Genome Biology

25/09/2022

Li and colleagues generated a comprehensive map of genomic variation in garlic by resequencing 84 germplasms. They explored the evolutionary history of garlic and found that two groups cultivated in China domesticated independently. They also revealed that independent domestication leads to distinct difference of transcriptomic architecture, few overlaps of deleterious substitutions, and differential selections for the bulb traits in these two garlic groups. These findings provide important insights into the evolutionary history of this Allium species. You can read the full article here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02756-1.

25/09/2022

To identify candidate causal variants at high resolution, Ramstein and Buckler introduced a machine learning method, Prediction of mutation Impact by Calibrated Nucleotide Conservation (PICNC), to predict the impact of mutations at single DNA sites. They demonstrated that nucleotide conservation predicted by this method performs better than the observed nucleotide conservation in maize. It leads to significant functional enrichments and improves genomic prediction for grain yield across elite populations. PICNC is useful for selecting polymorphisms for accurate genomic prediction, and candidate mutations for efficient base editing, which will improve crop breeding. You can read the full article here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02747-2 .

05/09/2022

Long non-coding RNAs, or lncRNAs, are a type of RNA that do not code for proteins but often still have functions regulating cell processes. In a new study Federico Ariel and colleagues report on the functions of a lncRNA, APOLO, in the mode plant Arabidopsis. They describe a new mechanism by which APOLO acts, coordinating a gene silencing function. They also find that another lncRNA, UPAT, which interacts with a lncRNA related to APOLO in humans, has a similar function to APOLO in plants. Strikingly this is despite APOLO and UPAT being unrelated and having little similarity in RNA sequence. The authors say this could point to a mechanism based on the lncRNA molecular structure rather than RNA sequence of the two lncRNAs, and there are also suggestions this could be a mechanism shared across animals and plants.

Read the full article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02750-7

Background RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Results Here, we show that in addit...

24/08/2022

Gui and colleagues generated a super pan-Zea genome from de novo draft assemblies of 721 pan-Zea individuals and 11 previously published assemblies of the Zea genus. They identified the patterns of presence/absence of pan-Zea genes, and constructed a comprehensive genetic variation map with structural variations. Further genetic analyses combined with multi-omics data revealed the impact of the pan-Zea genome and structural variations on maize phenotypic variations. These findings will improve our knowledge about the genetic bases of complex agronomic traits during domestication in maize and provide valuable information for breeding in maize.
You can read the full article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02742-7.

18/08/2022

Soto et al. reveal that OXPHOS complexes are synthesized proportionally across cellular compartments and proportionally to their relative final abundances, and a loss of this balance results in the induction of proteotoxicity pathways. Read the full article here:https: //genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02732-9

Background Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear....

15/08/2022

Detailed studies of the population genetics of African populations are scarce compared to those from other regions. In a new study, Gerald van Eeden and colleagues use genome sequence of individuals of the Nama Khoe-San ethnic group of southern African to develop a genomic map of recombination—the first such map in Africans outside of west Africa—and the demographic history of the population. The authors note that the recombination map, reflecting the complex history of the Nama, may represent the upper limit of how much divergence can be expected for a recombination map in humans.

Read the whole study here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02744-5

Background Recombination maps are  important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Kho...

04/08/2022

An-Yong Xie and coauthors examine how interactions between Cas9-sgRNA and DNA influence repair strategies after double-strand breaks are induced. Other cellular processes like DNA replication and transcription have differing effects on target residence, influencing both on-target and off-target editing. Read the full article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02736-5.

01/08/2022

Alex de Mendoza, Ryan Lister, and colleagues use an engineered zinc-finger fusion protein to force DNA methylation at thousands of promoters in a human cell line. While largely repressive, they surprisingly find that the response across the genome is largely context-specific. In some cases there is a lack of gene repression and in others even increased gene expression. Read the full manuscript here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02728-5.

