Magda Bienko

An integrated protocol for multiplexed DNA FISH and protein detection in large tissue sections

The paper presents a protocol combining DNA FISH and multiplexed immunofluorescence to analyze gene and protein expression in large tissue sections at the single-cell level.

A radial map of the budding yeast genome reveals novel organizational principles

The paper uses GPSeq to map the budding yeast genome's radial organization, revealing that centromeres and telomeres constrain chromatin positioning, and GC-content organizes chromatin in their absence.

Co-regulatory changes in Homo sapiens prefrontal cortex shape RNA-chromatin interactions

The paper maps RNA-chromatin interactions in human prefrontal cortex, revealing co-regulatory changes linked to brain evolution and disease pathways.

Extending cis-regulatory networks using chromatin-RNA interactions

The paper integrates enhancer-promoter interactions and RNA-DNA contacts to show RNA's role in modulating cis-regulatory networks during neural differentiation.

Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms

This study shows translocations can drive widespread gene expression changes across entire chromosome arms in MCL by altering chromatin organization and regulatory loops.

Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells

The paper identifies trans-contacting intronic RNAs (TIRs) in neuronal cells that form nuclear scaffolds called introsomes, influencing 3D genome organization and gene expression.

Genomic codes governing enhancer RNA fate

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis

This study shows that HNRNPU deficiency causes chromatin remodeling, transcriptional changes, and delayed neurogenesis in hindbrain-derived neural progenitors.

Separation of transcriptional repressor and activator functions in HDAC3

This study demonstrates that HDAC3's repressor and activator functions can be genetically separated in Drosophila, revealing distinct roles for catalytic activity and SMRTER interaction in transcriptional regulation.

Nuclear gene proximity and protein interactions shape transcript covariances in mammalian single cells

The paper identifies >80,000 gene pairs with intrinsic covariance in mouse embryonic stem cells, showing nuclear organization and protein interactions drive transcript covariances.

BLISS: quantitative and versatile genome-wide profiling of DNA breaks in situ

BLISS quantifies DNA double-strand breaks in situ with high sensitivity and efficiency, showing Cpf1 has higher specificity than Cas9.