Biology subjects

Chilaka, S.

Publications and source records attributed to Chilaka, S..

3 recordsLinked to original sources

bioRxiv2025

H3K4me3 is a post-transcriptional histone mark

Histone H3 Lysine 4 trimethylation (H3K4me3) is widely recognized as a hallmark of actively transcribed gene promoters, yet its precise role in transcriptional regulation remains unresolved1-4. Here we present the first direct evidence that H3K4me3 is not a cause but a consequence of transcriptional activation, functioning as a downstream epigenetic response. Using inducible gene models to study temporally resolved transcriptional dynamics, we demonstrate that H3K4me3 enrichment significantly lags behind the transcriptional peaks of inflammatory genes such as TNF- and IL-1{beta}, appearing hours after maximal RNA synthesis. This delayed deposition contrasts sharply with the early accumulation of other active histone marks, including H3K27ac and H4K8ac, and with the recruitment of canonical transcriptional regulators such as phosphorylated RNA polymerase II, NF-{kappa}B, and chromatin modifier, histone acetyltransferase p300. Pharmacological inhibition of transcription with Actinomycin D reduces H3K4me3 enrichment, while knockdown of MLL1 abolishes H3K4me3 without affecting gene activation, indicating that H3K4me3 deposition is transcription-dependent but dispensable for transcriptional initiation. Furthermore, analysis of the constitutively active MYC gene suggests that post-transcriptional H3K4me3 deposition may be a general feature of active transcription. Together, these findings redefine H3K4me3 as a post-transcriptional histone mark, revealing an unexpected layer of epigenetic regulation with broad implications for gene expression control.

molecular biology↗

bioRxiv2018

Replication dynamics of individual loci in single living cells reveal variation of stochasticity

Eukaryotic genomes are replicated under the control of a highly sophisticated program during the restricted time period corresponding to S-phase. The most widely used replication timing assays, which are performed on populations of millions of cells, suggest that most of the genome is synchronously replicated on homologous chromosomes. We investigated the stochastic nature of this temporal program, by comparing the precise replication times of allelic loci within single vertebrate cells progressing through S-phase at six loci replicated from very early to very late. We show that replication timing is strictly controlled for the three loci replicated in the first half of S-phase. Out of the three loci replicated in the second part of S-phase, two present a significantly more stochastic pattern. Surprisingly, we find that the locus replicated at the very end of S-phase, presents stochasticity similar to those replicated in early S-phase. We suggest that the richness of loci in efficient origins of replication, which decreases from early-to late-replicating regions, may underlie the variation of timing control during S-phase.

molecular biology↗

bioRxiv2018

Strong replicators associated with open chromatin are sufficient to establish an early replicating domain

Vertebrate genomes replicate according to a precise temporal program strongly correlated with their organization into topologically associating domains. However, the molecular mechanisms underlying the establishment of early-replicating domains remain largely unknown. We defined two minimal cis-element modules containing a strong replication origin and chromatin modifier binding sites capable of shifting a targeted mid-late replicating region for earlier replication. When inserted side-by-side, these modules acted in cooperation, with similar effects on two late-replicating regions. Targeted insertions of these two modules at two chromosomal sites separated by 30 kb brought these two modules into close physical proximity and induced the formation of an early-replicating domain. Thus, combinations of strong origins and cis-elements capable of opening the chromatin structure are the basic units of early-replicating domains, and are absent from late-replicated regions. These findings are consistent with those of genome-wide studies mapping strong initiation sites and open chromatin marks in vertebrate genomes.

molecular biology↗