Manuel Cañete, Chiara Lara Castellazzi, Anna Bartomeu, Anna Ferrer-Caelles, Oscar Reina, Adrià Caballé, Marina Gay, Gianluca Arauz-Garofalo, Eulalia Belloc, Raúl Mendez

{"title":"Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation.","authors":"Berta Duran-Arqué, Manuel Cañete, Chiara Lara Castellazzi, Anna Bartomeu, Anna Ferrer-Caelles, Oscar Reina, Adrià Caballé, Marina Gay, Gianluca Arauz-Garofalo, Eulalia Belloc, Raúl Mendez","doi":"10.1186/s13059-022-02759-y","DOIUrl":"10.1186/s13059-022-02759-y","url":null,"abstract":"Background: Vertebrate CPEB proteins bind mRNAs at cytoplasmic polyadenylation elements (CPEs) in their 3' UTRs, leading to cytoplasmic changes in their poly(A) tail lengths; this can promote translational repression or activation of the mRNA. However, neither the regulation nor the mechanisms of action of the CPEB family per se have been systematically addressed to date.Results: Based on a comparative analysis of the four vertebrate CPEBs, we determine their differential regulation by phosphorylation, the composition and properties of their supramolecular assemblies, and their target mRNAs. We show that all four CPEBs are able to recruit the CCR4-NOT deadenylation complex to repress the translation. However, their regulation, mechanism of action, and target mRNAs define two subfamilies. Thus, CPEB1 forms ribonucleoprotein complexes that are remodeled upon a single phosphorylation event and are associated with mRNAs containing canonical CPEs. CPEB2-4 are regulated by multiple proline-directed phosphorylations that control their liquid-liquid phase separation. CPEB2-4 mRNA targets include CPEB1-bound transcripts, with canonical CPEs, but also a specific subset of mRNAs with non-canonical CPEs.Conclusions: Altogether, these results show how, globally, the CPEB family of proteins is able to integrate cellular cues to generate a fine-tuned adaptive response in gene expression regulation through the coordinated actions of all four members.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"23 1","pages":"192"},"PeriodicalIF":12.3,"publicationDate":"2022-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33463627","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

Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation. 通过 CPEB4-repressor 复合物介导的 mRNA 降解控制即时早期基因的表达。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-09-12 DOI: 10.1186/s13059-022-02760-5

Fabian Poetz, Svetlana Lebedeva, Johanna Schott, Doris Lindner, Uwe Ohler, Georg Stoecklin

{"title":"Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.","authors":"Fabian Poetz, Svetlana Lebedeva, Johanna Schott, Doris Lindner, Uwe Ohler, Georg Stoecklin","doi":"10.1186/s13059-022-02760-5","DOIUrl":"10.1186/s13059-022-02760-5","url":null,"abstract":"Background: Cytoplasmic polyadenylation element-binding protein 4 (CPEB4) is known to associate with cytoplasmic polyadenylation elements (CPEs) located in the 3' untranslated region (UTR) of specific mRNAs and assemble an activator complex promoting the translation of target mRNAs through cytoplasmic polyadenylation.Results: Here, we find that CPEB4 is part of an alternative repressor complex that mediates mRNA degradation by associating with the evolutionarily conserved CCR4-NOT deadenylase complex. We identify human CPEB4 as an RNA-binding protein (RBP) with enhanced association to poly(A) RNA upon inhibition of class I histone deacetylases (HDACs), a condition known to cause widespread degradation of poly(A)-containing mRNA. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis using endogenously tagged CPEB4 in HeLa cells reveals that CPEB4 preferentially binds to the 3'UTR of immediate early gene mRNAs, at G-containing variants of the canonical U- and A-rich CPE located in close proximity to poly(A) sites. By transcriptome-wide mRNA decay measurements, we find that the strength of CPEB4 binding correlates with short mRNA half-lives and that loss of CPEB4 expression leads to the stabilization of immediate early gene mRNAs. Akin to CPEB4, we demonstrate that CPEB1 and CPEB2 also confer mRNA instability by recruitment of the CCR4-NOT complex.Conclusions: While CPEB4 was previously known for its ability to stimulate cytoplasmic polyadenylation, our findings establish an additional function for CPEB4 as the RNA adaptor of a repressor complex that enhances the degradation of short-lived immediate early gene mRNAs.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"23 1","pages":"193"},"PeriodicalIF":12.3,"publicationDate":"2022-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33470614","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

Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP. 位置主题分析揭示了 CLIP 观察到的蛋白质-RNA 相互作用的特异性程度。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-09-09 DOI: 10.1186/s13059-022-02755-2

Klara Kuret, Aram Gustav Amalietti, D Marc Jones, Charlotte Capitanchik, Jernej Ule

