Briefings in Functional Genomics - current issue

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CRISPR in medicine: applications and challenges

Initially discovered in bacteria and archaea as adaptive immune strategies against invading nucleic acids, the clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) system has now been repurposed as a practical tool for genome editing and other applications [1]. Owing to its flexibility, simplicity, efficiency and...

3D genome organization: setting the stage and introducing its players

The introduction of Chromosome Conformation Capture (3C) by Job Dekker and colleagues in 2002, followed by derivatives that incorporate high-throughput sequencing—most notably Hi-C—have transformed the study of eukaryotic 3D genome organization [1,2]. Whereas prior imaging-based studies mostly focused on the positioning of genomic regions within the...

Three-dimensional chromosome organization in flowering plants

AbstractResearch on plant three-dimensional (3D) genome architecture made rapid progress over the past 5 years. Numerous Hi-C interaction data sets were generated in a wide range of plant species, allowing for a comprehensive overview on 3D chromosome folding principles in the plant kingdom. Plants lack important genes reported to be vital for chromosome...

Plasmodium comparative genomics

Malaria is a serious infectious disease caused by unicellular eukaryotic parasites of the genus Plasmodium. Today more than 200 species exist [1], and whole-genome sequence data is available for around 22 species [2]. At least five different Plasmodium species can infect humans, of which Plasmodium falciparum is the major cause of morbidity and mortality...

Functional genomics in the era of cancer immunotherapy: challenges and clinical implications

The host immune system is comprised of both innate and adaptive immunity, which play critical roles in the immune surveillance, recognition and eradication of cancer cells [1, 2]. Cancer immunotherapy mainly aims to stimulate or modify immune cells to combat cancer cells without affecting normal cells. More recently, cancer immunotherapy has rapidly...

Emerging and threatening infectious diseases

The unpredictable appearance of new infectious diseases has been recognized as one of the emerging threats to human society. It has been made clear historically and scientifically that infectious diseases, which have been emerging over millennia, are driven by numerous factors. In spite of extraordinary advances in diagnostic-, therapeutic- and vaccine-related...

Single-cell genomics

The continual drop in sequencing costs and the steady improvement of platforms and protocols have allowed single-cell sequencing to become widely used over the past few years. The ability to profile individual cells—the fundamental building blocks of all organisms—has already provided important biological insights. Crucially, the rapid development of...

A decade of ChIP-seq

As it has become a tradition to point out, sequencing the first human genome as part of the Human Genome Project effort cost some $3 billion, and even after that, in the early to mid-2000s, it still cost several million to sequence and assemble a mammalian-sized genome using Sanger sequencing methods. The low throughput of Sanger sequencing had been...

Integrating ChIP-seq with other functional genomics data

AbstractTranscription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein–DNA interactions in vitro and...

ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation

AbstractAdvances in the methods for detecting protein–DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput...

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