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View article: Organization principles of dynamic three-dimensional genome architecture associated with centromere clustering states
Organization principles of dynamic three-dimensional genome architecture associated with centromere clustering states Open
Fungal centromeres are clustered near microtubule organizing centers to help adopt the Rabl chromosomal organization. The role of centromere clustering in driving large-scale changes in structural and functional chromatin assembly remains …
View article: <i>Xist</i> upstream deletion leads to dysregulation of <i>Xist</i> and autosomal gene expression
<i>Xist</i> upstream deletion leads to dysregulation of <i>Xist</i> and autosomal gene expression Open
Xist long noncoding RNA is the master regulator of the X-Chromosome inactivation (XCI) process. Xist is expressed from the inactive X and coats the inactive X to facilitate XCI. Cis -regulation of Xist expression remains poorly understood …
View article: Loss of tumour suppressor p53 rewires enhancer landscape and governs oncogenic progression
Loss of tumour suppressor p53 rewires enhancer landscape and governs oncogenic progression Open
Mutations in tumour suppressor p53 confer enhanced metastasis and chemoresistance in colorectal cancer (CRC). Though the genetic events regulating CRC with p53 loss/mutation have been documented, the epigenetic events accompanying the loss…
View article: Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain
Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain Open
Transcription activation of genes by estrogen is driven by enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven activation affects ne…
View article: Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer
Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer Open
Hypoxia influences the epithelial-mesenchymal transition (EMT) through the remodeling of the chromatin structure, epigenetics, and alternative splicing. Hypoxia drives CCCTC-binding factor (CTCF) induction through hypoxia-inducible factor …
View article: Nuclear myosin I mediates genomic clustering of estrogen receptor-α without affecting ligand-induced transcriptional robustness
Nuclear myosin I mediates genomic clustering of estrogen receptor-α without affecting ligand-induced transcriptional robustness Open
Ligand-induced transcriptional responses are rapid and robust. Estrogen, one such ligand, exerts its rapid effects through the steroid hormone receptor estrogen receptor-alpha (ERα). Upon stimulation, ERα binds to clustered enhancers to dr…
View article: Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry
Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry Open
Incidence and severity of prostate cancer (PrCa) substantially varies across ancestries. American men of African ancestry (AA) are more likely to be diagnosed with and die from PrCa than the those of European ancestry (EA). Published polyg…
View article: Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain
Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain Open
Transcription activation of genes by estrogen is driven by enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven activation affects ne…
View article: Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain
Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain Open
Transcription activation of genes by estrogens is driven by enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven activation affects n…
View article: Paused Polymerase synergises with transcription factors and RNA to enhance the transcriptional potential of promoters
Paused Polymerase synergises with transcription factors and RNA to enhance the transcriptional potential of promoters Open
Regulated pausing of RNA polymerase II (Pol II) is essential for enabling rapid and coordinated transcriptional responses to signalling cues. Pausing also contributes to the formation of nucleosome-free regions with the help of chromatin r…
View article: Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain
Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain Open
Transcription activation of genes by estrogen is driven by enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven activation affects ne…
View article: eLife assessment: Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9
eLife assessment: Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 Open
Full text Figures and data Peer review Side by side Abstract eLife assessment Introduction Results Discussion Materials and methods Data availability References Article and author information Metrics Abstract RNA polymerase II (RNAPII) tra…
View article: eLife Assessment: Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9
eLife Assessment: Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 Open
RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The bas…
View article: Compaction of Active Chromatin Domains and Promoters by H3S10 Phosphorylation during Mitosis Preserves Interphase-Specific Chromatin Structure and Function
Compaction of Active Chromatin Domains and Promoters by H3S10 Phosphorylation during Mitosis Preserves Interphase-Specific Chromatin Structure and Function Open
Mitotic chromosomes lose interphase-specific genome organization and transcription but gain histone phosphorylation, specifically H3S10p. This phosphorylation event compacts chromosomes in early mitosis by reducing inter-nucleosomal distan…
View article: eLife Assessment: Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9
eLife Assessment: Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9 Open
RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The bas…
View article: Cis‐regulatory effect of <scp>HPV</scp> integration is constrained by host chromatin architecture in cervical cancers
Cis‐regulatory effect of <span>HPV</span> integration is constrained by host chromatin architecture in cervical cancers Open
Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis‐regulatory effe…
View article: Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer
Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer Open
CCCTC-binding factor (CTCF) and cohesin play a significant role in the formation of chromatin loops and topologically associating domains (TADs), which influence gene expression and DNA replication. CTCF/cohesin-binding sites (CBSs) presen…
View article: Deletion of<i>Xist</i>upstream sequences alters TAD interactions and leads to defects in Xist coating and expression
Deletion of<i>Xist</i>upstream sequences alters TAD interactions and leads to defects in Xist coating and expression Open
The topological organization of the genome plays an important role in regulating gene expression. However, the connection between the two remains poorly understood. X-chromosome inactivation is a unique model system to explore the interlin…
View article: RNA binding limits the ligand induced transcriptional potential of estrogen receptor-alpha (ERα)
RNA binding limits the ligand induced transcriptional potential of estrogen receptor-alpha (ERα) Open
Transcription factors (TFs) primarily regulate gene expression by binding to DNA through their DNA binding domains (DBD). Additionally, approximately half of these TFs also interact with RNA. However, the role of RNA in enabling TF binding…
View article: Transcription factor condensates and signaling driven transcription
Transcription factor condensates and signaling driven transcription Open
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the …
View article: Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru
Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru Open
Genomic surveillance in response to coronavirus disease (COVID-19) pandemic is crucial for tracking spread, identify variants of concern (VoCs) and understand the evolution of its etiological agent, severe acute respiratory syndrome corona…
View article: Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries
Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries Open
Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulat…
View article: Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers
Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers Open
Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often the HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes (such as E6/E7) is well known, the cis-regula…
View article: Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms
Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms Open
9p21 locus is one of the most reproducible regions in genome-wide association studies (GWAS). The region harbors CDKN2A/B genes that code for p16 INK4a , p15 INK4b , and p14 ARF proteins, and it also harbors a long gene desert adjacent to …
View article: Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies
Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies Open
Reactivation of fetal hemoglobin (HbF) is the commonly adapted strategy to ameliorate β-hemoglobinopathies. However, the continued production of defective adult hemoglobin (HbA) limits the HbF tetramer production affecting the therapeutic …