{"title":"Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP.","authors":"Klara Kuret, Aram Gustav Amalietti, D Marc Jones, Charlotte Capitanchik, Jernej Ule","doi":"10.1186/s13059-022-02755-2","DOIUrl":"10.1186/s13059-022-02755-2","url":null,"abstract":"Background: Crosslinking and immunoprecipitation (CLIP) is a method used to identify in vivo RNA-protein binding sites on a transcriptome-wide scale. With the increasing amounts of available data for RNA-binding proteins (RBPs), it is important to understand to what degree the enriched motifs specify the RNA-binding profiles of RBPs in cells.Results: We develop positionally enriched k-mer analysis (PEKA), a computational tool for efficient analysis of enriched motifs from individual CLIP datasets, which minimizes the impact of technical and regional genomic biases by internal data normalization. We cross-validate PEKA with mCross and show that the use of input control for background correction is not required to yield high specificity of enriched motifs. We identify motif classes with common enrichment patterns across eCLIP datasets and across RNA regions, while also observing variations in the specificity and the extent of motif enrichment across eCLIP datasets, between variant CLIP protocols, and between CLIP and in vitro binding data. Thereby, we gain insights into the contributions of technical and regional genomic biases to the enriched motifs, and find how motif enrichment features relate to the domain composition and low-complexity regions of the studied proteins.Conclusions: Our study provides insights into the overall contributions of regional binding preferences, protein domains, and low-complexity regions to the specificity of protein-RNA interactions, and shows the value of cross-motif and cross-RBP comparison for data interpretation. Our results are presented for exploratory analysis via an online platform in an RBP-centric and motif-centric manner ( https://imaps.goodwright.com/apps/peka/ ).","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"23 1","pages":"191"},"PeriodicalIF":12.3,"publicationDate":"2022-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9461102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33460725","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

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2. 使用Cuttlefish构建压缩de Bruijn图的可伸缩、超快速和低内存。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-09-08 DOI: 10.1186/s13059-022-02743-6

Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro

引用次数: 3

Genomic insights into the evolutionary history and diversification of bulb traits in garlic. 大蒜鳞茎性状的进化历史和多样化的基因组见解。

IF 12.3 1区生物学

Genome Biology Pub Date : 2022-09-07 DOI: 10.1186/s13059-022-02756-1

Ningyang Li, Xueyu Zhang, Xiudong Sun, Siyuan Zhu, Yi Cheng, Meng Liu, Song Gao, Jiangjiang Zhang, Yanzhou Wang, Xiai Yang, Jianrong Chen, Fu Li, Qiaoyun He, Zheng Zeng, Xiaoge Yuan, Zhiman Zhou, Longchuan Ma, Taotao Wang, Xiang Li, Hanqiang Liu, Yupeng Pan, Mengyan Zhou, Chunsheng Gao, Gang Zhou, Zhenlin Han, Shiqi Liu, Jianguang Su, Zhihui Cheng, Shilin Tian, Touming Liu

{"title":"Genomic insights into the evolutionary history and diversification of bulb traits in garlic.","authors":"Ningyang Li, Xueyu Zhang, Xiudong Sun, Siyuan Zhu, Yi Cheng, Meng Liu, Song Gao, Jiangjiang Zhang, Yanzhou Wang, Xiai Yang, Jianrong Chen, Fu Li, Qiaoyun He, Zheng Zeng, Xiaoge Yuan, Zhiman Zhou, Longchuan Ma, Taotao Wang, Xiang Li, Hanqiang Liu, Yupeng Pan, Mengyan Zhou, Chunsheng Gao, Gang Zhou, Zhenlin Han, Shiqi Liu, Jianguang Su, Zhihui Cheng, Shilin Tian, Touming Liu","doi":"10.1186/s13059-022-02756-1","DOIUrl":"https://doi.org/10.1186/s13059-022-02756-1","url":null,"abstract":"Background: Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown.Results: Here we report a comprehensive map of garlic genomic variation, consisting of amazingly 129.4 million variations. Evolutionary analysis indicates that the garlic population diverged at least 100,000 years ago, and the two groups cultivated in China were domesticated from two independent routes. Consequently, 15.0 and 17.5% of genes underwent an expression change in two cultivated groups, causing a reshaping of their transcriptomic architecture. Furthermore, we find independent domestication leads to few overlaps of deleterious substitutions in these two groups due to separate accumulation and selection-based removal. By analysis of selective sweeps, genome-wide trait associations and associated transcriptomic analysis, we uncover differential selections for the bulb traits in these two garlic groups during their domestication.Conclusions: This study provides valuable resources for garlic genomics-based breeding, and comprehensive insights into the evolutionary history of this clonal-propagated crop.","PeriodicalId":48922,"journal":{"name":"Genome Biology","volume":"23 1","pages":"188"},"PeriodicalIF":12.3,"publicationDate":"2022-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9450234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33448119","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: 3