Simon Andrews

The paper investigates the chromosomal contacts of poised enhancers during the transition from naive to primed human pluripotency, revealing their dynamics and functional significance.

This study shows that senescent human cells secrete misfolded proteins via the endo-lysosomal system, driven by DNAJC5 and reduced intracellular proteostasis.

TrAEL-seq is a method for profiling DNA replication dynamics in mammalian cells without requiring synchronization or drugs, showing replication fork speed and initiation zone effects.

The paper investigates VH-replacement in B-cell development, finding it targets non-pairing productive VDJ rearrangements to reshape the antibody repertoire.

This study shows ZKSCAN3 represses enhancers by targeting retrotransposons without forming heterochromatin, linking it to neurodevelopmental processes and schizophrenia.

This study shows DDX1 promotes B-cell proliferation in germinal centres by enhancing mRNA translation through tRNA ligase activity, crucial for affinity maturation.

The paper shows that asymmetric bivalent nucleosomes at developmental gene promoters promote a poised state by recruiting repressive H3K27me3 binders and specific chromatin proteins like KAT6B, which is critical for ESC differentiation.

The paper introduces EM-seq, a new method for whole genome methylation sequencing that avoids the biases of WGBS by using enzymatic conversion, and demonstrates its advantages in accuracy and efficiency.

The paper compares protein dynamics in mouse and human neural progenitors, finding that human NPs have longer protein half-lives and lower proteasomal activity, which influences developmental tempo.

The paper investigates the role of GLP methyltransferase in oocyte development using multi-omics analysis and mouse models, finding that GLP contributes to transcriptional repression and is critical for oogenesis.

This study shows that loss of SETD1B in oocytes causes redistribution of H3K4me3, with loss at active promoters and gain at CpG-rich regions, revealing distinct roles for SETD1B and MLL2 in epigenetic regulation.

This study examines how 3D chromatin organization in mouse liver changes throughout the circadian cycle, revealing dynamic domain assignments and promoter-specific chromatin contacts.

The paper shows that histone modifications form cell-type-specific chromosomal patterns that remain stable through the cell cycle, helping maintain gene expression identity.

This study shows that ageing increases transcriptional heterogeneity and DNA methylation drift in muscle stem cells, disrupting transcriptional networks and stem cell function.

This study compares WGBS library preparation methods and identifies biases in sequencing data, finding that bisulfite conversion and PCR amplification are major sources of bias.

The paper introduces Proximity RNA-seq to study nuclear transcriptome organization, revealing bipartite compartments with distinct RNA density and transcription elongation rates.

The paper shows that differential mobility of chromatin segments, influenced by protein occupancy, drives 3D genome organisation in yeast.

This paper shows TET3 promotes open chromatin and enhances global transcription in embryonic stem cells, independent of its catalytic activity.