Boris Lenhard

Integrin α11 is enriched in quiescence and promotes cell-cycle re-entry through destabilisation of the CDK inhibitor p27

The paper identifies integrin α11 as a quiescence signature protein that promotes cell-cycle re-entry by destabilizing the CDK inhibitor p27 through YAP-dependent regulation.

Mapping non-coding functional elements in allotetraploid Cyprinus carpio embryo development reveals subgenome variation of transcription regulation

The paper maps non-coding regulatory elements in common carp embryos, revealing subgenome-specific regulatory divergence during development.

The role of long-range transcriptional regulation in interpretation of non-coding variants associated with human disease

This study introduces targPred, a method using genomic regulatory blocks to connect non-coding SNPs with target genes, and demonstrates its application to childhood obesity and psychiatric diseases.

Multimodal imaging reveals a lysosomal drug reservoir that drives heterogeneous distribution of PARP inhibitors

The paper uses multimodal imaging to show that lysosomes act as a reservoir for PARP inhibitors, leading to heterogeneous drug distribution and response in ovarian cancer.

Salmonids reveal principles of regulatory evolution following autotetraploidization

The paper studies gene regulatory evolution in salmonids after autotetraploidization, finding that it is influenced by developmental and tissue-specific factors, with constraints at advanced embryogenesis.

A dual enhancer-silencer element ensures transient Cdx2 expression during posterior body formation

The paper identifies a dual enhancer-silencer element at the Cdx2 locus that controls transient Cdx2 expression during posterior body formation in mice.

Conservation of Regulatory Elements with Highly Diverged Sequences Across Large Evolutionary Distances

The paper identifies functionally conserved regulatory elements across distantly related vertebrates despite sequence divergence using a synteny-based method.

Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states

This study shows that histone mark function, genomic distance, and cellular states collectively influence gene expression predictions using deep learning models, with no single mark consistently predicting expression across contexts.

Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism

The paper identifies widespread isoform switches of transcription factors across human tissues and predicts their functional consequences.

Abundant capped RNAs are derived from mRNA cleavage at 3'UTR G-Quadruplexes

The paper identifies 3UTR-derived capped RNAs, showing they are abundant and originate from AGO2-mediated cleavage at G-quadruplexes, with implications for APP protein regulation.

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.

Identification of transcription factor co-binding patterns with non-negative matrix factorization

COBIND identifies TF co-binding patterns using NMF on TFBS data, revealing both known and novel co-binding configurations across species.

Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells

This study shows that LKB1 deletion in mouse pancreatic beta cells causes widespread chromatin accessibility changes and affects gene expression, including neuronal genes.

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation

The paper introduces seqArchR, a method using non-negative matrix factorisation to classify promoters by motifs near reference points like TSS, identifying known and novel motifs and their functional roles.

Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

This study identifies DNA methylation changes associated with extreme obesity and finds causal effects on obesity and metabolic disturbances using Mendelian Randomisation.

Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics.

The paper identifies genes regulated by retinoic acid signaling in zebrafish endoderm using RNA-seq, ChIP-seq, and ATAC-seq, and finds conserved RAR binding sites across vertebrates.

TBPL2/TFIIA complex establishes the maternal transcriptome by an oocyte-specific promoter usage

The paper shows that the TBPL2/TFIIA complex establishes the oocyte transcriptome by using a specific TSS recognition code through oocyte-specific promoter usage.

Conservative route to extreme genome compaction in a miniature annelid

The paper decodes the compact genome of Dimorphilus gyrociliatus, revealing a conservative route to genome compaction with features similar to vertebrates.

Global regulatory transitions at core promoters demarcate the mammalian germline cycle

The paper identifies global regulatory transitions at core promoters during mammalian germline development, showing a shift from somatic to maternal promoter codes in oogenesis.

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

The paper investigates the evolution of DNA methylation patterns across arthropods, finding widespread conservation of exon methylation in specific genes and lineage-specific changes in TE and promoter methylation.

Integrator terminates promoter-proximal Pol II to generate C. elegans piRNA precursors

The paper shows that the Integrator complex cleaves nascent piRNA precursors to terminate promoter-proximal Pol II transcription in C. elegans.

HOTAIR ancient sequence suggests regulatory roles both in cis and trans

The paper identifies a conserved noncoding element in HOTAIR that functions both in cis and trans, regulating HOXC11 and HOXD11 expression.

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

RADICL-seq maps genome-wide RNA-chromatin interactions in intact nuclei, revealing general and cell type-specific patterns of transcript occupancy and the role of transcription in chromatin structure.

Germ plasm localisation dynamics mark distinct phases of transcriptional and post-transcriptional regulation control in primordial germ cells

The paper shows zebrafish primordial germ cells use germ plasm in two phases to regulate transcriptome divergence from somatic cells through post-transcriptional mechanisms and chromatin changes.

Intertwined canonical and non-canonical initiation in dual promoters are pervasive and differentially regulate Polymerase II transcription

The paper identifies dual-initiation promoters in zebrafish that use both canonical and non-canonical initiation motifs, showing differential regulation during development and conservation across species.

Zebrafish embryonic tissue differentiation is marked by concurrent cell cycle dynamic and gene promoter regulatory changes

The paper shows that during zebrafish embryonic development, core promoter architecture changes correlate with cell cycle dynamics and lineage-specific gene expression.

CNEr: a toolkit for exploring extreme noncoding conservation

CNEr identifies and analyzes conserved noncoding elements to study their genomic properties and relationships with chromatin structures.

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

The paper shows that the transcription start site landscape in Saccharomyces cerevisiae remains stable across different environmental conditions and identifies a negative correlation between TSS shape index and expression levels.

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

SLIC-CAGE enables high-resolution transcription start site mapping using nanogram-level total RNA, significantly reducing the required input compared to existing CAGE methods.