Joanna Wysocka

Regulation by partition predicts enhancer target selection in mammalian genomes

The paper introduces SPIE-seq to study enhancer target selection, finding that genomic context and distance-weighted competition, not enhancer identity, determine target choice.

Enhancer Tuning by Sequence-Specific Repressors

This study shows that SNAI1 and SNAI2 repressors tune enhancer activity by shifting chromatin states, affecting enhancer function and evolution.

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

TCOF1 dosage is limiting for transitional human neural crest cells; its enhancers buffer promoter output against MYC fluctuations rather than amplifying it, a pattern seen across 14 dosage-sensitive promoters.

The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions

The paper uses 3D craniofacial data and genome-wide association analysis to link craniofacial variation to genetic diversity, evolutionary processes, and clinical conditions in modern humans.

A human-specific regulatory mechanism revealed in a preimplantation model

The paper investigates the role of HERVK LTR5Hs elements in human preimplantation development, showing their cis-regulatory impact on the epiblast transcriptome and their essential role in blastoid formation through ZNF729 activation.

Promoter strength and position govern promoter competition via transcript-dependent insulation

This study investigates how promoter strength and position influence promoter competition by inserting diverse promoters into the Sox2 locus and measuring their effect on endogenous Sox2 expression.

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

The paper uses transfer learning to predict how TF dosage affects chromatin accessibility, finding that motif affinity and distribution determine sensitivity or buffering of TF concentration changes.

Long range regulation of transcription scales with genomic distance in a gene specific manner

The paper shows that enhancer-promoter communication scales with genomic distance in a gene-specific manner, independent of 3D contact frequency or chromatin state.

A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis

The paper identifies a SNP that regulates facial shape and disease risk by affecting PKDCC expression during chondrogenesis, showing its impact on both normal variation and clefting.

DNA-guided transcription factor cooperativity shapes face and limb mesenchyme

The paper shows how DNA motifs guide transcription factor cooperativity in embryonic face and limb mesenchyme, shaping cell identity and morphology.

Joint Multi-Ancestry and Admixed GWAS Reveals the Complex Genetics behind Human Cranial Vault Shape

This study performs a joint multi-ancestry and admixed GWAS on cranial vault shape, identifying 30 genome-wide significant loci and highlighting genetic pathways involved in craniofacial development.

Precise modulation of transcription factor levels reveals drivers of dosage sensitivity

The paper modulates SOX9 levels in human facial progenitors to study dosage sensitivity and identifies regulatory elements and genes that are sensitive to SOX9 changes.

Structural elements facilitate extreme long-range gene regulation at a human disease locus

The paper investigates how structural elements regulate SOX9 expression over long genomic distances in PRS patients by analyzing chromatin topology and modeling interactions.

Enhancer-associated H3K4 methylation safeguards in vitro germlinecompetence

The paper shows that H3K4me1 retention in enhancers supports germline competence by maintaining enhancer accessibility and responsiveness during in vitro differentiation.

Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements

The paper identifies an enhancer element that amplifies Fgf5 expression by accumulating paused RNA Polymerase II, revealing a new mechanism of enhancer collaboration during differentiation.

Insights into the genetic architecture of the human face

This study identifies 203 genomic regions associated with facial variation using GWAS on multivariate shape phenotypes, revealing novel regions and epistatic interactions.

Shared heritability of face and brain shape distinct from cognitive traits

This study identifies shared genetic loci influencing brain and facial shape, distinct from cognitive traits, suggesting a developmental link between brain and face formation.