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Effective and precise adenine base editing in mouse zygotes

, Hongwei Sun, Xiya Zhang, Xiaowei Xie, Jinran Zhang, Yaofu Bai, Xueling Ouyang, Shengyao Zhi, Yuanyan Xiong, Wenbin Ma, Dan Liu, Junjiu Huang and Zhou Songyang declare that they have no conflict of interest

Correction of β-thalassemia mutant by base editor in human embryos

, Xiya Zhang, Ying Sun, Yuanyan Xiong, Wenbin Ma, Yongxiang Liu, Yali Wang, Jianpei Fang, Dan Liu, Zhou Songyang, Canquan Zhou, and Junjiu Huang declare that they have no conflict of interest. All

Effective gene editing by high-fidelity base editor 2 in mouse zygotes

Zhang, Yuxi Chen, Chenhui Ding, Yuanyan Xiong, Wenbin Ma, Dan Liu, Junjiu Huang, and Zhou Songyang declare that they have no conflict of interest. All institutional and national guidelines for the care

Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures

Background Transcription factors (TF) regulate gene expression by binding DNA regulatory regions. Transcription factor binding sites (TFBSs) are conserved not only in primary DNA sequences but also in DNA structures. However, the global relationship between TFs and their preferred DNA structures remains to be elucidated. Results In this paper, we have developed a computational...

CCSI: a database providing chromatin–chromatin spatial interaction information

Distal regulatory elements have been shown to regulate gene transcription through spatial interactions, and single nucleotide polymorphisms (SNPs) are linked with distal gene expression by spatial proximity, which helps to explain the causal role of disease-associated SNPs in non-coding region. Therefore, studies on spatial interactions between chromatin have created a new avenue...

Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells

A recently developed strategy of sequencing alternative polyadenylation (APA) sites (SAPAS) with second-generation sequencing technology can be used to explore complete genome-wide patterns of tandem APA sites and global gene expression profiles. spermatogonial stem cells (SSCs) maintain long-term reproductive abilities in male mammals. The detailed mechanisms by which SSCs self...

Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome Analysis

University of Hong Kong. Author information Author notesQin Zhou & Yuanyan Xiong These authors contributed equally to this work. AffiliationsDepartment of Nephrology, The First Affiliated Hospital, Sun Yat ... ScholarSearch for Yuanyan Xiong in:Nature Research journals • PubMed • Google ScholarSearch for Xiao R. Huang in:Nature Research journals • PubMed • Google ScholarSearch for Patrick Tang in:Nature Research

The Pattern and Evolution of Looped Gene Bendability

Gene looping, defined as the physical interaction between the promoter and terminator regions of a RNA polymerase II-transcribed gene, is widespread in yeast and mammalian cells. Gene looping has been shown to play important roles in transcription. Gene-loop formation is dependent on regulatory proteins localized at the 5′ and 3′ ends of genes, such as TFIIB. However, whether...

TeloPIN: a database of telomeric proteins interaction network in mammalian cells

Interaction network surrounding telomeres has been intensively studied during the past two decades. However, no specific resource by integrating telomere interaction information data is currently available. To facilitate the understanding of the molecular interaction network by which telomeres are associated with biological process and diseases, we have developed TeloPIN...

The complete genome sequence of Dickeya zeae EC1 reveals substantial divergence from other Dickeya strains and species

Background Dickeya zeae is a bacterial species that infects monocotyledons and dicotyledons. Two antibiotic-like phytotoxins named zeamine and zeamine II were reported to play an important role in rice seed germination, and two genes associated with zeamines production, i.e., zmsA and zmsK, have been thoroughly characterized. However, other virulence factors and its molecular...

Human telomeric proteins occupy selective interstitial sites

Human telomeres are bound and protected by protein complexes assembled around the six core telomeric proteins RAP1, TRF1, TRF2, TIN2, TPP1, and POT1. The function of these proteins on telomeres has been studied extensively. Recently, increasing evidence has suggested possible roles for these proteins outside of telomeres. However, the non-canonical (extra-telomeric) function of...

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads

Background Next-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcript reads onto a reference genome and estimate minor allele frequency from sequences of population samples. Results We have designed and implemented MapNext, a...

A Comprehensive Expression Profile of MicroRNAs in Porcine Pituitary

MicroRNAs (miRNAs) are an abundant class of small RNAs that regulate expressions of most genes. miRNAs play important roles in the pituitary, the “master” endocrine organ.However, we still don't know which role miRNAs play in the development of pituitary tissue or how much they contribute to the pituitary function. By applying a combination of microarray analysis and Solexa...