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https://www.readbyqxmd.com/read/28637491/stable-centromere-positioning-in-diverse-sequence-contexts-of-complex-and-satellite-centromeres-of-maize-and-wild-relatives
#1
Jonathan I Gent, Na Wang, R Kelly Dawe
BACKGROUND: Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large (~2 Mb) centromeres are not dominated by satellite DNA. These centromeres, which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3)...
June 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629478/genetic-epigenetic-interactions-in-cis-a-major-focus-in-the-post-gwas-era
#2
REVIEW
Catherine Do, Alyssa Shearer, Masako Suzuki, Mary Beth Terry, Joel Gelernter, John M Greally, Benjamin Tycko
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS)...
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629467/chromatin-marks-and-ambient-temperature-dependent-flowering-strike-up-a-novel-liaison
#3
Alexander Steffen, Dorothee Staiger
A distinct chromatin mark, H3K36me3, has been found to engage in temperature-dependent alternative splicing and ambient temperature-dependent flowering-time control in Arabidopsis.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629446/increasing-mapping-precision-of-genome-wide-association-studies-to-genotype-and-impute-sequence-or-both
#4
Zhaoming Wang, Nilanjan Chatterjee
Fine-mapping to identify causal variants in genome-wide association studies remains challenging. A recent study provides guidance for future research.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28629399/epigenomics-dissecting-hybridization-and-polyploidization
#5
Scott A Jackson
Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication affect gene expression.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28622766/translational-contributions-to-tissue-specificity-in-rhythmic-and-constitutive-gene-expression
#6
Violeta Castelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich, David Gatfield
BACKGROUND: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney and contrasted our findings with liver data available from the same mice. RESULTS: Rhythmic translation of constantly abundant messenger RNAs (mRNAs) affects largely non-overlapping transcript sets with distinct phase clustering in the two organs...
June 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28619099/differentiated-demographic-histories-and-local-adaptations-between-sherpas-and-tibetans
#7
Chao Zhang, Yan Lu, Qidi Feng, Xiaoji Wang, Haiyi Lou, Jiaojiao Liu, Zhilin Ning, Kai Yuan, Yuchen Wang, Ying Zhou, Lian Deng, Lijun Liu, Yajun Yang, Shilin Li, Lifeng Ma, Zhiying Zhang, Li Jin, Bing Su, Longli Kang, Shuhua Xu
BACKGROUND: The genetic relationships reported by recent studies between Sherpas and Tibetans are controversial. To gain insights into the population history and the genetic basis of high-altitude adaptation of the two groups, we analyzed genome-wide data in 111 Sherpas (Tibet and Nepal) and 177 Tibetans (Tibet and Qinghai), together with available data from present-day human populations. RESULTS: Sherpas and Tibetans show considerable genetic differences and can be distinguished as two distinct groups, even though the divergence between them (~3200-11,300 years ago) is much later than that between Han Chinese and either of the two groups (~6200-16,000 years ago)...
June 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28619072/the-arabidopsis-swi-snf-protein-baf60-mediates-seedling-growth-control-by-modulating-dna-accessibility
#8
Teddy Jégu, Alaguraj Veluchamy, Juan S Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M Mahfouz, Heribert Hirt, Cécile Raynaud, Moussa Benhamed
BACKGROUND: Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored. RESULTS: In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes...
June 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615029/micrornas-control-mrna-fate-by-compartmentalization-based-on-3-utr-length-in-male-germ-cells
#9
Ying Zhang, Chong Tang, Tian Yu, Ruirui Zhang, Huili Zheng, Wei Yan
BACKGROUND: Post-transcriptional regulation of gene expression can be achieved through the control of mRNA stability, cytoplasmic compartmentalization, 3' UTR length and translational efficacy. Spermiogenesis, a process through which haploid male germ cells differentiate into spermatozoa, represents an ideal model for studying post-transcriptional regulation in vivo because it involves a large number of transcripts that are physically sequestered in ribonucleoprotein particles (RNPs) and thus subjected to delayed translation...
June 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615074/correspondence-on-lovell-et-al-response-to-bornel%C3%A3-v-et-al
#10
Peter V Lovell, Claudio V Mello
While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that specific groups of syntenic protein-coding genes are missing in birds.This is a response to the Correspondence article: https://www.dx.doi.org/10.1186/s13059-017-1231-1.
