Biology subjects

Kilic, S.

Publications and source records attributed to Kilic, S..

6 recordsLinked to original sources

bioRxiv2024

A unified model of gene expression control by cohesin and CTCF

Cohesin and CTCF fold vertebrate genomes into loops and topologically associating domains (TADs). The genome folding by cohesin and CTCF is considered crucial for enhancer-promoter communication and gene regulation. However, the extent of cohesin and CTCF-dependent looping in global enhancer function and their potential non-architectural roles in gene activation have remained unclear. Here, we demonstrate that the acute removal of cohesin or CTCF in mouse cells dysregulates hundreds of genes, albeit subtly. Among various possible enhancer types, cohesin almost exclusively facilitates gene activation by one enhancer type--the CBP/p300-dependent enhancers. Interestingly, CTCF plays a dual role, operating both with and without cohesin, and promoting gene activation both in an enhancer-dependent and independent manner. By anchoring cohesin loops, CTCF directs enhancers to specific target genes and prevents their mistargeting. Independently of cohesin and enhancers, CTCF acts as a transcriptional activator or repressor, depending on its precise binding position near promoters. Acting as a canonical transcription activator, CTCF directly activates hundreds of housekeeping genes, including those essential for mammalian cell proliferation. Mechanistically, promoter-bound CTCF controls DNA accessibility and RNA polymerase II recruitment. The transcriptional activator function of CTCF appears unique to vertebrates and is shared by its vertebrate-specific paralog, CTCFL, despite CTCFLs inability to anchor cohesin loops. These findings reveal the scope of cohesin and CTCF in gene regulation, delineate their shared and unique functions, define a specific class of enhancers using cohesin-mediated looping, and establish a crucial function of CTCF in gene regulation independent of its architectural role. The work reconciles conflicting views and provides a unified model for gene regulation by cohesin and CTCF.

genomics↗

bioRxiv2024

Characterization of a novel neurodevelopmental rare disease caused by a mutation within the autophagy gene ATG9B

Autophagy is a highly conserved eukaryotic cellular process whose dysfunction results in human pathologies including cancer and neurodegenerative disease. First identified in yeast, ATG genes are central players in autophagy. Although their roles in cancer and neurodegenerative disease are well known, Mendelian diseases associated with ATG genes are rare. Mutations in core autophagy genes ATG5 and ATG7 have been previously reported to cause rare genetic disorders with autosomal recessive inheritance pattern. Here we report, for the first time, a rare genetic disorder that results from a deletion/frameshift mutation in human ATG9B, the placenta specific homologue of yeast ATG9 in humans. The 11-nucleotide deletion causes a frameshift and addition of a premature stop codon, truncating the C-terminal cytosolic domain of the ATG9B protein. The pediatric patients carrying the mutant allele homozygous were children of a consanguineous marriage and displayed neurodevelopmental anomalies including mental retardation. We hypothesized that this phenotype originates during placental development. To characterize the effects of the mutation and gain insight on the specific functions of ATG9B in a physiological setting, we used mammalian cells and generated a knock-in mouse model. Truncated ATG9B was not stable when expressed in cells. It was localized to perinuclear vesicles like the WT protein, but not to peripheral vesicles. Homozygous knock-in mice were viable, fertile and displayed no gross phenotypical abnormalities. Histomorphometry analysis of the placenta layers did not reveal a significant difference between mutant and control embryos. The assessments of neurobehavioral tests were similar in wild-type and homozygous knock-in mice. However, knock-in mice had a reduced fear memory trend, which is an amygdala-involved response.

genetics↗

bioRxiv2022

The logic of native enhancer-promoter compatibility and cell-type-specific gene expression variation

Cis-regulatory enhancers are essential for differential expression of developmental and housekeeping genes. However, the specificity of native mammalian enhancers and how it shapes cell-type-specific gene expression landscapes remain largely unknown. We show that endogenous enhancers are broadly compatible with the promoters of developmental and housekeeping genes. Broad enhancer compatibility affords retrofitting new regulatory capabilities to housekeeping genes that evolved before the advent of enhancers. This enables cell-type-specific tuning of ubiquitously expressed genes. Segregation between enhancer-dependent and -independent type regulation is blurred. Within the same cell type, a single promoter can be activated by enhancers and non-enhancer promoter-regulatory elements (PREs). It is the tunable and integrated strengths of enhancers and PREs that quantitatively shape gene expression landscapes, within and across cell types. Our findings have broad implications for understanding cell-type-specific quantitative gene expression variation, as well as the emergence and rewiring of gene regulatory networks in disease and organismal evolution.

genomics↗

bioRxiv2022

A unique H2B acetylation signature marks active enhancers and predicts their target genes

Chromatin features are widely used for genome-scale mapping of enhancers. However, discriminating active enhancers from other cis-regulatory elements, predicting enhancer strength, and identifying their target genes remains challenging. Here we establish histone H2B N-terminus multisite lysine acetylation (H2BNTac) as a genuine signature of active enhancers. H2BNTac prominently marks candidate active enhancers and their target promoters and discriminates them from ubiquitously active promoters. Two mechanisms afford the distinct H2BNTac specificity. (1) Unlike H3K27ac, H2BNTac is specifically catalyzed by CBP/p300. (2) H2A-H2B, but not H3-H4, are rapidly exchanged through transcription-induced nucleosome remodeling. H2BNTac-positive candidate enhancers show a high validation rate in orthogonal enhancer activity assays, and a vast majority of endogenously active enhancers are marked by H2BNTac and H3K27ac. Notably, H2BNTac intensity predicts enhancer strength and outperforms the current state-of-the-art models in predicting enhancer target genes. These findings have broad implications for generating fine-grained enhancer maps and modeling enhancer-dependent gene regulation.

genomics↗

bioRxiv2020

SUV39 SET domains mediate crosstalk of heterochromatic histone marks

The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast S. pombe and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remains to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to clr4 deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbours a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.

molecular biology↗

bioRxiv2020

Disordered Proteins Enable Histone Chaperoning on the Nucleosome

Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin . Consequently, prothymosin can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation.

biophysics↗