{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T12:04:57Z","timestamp":1790337897132,"version":"4.1.0"},"reference-count":210,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Epigenet. Epigenom."],"abstract":"<jats:p>Pathogenic variation can alter gene output at multiple levels, from chromatin accessibility and enhancer-promoter communication to RNA processing, translation and protein turnover. The diagnostic challenge is not to catalogue these layers, but to determine which regulatory mechanism is plausible for a given variant, phenotype, tissue and developmental context. This targeted narrative review synthesises representative Mendelian mechanisms across five linked levels: chromatin, transcription, RNA processing and stability, translation, and post-translational proteostasis. Three cross-cutting principles recur. First, distinct molecular lesions may converge on the same functional bottleneck: altered dosage, timing, localisation or disrupted protein homeostasis. Second, regulatory effects are often cell-type-, isoform-, developmental-stage- and state-specific, so assay and tissue selection are integral to interpretation. Third, a negative result in an accessible surrogate such as blood does not exclude a disease-relevant effect in brain, muscle, liver or stimulated immune cells. From these principles, the review derives a mechanism-directed diagnostic framework that links variant class to orthogonal assays, including DNA methylation profiling, chromatin and reporter assays, RNA sequencing, ribosome-level methods and protein-based studies. The framework is offered as an integrative clinical synthesis rather than a new model of gene regulation, to support variant interpretation, functional-test selection and translational prioritisation in unsolved Mendelian disease.<\/jats:p>","DOI":"10.3389\/freae.2026.1944086","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T11:48:55Z","timestamp":1790336935000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["From chromatin to proteostasis: multilevel gene regulation in Mendelian diseases"],"prefix":"10.3389","volume":"4","author":[{"given":"Himanshu","family":"Goel","sequence":"first","affiliation":[{"name":"Hunter Genetics, Hunter New England Local Health District","place":["Waratah, NSW, Australia"]},{"name":"School of Medicine and Public Health, University of Newcastle","place":["Newcastle, NSW, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunjan","family":"Garg","sequence":"additional","affiliation":[{"name":"Hunter Genetics, Hunter New England Local Health District","place":["Waratah, NSW, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,25]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1016\/j.ajhg.2010.10.031","article-title":"PSMB8 encoding the beta5i proteasome subunit is mutated in joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy syndrome","volume":"87","author":"Agarwal","year":"2010","journal-title":"Am. 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