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615073/crispr-cas9-mediated-genome-editing-induces-exon-skipping-by-alternative-splicing-or-exon-deletion
#11
Haiwei Mou, Jordan L Smith, Lingtao Peng, Hao Yin, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M Ozata, Yingxiang Li, Daniel G Anderson, Charles P Emerson, Erik J Sontheimer, Melissa J Moore, Zhiping Weng, Wen Xue
CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exons. For example, CRISPR-mediated editing of β-catenin exon 3, which encodes an autoinhibitory domain, induces partial skipping of the in-frame exon and nuclear accumulation of β-catenin. A single sgRNA can induce small insertions or deletions that partially alter splicing or unexpected larger deletions that remove exons...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615069/regulatory-landscape-fusion-in-rhabdomyosarcoma-through-interactions-between-the-pax3-promoter-and-foxo1-regulatory-elements
#12
Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D Acemel, Juan J Tena, Peter W J Rigby, Damien P Devos, Jose L Gómez-Skarmeta, Jaime J Carvajal
BACKGROUND: The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation is achieved through the interactions of the regulatory elements within them or if these interactions are favoured by the pre-existence of TADs. If the latter is true, the fusion of two independent TADs should result in the rewiring of the transcriptional landscape and the generation of ectopic contacts...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615067/correspondence-on-lovell-et-al-identification-of-chicken-genes-previously-assumed-to-be-evolutionarily-lost
#13
Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Ken Pendavis, Shane C Burgess, Manfred Grabherr, Miriam Friedman-Einat, Leif Andersson
Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases. Hence, the occurrence of syntenic groups of vertebrate genes that have not been observed in Aves does not prove the evolutionary loss of such genes.Please see related Research article: http://dx.doi.org/10.1186/s13059-014-0565-1 and Please see response from Lovell et al: https://www...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615063/lineage-specific-rediploidization-is-a-mechanism-to-explain-time-lags-between-genome-duplication-and-evolutionary-diversification
#14
Fiona M Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R Hvidsten, Anthony K Redmond, Sigbjørn Lien, Samuel A M Martin, Peter W H Holland, Simen R Sandve, Daniel J Macqueen
BACKGROUND: The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615043/-like-sugar-in-milk-reconstructing-the-genetic-history-of-the-parsi-population
#15
Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi, Kurush Dalal, Shagufta Khaliq, Syed Qasim Mehdi, Lalji Singh, Mait Metspalu, Toomas Kivisild, Chris Tyler-Smith, Richard Villems, Kumarasamy Thangaraj
BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615041/epigenetic-aging-clocks-in-mice-and-men
#16
Wolfgang Wagner
Epigenetic clocks provide powerful tools to evaluate nutritional, hormonal, and genetic effects on aging. What can we learn from differences between species in how these clocks tick?Please see related Research articles: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1203-5 , http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1186-2 , http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1187-1 and http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1185-3...
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28615035/unexpected-consequences-exon-skipping-caused-by-crispr-generated-mutations
#17
Joshua J Sharpe, Thomas A Cooper
A new study finds that splicing disruption is a frequent consequence of mutations generated by CRISPR/Cas9 gene-editing technology, and alleles designed to be null can express aberrant proteins. This new information allows enhanced quality control procedures to select the best mutant alleles generated by CRISPR/Cas9.Please see related Method article: https://www.doi.org/10.1186/s13059-017-1237-8.
June 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28595587/multiple-gene-movements-into-and-out-of-haploid-sex-chromosomes
#18
Agnieszka P Lipinska, Nicholas R T Toda, Svenja Heesch, Akira F Peters, J Mark Cock, Susana M Coelho
BACKGROUND: Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out for haploid phase UV sex chromosomes. Here, we explore sex-specific sequences of seven brown algal species to understand the dynamics of the sex-determining region (SDR) gene content across 100 million years of evolution. RESULTS: A core set of sex-linked genes is conserved across all the species investigated, but we also identify modifications of both the U and the V SDRs that occurred in a lineage-specific fashion...
June 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28566089/histone-h3-lysine-36-methylation-affects-temperature-induced-alternative-splicing-and-flowering-in-plants
#19
A Pajoro, E Severing, G C Angenent, R G H Immink
BACKGROUND: Global warming severely affects flowering time and reproductive success of plants. Alternative splicing of pre-messenger RNA (mRNA) is an important mechanism underlying ambient temperature-controlled responses in plants, yet its regulation is poorly understood. An increase in temperature promotes changes in plant morphology as well as the transition from the vegetative to the reproductive phase in Arabidopsis thaliana via changes in splicing of key regulatory genes. Here we investigate whether a particular histone modification affects ambient temperature-induced alternative splicing and flowering time...
June 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/28569170/the-developmental-regulator-pkl-is-required-to-maintain-correct-dna-methylation-patterns-at-rna-directed-dna-methylation-loci
#20
Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He, Heng Zhang
BACKGROUND: The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana. RESULTS: Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter...
May 31, 2017: Genome Biology
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