Functional genomics

Functional genomics uses genomic data to study gene and protein expression and function on a global scale (genome-wide or system-wide), focusing on gene transcription, translation and protein-protein interactions, and often involving high-throughput methods.

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News & Views | 13 January 2023

A scalable technology for measuring cell-type-specific activity of cis-regulatory sequences

Nature Genetics, 1-2
News & Views | 13 January 2023

Identifying type 2 diabetes risk genes by β-cell CRISPR screening
- Bridget K. Wagner
Nature Genetics 55, 4-5

Latest Research and Reviews

Research
27 January 2023 | Open Access

Chromatin complex dependencies reveal targeting opportunities in leukemia

Epigenetic regulators are potential therapeutic drug targets in leukemia. Here, the authors perform combinatorial CRISPR knockouts to test gene-gene pairings in leukemia cells to discover compensatory non-lethal or synergistic lethal combinations with therapeutic potential.
- Fadi J. Najm
- , Peter DeWeirdt
- & Bradley E. Bernstein
Nature Communications 14, 448
Reviews | 25 January 2023

Molecular quantitative trait loci

Molecular quantitative trait locus (molQTL) mapping associates genetic variation with molecular traits that can be measured as gene expression, splicing and chromatin accessibility. In this Primer, Aguet et al. discuss the study design and implementation of molQTL mapping in various applications, with a focus on technical developments for functional characterization.
- François Aguet
- , Kaur Alasoo
- & Tuuli Lappalainen
Nature Reviews Methods Primers 3, 4
Research
23 January 2023 | Open Access

Precise transcript targeting by CRISPR-Csm complexes

The bacterial Csm complex efficiently knocks down eukaryotic nuclear and cytoplasmic RNAs.
- David Colognori
- , Marena Trinidad
- & Jennifer A. Doudna
Nature Biotechnology, 1-9
Research
19 January 2023 | Open Access

Genome-wide RNA polymerase stalling shapes the transcriptome during aging

In aging mouse livers, 40% of elongating RNA polymerases are stalled, biasing transcriptional output dependent on gene length. This transcriptional stress appears to be caused by endogenous DNA damage.
- Akos Gyenis
- , Jiang Chang
- & Joris Pothof
Nature Genetics, 1-12
Research
17 January 2023 | Open Access

Efficient CRISPR-Cas9 based cytosine base editors for phytopathogenic bacteria

A versatile cytosine base editor system is developed to achieve highly efficient C to T conversion in the genome of a series of phytopathogenic bacteria, including Xanthomonas, Pseudomonas, Erwinia, and Agrobacterium.
- Chenhao Li
- , Longfei Wang
- & Bing Yang
Communications Biology 6, 56
Research
16 January 2023 | Open Access

Micro and macroevolution of sea anemone venom phenotype

Venom is a complex trait with unresolved underlying toxin expression dynamics. Here, the authors compare expression across sea anemone species, revealing variation in dominant toxin diploid copy number across populations which generates distinct haplotypes.
- Edward G. Smith
- , Joachim M. Surm
- & Yehu Moran
Nature Communications 14, 249

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News and Comment

Research Highlights | 13 January 2023

NR5A2 activates the zygotic genome
- Tiago Faial
Nature Genetics 55, 1
News & Views | 13 January 2023

A scalable technology for measuring cell-type-specific activity of cis-regulatory sequences

A high-throughput reporter gene assay for use in living tissues has been developed. The assay allows investigators to quantify, in parallel, the activities of reporter genes in each of the cell types that constitute a tissue.

Nature Genetics, 1-2
News & Views | 13 January 2023

Identifying type 2 diabetes risk genes by β-cell CRISPR screening

A major challenge in human genetics is the prioritization of causal genes in common complex diseases. A genome-wide CRISPR screen for intracellular insulin content in a human β-cell line has now identified a new candidate gene for type 2 diabetes, demonstrating the utility of this screening approach in β-cells.
- Bridget K. Wagner
Nature Genetics 55, 4-5
Research Highlights | 20 December 2022

CRC malignancy continuum
- Tim Thomas
Nature Cancer 3, 1439
News & Views | 19 December 2022

The discovery of human agouti-induced obesity and its implication for genetic diagnosis

Multiomic analyses in an individual with severe, early-onset obesity, followed by targeted screening in additional patients identifies a tandem duplication at the ASIP gene (encoding agouti-signalling protein) as a novel cause of monogenic obesity, with implications for genetic diagnosis of obesity.
- Philippe Froguel
- & Amélie Bonnefond
Nature Metabolism 4, 1614-1615
Research Highlights | 05 December 2022

Butterfly wing pattern diversity
- Michael Fletcher
Nature Genetics 54, 1764

All News & Comment

Functional genomics

Featured

A scalable technology for measuring cell-type-specific activity of cis-regulatory sequences

Identifying type 2 diabetes risk genes by β-cell CRISPR screening

Latest Research and Reviews

Chromatin complex dependencies reveal targeting opportunities in leukemia

Molecular quantitative trait loci

Precise transcript targeting by CRISPR-Csm complexes

Genome-wide RNA polymerase stalling shapes the transcriptome during aging

Efficient CRISPR-Cas9 based cytosine base editors for phytopathogenic bacteria

Micro and macroevolution of sea anemone venom phenotype

News and Comment

NR5A2 activates the zygotic genome

A scalable technology for measuring cell-type-specific activity of cis-regulatory sequences

Identifying type 2 diabetes risk genes by β-cell CRISPR screening

CRC malignancy continuum

The discovery of human agouti-induced obesity and its implication for genetic diagnosis

Butterfly wing pattern diversity

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Functional genomics

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