29/07/2022

The double helix structure of DNA is familiar to many, but it is often overlooked that DNA can form a number of different structures in the nucleus. As well as the canonical B-form helix, these include A-form helix, left-handed Z-form, four-stranded G-quadruplex, and RNA-DNA hybrid R-loops. Ilias Georgakopoulos-Soares and colleagues have reviewed these structures, and corresponding structures in RNA, and their functional roles in the cell such as at gene promoters and termination sites.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02727-6

25/07/2022

Cancer biopsies are often stored as formalin-fixed, paraffin-embedded (FFPE) samples. Yifan Zhang and colleagues in the Sequencing Quality Control phase II (SEQC2) consortium have looked to see if that damages the DNA in a way that affects sequencing. They experimented with different protocols and find that fixation time does not affect quality. Samples from the edges of blocks show increased errors. You can read their study here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02709-8

22/07/2022

Emma Roberts, Daniel Hardy, and coauthors describe Zan, a speciation gene in mammals. This gene encodes a s***m acrosomal protein zonadhesin that mediates adhesion to the egg’s zona pellucida. This gene arose in the stem vertebrates but was lost in multiple lineages while retained in Eutheria. Read the full manuscript: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02721-y.

18/07/2022

Cao and colleagues performed comprehensive metabolic profiling, mGWAS, and expression quantitative trait loci analyses of peach fruits. They identified novel metabolites that are involved in adaptation to different environments, and also found footprints of artificial selection associated with fruit flavor and nutrition. Their findings demonstrated the molecular mechanism of metabolite changes underlying peach evolution.
You can read the full article here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02719-6 .

08/07/2022

There has been a lot of talk about how blockchains could be used in genomics analysis. However, the large size of genomics datasets makes storing them on the chain difficult. Speeds are slow, and approaches for querying the data are limited. Gürsoy, Gerstein and colleagues have preformed a proof-of-principle analysis, allowing efficient storage and retrieval of genome sequences on the blockchain, optimizing data storage, and allowing analysis of the sequence. The benefit is that the owner of the data can control who sees the data. You can read more here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02699-7

07/07/2022

Brandes, Weissbrod and Linial have written a review on the unsolved problems in the human genetics field. They discuss how genome-wide association studies are confounded by factors such as population structure, environmental effects, and genetic interactions. They explore how knowledge of genetic origins of disease can be used to inform treatment. They talk about various biases that can affect studies. You can read about these, and the other problems, here:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02697-9/

20/06/2022

Zhou and colleagues detected novel fusion genes across four Oryza species using their newly developed pipelines. They validated the role of newly formed fusion genes in regulating important phenotype traits by analyzing the CRISPR/Cas9 knockout lines. They also found that novel fusion genes show strong signals of purifying selection. Their findings will provide novel insights into the genome evolution of Oryza.
You can read the full article here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02696-w

14/06/2022

Michael Guo and coauthors examine genetic and epigenetic determinants in multiple sclerosis. Using chromatin accessibility and GWAS data, they identify memory B cells and CD4+ T cells independently drive MS genetic signals. Immunomodulatory treatments suppress chromatin accessibility in these driver cells. Read the full article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02694-y.

10/06/2022

There have been various genome-wide association studies linking genomic variants with severity of COVID-19, but the functional relevance of these variants is so far not clear. Matthew Pahl and colleagues try to dissect these further by mapping the variants to regions of open chromatin in immune cells. These regions are likely to be involved in regulation of gene expression, and this is further strengthened by identifying contacts between the regions and gene promoters. The authors identify a number of candidate genes, which are differentially expressed between patients with mild or severe COVID. You can read the research here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02691-1

30/05/2022

There are many tools for analyzing and comparing ChIP-seq datasets. Thomas Eder and Florian Grebien assess the performance of 33 methods for calling differential peaks. They use simulated and real data to assess the tools, and find that the shape and size of peaks is a major contributor to tool performance. You can read more here:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02686-y

28/05/2022

Lopez-Gomollon and colleagues investigated the mechanism of changes in gene expression in response to interspecific hybridization in tomato. They demonstrated that small RNAs derived from endogenous (para)retroviruses (EPRV) and perturbation of DCL2-mediated sRNA silencing drive altered gene expression in interspecific Solanum hybrids.
You can read the full article here:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02685-z.

19/05/2022

Khaliq et al. use single-cell sequencing to investigates the drivers of poor prognosis in colorectal cancer with high content of cancer-associated fibroblasts and C1Q+TAM. They uncover distinct cellular phenotypes of fibroblasts, T cells, and the myeloid compartment within the colorectal cancer CMS classification scheme. Results further show that colorectal cancers fit better to a tumour immune stromal continuum rather than discrete subtypes proposed by bulk transcriptomics. These results will assist in more precise prognosis and the design of more effective treatment strategies.
Read the full article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02677-z

13/05/2022

Translation of mRNAs in eukaryotes typically starts at the codon AUG. Non-AUG initiation, when it occurs, is said to be leaky, starting translation at an alternative site. In a new review article Dmitry Andreev, Pavel Baranov and colleagues, discuss the current understating of non-AUG initiation in mammals, and argue that it has a substantial role in diversity of the proteome.

Read the article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02674-2

Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due to start codon plurality within the same RNA. This plurality is often due to the failure o...

11/05/2022

Li Fang and colleagues present DeepRepeat, a method for detecting short tandem repeats in Oxford Nanopore sequencing data. Nanopores read sequencing by measuring changes in electrical current as DNA is pulled through a pore. Usually, these 'squiggle' traces are converted into bases by machine learning methods, but increasingly methods are being developed that work with the current traces directly. DeepRepeat is one such method which converts the squiggle into a colored image, which can be interpreted by image analysis software to identify short tandem repeats. Short tandem repeats are areas of the genome featuring a string of repeats of a short sequence. They are frequently associated with disease, and are hard to resolve from standard short-read sequencing methods. Thus DeepRepeat is a promising approach for analysis of genetic disease. You can read more here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02670-6

03/05/2022

Madsen-Østerbye and colleagues map genome associations with the nuclear lamina in adipose stem cells differentiating into adipocytes. Adipogenic genes are released from lamina-associated domains in order to be expressed, whereas genes not involved in differentiation are sequestered at the lamina. Differentially expressed genes associated with short-range enhancers within lamina associated domains. You can read the research here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02662-6

25/04/2022

Ferrero-Serrano and colleagues demonstrated the existence of climate-related riboSNitches in plants by experimental analyses. They also provided the first pan-genome-wide prediction of riboSNitches in plants. They expanded the CLIMtools web resource and developed a novel web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation. You can read the full article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02656-4 .

11/04/2022

Jiang, Raj, and coauthors examine whether intrinsic differences in the initial population of induced pluripotent stem cells influence different outcomes in cardiac cardiac differentiation. Using barcoding and imaging approaches, they show that there is substantial heterogeneity in the initial population, this is not the main factor in influencing the outcome. Cell type specification occurs early and is maintained during differentiation. Read the full article: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02654-6.

08/04/2022

Promoter sequences in the genome are sites of a lot of consequential genetic variation, and also sites of pervasive loss and gain in the evolution between species. In a new study, Robert Young, Lana Talmane, Sophie Marion de Procé and Martin Taylor, describe this in the human genome, and show that promoters subject to turnover, have been subject to natural selection and are also sites of mutation and variants that influence important traits. This shows that these evolutionarily volatile promoters are a source of evolutionary innovation.

Read the study here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02634-w

Background Promoters are sites of transcription initiation that harbour a high concentration of phenotype-associated genetic variation. The evolutionary gain and loss of promoters between species (collectively, termed turnover) is pervasive across mammalian genomes and may play a prominent role in d...

04/04/2022

Shi et al. investigate the single-cell ecosystem of tumor thrombus in renal cell carcinoma. They show evidence of phenotypic heterogeneity between primary tumors and tumor thrombus, in terms of tumor cells, immune cells, and stromal cells, and enhanced remodelling of the extracellular matrix in the tumor thrombus.
Read the full paper here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02651-9

04/04/2022

By a combination of transcriptome-wide association studies, genome-wide association studies and gene module analysis using 382 Brassica napus accessions, Zhang and colleagues identified genes, loci, and regulatory networks that are associated with the seed coat content (SCC), which provides insights into the genetic basis of SCC trait and will accelerate B. napus breeding. You can read the full article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02647-5.

21/03/2022

Paralogs that arise from gene duplications during genome evolution enable genetic redundancy and phenotypic robustness. How paralogs regulate such robustness is unknown. Huang and colleagues explored the genetic relationship and protein behavior of ALOG family transcriptional factors with diverse transcriptional abundance in tomato shoot meristems. They demonstrated how TFAM (TERMINATING FLOWER FAMILY MEMBERs) proteins work together via heterotypic condensation to achieve a robust transcriptional control of stem cell fate transition in tomato. You can read the full article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02646-6.

21/03/2022

Ma and colleagues generated a high-quality YY genome assembly of spinach by long-read sequencing. They characterized a s*x determination region on chromosome 1, and identified a Y-specific gene as strong candidate for the s*x determination or differentiation factor. Further comprehensive population genomic analyses based on resequenced genomes provide insights into spinach domestication, introgression, and genetic basis of important agronomic traits. You can read the full article here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02633-x .